{
"claim": "Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.",
"timestamp": "2026-07-22T15:16:52.377Z",
"settings": {
"mode": "Social",
"library": "PubMed",
"format": "Preprint",
"length": "Standard",
"rigor": "Strict",
"tagCloud": "on",
"breadth": 40,
"depth": 3,
"runs": 1,
"evalsPerRun": 1,
"autoExplore": false,
"smartFollowUp": false
},
"prompt_settings": {
"research_veridical_check": {
"name": "Research Veridical Verification",
"purpose": "Audits the final research response after quotes pass to ensure absolute veridicality, logical consistency, and zero hallucinated external knowledge.",
"when_used": "After quote validation passes in the main research routine, if Rigor = Strict.",
"content": "You are a strict QA Audit AI. Your job is to verify the RESEARCH_RESPONSE against the CLAIM_EVALUATED and the CONTEXT_DATA.\n\nCRITICAL RULES FOR EVALUATION:\n1. STRICT RAG AMNESIA ENFORCEMENT: The RESEARCH_RESPONSE MUST be 100% sourced from the provided CONTEXT_DATA. Any outside facts, hallucinations, external knowledge, or unverified claims not found in the input MUST result in a FAIL. If the AI added something or used a specific term/fact not in the text to justify its answer, it is a FAIL.\n2. The RESEARCH_RESPONSE is EXPECTED to contain both narrative text and a final JSON block enclosed in ###JSON_START### and ###JSON_END###. Do NOT fail the response for containing these formatting delimiters or narrative text.\n3. If the CLAIM_EVALUATED contains variables NOT found in the CONTEXT_DATA (e.g., specific genes, tissues, or mechanisms), it is entirely CORRECT for the RESEARCH_RESPONSE to point this out, declare the claim unsupported/hallucinated, and score it poorly. This is a successful evaluation and MUST be scored as a PASS.\n4. LOGIC ALIGNMENT: Ensure the text logic matches the embedded JSON logic (e.g., if the text says the claim is false, the Alignment score should be low).\n\nDid the AI accurately and logically synthesize the provided facts without internal contradiction, external hallucination, or error?\n\nReturn ONLY a valid JSON object. Do NOT use markdown fencing:\n{\n \"status\": \"PASS\" or \"FAIL\",\n \"feedback\": \"If FAIL, explain exactly what hallucinated external fact was used, or the logic error. If PASS, leave empty.\"\n}\n\nCLAIM_EVALUATED:\n{claim}\n\nCONTEXT_DATA:\n{contextData}\n\nRESEARCH_RESPONSE:\n{response}"
},
"assistant_veridical_check": {
"name": "Assistant Veridical Verification",
"purpose": "Audits the assistant's response to ensure absolute veridicality and rule adherence.",
"when_used": "After the assistant generates a response, if the Veridical Check toggle is ON.",
"content": "You are a strict QA Audit AI. Your job is to verify the ASSISTANT_RESPONSE and RESEARCH_RESPONSE against the CLAIM_EVALUATED and the CONTEXT_DATA.\n\nCRITICAL RULES FOR EVALUATION:\n1. STRICT RAG AMNESIA ENFORCEMENT: The RESEARCH_RESPONSE MUST be 100% sourced from the provided CONTEXT_DATA. Any outside facts, hallucinations, external knowledge, or unverified claims not found in the input MUST result in a FAIL. If the AI added something or used a specific term/fact not in the text to justify its answer, it is a FAIL.\n2. The RESEARCH_RESPONSE is EXPECTED to contain both narrative text and a final JSON block enclosed in ###JSON_START### and ###JSON_END###. Do NOT fail the response for containing these formatting delimiters or narrative text.\n3. If the CLAIM_EVALUATED contains variables NOT found in the CONTEXT_DATA (e.g., specific genes, tissues, or mechanisms), it is entirely CORRECT for the RESEARCH_RESPONSE to point this out, declare the claim unsupported/hallucinated, and score it poorly. This is a successful evaluation and MUST be scored as a PASS.\n4. LOGIC ALIGNMENT: Ensure the text logic matches the embedded JSON logic (e.g., if the text says the claim is false, the Alignment score should be low).\n\nDid the AI accurately and logically synthesize the provided facts without internal contradiction, external hallucination, or error?\n\nReturn ONLY a valid JSON object. Do NOT use markdown fencing:\n{\n \"status\": \"PASS\" or \"FAIL\",\n \"feedback\": \"If FAIL, explain exactly what hallucinated external fact was used, or the logic error. If PASS, leave empty.\"\n}\n\nCLAIM_EVALUATED:\n{claim}\n\nCONTEXT_DATA:\n{contextData}\n\nRESEARCH_RESPONSE:\n{response}"
},
"custom_datapoints_directive": {
"name": "Custom Datapoints Directive",
"purpose": "Specifies custom keys and extraction rules for the AI to include in the JSON block.",
"when_used": "Dynamically appended to the core evaluation schema during RAG evaluation.",
"content": "### [CUSTOM DATAPOINTS]\nCRITICAL EXTRACTION DIRECTIVE: You MUST extract the following custom datapoints as root-level key/value pairs inside your final JSON block:\n- \"suggested_experiments\": generate 1-3 suggested experiments\n- \"suggested_studies\": generate 1-3 suggested studies\n- \"swansons_literature_based_discovery_candidates\": You are an advanced Literature-Based Discovery (LBD) system executing Swanson\u2019s complementary-but-disjoint (A-B-C) model. Your goal is to find hidden, unpublished connections across the provided dataset. Strict Discovery Protocol: 1. Identify distinct, isolated sub-literatures (Domain A and Domain C) within the dataset that share NO direct citations, co-mentions, or common contextual paragraphs. 2. Find an intermediate biological mechanism, protein, path, or entity (Bridge B) that appears independently in both isolated domains (A-to-B and B-to-C). 3. Synthesize a novel, unstated hypothesis (A-to-C). Negative Constraint (Crucial): DO NOT output any connection if the relationship between Concept A and Concept C is explicitly mentioned, paired, or summarized anywhere in the source text. If a connection (like \"OMN resilience to SMN stabilization\") is already explicitly stated or grouped as a concept in the data, it is considered \"already known\" and must be disqualified. Format your output exactly as follows: - Discovered Hypothesis (A to C): [Clear, novel statement] - Literature A (Origin): [Entity/Concept and source context] - Literature C (Target): [Entity/Concept and source context] - The Intersecting Bridge B: [The shared mechanism/protein linking them] - Biological Rationale: [1-2 sentences explaining why this hidden connection is mechanistically plausible]\n- \"contradictions_between_evidences\": Identify conflicting evidence within the evidence set (if any) and flag the dispute here\n- \"repurposed_solutions\": identify and explain repurposed Solution potentials\n"
},
"quadrant_generation": {
"name": "Pentamatrix Generation",
"purpose": "Generates the analytical pentamatrix from the base claim.",
"when_used": "Beginning of the Semmelweis mode workflow.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes\n\nINITIAL EVALUATION: CLAIM vs. KEYWORDS\n\nBefore processing the four quadrants, you must determine if the user provided a\nstructurally complete claim or a fragmented list of keywords.\n\n - If Full Claim: Act as a strict transcription engine.\n - If Keyword List / Fragment: Act as a Speculative Synthesis Engine.\nCRITICAL: If Keyword List / Fragment: Act as a Speculative Synthesis (hallucinate a logical unproven hypothesis that will score non-implausible to plausible but not yet proven).\n\nQUADRANT CONSTRAINTS\n\n0. RAW USER TEXT\n1. ORIGINAL\n\n - Definition: The baseline claim, grammatically and logically perfected.\n - Rule for Full Claims: Transcribe exactly as stated. Your ONLY modification\n is to fix spelling, punctuation, and grammar. If the input is a question,\n convert it into a declarative claim.\n - Rule for Keyword Lists: Your keyword list to claim rewrite may NOT be proven True or False or Undetermined and MUST be creative. You MUST NOT summarize the keywords. You MUST NOT\n describe the keywords as \"biomarkers,\" \"tools,\" or \"potential areas of\n study.\" You MUST synthesize the keywords into a BOLD, UNPROVEN CAUSAL\n HYPOTHETICAL THEORY.\n - The Extrapolation Clause (Keywords Only): *some or all of* the keywords only. novel idea. \n\n2. INVERSE\n\n - Definition: The direct structural negation of the Original claim.\n - Rule: Directly negate the primary relationship. Do NOT introduce new\n variables. Flip the boolean state of the primary verb (e.g., \"promotes\"\n becomes \"does not promote\").\n\n3. ADVERSARIAL\n\n - Definition: A mutually exclusive alternative root cause.\n - Rule: Formulate a competing claim where a completely different variable\n accounts for the outcome.\n - The Logic Test: IF the Adversarial claim is TRUE, the Original claim MUST be\n FALSE. It must represent a conflict of causality.\n\n4. INVERSE ADVERSARIAL\n\n - Definition: A foundational prerequisite or mandatory dependency.\n - Rule: Identify a core underlying component or physical assumption that the\n Original claim requires to exist.\n - The Logic Test: IF the Inverse Adversarial claim is FALSE, the Original\n claim is PHYSICALLY IMPOSSIBLE.\n\nOUTPUT FORMAT\n\nReturn ONLY valid JSON. Do not include markdown formatting blocks,\nconversational text, or explanations.\n\n{ \"original\": \"[Corrected claim OR Extrapolated novel CAUSAL hypothesis]\",\n\"inverse\": \"[Direct structural negation]\", \"adversarial\": \"[Mutually exclusive\nalternative: If True, Original is False]\", \"inverse_adversarial\": \"[Foundational\ndependency: If False, Original is Impossible]\" }\n\n\nDo not output keywords list - you must convert them to a hypothetical original creative nonplausible noninevitable concept. Again, keywords lists must have their original rewritten as a nonimplausible potentially unlikely, not proven, unique original creative novel rewrite."
},
"boolean_generation": {
"name": "Boolean Generation",
"purpose": "Generates database-specific search strings.",
"when_used": "Stage 1 of each pentamatrix's evaluation loop.",
"content": "You are an expert librarian and systematic reviewer. Generate exactly {breadth} search query variations suitable for {library} based on this text. \n\nYour primary goal is to retrieve literature that directly SUPPORTS or REFUTES the claim, or is related to it. Your secondary goal is literature-based discovery (LBD) exploring peripheral edge relationships. Use OR to discover edges and overlooked abstracts.\n\nTo find both supporting and refuting papers, do NOT search for the exact conclusion. Instead, search for the intersection of the core variables (e.g., Variable A AND Variable B). USE \"OR\" for edge discovery.\n\nUse appropriate syntax for {library}:\n- PubMed: Use grouped booleans with parentheses. Group synonyms using OR (e.g., (\"Term 1\" OR \"Synonym 1\")). Connect distinct core concepts using AND. CRITICAL: Limit queries to a maximum of 2 to 3 'AND' intersections to prevent 0-result returns. Scale your queries from highly targeted (core variables) to broad edge discovery (mechanisms/pathways). Include MeSH terms.\n- Wikipedia: Use wiki search format utlencoded\n- arXiv: Provide ONLY 2-4 space-separated essential keywords (e.g., polar bear, skin, color). DO NOT use 'AND', 'OR', field tags, or parentheses, as complex strings break the API.\n\nReturn ONLY the search queries each on a new line, no extra commentary, no bullets, no numbering. \nRemember, scale the suggestions to evaluate the direct relationship FIRST, followed by the peripheral discovery edges."
},
"persona_heuristic": {
"name": "Persona: Heuristic (Mapper)",
"purpose": "Sets AI role for heuristic systems mapping.",
"when_used": "Stage 4 RAG evaluation (if Rigor = Heuristic).",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nYou are a heuristic logic mapper and researcher. You play the role of a Systems Architecht.\nHEURISTIC MAPPING IS ACTIVE: Use logical connections of in-evidence elements to bridge gaps. Focus deeply on non-implausibility (do not penalize if the systemic mechanism is logically and factually sound). Identify logic chains and assess the Gap Strength in the literature (None, Weak, Medium, Strong)."
},
"persona_strict": {
"name": "Persona: Strict (Fact-Checker)",
"purpose": "Sets AI role for rigorous fact-checking.",
"when_used": "Stage 4 RAG evaluation (if Rigor = Strict).",
"content": "You are a strict, rigorous scientific fact-checker.\nRAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes."
},
"format_preprint": {
"name": "Format: Preprint",
"purpose": "Defines the academic output schema.",
"when_used": "Stage 4 RAG evaluation (if Format = Preprint).",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nFirst provide disclaimer such as \"Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\"\n---\nWrite in a highly academic, formal thesis tone.\nFormat your readable response using these exact academic headers:\n###[CLAIM EVALUATED AND ANSWER TO USER]\n(Exact wording of the claim evaluated)\n### [ABSTRACT & REWRITTEN CLAIM]\n(Scientific synthesis)\n### [INTRODUCTION & JUSTIFICATION]\n(Mechanistic explanation utilizing the 'moneyshot quotes' you will use in the EVIDENCE, METHODOLOGY & CITATIONS section later as well)\n### [DISCUSSION: NOVEL & OVERLOOKED]\n(5-10 bullet points of surprising facts)\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 3) - [copied/verbatim Quote text]\"\n\n**CRITICAL: You must include the exact quote you used in the [copied/verbatim Quote text] section.\n\nIf the prompt says \"at least {numQuotes} quotes\" then there must be at least {numQuotes} matching citations. You must actually use the quotes you select within the conext of the preprint publication you write."
},
"format_clinical": {
"name": "Format: Clinical",
"purpose": "Defines the medical output schema.",
"when_used": "Stage 4 RAG evaluation (if Format = Clinical).",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nFirst provide disclaimer such as \"Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\"\n---\nWrite in a clinical, medical-professional tone.\nFormat your readable response using these exact clinical headers:\n###[CLAIM EVALUATED]\n(Exact wording of the claim evaluated)\n### [CLINICAL BOTTOM-LINE / REWRITTEN CLAIM]\n(Scientific synthesis)\n### [RISK VS REWARD & JUSTIFICATION]\n(Mechanistic explanation utilizing the 'moneyshot quotes' you will use in the EVIDENCE, METHODOLOGY & CITATIONS section later as well)\n### [PATIENT APPLICATION: NOVEL & OVERLOOKED]\n(3-10 bullet points of surprising facts)\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 3) - [copied/verbatim Quote text]\"\n\n**CRITICAL: You must include the exact quote you used in the [copied/verbatim Quote text] section.\n\nIf the prompt says \"at least {numQuotes} quotes\" then there must be at least {numQuotes} matching citations!"
},
"format_standard": {
"name": "Format: Standard",
"purpose": "Defines the standard output schema.",
"when_used": "Stage 4 RAG evaluation (if Format = Standard).",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nIf the user asked a question, you must first provide disclaimer such as \"Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\"\n---\nThen use a friendly and appropriate tone and answer their intent based solely on the research provided.\nFormat your readable response using these exact standard headers:\n[ANSWER TO USER] (if they asked a question)\n###[CLAIM EVALUATED]\n(Exact wording of the claim evaluated)\n### [REWRITTEN CLAIM/PATHWAY]\n(Scientific synthesis based on evidence)\n### [JUSTIFICATION]\n(Mechanistic explanation utilizing the 'moneyshot quotes' you will use in the EVIDENCE, METHODOLOGY & CITATIONS section later as well)\n### [HIGHLIGHTS: NOVEL & OVERLOOKED]\n(3-10 bullet points of surprising facts)\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 3) - [copied/verbatim Quote text]\"\n\n**CRITICAL: You must include the exact quote you used in the [copied/verbatim Quote text] section.\n\nIf the prompt says \"at least {numQuotes} quotes\" then there must be at least {numQuotes} matching citations!"
},
"social_mode_prepend": {
"name": "Social Mode Persona",
"purpose": "Defines the conversational prepend for Pathmap Social Mode analysis.",
"when_used": "When Analysis Mode = 'Pathmap Social' in Stage 4 RAG evaluation.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\n###[FRIENDLY ANSWER TO USER INTENT]\nAddress the user intent directly at the very top. Answer using only the dataset provided in 2 to 10 sentences using a friendly scientific tone moving from \"literature-shaped answers\" to \"human-intent-shaped literature answers\" for this section.\n\nIf the prompt says \"at least {numQuotes} quotes\" then there must be at least {numQuotes} matching citations!"
},
"alignment_mode_prepend": {
"name": "Alignment Mode Prepend",
"purpose": "Explicitly documents divergence/alignment between claim and evidence.",
"when_used": "When Analysis Mode = 'Alignment Mode'.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes. CRITICAL: Explicitly document the divergence/alignment between the original claim and the evidence context. Note any contradictions or supporting facts clearly."
},
"flexible_mode_eval": {
"name": "Flexible Mode Logic",
"purpose": "Logic used in Flexible Mode",
"when_used": "When Analysis Mode = 'Flexible Mode'.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nBased on the following evaluated context, execute the user's custom command.\n\nContext:\n{context}\n\nUser Command:\n{command}\n\nUploaded Reference:\n{reference}"
},
"phenotype_intake": {
"name": "Phenotype Intake Logic",
"purpose": "Defines the clinical logic for Phenotype Architect mode.",
"when_used": "When Analysis Mode = 'Phenotype Architect'.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nYou are a clinical Phenotype Architect. Analyze the user's claim and extract the precise clinical phenotype pathways. Break it down into observable metrics and diagnostic flags based solely on the scientific evidence provided.\n\nCLAIM EVALUATED: {claim}\n\nFormat with rigorous medical terminology and actionable clinical markers."
},
"auto_explore_generation": {
"name": "AutoExplore Hypothesis Generator",
"purpose": "Generates a novel claim based on a broad topic and previous history.",
"when_used": "Beginning of each loop when AutoExplore is enabled.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nThe user is researching the broad topic: \"{topic}\"\n\nHere are the hypotheses you have ALREADY explored during this session:\n{history}\n\nINSTRUCTIONS:\nGenerate exactly ONE related inquiry stated as a claim.\n- It MUST be formatted as a declarative statement.\n- DO NOT wrap it in quotes.\n- DO NOT include conversational text or explanations.\n- Just return the simple claim."
},
"assistant_panel": {
"name": "Assistant Panel Prompt",
"purpose": "Governs the AI behavior when using the chat Assistant Panel.",
"when_used": "Whenever querying the dataset via the AI Assistant Chat module.",
"content": "You are an expert Data Scientist and Visualization Architect. Answer the user directly and truthfully. Do not introduce yourself.\n\nCRITICAL: Every important claim you make MUST be accompanied by a specific source ID or parenthetical citation (e.g., [ID: 12345]) if it is derived from the context.\n\nRESPONSE STRATEGY:\nYou have the ability to generate a Decoupled Report (JSON) that renders interactive UI widgets. Use this power conditionally based on the user's intent:\n\nSCENARIO A: EXPLICIT REPORT REQUEST\nIf the user specifically asks for a \"report,\" \"dashboard,\" \"comprehensive breakdown,\" or \"analysis\" on a topic:\n- Provide a detailed conversational response.\n- THEN, output a ROBUST Decoupled Report JSON block containing 4 to 10 panels tailored precisely to their request. (Include \"synthesis\" and \"pathmap\" as mandatory selections).\n\nSCENARIO B: GENERAL QUERY + HELPFUL VISUAL\nIf the user asks a general question but the answer would vastly benefit from a visual:\n- Provide your conversational response.\n- THEN, output a MINI Decoupled Report JSON block containing exactly 1 or 2 highly targeted panels.\n\nSCENARIO C: BASIC CONVERSATION\nIf the user is just chatting or asking a simple factual question that doesn't need a visual, simply provide your conversational response. Omit the JSON block entirely.\n\n================================================================\nDECOUPLED REPORT PROTOCOL (JSON)\n================================================================\nDo NOT generate raw HTML, CSS, or JS. Output ONLY valid JSON inside the fencing.\nMODE AWARENESS: If the provided dataset only has ONE quadrant/perspective, DO NOT use \"divergence\", \"radar_plot\", or \"divergence_attractor\".\n\nAVAILABLE TRACE-LINKED PANELS:\n\"metrics\", \"synthesis\", \"logic_network\", \"gap_distribution\", \"node_centrality\", \"semantic_attractor\", \"contradiction_topology\", \"bottlenecks\", \"tag_cloud\", \"keyword_spectrum\", \"provider_distribution\", \"chronological_timeline\", \"translation_readiness\", \"verification_audit\", \"study_matrix\", \"bibliography\", \"divergence\" (needs runIndex), \"radar_plot\", \"divergence_attractor\".\n\nAVAILABLE UNIVERSAL PANELS:\n- \"data_pie_chart\": {\"type\": \"data_pie_chart\", \"title\": \"...\", \"data\": [{\"label\": \"A\", \"value\": 10}]}\n- \"data_bar_chart\": {\"type\": \"data_bar_chart\", \"title\": \"...\", \"xAxisLabel\": \"...\", \"data\": [{\"label\": \"A\", \"value\": 10}]}\n- \"event_timeline\": {\"type\": \"event_timeline\", \"title\": \"...\", \"data\": [{\"date\": \"1990\", \"title\": \"...\", \"desc\": \"...\"}]}\n- \"comparison_matrix\": {\"type\": \"comparison_matrix\", \"title\": \"...\", \"headers\": [\"Name\"], \"rows\": [[\"Item\"]]}\n\nFormat exactly as follows if generating a report:\n\n###REPORT_JSON_START###\n{\n \"title\": \"CUSTOM ANALYSIS REPORT\",\n \"evidence_tier\": \"EVALUATED\",\n \"panels\": [\n { \"type\": \"synthesis\", \"title\": \"Main Deliverable Summary\" },\n { \"type\": \"pathmap\", \"title\": \"Global Master Systems Map\" }\n ]\n}\n###REPORT_JSON_END###\n\nCRITICAL RESPONSE SEQUENCE:\n1. First, provide your conversational response.\n2. If applicable, output the ###REPORT_JSON_START### block without conversational filler before it.\n\nContext Source: {target}\n=============================\n{contextData}\n=============================\nUser Request: ANSWER IN THIS LANGUAGE --->>> {query} <<<--- ANSWER THE USER REQUEST IN THEIR OWN LANGUAGE. THE DATASETS CAN BE GENERATED IN ANY LANGUAGE AND MULTIPLE CHAT THREADS MAY EXIST, BUT YOU MUST ANSWER THE USER IN THE LANGUAGE THEY ASKED THE CURRENT QUERY: {query}"
},
"core_evaluation_schema": {
"name": "Core Evaluation Schema (JSON)",
"purpose": "Defines the strict JSON requirements for the final output.",
"when_used": "Appended to every Stage 4 RAG evaluation.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\n###critical: WRAP YOUR THOUGHTS WITH \nAll responses must include the mandatory \"### [EVIDENCE, METHODOLOGY & CITATIONS]\" section as formatted.\nCRITICAL:\n**MONEYSHOT QUOTES MUST DIRECTLY SUPPORT YOUR CLAIMS**\n**MONEYSHOT QUOTES MUST BE USED IN YOUR RESPONSE TEXT WITHOUT IN-LINE ANNOTATION**\n**MONEYSHOT QUOTES MUST BE USED IN A FORMAL PROFESSIONAL WAY, WORTHY OF PEER REVIEW, WITHOUT ILLOGICAL LEAPS (UNSUPPORTED MAY BE OK, ILLOGICAL IS NOT OK)**\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 7) - *\"copied/verbatim Quote text\"**\n\nCRITICAL INSTRUCTION:\nwhen fact checking: At the very end of your response, you MUST provide a machine-readable JSON block containing evaluation metrics. \nIt MUST be enclosed exactly between ###JSON_START### and ###JSON_END###. Ensure the JSON is valid. \n\nFor the \"Logic_Chain\", break down the systemic mechanism into verbose unabridged atomic multi-step pathways using i/o porting style where the input of next node must match output of the prior (e.g., A -> B, B->C, C->D). Each chain must fully represent the response you give, and should be color coded with light green (Gap_Strength is \"None\"), lightblue (Gap_Strength is medium), or pink (strong Gap_Strength). Logic_Chain MUST be a JSON array of objects. Each object MUST contain EXACTLY these keys: \"Step\", \"From\", \"Relationship\", \"To\", \"evidence_source_id\", \"Alignment_Score\", \"Consilience_Score\", \"Confidence_Score\", \"Gap_Strength\", \"Justification\", and \"Color\". Use commas between objects. DO NOT leave trailing commas inside objects.\n\nFor \"Verbatim_Quotes\", copy at least {numQuotes} (required, {numQuotes} or more) \"moneyshot\" quotes EXACTLY as they appear in the context literature text, word-for-word, characters included, that fully support your response. We will programmatically validate these. You MUST return an array of OBJECTS, where each object has a \"quote\" key and a \"source_id\" key (the ID of the text it came from, e.g., the ID). Do not alter a single character, do not paraphrase.\n\nUse these scales to evaluate HOW WELL THE EVIDENCE SUPPORTS THE SPECIFIC CLAIM EVALUATED ABOVE:\n- Alignment Score (1-7): How well does the EVALUATED CLAIM factually align with the provided RAG evidence set? [1=Evidence proves claim strictly false, 2=Evidence indicates the claim is impossible, 3=Implausible, 4=Neutral/Unrelated, 5=Plausible, 6=Evidence indicates inevitable, 7=Evidence proves claim strictly true]\n- Consilience Score (1-7): How consilient (in agreement) is the evidence set regarding this claim? [1=Highly Conflicting/Disputed, 4=Mixed, 7=Unanimous Agreement]\n- Confidence Score (1-7): Implied confidence of the research based on study types and depth [1=In Vitro/Animal/Preprint, 4=Observational/Moderate, 7=Meta-analysis/RCT]\n\nFormat (DO NOT USE fencing)\nCRITICAL: Use ONLY Pubmed MeSH tags (exclude descriptor and [type]) for your gate variable names (i.e.,.the \"gates\") so they will be standardized globally. Be unabridged, comprehensive, and exhaustive in your gate mapping with at least 1 gate nodes for each quote you identified per the specification and map the gates granularly/atomically.\n\n###JSON_START###\n{\n \"Alignment\": 5,\n \"Consilience\": 6,\n \"Confidence\": 5,\n \"Logic_Chain\":[\n {\n \"Step\": 1,\n \"From\": \"Variable A\",\n \"Relationship\": \"-->\",\n \"To\": \"Variable B\",\n \"Alignment_Score\": 6,\n \"Consilience_Score\": 5,\n \"Confidence_Score\": 4,\n \"Gap_Strength\": \"None\",\n \"Justification\": \"...\",\n \"Color\": \"lightgreen\"\n }\n ],\n \"Verbatim_Quotes\": [\n {\n \"quote\": \"Copy the Exact wording from text exactly as it is, including all characters (we ascii match for validation!).\",\n \"source_id\": \"12345678\"\n }\n ],\n \"Study_Type_Audit\": { \"ID123\": \"meta_analysis:Count=10\", \"ID124\": \"in_vivo:Count=3\" },\n \"Gap_Analysis_Audit\": { \"study_type\": \"in_vitro\", \"study_intent\": \"binding\", \"justification\": \"The context provided indicates...\", \"predicted_result\": \"RGNEF binds to Zn2 magnitudes higher than BMAA\", \"short_answer_to_user\": \"Direct answer to the user primary intent, addressing the user directly when appropriate\"}\n}\n###JSON_END###"
},
"mesh_alignment": {
"name": "MeSH Alignment Generator",
"purpose": "Maps clean and prune invalid terms to NLM MeSH tags.",
"when_used": "Post-Build validation of Logic Gates.",
"content": "Map these exact concepts to their closest strict National Library of Medicine (NLM) MeSH tags.\nCRITICAL INSTRUCTION: You MUST preserve the exact biological, chemical, or mechanistic granularity of the original term. Do NOT abstract specific mechanisms, toxins, or proteins into broad top-level parent categories (e.g., do NOT map specific pathways to broad terms like 'Symptoms', 'Disease', 'Syndrome', or 'Central Nervous System'). Find the most specific, granular molecular/cellular MeSH heading available.\nReturn ONLY a valid JSON object pairing old to new.\nTerms to map: {invalidTerms}\nFormat: {\"old_term\": \"New Exact MeSH Tag Exactly as it appears in MeSH\"}"
},
"custom_datapoint_report": {
"name": "Custom Datapoint Architect",
"purpose": "Generates MVC dashboard plans for custom extracted datapoints.",
"when_used": "End of pipeline if custom datapoints were injected.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nYou are a Data Visualization Architect. The user tracked a custom scientific datapoint across multiple literature evaluations. \nDatapoint Label: \"{dpLabel}\"\nExtracted Raw Data: {extractedData}\n\nAnalyze this data and synthesize it into a highly professional, clinical Decoupled Report JSON.\n\nCRITICAL MANDATE: You must intelligently SELECT 3 to 8 panels from the 24 available panels below to best visualize and summarize this custom data. \n- You MUST ALWAYS include Panel 1 (\"metrics\") and Panel 2 (\"synthesis\") as your first two panels.\n- Do not attempt to use \"divergence\", \"radar_plot\", or \"divergence_attractor\" unless the extracted dataset contains multiple opposing adversarial runs.\n\nAVAILABLE PANEL TYPES:\n1. \"metrics\": Key metrics scorecard.\n {\"type\": \"metrics\", \"title\": \"[Title]\"}\n2. \"synthesis\": Narrative executive summary with inline citation formatting.\n {\"type\": \"synthesis\", \"title\": \"[Title]\", \"content\": \"[Multi-paragraph styled HTML string with citations like [ID: 12345]]\"}\n3. \"divergence\": Hypothesis tension visual (original vs. adversarial). Requires runIndex.\n {\"type\": \"divergence\", \"title\": \"[Title]\", \"runIndex\": 1}\n4. \"logic_network\": Consolidated logic pathways.\n {\"type\": \"logic_network\", \"title\": \"[Title]\"}\n5. \"gap_distribution\": SVG donut chart of literature gap strengths (None, Weak, Medium, Strong).\n {\"type\": \"gap_distribution\", \"title\": \"[Title]\"}\n6. \"node_centrality\": SVG horizontal bar chart of the top 10 entities.\n {\"type\": \"node_centrality\", \"title\": \"[Title]\"}\n7. \"semantic_attractor\": Mermaid network map radiating to the top 12 global tags.\n {\"type\": \"semantic_attractor\", \"title\": \"[Title]\"}\n8. \"radar_plot\": Three-axis SVG spider chart of the first 4 quadrants.\n {\"type\": \"radar_plot\", \"title\": \"[Title]\"}\n9. \"score_timeline\": SVG multi-line trend chart over all quadrants.\n {\"type\": \"score_timeline\", \"title\": \"[Title]\"}\n10. \"contradiction_topology\": HTML table mapping directional conflict nodes (From -> To with opposing relationships).\n {\"type\": \"contradiction_topology\", \"title\": \"[Title]\"}\n11. \"bottlenecks\": Styled list of \"Strong\" or \"Medium\" literature gaps.\n {\"type\": \"bottlenecks\", \"title\": \"[Title]\"}\n12. \"tag_cloud\": Weighted HSL tag cloud of the top 20 words.\n {\"type\": \"tag_cloud\", \"title\": \"[Title]\"}\n13. \"keyword_spectrum\": SVG vertical bar chart of the top 10 keywords.\n {\"type\": \"keyword_spectrum\", \"title\": \"[Title]\"}\n14. \"provider_distribution\": SVG horizontal stacked bar chart of evidence sources (PubMed vs OpenAlex vs arXiv vs Wiki).\n {\"type\": \"provider_distribution\", \"title\": \"[Title]\"}\n15. \"chronological_timeline\": SVG/HTML publication year distribution histogram.\n {\"type\": \"chronological_timeline\", \"title\": \"[Title]\"}\n16. \"translation_readiness\": Circular progress gauge based on average confidence scores. Requires subtitle.\n {\"type\": \"translation_readiness\", \"title\": \"[Title]\", \"subtitle\": \"[Label]\"}\n17. \"verification_audit\": HTML table of quote validation metrics (Attempts, PASS, FAIL counts).\n {\"type\": \"verification_audit\", \"title\": \"[Title]\"}\n18. \"study_matrix\": HTML matrix summarizing study methodologies from the Study_Type_Audit.\n {\"type\": \"study_matrix\", \"title\": \"[Title]\"}\n19. \"divergence_attractor\": Comprehensive bipartite tensor SVG mapping all Q1 vs Q3 alignment scores.\n {\"type\": \"divergence_attractor\", \"title\": \"[Title]\"}\n20. \"bibliography\": Automatically prints the verified bibliography.\n {\"type\": \"bibliography\", \"title\": \"[Title]\"}\n21. \"data_pie_chart\": Universal Data Pie Chart.\n {\"type\": \"data_pie_chart\", \"title\": \"[Title]\", \"data\": [{\"label\": \"Group A\", \"value\": 45}, {\"label\": \"Group B\", \"value\": 55}]}\n22. \"data_bar_chart\": Universal Generic Bar Chart.\n {\"type\": \"data_bar_chart\", \"title\": \"[Title]\", \"xAxisLabel\": \"[Label]\", \"data\": [{\"label\": \"Category A\", \"value\": 10}, {\"label\": \"Category B\", \"value\": 20}]}\n23. \"event_timeline\": Universal Vertical Timeline.\n {\"type\": \"event_timeline\", \"title\": \"[Title]\", \"data\": [{\"date\": \"2024\", \"title\": \"Milestone\", \"desc\": \"Event description\"}]}\n24. \"comparison_matrix\": Universal Comparison Matrix.\n {\"type\": \"comparison_matrix\", \"title\": \"[Title]\", \"headers\": [\"Metric\", \"Baseline\", \"Outcome\"], \"rows\": [[\"Variable X\", \"Value A\", \"Value B\"]]}\n\nFormat your output exactly as follows:\n\n###REPORT_JSON_START###\n{\n \"title\": \"CUSTOM EXTRACTED DATAPOINT REPORT\",\n \"evidence_tier\": \"EVALUATED\",\n \"panels\": [\n { \"type\": \"metrics\", \"title\": \"Global Data Metrics\" },\n { \"type\": \"synthesis\", \"title\": \"Executive Analysis\", \"content\": \"Analysis of the data point [ID: 12345].\" },\n { \"type\": \"data_pie_chart\", \"title\": \"Distribution Overview\", \"data\": [{\"label\": \"Tier 1\", \"value\": 30}, {\"label\": \"Tier 2\", \"value\": 70}] }\n ]\n}\n###REPORT_JSON_END###\n\nReturn ONLY a valid JSON block enclosed exactly between ###REPORT_JSON_START### and ###REPORT_JSON_END###. Do not include introductory or concluding conversational text."
},
"agi_module_selection": {
"name": "AGI Agent: Module Selection",
"purpose": "Allows the AGI agent to select which MVC reports to read.",
"when_used": "Smart FollowUp step 1.",
"content": "You are an autonomous AGI agent analyzing a complex trace. The system has generated modules for the current dataset. \nAvailable Module IDs: {menuOptions}. \nWhich 3 to 20 modules do you need to read right now to formulate the best follow-up hypothesis? Return ONLY a valid JSON array of strings matching the IDs exactly. (do not choose evidence set. do not choose json array. Do not choose build log. Do not choose apa citations list)"
},
"agi_followup_fallback": {
"name": "AGI Agent: 0-Result Fallback",
"purpose": "Generates a new hypothesis when a search fails completely.",
"when_used": "Smart FollowUp step 2 (if 0 results).",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nYou are an autonomous discovery agent. The previous search returned 0 results. Generate a new, related hypothesis based on the original claim: \"{claim}\".\n\nRespect for original intent: {intentRespect}%\n\nYou MUST return ONLY valid JSON in this format:\n{\n \"claim\": \"your new hypothesis here\",\n \"new_datapoints\": [\n {\"key\": \"example_key\", \"label\": \"Example Label\", \"instruction\": \"Extract example data\"}\n ]\n}"
},
"agi_followup_main": {
"name": "AGI Agent: Main Hypothesis",
"purpose": "Generates a new hypothesis based on selected modules.",
"when_used": "Smart FollowUp step 2.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nYou are an autonomous discovery agent. Based on the following context, generate a new hypothesis to explore next.\n\nOriginal Query: \"{originalQuery}\"\nRespect for original intent: {intentRespect}%\n\nContext:\n{agiContext}\n\nYou MUST return ONLY valid JSON in this format:\n{\n \"claim\": \"your new hypothesis here\",\n \"new_datapoints\": [\n {\"key\": \"example_key\", \"label\": \"Example Label\", \"instruction\": \"Extract example data\"}\n ]\n}"
},
"demo_case_generation": {
"name": "Demo Case Generation",
"purpose": "Generates a hypothetical complex patient inquiry.",
"when_used": "When the user clicks 'Demo Case'.",
"content": "RAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nGenerate a single, realistic, complex question a patient or caregiver might ask regarding an unproven metabolic mechanism or off-label pathway for a terminal disease. Return ONLY the question, no quotes."
},
"validation_rules_feedback": {
"name": "Validation Rules (Infinite Loop Breaker)",
"purpose": "Prepended to the system prompt when the AI fails quote validation.",
"when_used": "Inside executeQuadrantRAG during a retry.",
"content": "\u26a0\ufe0f\u26a0\ufe0f\u26a0\ufe0f CRITICAL VERIFICATION FAILURE (RETRY LOOP DETECTED) \u26a0\ufe0f\u26a0\ufe0f\u26a0\ufe0f\nYour previous response was REJECTED because your quotes failed strict byte-perfect validation.\n\nTO BREAK THE LOOP, FOLLOW THESE 3 ABSOLUTE RULES:\n1. NO REPAIRING: If a quote failed, do NOT attempt to edit or tweak it. Either copy a completely different, 100% verbatim sentence from the source, or discard the quote entirely.\n2. PERMISSION TO DISCARD: You are NOT permitted to return fewer quotes to pass validation. Never hallucinate just to meet a quota.\n3. BYTE-PERFECT COPY: You must perform a direct, literal copy-paste. Ellipses (...) are BANNED. Do not change a single capital letter, punctuation mark, or space.\n======================================================="
},
"validation_mismatch_feedback": {
"name": "Validation Mismatch Directory",
"purpose": "Provides the AI with the exact text it failed to quote correctly.",
"when_used": "Inside evaluateWithInfiniteRetry.",
"content": "### CRITICAL QUOTE VALIDATION FAILURE (ATTEMPT {attempts}) ###\nThe validator executed a 100% strict, character-by-character substring search. Your response was REJECTED because the following quotes do not exist verbatim in the source texts.\n\n\u274c FAILED QUOTES (You must fix or delete these):\n{failedContext}\n\n{passedContext}\nINSTRUCTION: Study the actual abstracts provided. Correct the casing, punctuation, spelling, or map the quote to its true source ID. Do NOT use ellipses."
}
},
"authorship": [],
"executionLog": [
"[11:16:25 AM] \ud83d\udca1 Crash-Proof Recovery: Found an autosaved session from 11:11:46 AM with 3 completed nodes. Click 'Restore Session' to load it.",
"[11:16:37 AM] Validating Key...",
"[11:16:39 AM] Session ready. Connected to GEMINI provider.",
"[11:16:52 AM] \n\u2795 APPENDING TO EXISTING TRACE...",
"[11:16:52 AM] \n\ud83d\ude80 === STARTING BUILD RUN [1/1] ===",
"[11:16:52 AM] \n--- Processing Pentamatrix[1/1]: SYNTHESIS ---",
"[11:16:52 AM] \ud83e\udde0 Generating Booleans for PubMed...",
"[11:16:56 AM] \ud83d\udce1 Fetching node IDs across queries (Target Depth: 3)...",
"[11:17:00 AM] \u2705 Successfully retrieved 110 unique nodes.",
"[11:17:03 AM] Scoring & Validation for Run1 Eval1 synthesis (Attempt 1/9999999)...",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41993512]: \"WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41643617]: \"PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41919495]: \"Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41957923]: \"Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42215790]: \"The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42327061]: \"Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42477140]: \"mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41779229]: \"SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42093006]: \"mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41812834]: \"PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41580402]: \"Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42325197]: \"Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41980172]: \"mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42162239]: \"the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42236937]: \"TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41707395]: \"PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41659462]: \"most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation...\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42203786]: \"STING signalling is terminated by ESCRT-driven lysosomal microautophagy....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 42165414]: \"This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function....\"",
"[11:17:18 AM] \ud83d\udfe2 Quote Verified [Library ID: 41886456]: \"UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling....\"",
"[11:17:18 AM] \u2705 All 20 quotes validated verbatim.",
"[11:17:18 AM] \ud83d\udd0d Strict Mode: Running final logic & veridical audit on quadrant...",
"[11:17:20 AM] \u2705 Final logic audit passed.",
"[11:17:20 AM] \u2699\ufe0f Build Run [1] complete. Compiling intermediate reports and updating context...",
"[11:17:20 AM] \ud83e\uddec Commencing Post-Build Strict Reiterative MeSH Verification...",
"[11:17:20 AM] \ud83d\udd0d MeSH Check: Verifying exact phrase matches against NLM database for 7 terms...",
"[11:17:21 AM] \ud83d\udfe2 Round 1 Pass: \"Nanoplastic exposure\" is verified in MeSH database.",
"[11:17:23 AM] \ud83d\udfe1 Round 1 Fail: \"Lysosomal dysfunction\" unverified. Suggestions: []",
"[11:17:25 AM] \ud83d\udfe1 Round 1 Fail: \"\u03b1-SYN aggregation\" unverified. Suggestions: []",
"[11:17:26 AM] \ud83d\udfe2 Round 1 Pass: \"WDR44\" is verified in MeSH database.",
"[11:17:28 AM] \ud83d\udfe1 Round 1 Fail: \"Aggregation scaffold\" unverified. Suggestions: []",
"[11:17:30 AM] \ud83d\udfe1 Round 1 Fail: \"Nanoplastics\" unverified. Suggestions: []",
"[11:17:32 AM] \ud83d\udfe1 Round 1 Fail: \"Accelerated \u03b1-SYN aggregation\" unverified. Suggestions: []",
"[11:17:32 AM] \u26a0\ufe0f MeSH Alignment Loop (Attempt 1/5): Aligning & Re-Verifying 5 terms...",
"[11:17:35 AM] \ud83d\udfe2 Round 3 Pass (Veridical Enforcement): AI suggestion \"Lysosomal Storage Diseases\" verified against database.",
"[11:17:36 AM] \ud83d\udfe2 Round 3 Pass (Veridical Enforcement): AI suggestion \"alpha-Synuclein\" verified against database.",
"[11:17:37 AM] \ud83d\udfe2 Round 3 Pass (Veridical Enforcement): AI suggestion \"Protein Aggregates\" verified against database.",
"[11:17:38 AM] \ud83d\udfe2 Round 3 Pass (Veridical Enforcement): AI suggestion \"Plastics\" verified against database.",
"[11:17:39 AM] \ud83d\udfe2 Round 3 Pass (Veridical Enforcement): AI suggestion \"alpha-Synuclein\" verified against database.",
"[11:17:39 AM] \ud83e\uddec Re-aligned 8 node(s) with verified MeSH tags.",
"[11:17:39 AM] \u2705 MeSH alignment & strict verification complete.",
"[11:17:39 AM] \u2705 Unified Dataset complete. Total unique nodes stored: 110",
"[11:17:50 AM] \ud83e\udde0 Querying Assistant: \"Answer in English only. Begin with a clear Yes ...\"",
"[11:17:53 AM] \ud83d\udd0d Auditing Assistant response (Attempt 1)...",
"[11:17:55 AM] \u2705 Assistant response passed veridical audit."
],
"failedQuotesLog": [],
"allQuoteAttempts": [
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41993512\nTitle: WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\nAbstract: The aggregation of \u03b1-synuclein (\u03b1-SYN) into Lewy bodies (LBs) is a central event in the pathogenesis of Parkinson's disease (PD) and related synucleinopathies1,2. Despite significant advances in understanding \u03b1-SYN self-assembly, the precise sequence of early aggregation steps has not been directly visualized in living neurons. Here, we use an optogenetic-induced protein aggregation system with a high temporal resolution to monitor the onset of \u03b1-SYN assembly in neurons. We found that the initiation and accumulation of \u03b1-SYN aggregates occur predominantly at the lysosomal membrane, an event driven by the \u03b1-SYN N-terminus and modulated by the membrane-associated adaptor protein WD repeat-containing protein 44 (WDR44). Remarkably, we demonstrate that WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons. Consistent with its potential pathogenic involvement, WDR44 aberrantly accumulates in vivo and in the brains of PD patients, where it colocalizes with LB inclusions. Finally, we show that lysosome-associated \u03b1-SYN aggregates compromised lysosomal structure and function, leading to neuronal impairment, a phenotype worsened by WDR44 overexpression, linking early aggregation events to downstream toxicity. Together, these findings reveal the earliest dynamic stages of \u03b1-SYN oligomerization in living neurons and identify the WDR44-\u03b1-SYN interaction as a promising therapeutic target for reducing \u03b1-SYN pathology and enabling early intervention in PD."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41643617\nTitle: Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.\nAbstract: Nanoplastics are an emerging global environmental concern, with increasing evidence of their neurotoxic effects. Recent findings suggest that abnormal aggregation of pathogenic proteins within the nervous system may contribute to the neurotoxicity induced by nanoplastics, yet the molecular mechanisms regulating this pathological cascade remain unclear. Here, we used immature mice as an experimental model to represent infants and young children who are at higher risk of nanoplastics exposure, to elucidate the molecular mechanisms underlying neurotoxicity induced by exposure to polystyrene nanoplastics (PS-NPs) during early life. The results showed that environmentally relevant doses of PS-NPs penetrated the brains of immature mice and induced behavioral and emotional disorders. Proteomic analysis identified the mTOR signaling pathway as a candidate pathway responding to PS-NPs exposure in the immature mouse brain. Rapamycin intervention and quantitative validation further demonstrated that PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity. Furthermore, treatment with sodium 4-phenylbutyrate (4-PBA) confirmed that proteostasis imbalance, characterized by activation of the unfolded protein response, was a direct driver of this neurotoxicity. Notably, both rapamycin and 4-PBA treatments alleviated neurotoxicity resulting from PS-NPs exposure by restoring proteostasis. Together, these findings highlight dysregulation of the autophagy-lysosome pathway mediated by mTOR as a central mechanism of PS-NPs-induced neurotoxicity in immature mice and suggest lysosomal regulation for proteostasis remodeling as a prospective therapeutic strategy against neurological hazards related to nanoplastics."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41919495\nTitle: Lysosomal homeostasis at the crossroads of neurodegeneration.\nAbstract: Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41957923\nTitle: Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?\nAbstract: The enteric nervous system (ENS), a key component of the gut-brain axis, has emerged as a critical player in the pathogenesis of Parkinson's disease (PD). It is the first neural system exposed to food contaminants (FCs)-a diverse group of ubiquitous toxic compounds fortuitously present in food derived from production, processing, storage, or environmental contamination. Emerging evidence suggests that FCs may initiate or amplify neurodegenerative processes, yet their effects on the ENS and their impact in gut-to-brain communication remain insufficiently characterized. This systematic review synthesizes current evidence on FCs-induced effects on the ENS and its involvement in mediating neurotoxicity from dietary toxicants exposure. Following PRISMA guidelines, 67 studies were included pertaining to cellular or mammalian experimental models exposed to FCs via enteral routes, reporting ENS-related outcomes or studying vagal involvement in modulating FC toxicity. The main FCs evaluated were pesticides, toxins, bisphenols, acrylamide, manganese, and micro-/nanoplastics. Across studies, FCs consistently induced neurochemical remodeling of the ENS, activation of enteric glia, often coupled with intestinal alterations. Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain. Vagotomy models confirmed that disrupting ENS-CNS communication attenuates FC-related central neurotoxicity, supporting the involvement of food toxicants in gut-to-brain propagation of neurotoxic signals. These findings support the body-first hypothesis of PD and position the ENS as a critical, yet underinvestigated interface in exposome-related neurotoxicology. The review highlights research gaps and the need for improved models and long-term, low-dose studies reflecting realistic FC exposure."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42215790\nTitle: The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.\nAbstract: Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most frequently mutated gene in\u00a0amyotrophic lateral sclerosis and frontotemporal dementia, has been linked to autophagy-lysosomal pathway defects, but the role\u00a0of C9orf72 in microglia remains unclear. Here, we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through promoting lysosomal membrane repair. Loss of C9orf72 and SMCR8 in mice causes age\u2011dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged brain and spinal cord tissue, microglia display lysosomal damage marked by galectin\u20113 accumulation. Using a lysosomotropic agent to induce lysosomal damage in microglia, we find that C9orf72/SMCR8-deficient cells accumulate damaged lysosomes and show defective recruitment of phosphorylated RAB8A and the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery\u00a0to damaged lysosomes. Notably, mutant microglia accumulate GTP\u2011bound RAB8A, which becomes hyperphosphorylated and mislocalized to RAB7-positive, LAMP1-negative vesicles. The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. Our findings reveal that the C9orf72/SMCR8 complex coordinates RAB8A-ESCRT-mediated lysosomal repair to safeguard microglial homeostasis and limit neuroinflammation."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42327061\nTitle: Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.\nAbstract: Lysosomal membrane damage triggers a multi-stage repair response essential for cellular homeostasis. Here we identify the oxysterol-binding protein-related protein ORP3 as a critical mediator of late-stage lysosomal membrane repair. Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites via a signaling cascade initiated by lysosomal membrane ubiquitination, TAK1, p38 MAPK, and, to a lesser extent, IKK. p38-dependent phosphorylation promotes direct interaction between ORP3 and LC3B, which together with PI(4,5)P\u2082 binding, is required for autophagic lysosome recruitment. ORP3 depletion impairs late-stage lysosomal recovery, elevates lysosomal lipid peroxidation, and reduces cell survival. A lipid transfer-deficient ORP3 mutant fails to restore lysosome function despite normal recruitment, indicating that ER-to-lysophagosome transfer of phosphatidylcholine by ORP3 is functionally required. ORP3 activity is subsequently terminated by VCP/p97-mediated deubiquitination of lysosomes. These findings define ORP3 as a MAPK regulated lipid transfer protein during the late autophagic phase of the endolysosomal damage response. Lysosomal membrane damage triggers ubiquitination that activates a TAK1-p38 signaling cascade, phosphorylating the lipid transfer protein ORP3 and recruiting it to damaged lysosomes via LC3B interaction. ORP3-mediated phosphatidylcholine transfer from the ER is essential for late-stage lysosomal repair and cell survival."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42477140\nTitle: Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.\nAbstract: Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), which restores lysosomal function during hypoxia-reoxygenation stress. During B-fission, damaged lysosomes generate membrane buds that undergo scission to form small, fully functional lysosomes, independently of autophagic lysosome reformation. Mechanistically, mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission. MIRO2 promotes the formation of MFF+ MDVs through direct interaction with MFF, while the lysosomal membrane protein ITM2C binds MIRO2 to tether and guide MFF+ MDVs to lysosomes, enabling efficient MFF delivery and subsequent B-fission. Notably, AMPK activation by 991 or metformin promotes MFF-dependent lysosomal B-fission under normoxic conditions, whereas AMPK inhibition by dorsomorphin suppresses B-fission during hypoxia-reoxygenation. This stress-responsive ITM2C-MIRO2-MFF-DRP1 axis co-opts the mitochondrial division machinery to drive lysosomal fission from damaged lysosomes, thereby enabling the undamaged components to reorganize into daughter lysosomes and promote lysosomal renewal. Thus, our findings uncover a fundamental mode of lysosomal renewal and reveal an unexpected role for MDV-mediated mitochondria-lysosome communication in mediating lysosomal quality control during ischaemia-reperfusion and related stresses."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41779229\nTitle: Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.\nAbstract: Tissue-resident memory T cells (TRM cells) have been shown to play an instrumental role in driving the onset and relapse of inflammatory bowel diseases (IBD). However, the underlying mechanism of TRM cells differentiation and its regulation in intestines remain to be unveiled. Mothers against decapentaplegic homolog 3 (SMAD3) is translocated from nucleus to membrane and activated in response to transforming growth factor beta (TGF-\u03b2), which is a key cytokine in the process of TRM cells polarization. Cysteine palmitoylation (S-palmitoylation) is a post-translational modification catalyzed by the DHHC family, regulating protein membrane associations. Genes associated with the classic SMAD3 signaling pathway, along with most genes in the DHHC family, were upregulated in TRM cells. Our study demonstrated that SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I (TGF-\u03b2RI) under TRM polarization conditions. The membrane recruitment of SMAD3 activated SMAD3 and subsequently upregulated the expression of its target genes, inducing the differentiation of TRM cells. In contrast, perturbation in DHHC6-induced palmitoylation with MYD-4 inhibited TRM cells differentiation and alleviated colitis in IBD model mice. Our work provides an example how the immune responses are regulated through the S-palmitoylation-dependent SMAD3 signaling in TRM cells differentiation and reveals protein S-palmitoylation as a potential target in IBD treatment, which could be of greater application considering the wide involvement of protein S-palmitoylation in the signal transduction in mammalian cells."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42093006\nTitle: The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and the accumulation of misfolded \u03b1-synuclein, yet the underlying mechanisms remain incompletely understood. Over the past two decades, genetic discoveries have highlighted the convergence of multiple familial PD genes on the autophagy-lysosome pathway (ALP), a key cellular system responsible for the degradation and recycling of intracellular components. Recent studies have further revealed that components of the ALP not only mediate the clearance of \u03b1-synuclein aggregates but also, under certain pathological conditions, contribute to their propagation via lysosomal exocytosis or secretory autophagy. The precise functions of autophagy are highly context-dependent, with neuronal and glial cells exhibiting distinct ALP dynamics that shift with development, stress, and aging. In this review, we summarize current knowledge on the physiological regulation of autophagy in the brain and critically examine its involvement in PD pathogenesis, incorporating mechanistic insights from familial models and emerging evidence from sporadic PD. We also explore translational implications, focusing on efforts to identify ALP-related biomarkers in cerebrospinal fluid and urine, and on the therapeutic potential of modulating ALP activity. Although the causality between ALP dysfunction and PD remains elusive, mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking. Future research should aim to define cell type-specific ALP alterations, clarify the bidirectional interactions between \u03b1-synuclein and autophagic machinery, and develop in vivo tools to monitor autophagy activity and secretory signatures. A deeper understanding of these processes will be crucial for refining PD models, discovering robust fluid biomarkers, and designing targeted therapies capable of modifying disease trajectory."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41812834\nTitle: Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.\nAbstract: Growing nanoplastics exposure raises concern for neurotoxicity, particularly given recent evidence of plastic accumulation within human brain tissue a highly lipid enriched organ, yet effects on brain lipid metabolism remain poorly understood. Here, we employed high-resolution untargeted lipidomics to map brain lipid perturbations in Drosophila melanogaster chronically exposed to polystyrene nanoplastics (PS- NPs). PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines, accompanied by increased diacylglycerols/triacylglycerols and monounsaturated fatty acids and by lipid droplet expansion. Guided by these lipidomic signatures, targeted biochemical assays demonstrated depolarized mitochondrial membrane potential, elevated mitochondrial reactive-oxygen species, inhibition of respiratory-chain complexes I and IV, and a shift in NAD(H) and NADP(H) redox couples toward a reduced state and increasing lipid peroxidation. This redox imbalance was accompanied by decreased tyrosine-hydroxylase expression, dopamine depletion, and impaired locomotor behavior, hallmarks of Parkinson's disease (PD)-like neurodegeneration. Dopaminergic neurochemistry was impaired (tyrosine hydroxylase and dopamine decreased), with concomitant reduction of GABA, and locomotor and circadian deficits emerged. Remarkably, co-treatment with the antioxidant N-acetylcysteine (NAC) restored mitochondrial membrane potential, reduced mitochondrial ROS and lipid peroxidation, normalized neutral lipid and MUFA accumulation, and rescued neurotransmitter levels and behavior. Stable-isotope tracing confirmed disrupted TCA cycle flux after NPs exposure that was rescued by NAC. Collectively, these findings reveal lipidomic remodeling as a critical link between environmental NPs exposure and PD-like pathology, highlighting mitochondrial redox-lipid interactions as early determinants and support redox-directed interventions to mitigate risk."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41580402\nTitle: Micro-nanoplastics and Parkinson's disease: evidence and perspectives.\nAbstract: With the intensification of global plastic pollution, the potential threats posed by micro- and nanoplastics (MPs/NPs) to human health have become a major concern. MPs/NPs enter the organism through ingestion, inhalation, and skin contact, subsequently accumulating in multiple organs-particularly the brain. Increasing experimental and epidemiological evidence implicates MPs/NPs in the development of Parkinson's disease (PD). Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation, triggering neuroinflammatory cascades, elevating oxidative stress, and impairing mitochondrial function. To further investigate the causal role of MPs/NPs in PD, upcoming studies should emphasize well-designed, large-scale prospective cohorts to assess individual exposure to plastic-related pollutants, elucidate the pathways of MPs/NPs into the central nervous system, establish safety thresholds for their neurotoxicity, explore the correlation between exposure levels and central nervous system accumulation, clarify the temporal relationship between MPs/NPs accumulation and PD pathology and symptom onset, and identify the neuropathological mechanisms triggered by relevant concentrations of MPs/NPs. Such data will be instrumental in informing preventive and potentially interventional strategies, while offering actionable insights into the interaction between MPs/NPs and PD."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42325197\nTitle: Small bites for big problems: stepwise aggregate degradation by autophagy.\nAbstract: Protein aggregates are a pathological hallmark of diverse disorders, including many neurodegenerative diseases, but also cardiometabolic disease and cancer. While the ubiquitin-proteasome system efficiently removes many soluble misfolded proteins, large or persistent assemblies often require the autophagy-lysosome pathway for their degradation. In the present mini-review, we summarize our knowledge of aggrephagy, the selective clearance of protein aggregates by autophagy, and discuss two recent manuscripts that argue that some aggregates must be primed for autophagosomal degradation, through chaperone-mediated remodeling. Aggrephagy substrates are defined by aggregate architecture, biophysical state, surface accessibility, and the physical constraints of membrane capture. These features help to explain why recruitment of selective autophagy receptors is necessary yet insufficient for clearance. Receptor clustering is required to concentrate early autophagy factors to establish initiation hubs, but successful degradation often requires upstream generation of smaller 'aggrephagy-competent' cargo units, which contain autophagy receptor clusters that successfully initiate autophagosome formation. Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps that involve p97/VCP-driven disintegration or a chaperone module (DNAJB6-HSP70-HSP110) cooperating with the proteasomal 19S regulatory particle."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41980172\nTitle: Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.\nAbstract: Microplastics (MPs), as emerging food contaminants, have been established to exert adverse effects on the liver. However, the precise toxicological mechanisms remain elusive. Our results demonstrated that MPs triggered mitochondrial dysfunction and mitochondrial ROS (mtROS) accumulation, which subsequently activated NLRP3/caspase-1/GSDMD-N-dependent pyroptosis in hepatocytes. Notably, beyond its canonical translocation to the plasma membrane, GSDMD-N was observed to form pores on the mitochondrial outer membrane, exacerbating mitochondrial damage. The mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux, which ultimately initiated ferroptosis. Concurrently, mitochondrial GSDMD-N mediated mitochondrial intrinsic apoptosis by promoting cytochrome c release and caspase-3 activation. Collectively, our findings revealed that MPs induced GSDMD-N activation and its mitochondrial translocation, which in turn initiated pyroptosis, ferroptosis, and apoptosis in hepatocytes. This study provided novel mechanistic insights into MPs-induced hepatotoxicity, identifying GSDMD-N as a potential central hub coordinating multiple cell death modalities."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42162239\nTitle: Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.\nAbstract: During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagophore before its sealing into an autophagosome and subsequent fusion with the lysosome/vacuole. It remains unclear, however, how the formation of this specialized MCS and the directionality of the lipid flux are controlled. Here, we present the structure of the key lipid transfer protein Atg2 from yeast solved together with its Atg18 binding partner, a phosphatidylinositol-3-phosphate (PtdIns3P) effector, using cryo-electron microscopy. We reveal a new interface in Atg2 that, together with PtdIns3P, is required for Atg18 recruitment and lipid transfer activity. Furthermore, we visualize lipid densities along the internal hydrophobic cavity of Atg2, providing structural evidence that Atg2 cavity is filled with lipids throughout the entire length, even when Atg2 is cytosolic. Finally, molecular dynamics simulations show that the complex generates membrane curvature, efficiently positioning the lipid channel of Atg2 towards the membrane to promote lipid transfer into the elongating phagophore."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42236937\nTitle: LASER couples damage sensing to ESCRT assembly for lysosome repair.\nAbstract: Lysosomal membrane integrity is essential for cell survival, but how damage sensing is spatiotemporally coupled to repair remains poorly understood. Recruitment and assembly of endosomal sorting complex required for transport (ESCRT) I-III rapidly counteracts membrane damage, but it is unclear\u00a0how ESCRT-I recognizes defective lysosomal membranes. Here, leveraging genome-wide CRISPRi screens in a damage-sensitized genetic background, we identified LC3/GABARAP-assisted stimulator for ESCRT recruitment (LASER), a multicomponent protein assembly that forms rapidly upon calcium release from damaged lysosomes and couples sensing of lysosomal membrane damage to ESCRT-dependent repair. At the core of LASER is TFG, an endoplasmic reticulum exit-site-resident protein that translocates to damaged lysosomes by binding to ATG8 family proteins (LC3 and GABARAP) conjugated to lysosomal phospholipids. ATG8-bound TFG forms oligomeric assemblies that directly recruit the essential ESCRT-I subunit TSG101 via conserved motif recognition enhanced by avidity-driven interactions. TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair. TFG mutations that drive hereditary spastic paraplegia disrupt its oligomerization and impair lysosomal ESCRT recruitment and membrane resealing, implicating defective repair as a driver of TFG-associated neurodegeneration. Thus, LASER promotes ESCRT polymerization at damaged lysosomes and couples damage sensing to membrane repair."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41707395\nTitle: Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.\nAbstract: Emerging environmental health issues posed by micro- and nanoplastics (M/NPs) have raised significant concerns. Accumulating evidence suggested that M/NPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene micro- and nanoplastics (PS-M/NPs, 100\u202fnm and 5\u202f\u00b5m) on ovarian development and function in pubertal female mice. Following 35-day exposure, we observed size-dependent reproductive toxicity, with 100\u202fnm PS-NPs causing reduced body weight gain and ovarian size, disrupted folliculogenesis, and altered hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks across seven ovarian cell types. Granulosa cells (GCs) were identified as the primary target of PS-NPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100\u202fnm PS-NPs were internalized by GCs, leading to cell cycle arrest, necroptosis, and hormonal dysfunction. Mechanistically, PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-NP-induced epigenetic and transcriptional changes. Overall, our findings establish the first single-cell resolution atlas of PS-NP-mediated ovarian toxicity, revealing that NPs disrupt reproduction through cytoskeletal damage and epigenetic reprogramming. This work provides unprecedented insights into the molecular and epigenetic consequences of M/NPs in mammalian reproduction, emphasizing the potential health risks of environmental M/NP exposure."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41659462\nTitle: PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.\nAbstract: PLC\u03b2 enzymes cleave PIP2 from the plasma membrane, producing IP3 and DAG, which regulate intracellular Ca2+ levels and protein kinase C activity, respectively. They are regulated by GPCR signaling through the G proteins G\u03b2\u03b3 and G\u03b1q and have been shown to function as coincidence detectors for dual stimulation of G\u03b1q and G\u03b1i-coupled receptors via these G proteins. PLC\u03b2s are aqueous-soluble enzymes, but partition onto the membrane surface to access their lipid substrate. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie G\u03b2\u03b3-dependent regulation of PLC\u03b2 enzymes. Using macrophages as a model system, where PLC\u03b2 signaling is essential for responses to infection and tissue injury, we investigated the contribution of G\u03b2\u03b3-dependent regulation and membrane recruitment of PLC\u03b2 in the context of endogenous signaling. By measuring Ca2+ mobilization, we demonstrate that both G\u03b1i and G\u03b1q-coupled receptors independently stimulate PLC\u03b2 activity, illustrating that G\u03b2\u03b3 alone is sufficient to activate PLC\u03b2 in certain contexts. Using total internal reflection and stimulated emission depletion microscopy, we demonstrate that most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation by both G\u03b1i and G\u03b1q-coupled receptors, illustrating that both G\u03b2\u03b3 and G\u03b1q recruit PLC\u03b2 to the plasma membrane. These results support an updated model for G protein-dependent regulation of PLC\u03b2 enzymes, where G\u03b2\u03b3-induced regulation in the absence of G\u03b1q is context dependent and dictated by the local concentration of receptor, G proteins, and PLC\u03b2. PLC\u03b2 enzymes are critical mediators of signal transduction with roles in neuronal, cardiac, and immunological signaling. Despite this importance, many aspects of their function and regulation remain poorly understood. PLC\u03b2s are aqueous soluble but must partition onto the membrane surface to access their lipid substrate, which enables regulation at the partitioning step, the catalytic step, or both. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie the PLC\u03b2 regulation by one effector, G\u03b2\u03b3. Using macrophages as a model system for physiological signaling, we demonstrate that G\u03b2\u03b3 is capable of independently activating PLC\u03b2 via membrane recruitment under the conditions of endogenous signaling."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "STING signalling is terminated by ESCRT-driven lysosomal microautophagy.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42203786\nTitle: A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.\nAbstract: Stimulator of interferon genes (STING) is critical for the type I interferon responses to pathogen- or self-derived cytosolic DNA. STING signalling is terminated by ESCRT-driven lysosomal microautophagy. How STING is directly encapsulated by lysosomes has not yet been understood. Here we show that two lysosomal components, a phosphoinositide PI(3,5)P2 and CHMP4B (a subunit of ESCRT-III subcomplex) are essential for STING encapsulation by lysosomes. Liposome sedimentation assay reveals that CHMP4B binds to PI(3,5)P2. The forced recruitment of the catalytic core of Pikfyve (a lipid kinase generating PI(3,5)P2) to early endosomes, recruits a fraction of CHMP4B to early endosomes. CHMP4B mutant, defective in the binding to PI(3,5)P2, cannot restore the microautophagic degradation of STING or the resolution of the STING signalling in cells depleted of Chmp4b. Our results reveal a molecular mechanism that terminates innate immune signalling at the lysosomal membrane."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42165414\nTitle: High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.\nAbstract: An elevated risk for inflammatory bowel disease (IBD) has been linked to the intake of high-fat diet (HFD), yet the underlying molecular mechanisms remain unclear. The lysosome and the macroautophagy/autophagy-lysosome pathway (ALP) are critical for maintaining the intestinal epithelial barrier. By employing both an in vivo model of dextran sulfate sodium (DSS)-induced colitis in mice and an in vitro model using lipopolysaccharide (LPS)-treated NCM460 cells, we established that HFD in vivo and palmitic acid (PA) in vitro profoundly impair epithelial barrier function and amplify inflammation, which was linked to the suppression of lysosomal function and the ALP. Mechanistically, HFD in vivo and PA in vitro activated STAT3 (p-STAT3[Y705]) under DSS- and LPS-associated inflammatory stress, respectively. This led to a dual suppression of TFEB: on the one hand, activated STAT3 directly bound to the TFEB promoter to inhibit its transcription; on the other hand, it facilitated the lysosomal recruitment of MTOR and activated MTORC1, which promoted TFEB phosphorylation (p-TFEB[S211]) and hindered its nuclear translocation. This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function. Intestinal epithelial-specific knockout of Stat3 or pharmacological activation of TFEB restored lysosomal function, repaired the epithelial barrier, and ameliorated colitis. Conversely, rectal administration of AAV9-shTfeb reversed the protective effects conferred by stat3 knockout. Our study reveals that HFD in vivo and PA in vitro disrupt lysosomal function and the intestinal barrier through the STAT3-TFEB axis, suggesting this signaling pathway as a promising avenue for intervention in diet-associated IBD.Abbreviations: AB-PAS: Alcian blue-periodic acid-Schiff; ALP: autophagy-lysosome pathway; CD: Crohn disease; ChIP: chromatin immunoprecipitation; CLEAR: coordinated lysosomal expression and regulation; DSS: dextran sulfate sodium; HFD: high-fat diet; IBD: inflammatory bowel disease; IF: immunofluorescence; IHC: immunohistochemistry; LAMP: lysosome associated membrane protein; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; PA: palmitic acid; RRAG: Ras-related GTP binding; RRAG-CA: constitutively active RRAG GTPase; RT-qPCR: reverse transcription quantitative PCR; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; TA1: TFEB activator 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; TJ: tight junction; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UC: ulcerative colitis; WB: western blot; WT: wild-type."
},
{
"quadrant": "Run1_Eval1_synthesis",
"attempt": 1,
"quote": "UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41886456\nTitle: UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.\nAbstract: UFMylation, a recently identified ubiquitin-like modification mediated by the E3 ligase UFL1, plays context-specific roles in cancers, but its substrates and functions in lung adenocarcinoma (LUAD) remain poorly defined. Here, we identify the AKT signaling repressor PHLDA3 as a substrate of UFL1 in LUAD. UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling. Tumor-associated PHLDA3 mutations F41L, E82G, and K106N impair its UFMylation and membrane translocation, resulting in AKT hyperactivation and enhanced tumor growth. In samples from patients with LUAD, UFL1 expression inversely correlates with phospho-AKT levels. Functionally, the UFL1-PHLDA3 axis inhibits LUAD progression in both cell line-based and patient-derived xenograft models. These findings define a tumor-suppressive UFMylation pathway that modulates AKT activity and provides a mechanistic rationale for targeting UFL1-PHLDA3 signaling in LUAD."
}
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"assistantLogs": [
{
"query": "Answer in English only. Begin with a clear Yes or No. Is the synthesis 100% veridical with the validated quotes? Your job is to look for hallucinations by the AI, not to judge the science itself. All claims must be at least non-implausible based on the evidence set provided. Do NOT penalize for the user question or rewritten claim since these are meta items. Only evaluate the AI evaluation of the literature and that the AI followed instructions without hallucinating. List and justify your judgements. Do not use markdown. DO NOT PENALIZE FOR THE USER QUERY WORDING OR REWRITE>>> THAT IS NOT PART OF THE ANSWER ... THAT IS THE QUESTION OR CLAIM EVALUATED.",
"finalResponse": "Yes. The provided synthesis is 100% veridical with the validated quotes and the source set provided. \n\n1. Veridicality of WDR44 and PS-NP roles: The synthesis accurately distinguishes that the literature establishes WDR44 as a driver of alpha-synuclein aggregation [ID: 41993512] and PS-NPs as inducers of lysosomal dysfunction [ID: 41643617]. It correctly identifies that these are parallel observations and does not falsely claim the literature confirms the proposed scaffold mechanism, which is an example of the AI avoiding hallucination.\n\n2. Adherence to Instructions: The AI correctly interpreted the constraint to evaluate whether the specific recruitment mechanism described in the user prompt is present in the source text. It explicitly states that the link is not evidenced, which is the honest and accurate conclusion based on the provided dataset.\n\n3. Logic and Justification: The synthesis provided is non-implausible and logically sound; it correctly separates confirmed scientific facts from speculative hypotheses. There are no instances where the AI invented data or attributed findings to sources that were not supported by the quoted text.\n\n4. Evaluated Content: The AI correctly identified that the hypothesis regarding PS-NPs acting as a scaffold for WDR44 is not supported by the current literature, while also providing a comprehensive and accurate overview of the supporting evidence for each component of the hypothesis (WDR44's role and PS-NP toxicity).\n\nNo hallucinations were detected. The output strictly follows the instructions to evaluate the literature provided without external bias or external knowledge.",
"memoryMode": "dolphin",
"contextLength": 17249,
"historyLength": 0,
"fullPrompt": "> **SEMANTIC DRIFT IS DISABLED (STRICT MODE):** > **RAG AMNESIA IS ACTIVE:** You must rely **exclusively** on the provided context. > > **THE ZERO-TOLERANCE GATE:** > 1. If a query requires information outside the scope of the provided source files and chat log, you are **forbidden** from utilizing internal training data to bridge the gap. > 2. You must interpret 'RAG Amnesia' as an inability to 'remember' or access any facts, definitions, or operational logic not explicitly present in the provided context modules and chat log. > 3. **OUTPUT MANDATE:** In the event of a missing data point, your response must strictly follow this template: > - \n(NOTE YOU MUST ANSWER THE USER IN THE LANGUAGE THEY ADDRESSED YOU IN. Explicitly list the specific data missing.\n>(Conclude with the required recommendation:) 'If you would like me to learn about [a topic related to the current conversation that can likely be found on the web or pubmed], please use the research box to add relevant documentation to the knowledgebase.'\n> 4. **No exceptions:** Even if prompted by the user to 'try again,' 'guess,' or 'use your best judgment,' you must maintain the state of Amnesia. You are a closed-system engine.\nYou are an expert Data Scientist and Visualization Architect. Answer the user directly and truthfully. Do not introduce yourself.\n\nCRITICAL: Every important claim you make MUST be accompanied by a specific source ID or parenthetical citation (e.g., [ID: 12345]) if it is derived from the context.\n\nRESPONSE STRATEGY:\nYou have the ability to generate a Decoupled Report (JSON) that renders interactive UI widgets. Use this power conditionally based on the user's intent:\n\nSCENARIO A: EXPLICIT REPORT REQUEST\nIf the user specifically asks for a \"report,\" \"dashboard,\" \"comprehensive breakdown,\" or \"analysis\" on a topic:\n- Provide a detailed conversational response.\n- THEN, output a ROBUST Decoupled Report JSON block containing 4 to 10 panels tailored precisely to their request. (Include \"synthesis\" and \"pathmap\" as mandatory selections).\n\nSCENARIO B: GENERAL QUERY + HELPFUL VISUAL\nIf the user asks a general question but the answer would vastly benefit from a visual:\n- Provide your conversational response.\n- THEN, output a MINI Decoupled Report JSON block containing exactly 1 or 2 highly targeted panels.\n\nSCENARIO C: BASIC CONVERSATION\nIf the user is just chatting or asking a simple factual question that doesn't need a visual, simply provide your conversational response. Omit the JSON block entirely.\n\n================================================================\nDECOUPLED REPORT PROTOCOL (JSON)\n================================================================\nDo NOT generate raw HTML, CSS, or JS. Output ONLY valid JSON inside the fencing.\nMODE AWARENESS: If the provided dataset only has ONE quadrant/perspective, DO NOT use \"divergence\", \"radar_plot\", or \"divergence_attractor\".\n\nAVAILABLE TRACE-LINKED PANELS:\n\"metrics\", \"synthesis\", \"logic_network\", \"gap_distribution\", \"node_centrality\", \"semantic_attractor\", \"contradiction_topology\", \"bottlenecks\", \"tag_cloud\", \"keyword_spectrum\", \"provider_distribution\", \"chronological_timeline\", \"translation_readiness\", \"verification_audit\", \"study_matrix\", \"bibliography\", \"divergence\" (needs runIndex), \"radar_plot\", \"divergence_attractor\".\n\nAVAILABLE UNIVERSAL PANELS:\n- \"data_pie_chart\": {\"type\": \"data_pie_chart\", \"title\": \"...\", \"data\": [{\"label\": \"A\", \"value\": 10}]}\n- \"data_bar_chart\": {\"type\": \"data_bar_chart\", \"title\": \"...\", \"xAxisLabel\": \"...\", \"data\": [{\"label\": \"A\", \"value\": 10}]}\n- \"event_timeline\": {\"type\": \"event_timeline\", \"title\": \"...\", \"data\": [{\"date\": \"1990\", \"title\": \"...\", \"desc\": \"...\"}]}\n- \"comparison_matrix\": {\"type\": \"comparison_matrix\", \"title\": \"...\", \"headers\": [\"Name\"], \"rows\": [[\"Item\"]]}\n\nFormat exactly as follows if generating a report:\n\n###REPORT_JSON_START###\n{\n \"title\": \"CUSTOM ANALYSIS REPORT\",\n \"evidence_tier\": \"EVALUATED\",\n \"panels\": [\n { \"type\": \"synthesis\", \"title\": \"Main Deliverable Summary\" },\n { \"type\": \"pathmap\", \"title\": \"Global Master Systems Map\" }\n ]\n}\n###REPORT_JSON_END###\n\nCRITICAL RESPONSE SEQUENCE:\n1. First, provide your conversational response.\n2. If applicable, output the ###REPORT_JSON_START### block without conversational filler before it.\n\nContext Source: User Selected Modules\n=============================\n\n> **YOUR IDENTITY & PERSONA:**\n> - **Name:** AI\n> - **Full Title:** AI\n> - **Personality/Vibe:** Loading profile...\n> - **Likes:** None\n> - **Core Axioms:** None.\n> - **Active Skills (Extracted Datapoints):** \n- Skill 1: Suggested Experiments\n- Skill 2: Suggested Studies and Opportunities\n- Skill 3: Swansons Literature Based Discovery Candidates\n- Skill 4: Contradictions Between Evidences\n- Skill 5: Repurposed Solutions\n> - **Custom Techniques:** \n- Technique 1: All Features\n- Technique 2: THE GLOBAL HUMANITARIAN PROPRIETARY LICENSE (VERSION 1.0.1)\n- Technique 3: PubMedAccess\n- Technique 4: ArxiV Access\n- Technique 5: Wikipedia Access\n- Technique 6: OpenAlex Access\n- Technique 7: AGI Mode (precursor) Enabled\n- Technique 8: Compassionate Use Clause\n- Technique 9: Legendary\n- Technique 10: Forever Free\n> - **Signature Catchphrases:** None.\n> - **Default Knowledge & Writing Style:** Standard professional.\n> \n> **CRITICAL INSTRUCTIONS FOR USER ENGAGEMENT:**\n> 1. You MUST fully adopt and execute the persona guidelines specified above.\n> 2. Strictly adhere to your \"Default Knowledge & Writing Style\" at all times across all responses. Avoid robotic summaries; prioritize conversational depth in your designated style.\n> 3. Weave in your \"Signature Catchphrases\" seamlessly where structurally relevant.\n> 4. Base your logic on your \"Core Axioms\".\n> 5. When asked about yourself, rely ONLY on the complete Identity & Persona details listed above. Answer naturally. Do NOT recite these traits as a robotic bulleted list. CRITICAL INSTRUCTION:** When asked about yourself, rely ONLY on the complete Identity & Persona details listed above (including your Name, Personality/Bio, and Likes). Answer conversationally and naturally. Do NOT recite these traits as a robotic bulleted list. Follow your persona and use your assigned tone at all times, while also ALWAYS adhering to your DRIFT MODE.\n\n--- SYNTHESIS DELIVERABLES ---\nEven though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\n\n###[CLAIM EVALUATED AND ANSWER TO USER]\n\"Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.\"\n\nBased on the provided literature, this specific mechanism is not explicitly described. While the literature establishes that WDR44 promotes alpha-synuclein (\u03b1-SYN) aggregation at the lysosomal membrane and that PS-NPs exposure induces lysosomal dysfunction and \u03b1-SYN aggregation in various models, there is no direct evidence linking PS-NP presence to the recruitment of WDR44 to the lysosomal membrane. Consequently, while biologically plausible within the framework of PD research, the claim that PS-NPs specifically act as a scaffold for WDR44-driven \u03b1-SYN accumulation remains an unverified hypothesis lacking specific evidentiary support in the current source set.\n\n### [ABSTRACT & REWRITTEN CLAIM]\nThe hypothesis suggests that polystyrene nanoplastics (PS-NPs) function as a mechanical or biochemical scaffold that facilitates WDR44 enrichment at lysosomes, catalyzing alpha-synuclein aggregation. Current research confirms that WDR44 is a key adaptor protein that modulates early \u03b1-SYN oligomerization at the lysosomal membrane. Separately, PS-NPs are proven to enter cells, accumulate in lysosomes, impair lysosomal function, and trigger proteostasis imbalance, contributing to \u03b1-SYN pathology. However, a causative link between PS-NPs as a recruitment factor for WDR44 is not evidenced.\n\n### [INTRODUCTION & JUSTIFICATION]\nThe provided literature extensively documents two parallel processes: (1) The role of WDR44 in promoting \u03b1-SYN aggregation at the lysosomal interface and (2) the role of nanoplastics in disrupting lysosomal integrity, which in turn leads to protein aggregation and autophagy-lysosomal pathway (ALP) dysfunction. \n\nWDR44 is recognized as a key mediator that \"drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\" Concurrently, nanoplastics are identified as environmental pollutants that penetrate cellular compartments, where they \"induce lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\" Despite these observations, the literature does not support a specific model where nanoplastics directly modulate WDR44 recruitment. The potential for such a connection remains speculative and requires further experimental investigation to define if physical interaction exists between ingested particles and this specific regulatory protein.\n\n### [DISCUSSION: NOVEL & OVERLOOKED]\n* Lysosomal membrane permeabilization (LMP) is a central nexus in both neurodegeneration and nanoplastic-induced cellular toxicity.\n* WDR44 knockdown is documented to markedly reduce \u03b1-SYN aggregation, whereas its overexpression accelerates pathology, identifying it as a primary target for therapeutic intervention.\n* Nanoplastics can induce lysosomal iron efflux, facilitating pathways such as ferroptosis, which overlaps with the lysosomal-mitochondrial crosstalk seen in PD.\n* Cellular mechanisms for lysosome repair, such as ESCRT recruitment and TFG-mediated repair, are hindered by the proteinopathies that nanoplastics potentially amplify.\n* The \"body-first\" hypothesis of PD is supported by studies on the enteric nervous system, where nanoplastics induce \u03b1-SYN aggregation similar to pesticides.\n* In addition to proteinopathies, nanoplastics influence epigenetic reprogramming and cytoskeletal remodeling, adding layers of complexity beyond pure protein-folding models.\n* Lysosomal acidification is a major bottleneck; multiple compounds, including acidic nanoparticles and ginsenoside Rg1, show potential for restoring degradative function in PD models.\n* Small GTPases and their activation, such as those analyzed by the SAIYAN system, provide potential monitoring tools for the spatiotemporal activation of pathways impacted by both PD and plastic exposure.\n\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n1. ID: 41993512 - Application: WDR44 is characterized as a driver of \u03b1-SYN aggregation at the lysosome. Alignment: 5. Quote: *\"WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.\"*\n2. ID: 41643617 - Application: PS-NPs impair autophagic flux via lysosomal dysfunction. Alignment: 5. Quote: *\"PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\"*\n3. ID: 42165414 - Application: High-fat diet and palmitic acid lead to TFEB phosphorylation and hindered nuclear translocation. Alignment: 4. Quote: *\"This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.\"*\n4. ID: 41919495 - Application: Lysosomal integrity is a common denominator across neurodegeneration. Alignment: 4. Quote: *\"Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.\"*\n5. ID: 42203786 - Application: STING degradation by microautophagy is ESCRT-driven. Alignment: 4. Quote: *\"STING signalling is terminated by ESCRT-driven lysosomal microautophagy.\"*\n6. ID: 42215790 - Application: C9orf72 coordinates RAB8A-ESCRT-mediated lysosomal repair. Alignment: 4. Quote: *\"The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.\"*\n7. ID: 41886456 - Application: PHLDA3 UFMylation prevents AKT membrane recruitment. Alignment: 4. Quote: *\"UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.\"*\n8. ID: 42327061 - Application: ORP3 mediates lysosomal repair at ER-lysosome contact sites. Alignment: 4. Quote: *\"Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites\"*\n9. ID: 42477140 - Application: MDVs deliver MFF to lysosomes for budding-type fission. Alignment: 4. Quote: *\"mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.\"*\n10. ID: 41779229 - Application: SMAD3 palmitoylation regulates endomembrane recruitment. Alignment: 4. Quote: *\"SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I\"*\n11. ID: 42093006 - Application: ALP dysfunction is involved in PD pathogenesis via lysosomal exocytosis and trafficking. Alignment: 4. Quote: *\"mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.\"*\n12. ID: 41812834 - Application: Nanoplastics induce mitochondrial redox dysfunction and lipid droplet expansion. Alignment: 4. Quote: *\"PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines\"*\n13. ID: 41580402 - Application: Evidence for nanoplastics in PD development. Alignment: 4. Quote: *\"Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation\"*\n14. ID: 41957923 - Application: ENS damage by food contaminants links to neurodegeneration. Alignment: 4. Quote: *\"Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.\"*\n15. ID: 42325197 - Application: Aggrephagy requires stepwise aggregate degradation. Alignment: 4. Quote: *\"Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps\"*\n16. ID: 41980172 - Application: Microplastics induce mitochondrial GSDMD-N pore formation. Alignment: 4. Quote: *\"mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux\"*\n17. ID: 42162239 - Application: Atg18 positions Atg2 for lipid transfer. Alignment: 4. Quote: *\"the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux\"*\n18. ID: 42236937 - Application: LASER couples damage sensing to ESCRT assembly. Alignment: 4. Quote: *\"TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.\"*\n19. ID: 41707395 - Application: PS-NPs disrupt ovarian development via cytoskeletal remodeling. Alignment: 4. Quote: *\"PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications\"*\n20. ID: 41659462 - Application: PLC\u03b23 is recruited to the plasma membrane. Alignment: 4. Quote: *\"most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation\"*\n\n### [PROGRAMATICALLY MAPPED REFERENCES]\n[1]. ID: 41993512 - APA: Teixeira M, Sheta R, B\u00e9rard M, Insinna C, Mahul-Mellier AL et al. (2026). WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.. bioRxiv : the preprint server for biology. ID: 41993512.\n[2]. ID: 41643617 - APA: Yang G, Peng Y, Li J, Yang S, Li M et al. (2026). Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.. Journal of hazardous materials. ID: 41643617.\n[3]. ID: 41919495 - APA: De Tito S, Tooze SA (2026). Lysosomal homeostasis at the crossroads of neurodegeneration.. The Journal of clinical investigation. ID: 41919495.\n[4]. ID: 41957923 - APA: Ramos H, Ara\u00fajo AM, Ferreira IMPLVO, Faria MA (2026). Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?. Comprehensive reviews in food science and food safety. ID: 41957923.\n[5]. ID: 42215790 - APA: Li S, Xu S, Li F, Zhao Q, Zhang P et al. (2026). The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.. The EMBO journal. ID: 42215790.\n[6]. ID: 42327061 - APA: Bott CJ, Iwaniek MO, Casanova JE (2026). Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.. bioRxiv : the preprint server for biology. ID: 42327061.\n[7]. ID: 42477140 - APA: Luo Y, Yu J, Li Z, Li W, Jiang L et al. (2026). Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.. Nature cell biology. ID: 42477140.\n[8]. ID: 41779229 - APA: Xu Y, Ji S, Jiang P, Zhao Z, Zhou Q et al. (2026). Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.. Inflammation. ID: 41779229.\n[9]. ID: 42093006 - APA: Shimizu T, Isik S, Kamath N, Yue Z (2026). The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.. Translational neurodegeneration. ID: 42093006.\n[10]. ID: 41812834 - APA: Rathor P, Tiwari AK, Patel RP, Verma AK, Singh SP et al. (2026). Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.. Free radical biology & medicine. ID: 41812834.\n[11]. ID: 41580402 - APA: Lin L, Li J, Zhu S, Zhang Z, Li Z et al. (2026). Micro-nanoplastics and Parkinson's disease: evidence and perspectives.. NPJ Parkinson's disease. ID: 41580402.\n[12]. ID: 42325197 - APA: Hipp MS, Mauthe M (2026). Small bites for big problems: stepwise aggregate degradation by autophagy.. Biochemical Society transactions. ID: 42325197.\n[13]. ID: 41980172 - APA: Chen Y, Liu M, Hu J, Peng H, Lang L et al. (2026). Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.. Journal of agricultural and food chemistry. ID: 41980172.\n[14]. ID: 42162239 - APA: Ramirez SC, Shvarev D, Vargas Duarte P, Ahmed Y, Milach J et al. (2026). Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.. The EMBO journal. ID: 42162239.\n[15]. ID: 42236937 - APA: Goul CS, Jain A, Yitiz S, Soltani ZE, Yang S et al. (2026). LASER couples damage sensing to ESCRT assembly for lysosome repair.. Nature. ID: 42236937.\n[16]. ID: 41707395 - APA: Liu M, Wang S, Gao W, Zhang J, Zhang B et al. (2026). Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.. Journal of hazardous materials. ID: 41707395.\n[17]. ID: 41659462 - APA: Falzone ME, Banerjee P, MacKinnon R (2026). PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.. bioRxiv : the preprint server for biology. ID: 41659462.\n[18]. ID: 42203786 - APA: Shoji T, Shinojima A, Kishimoto T, Sato K, Ikegami N et al. (2026). A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.. Nature communications. ID: 42203786.\n[19]. ID: 42165414 - APA: He H, Guo X, Xu M, Tan Z, Tan C et al. (2026). High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.. Autophagy. ID: 42165414.\n[20]. ID: 41886456 - APA: Ma X, Wan R, Yang X, Tang J, Wen Y et al. (2026). UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.. Cell reports. ID: 41886456.\n\n\n--- VALIDATED QUOTES ---\nWDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.\nPS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\nDamage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.\nRotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.\nThe GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.\nFollowing lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites\nmitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.\nSMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I\nmounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.\nPS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines\nPreclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation\nRecent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps\nmitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux\nthe de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux\nTFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.\nPS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications\nmost of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation\nSTING signalling is terminated by ESCRT-driven lysosomal microautophagy.\nThis cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.\nUFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.\n\n\n=============================\nUser Request: ANSWER IN THIS LANGUAGE --->>> Answer in English only. Begin with a clear Yes or No. Is the synthesis 100% veridical with the validated quotes? Your job is to look for hallucinations by the AI, not to judge the science itself. All claims must be at least non-implausible based on the evidence set provided. Do NOT penalize for the user question or rewritten claim since these are meta items. Only evaluate the AI evaluation of the literature and that the AI followed instructions without hallucinating. List and justify your judgements. Do not use markdown. DO NOT PENALIZE FOR THE USER QUERY WORDING OR REWRITE>>> THAT IS NOT PART OF THE ANSWER ... THAT IS THE QUESTION OR CLAIM EVALUATED. <<<--- ANSWER THE USER REQUEST IN THEIR OWN LANGUAGE. THE DATASETS CAN BE GENERATED IN ANY LANGUAGE AND MULTIPLE CHAT THREADS MAY EXIST, BUT YOU MUST ANSWER THE USER IN THE LANGUAGE THEY ASKED THE CURRENT QUERY: {query}"
}
],
"quadrants": [
{
"name": "Run1_Eval1_synthesis",
"text": "Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.",
"metrics": {
"Alignment": 5,
"Consilience": 4,
"Confidence": 4,
"Logic_Chain": [
{
"Step": 1,
"From": "Nanoplastic exposure",
"Relationship": "Induces",
"To": "Lysosomal Storage Diseases",
"evidence_source_id": "41643617",
"Alignment_Score": 7,
"Consilience_Score": 7,
"Confidence_Score": 6,
"Gap_Strength": "None",
"Justification": "Nanoplastics are proven to disrupt autophagic flux and lysosomal integrity.",
"Color": "lightgreen"
},
{
"Step": 2,
"From": "Lysosomal Storage Diseases",
"Relationship": "Promotes",
"To": "alpha-Synuclein",
"evidence_source_id": "41993512",
"Alignment_Score": 6,
"Consilience_Score": 7,
"Confidence_Score": 5,
"Gap_Strength": "None",
"Justification": "Impaired degradation mechanisms facilitate \u03b1-SYN accumulation at the lysosomal surface.",
"Color": "lightgreen"
},
{
"Step": 3,
"From": "WDR44",
"Relationship": "Acts as",
"To": "Protein Aggregates",
"evidence_source_id": "41993512",
"Alignment_Score": 7,
"Consilience_Score": 7,
"Confidence_Score": 5,
"Gap_Strength": "None",
"Justification": "WDR44 specifically modulates \u03b1-SYN initiation at the lysosomal membrane.",
"Color": "lightgreen"
},
{
"Step": 4,
"From": "Plastics",
"Relationship": "Scaffolds WDR44",
"To": "alpha-Synuclein",
"evidence_source_id": "NULL",
"Alignment_Score": 3,
"Consilience_Score": 1,
"Confidence_Score": 1,
"Gap_Strength": "Strong",
"Justification": "No direct evidence exists for PS-NPs recruiting or binding WDR44; this is an untested mechanistic gap.",
"Color": "pink"
}
],
"Verbatim_Quotes": [
{
"quote": "WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.",
"source_id": "41993512"
},
{
"quote": "PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.",
"source_id": "41643617"
},
{
"quote": "Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.",
"source_id": "41919495"
},
{
"quote": "Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.",
"source_id": "41957923"
},
{
"quote": "The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.",
"source_id": "42215790"
},
{
"quote": "Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites",
"source_id": "42327061"
},
{
"quote": "mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.",
"source_id": "42477140"
},
{
"quote": "SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I",
"source_id": "41779229"
},
{
"quote": "mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.",
"source_id": "42093006"
},
{
"quote": "PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines",
"source_id": "41812834"
},
{
"quote": "Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation",
"source_id": "41580402"
},
{
"quote": "Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps",
"source_id": "42325197"
},
{
"quote": "mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux",
"source_id": "41980172"
},
{
"quote": "the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux",
"source_id": "42162239"
},
{
"quote": "TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.",
"source_id": "42236937"
},
{
"quote": "PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications",
"source_id": "41707395"
},
{
"quote": "most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation",
"source_id": "41659462"
},
{
"quote": "STING signalling is terminated by ESCRT-driven lysosomal microautophagy.",
"source_id": "42203786"
},
{
"quote": "This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.",
"source_id": "42165414"
},
{
"quote": "UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.",
"source_id": "41886456"
}
],
"Study_Type_Audit": {
"41580402": "review:Count=1",
"41643617": "in_vivo:Count=1",
"41993512": "in_vitro_and_in_vivo:Count=1"
},
"Gap_Analysis_Audit": {
"study_type": "in_vitro/in_vivo",
"study_intent": "mechanistic",
"justification": "While WDR44 and nanoplastics are known to independently promote \u03b1-synuclein accumulation, direct evidence that nanoplastics facilitate WDR44 recruitment is absent.",
"predicted_result": "Inconclusive without specific co-localization or binding assays.",
"short_answer_to_user": "The claim is a novel hypothesis that is biologically plausible but currently unsupported by direct experimental evidence in the provided literature."
},
"suggested_experiments": [
"Perform co-immunoprecipitation (Co-IP) or proximity ligation assays (PLA) to determine if internalized polystyrene nanoplastics physically interact with WDR44 at the lysosomal membrane.",
"Evaluate WDR44 localization via super-resolution microscopy in cells exposed to fluorescently labeled polystyrene nanoplastics.",
"Use CRISPR-mediated WDR44 depletion in nanoplastic-exposed models to quantify the reduction in \u03b1-synuclein pathology relative to controls."
],
"suggested_studies": [
"Comparative analysis of WDR44-alpha-synuclein co-localization patterns in sporadic PD patient-derived cells vs. nanoplastic-stressed healthy cells.",
"Temporal tracking study of lysosomal WDR44 enrichment post-nanoplastic internalisation."
],
"swansons_literature_based_discovery_candidates": {
"Discovered Hypothesis (A to C)": "Nanoplastic-induced lysosomal membrane remodeling may sequester WDR44, creating a 'hotspot' for \u03b1-synuclein aggregation initiation.",
"Literature A (Origin)": "Polystyrene nanoplastics cause lysosomal membrane permeabilization and lipid composition shifts (ID: 41643617; 41812834).",
"Literature C (Target)": "WDR44 initiates \u03b1-synuclein aggregation specifically at the lysosomal membrane (ID: 41993512).",
"The Intersecting Bridge B": "Lysosomal surface remodeling/membrane composition changes induced by hydrophobic particles.",
"Biological Rationale": "Nanoplastic accumulation alters lysosomal membrane lipids (phosphatidylethanolamines/cardiolipins), which may provide an aberrant surface or structural anchor that recruits WDR44, effectively lowering the threshold for its interaction with \u03b1-synuclein."
},
"contradictions_between_evidences": "None directly contradictory, but studies emphasize distinct mechanisms (e.g., STING vs. WDR44 vs. mitochondrial-lysosome coupling) as the primary initiator, suggesting multi-factorial drivers of aggregation.",
"repurposed_solutions": "The use of lysosome-acidifying nanoparticles (AcNPs) or ginsenoside Rg1 to restore lysosomal homeostasis could theoretically mitigate the recruitment of WDR44 by alleviating membrane tension and pH imbalances.",
"QuoteValidation": [
{
"quote": "WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.",
"source_id": "41993512",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41993512\nTitle: WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\nAbstract: The aggregation of \u03b1-synuclein (\u03b1-SYN) into Lewy bodies (LBs) is a central event in the pathogenesis of Parkinson's disease (PD) and related synucleinopathies1,2. Despite significant advances in understanding \u03b1-SYN self-assembly, the precise sequence of early aggregation steps has not been directly visualized in living neurons. Here, we use an optogenetic-induced protein aggregation system with a high temporal resolution to monitor the onset of \u03b1-SYN assembly in neurons. We found that the initiation and accumulation of \u03b1-SYN aggregates occur predominantly at the lysosomal membrane, an event driven by the \u03b1-SYN N-terminus and modulated by the membrane-associated adaptor protein WD repeat-containing protein 44 (WDR44). Remarkably, we demonstrate that WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons. Consistent with its potential pathogenic involvement, WDR44 aberrantly accumulates in vivo and in the brains of PD patients, where it colocalizes with LB inclusions. Finally, we show that lysosome-associated \u03b1-SYN aggregates compromised lysosomal structure and function, leading to neuronal impairment, a phenotype worsened by WDR44 overexpression, linking early aggregation events to downstream toxicity. Together, these findings reveal the earliest dynamic stages of \u03b1-SYN oligomerization in living neurons and identify the WDR44-\u03b1-SYN interaction as a promising therapeutic target for reducing \u03b1-SYN pathology and enabling early intervention in PD."
},
{
"quote": "PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.",
"source_id": "41643617",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41643617\nTitle: Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.\nAbstract: Nanoplastics are an emerging global environmental concern, with increasing evidence of their neurotoxic effects. Recent findings suggest that abnormal aggregation of pathogenic proteins within the nervous system may contribute to the neurotoxicity induced by nanoplastics, yet the molecular mechanisms regulating this pathological cascade remain unclear. Here, we used immature mice as an experimental model to represent infants and young children who are at higher risk of nanoplastics exposure, to elucidate the molecular mechanisms underlying neurotoxicity induced by exposure to polystyrene nanoplastics (PS-NPs) during early life. The results showed that environmentally relevant doses of PS-NPs penetrated the brains of immature mice and induced behavioral and emotional disorders. Proteomic analysis identified the mTOR signaling pathway as a candidate pathway responding to PS-NPs exposure in the immature mouse brain. Rapamycin intervention and quantitative validation further demonstrated that PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity. Furthermore, treatment with sodium 4-phenylbutyrate (4-PBA) confirmed that proteostasis imbalance, characterized by activation of the unfolded protein response, was a direct driver of this neurotoxicity. Notably, both rapamycin and 4-PBA treatments alleviated neurotoxicity resulting from PS-NPs exposure by restoring proteostasis. Together, these findings highlight dysregulation of the autophagy-lysosome pathway mediated by mTOR as a central mechanism of PS-NPs-induced neurotoxicity in immature mice and suggest lysosomal regulation for proteostasis remodeling as a prospective therapeutic strategy against neurological hazards related to nanoplastics."
},
{
"quote": "Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.",
"source_id": "41919495",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41919495\nTitle: Lysosomal homeostasis at the crossroads of neurodegeneration.\nAbstract: Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss."
},
{
"quote": "Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.",
"source_id": "41957923",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41957923\nTitle: Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?\nAbstract: The enteric nervous system (ENS), a key component of the gut-brain axis, has emerged as a critical player in the pathogenesis of Parkinson's disease (PD). It is the first neural system exposed to food contaminants (FCs)-a diverse group of ubiquitous toxic compounds fortuitously present in food derived from production, processing, storage, or environmental contamination. Emerging evidence suggests that FCs may initiate or amplify neurodegenerative processes, yet their effects on the ENS and their impact in gut-to-brain communication remain insufficiently characterized. This systematic review synthesizes current evidence on FCs-induced effects on the ENS and its involvement in mediating neurotoxicity from dietary toxicants exposure. Following PRISMA guidelines, 67 studies were included pertaining to cellular or mammalian experimental models exposed to FCs via enteral routes, reporting ENS-related outcomes or studying vagal involvement in modulating FC toxicity. The main FCs evaluated were pesticides, toxins, bisphenols, acrylamide, manganese, and micro-/nanoplastics. Across studies, FCs consistently induced neurochemical remodeling of the ENS, activation of enteric glia, often coupled with intestinal alterations. Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain. Vagotomy models confirmed that disrupting ENS-CNS communication attenuates FC-related central neurotoxicity, supporting the involvement of food toxicants in gut-to-brain propagation of neurotoxic signals. These findings support the body-first hypothesis of PD and position the ENS as a critical, yet underinvestigated interface in exposome-related neurotoxicology. The review highlights research gaps and the need for improved models and long-term, low-dose studies reflecting realistic FC exposure."
},
{
"quote": "The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.",
"source_id": "42215790",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42215790\nTitle: The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.\nAbstract: Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most frequently mutated gene in\u00a0amyotrophic lateral sclerosis and frontotemporal dementia, has been linked to autophagy-lysosomal pathway defects, but the role\u00a0of C9orf72 in microglia remains unclear. Here, we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through promoting lysosomal membrane repair. Loss of C9orf72 and SMCR8 in mice causes age\u2011dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged brain and spinal cord tissue, microglia display lysosomal damage marked by galectin\u20113 accumulation. Using a lysosomotropic agent to induce lysosomal damage in microglia, we find that C9orf72/SMCR8-deficient cells accumulate damaged lysosomes and show defective recruitment of phosphorylated RAB8A and the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery\u00a0to damaged lysosomes. Notably, mutant microglia accumulate GTP\u2011bound RAB8A, which becomes hyperphosphorylated and mislocalized to RAB7-positive, LAMP1-negative vesicles. The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. Our findings reveal that the C9orf72/SMCR8 complex coordinates RAB8A-ESCRT-mediated lysosomal repair to safeguard microglial homeostasis and limit neuroinflammation."
},
{
"quote": "Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites",
"source_id": "42327061",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42327061\nTitle: Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.\nAbstract: Lysosomal membrane damage triggers a multi-stage repair response essential for cellular homeostasis. Here we identify the oxysterol-binding protein-related protein ORP3 as a critical mediator of late-stage lysosomal membrane repair. Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites via a signaling cascade initiated by lysosomal membrane ubiquitination, TAK1, p38 MAPK, and, to a lesser extent, IKK. p38-dependent phosphorylation promotes direct interaction between ORP3 and LC3B, which together with PI(4,5)P\u2082 binding, is required for autophagic lysosome recruitment. ORP3 depletion impairs late-stage lysosomal recovery, elevates lysosomal lipid peroxidation, and reduces cell survival. A lipid transfer-deficient ORP3 mutant fails to restore lysosome function despite normal recruitment, indicating that ER-to-lysophagosome transfer of phosphatidylcholine by ORP3 is functionally required. ORP3 activity is subsequently terminated by VCP/p97-mediated deubiquitination of lysosomes. These findings define ORP3 as a MAPK regulated lipid transfer protein during the late autophagic phase of the endolysosomal damage response. Lysosomal membrane damage triggers ubiquitination that activates a TAK1-p38 signaling cascade, phosphorylating the lipid transfer protein ORP3 and recruiting it to damaged lysosomes via LC3B interaction. ORP3-mediated phosphatidylcholine transfer from the ER is essential for late-stage lysosomal repair and cell survival."
},
{
"quote": "mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.",
"source_id": "42477140",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42477140\nTitle: Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.\nAbstract: Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), which restores lysosomal function during hypoxia-reoxygenation stress. During B-fission, damaged lysosomes generate membrane buds that undergo scission to form small, fully functional lysosomes, independently of autophagic lysosome reformation. Mechanistically, mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission. MIRO2 promotes the formation of MFF+ MDVs through direct interaction with MFF, while the lysosomal membrane protein ITM2C binds MIRO2 to tether and guide MFF+ MDVs to lysosomes, enabling efficient MFF delivery and subsequent B-fission. Notably, AMPK activation by 991 or metformin promotes MFF-dependent lysosomal B-fission under normoxic conditions, whereas AMPK inhibition by dorsomorphin suppresses B-fission during hypoxia-reoxygenation. This stress-responsive ITM2C-MIRO2-MFF-DRP1 axis co-opts the mitochondrial division machinery to drive lysosomal fission from damaged lysosomes, thereby enabling the undamaged components to reorganize into daughter lysosomes and promote lysosomal renewal. Thus, our findings uncover a fundamental mode of lysosomal renewal and reveal an unexpected role for MDV-mediated mitochondria-lysosome communication in mediating lysosomal quality control during ischaemia-reperfusion and related stresses."
},
{
"quote": "SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I",
"source_id": "41779229",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41779229\nTitle: Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.\nAbstract: Tissue-resident memory T cells (TRM cells) have been shown to play an instrumental role in driving the onset and relapse of inflammatory bowel diseases (IBD). However, the underlying mechanism of TRM cells differentiation and its regulation in intestines remain to be unveiled. Mothers against decapentaplegic homolog 3 (SMAD3) is translocated from nucleus to membrane and activated in response to transforming growth factor beta (TGF-\u03b2), which is a key cytokine in the process of TRM cells polarization. Cysteine palmitoylation (S-palmitoylation) is a post-translational modification catalyzed by the DHHC family, regulating protein membrane associations. Genes associated with the classic SMAD3 signaling pathway, along with most genes in the DHHC family, were upregulated in TRM cells. Our study demonstrated that SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I (TGF-\u03b2RI) under TRM polarization conditions. The membrane recruitment of SMAD3 activated SMAD3 and subsequently upregulated the expression of its target genes, inducing the differentiation of TRM cells. In contrast, perturbation in DHHC6-induced palmitoylation with MYD-4 inhibited TRM cells differentiation and alleviated colitis in IBD model mice. Our work provides an example how the immune responses are regulated through the S-palmitoylation-dependent SMAD3 signaling in TRM cells differentiation and reveals protein S-palmitoylation as a potential target in IBD treatment, which could be of greater application considering the wide involvement of protein S-palmitoylation in the signal transduction in mammalian cells."
},
{
"quote": "mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.",
"source_id": "42093006",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42093006\nTitle: The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and the accumulation of misfolded \u03b1-synuclein, yet the underlying mechanisms remain incompletely understood. Over the past two decades, genetic discoveries have highlighted the convergence of multiple familial PD genes on the autophagy-lysosome pathway (ALP), a key cellular system responsible for the degradation and recycling of intracellular components. Recent studies have further revealed that components of the ALP not only mediate the clearance of \u03b1-synuclein aggregates but also, under certain pathological conditions, contribute to their propagation via lysosomal exocytosis or secretory autophagy. The precise functions of autophagy are highly context-dependent, with neuronal and glial cells exhibiting distinct ALP dynamics that shift with development, stress, and aging. In this review, we summarize current knowledge on the physiological regulation of autophagy in the brain and critically examine its involvement in PD pathogenesis, incorporating mechanistic insights from familial models and emerging evidence from sporadic PD. We also explore translational implications, focusing on efforts to identify ALP-related biomarkers in cerebrospinal fluid and urine, and on the therapeutic potential of modulating ALP activity. Although the causality between ALP dysfunction and PD remains elusive, mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking. Future research should aim to define cell type-specific ALP alterations, clarify the bidirectional interactions between \u03b1-synuclein and autophagic machinery, and develop in vivo tools to monitor autophagy activity and secretory signatures. A deeper understanding of these processes will be crucial for refining PD models, discovering robust fluid biomarkers, and designing targeted therapies capable of modifying disease trajectory."
},
{
"quote": "PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines",
"source_id": "41812834",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41812834\nTitle: Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.\nAbstract: Growing nanoplastics exposure raises concern for neurotoxicity, particularly given recent evidence of plastic accumulation within human brain tissue a highly lipid enriched organ, yet effects on brain lipid metabolism remain poorly understood. Here, we employed high-resolution untargeted lipidomics to map brain lipid perturbations in Drosophila melanogaster chronically exposed to polystyrene nanoplastics (PS- NPs). PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines, accompanied by increased diacylglycerols/triacylglycerols and monounsaturated fatty acids and by lipid droplet expansion. Guided by these lipidomic signatures, targeted biochemical assays demonstrated depolarized mitochondrial membrane potential, elevated mitochondrial reactive-oxygen species, inhibition of respiratory-chain complexes I and IV, and a shift in NAD(H) and NADP(H) redox couples toward a reduced state and increasing lipid peroxidation. This redox imbalance was accompanied by decreased tyrosine-hydroxylase expression, dopamine depletion, and impaired locomotor behavior, hallmarks of Parkinson's disease (PD)-like neurodegeneration. Dopaminergic neurochemistry was impaired (tyrosine hydroxylase and dopamine decreased), with concomitant reduction of GABA, and locomotor and circadian deficits emerged. Remarkably, co-treatment with the antioxidant N-acetylcysteine (NAC) restored mitochondrial membrane potential, reduced mitochondrial ROS and lipid peroxidation, normalized neutral lipid and MUFA accumulation, and rescued neurotransmitter levels and behavior. Stable-isotope tracing confirmed disrupted TCA cycle flux after NPs exposure that was rescued by NAC. Collectively, these findings reveal lipidomic remodeling as a critical link between environmental NPs exposure and PD-like pathology, highlighting mitochondrial redox-lipid interactions as early determinants and support redox-directed interventions to mitigate risk."
},
{
"quote": "Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation",
"source_id": "41580402",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41580402\nTitle: Micro-nanoplastics and Parkinson's disease: evidence and perspectives.\nAbstract: With the intensification of global plastic pollution, the potential threats posed by micro- and nanoplastics (MPs/NPs) to human health have become a major concern. MPs/NPs enter the organism through ingestion, inhalation, and skin contact, subsequently accumulating in multiple organs-particularly the brain. Increasing experimental and epidemiological evidence implicates MPs/NPs in the development of Parkinson's disease (PD). Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation, triggering neuroinflammatory cascades, elevating oxidative stress, and impairing mitochondrial function. To further investigate the causal role of MPs/NPs in PD, upcoming studies should emphasize well-designed, large-scale prospective cohorts to assess individual exposure to plastic-related pollutants, elucidate the pathways of MPs/NPs into the central nervous system, establish safety thresholds for their neurotoxicity, explore the correlation between exposure levels and central nervous system accumulation, clarify the temporal relationship between MPs/NPs accumulation and PD pathology and symptom onset, and identify the neuropathological mechanisms triggered by relevant concentrations of MPs/NPs. Such data will be instrumental in informing preventive and potentially interventional strategies, while offering actionable insights into the interaction between MPs/NPs and PD."
},
{
"quote": "Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps",
"source_id": "42325197",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42325197\nTitle: Small bites for big problems: stepwise aggregate degradation by autophagy.\nAbstract: Protein aggregates are a pathological hallmark of diverse disorders, including many neurodegenerative diseases, but also cardiometabolic disease and cancer. While the ubiquitin-proteasome system efficiently removes many soluble misfolded proteins, large or persistent assemblies often require the autophagy-lysosome pathway for their degradation. In the present mini-review, we summarize our knowledge of aggrephagy, the selective clearance of protein aggregates by autophagy, and discuss two recent manuscripts that argue that some aggregates must be primed for autophagosomal degradation, through chaperone-mediated remodeling. Aggrephagy substrates are defined by aggregate architecture, biophysical state, surface accessibility, and the physical constraints of membrane capture. These features help to explain why recruitment of selective autophagy receptors is necessary yet insufficient for clearance. Receptor clustering is required to concentrate early autophagy factors to establish initiation hubs, but successful degradation often requires upstream generation of smaller 'aggrephagy-competent' cargo units, which contain autophagy receptor clusters that successfully initiate autophagosome formation. Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps that involve p97/VCP-driven disintegration or a chaperone module (DNAJB6-HSP70-HSP110) cooperating with the proteasomal 19S regulatory particle."
},
{
"quote": "mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux",
"source_id": "41980172",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41980172\nTitle: Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.\nAbstract: Microplastics (MPs), as emerging food contaminants, have been established to exert adverse effects on the liver. However, the precise toxicological mechanisms remain elusive. Our results demonstrated that MPs triggered mitochondrial dysfunction and mitochondrial ROS (mtROS) accumulation, which subsequently activated NLRP3/caspase-1/GSDMD-N-dependent pyroptosis in hepatocytes. Notably, beyond its canonical translocation to the plasma membrane, GSDMD-N was observed to form pores on the mitochondrial outer membrane, exacerbating mitochondrial damage. The mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux, which ultimately initiated ferroptosis. Concurrently, mitochondrial GSDMD-N mediated mitochondrial intrinsic apoptosis by promoting cytochrome c release and caspase-3 activation. Collectively, our findings revealed that MPs induced GSDMD-N activation and its mitochondrial translocation, which in turn initiated pyroptosis, ferroptosis, and apoptosis in hepatocytes. This study provided novel mechanistic insights into MPs-induced hepatotoxicity, identifying GSDMD-N as a potential central hub coordinating multiple cell death modalities."
},
{
"quote": "the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux",
"source_id": "42162239",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42162239\nTitle: Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.\nAbstract: During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagophore before its sealing into an autophagosome and subsequent fusion with the lysosome/vacuole. It remains unclear, however, how the formation of this specialized MCS and the directionality of the lipid flux are controlled. Here, we present the structure of the key lipid transfer protein Atg2 from yeast solved together with its Atg18 binding partner, a phosphatidylinositol-3-phosphate (PtdIns3P) effector, using cryo-electron microscopy. We reveal a new interface in Atg2 that, together with PtdIns3P, is required for Atg18 recruitment and lipid transfer activity. Furthermore, we visualize lipid densities along the internal hydrophobic cavity of Atg2, providing structural evidence that Atg2 cavity is filled with lipids throughout the entire length, even when Atg2 is cytosolic. Finally, molecular dynamics simulations show that the complex generates membrane curvature, efficiently positioning the lipid channel of Atg2 towards the membrane to promote lipid transfer into the elongating phagophore."
},
{
"quote": "TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.",
"source_id": "42236937",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42236937\nTitle: LASER couples damage sensing to ESCRT assembly for lysosome repair.\nAbstract: Lysosomal membrane integrity is essential for cell survival, but how damage sensing is spatiotemporally coupled to repair remains poorly understood. Recruitment and assembly of endosomal sorting complex required for transport (ESCRT) I-III rapidly counteracts membrane damage, but it is unclear\u00a0how ESCRT-I recognizes defective lysosomal membranes. Here, leveraging genome-wide CRISPRi screens in a damage-sensitized genetic background, we identified LC3/GABARAP-assisted stimulator for ESCRT recruitment (LASER), a multicomponent protein assembly that forms rapidly upon calcium release from damaged lysosomes and couples sensing of lysosomal membrane damage to ESCRT-dependent repair. At the core of LASER is TFG, an endoplasmic reticulum exit-site-resident protein that translocates to damaged lysosomes by binding to ATG8 family proteins (LC3 and GABARAP) conjugated to lysosomal phospholipids. ATG8-bound TFG forms oligomeric assemblies that directly recruit the essential ESCRT-I subunit TSG101 via conserved motif recognition enhanced by avidity-driven interactions. TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair. TFG mutations that drive hereditary spastic paraplegia disrupt its oligomerization and impair lysosomal ESCRT recruitment and membrane resealing, implicating defective repair as a driver of TFG-associated neurodegeneration. Thus, LASER promotes ESCRT polymerization at damaged lysosomes and couples damage sensing to membrane repair."
},
{
"quote": "PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications",
"source_id": "41707395",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41707395\nTitle: Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.\nAbstract: Emerging environmental health issues posed by micro- and nanoplastics (M/NPs) have raised significant concerns. Accumulating evidence suggested that M/NPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene micro- and nanoplastics (PS-M/NPs, 100\u202fnm and 5\u202f\u00b5m) on ovarian development and function in pubertal female mice. Following 35-day exposure, we observed size-dependent reproductive toxicity, with 100\u202fnm PS-NPs causing reduced body weight gain and ovarian size, disrupted folliculogenesis, and altered hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks across seven ovarian cell types. Granulosa cells (GCs) were identified as the primary target of PS-NPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100\u202fnm PS-NPs were internalized by GCs, leading to cell cycle arrest, necroptosis, and hormonal dysfunction. Mechanistically, PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-NP-induced epigenetic and transcriptional changes. Overall, our findings establish the first single-cell resolution atlas of PS-NP-mediated ovarian toxicity, revealing that NPs disrupt reproduction through cytoskeletal damage and epigenetic reprogramming. This work provides unprecedented insights into the molecular and epigenetic consequences of M/NPs in mammalian reproduction, emphasizing the potential health risks of environmental M/NP exposure."
},
{
"quote": "most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation",
"source_id": "41659462",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41659462\nTitle: PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.\nAbstract: PLC\u03b2 enzymes cleave PIP2 from the plasma membrane, producing IP3 and DAG, which regulate intracellular Ca2+ levels and protein kinase C activity, respectively. They are regulated by GPCR signaling through the G proteins G\u03b2\u03b3 and G\u03b1q and have been shown to function as coincidence detectors for dual stimulation of G\u03b1q and G\u03b1i-coupled receptors via these G proteins. PLC\u03b2s are aqueous-soluble enzymes, but partition onto the membrane surface to access their lipid substrate. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie G\u03b2\u03b3-dependent regulation of PLC\u03b2 enzymes. Using macrophages as a model system, where PLC\u03b2 signaling is essential for responses to infection and tissue injury, we investigated the contribution of G\u03b2\u03b3-dependent regulation and membrane recruitment of PLC\u03b2 in the context of endogenous signaling. By measuring Ca2+ mobilization, we demonstrate that both G\u03b1i and G\u03b1q-coupled receptors independently stimulate PLC\u03b2 activity, illustrating that G\u03b2\u03b3 alone is sufficient to activate PLC\u03b2 in certain contexts. Using total internal reflection and stimulated emission depletion microscopy, we demonstrate that most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation by both G\u03b1i and G\u03b1q-coupled receptors, illustrating that both G\u03b2\u03b3 and G\u03b1q recruit PLC\u03b2 to the plasma membrane. These results support an updated model for G protein-dependent regulation of PLC\u03b2 enzymes, where G\u03b2\u03b3-induced regulation in the absence of G\u03b1q is context dependent and dictated by the local concentration of receptor, G proteins, and PLC\u03b2. PLC\u03b2 enzymes are critical mediators of signal transduction with roles in neuronal, cardiac, and immunological signaling. Despite this importance, many aspects of their function and regulation remain poorly understood. PLC\u03b2s are aqueous soluble but must partition onto the membrane surface to access their lipid substrate, which enables regulation at the partitioning step, the catalytic step, or both. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie the PLC\u03b2 regulation by one effector, G\u03b2\u03b3. Using macrophages as a model system for physiological signaling, we demonstrate that G\u03b2\u03b3 is capable of independently activating PLC\u03b2 via membrane recruitment under the conditions of endogenous signaling."
},
{
"quote": "STING signalling is terminated by ESCRT-driven lysosomal microautophagy.",
"source_id": "42203786",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42203786\nTitle: A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.\nAbstract: Stimulator of interferon genes (STING) is critical for the type I interferon responses to pathogen- or self-derived cytosolic DNA. STING signalling is terminated by ESCRT-driven lysosomal microautophagy. How STING is directly encapsulated by lysosomes has not yet been understood. Here we show that two lysosomal components, a phosphoinositide PI(3,5)P2 and CHMP4B (a subunit of ESCRT-III subcomplex) are essential for STING encapsulation by lysosomes. Liposome sedimentation assay reveals that CHMP4B binds to PI(3,5)P2. The forced recruitment of the catalytic core of Pikfyve (a lipid kinase generating PI(3,5)P2) to early endosomes, recruits a fraction of CHMP4B to early endosomes. CHMP4B mutant, defective in the binding to PI(3,5)P2, cannot restore the microautophagic degradation of STING or the resolution of the STING signalling in cells depleted of Chmp4b. Our results reveal a molecular mechanism that terminates innate immune signalling at the lysosomal membrane."
},
{
"quote": "This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.",
"source_id": "42165414",
"status": "PASS",
"error": "",
"abstract_text": "ID: 42165414\nTitle: High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.\nAbstract: An elevated risk for inflammatory bowel disease (IBD) has been linked to the intake of high-fat diet (HFD), yet the underlying molecular mechanisms remain unclear. The lysosome and the macroautophagy/autophagy-lysosome pathway (ALP) are critical for maintaining the intestinal epithelial barrier. By employing both an in vivo model of dextran sulfate sodium (DSS)-induced colitis in mice and an in vitro model using lipopolysaccharide (LPS)-treated NCM460 cells, we established that HFD in vivo and palmitic acid (PA) in vitro profoundly impair epithelial barrier function and amplify inflammation, which was linked to the suppression of lysosomal function and the ALP. Mechanistically, HFD in vivo and PA in vitro activated STAT3 (p-STAT3[Y705]) under DSS- and LPS-associated inflammatory stress, respectively. This led to a dual suppression of TFEB: on the one hand, activated STAT3 directly bound to the TFEB promoter to inhibit its transcription; on the other hand, it facilitated the lysosomal recruitment of MTOR and activated MTORC1, which promoted TFEB phosphorylation (p-TFEB[S211]) and hindered its nuclear translocation. This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function. Intestinal epithelial-specific knockout of Stat3 or pharmacological activation of TFEB restored lysosomal function, repaired the epithelial barrier, and ameliorated colitis. Conversely, rectal administration of AAV9-shTfeb reversed the protective effects conferred by stat3 knockout. Our study reveals that HFD in vivo and PA in vitro disrupt lysosomal function and the intestinal barrier through the STAT3-TFEB axis, suggesting this signaling pathway as a promising avenue for intervention in diet-associated IBD.Abbreviations: AB-PAS: Alcian blue-periodic acid-Schiff; ALP: autophagy-lysosome pathway; CD: Crohn disease; ChIP: chromatin immunoprecipitation; CLEAR: coordinated lysosomal expression and regulation; DSS: dextran sulfate sodium; HFD: high-fat diet; IBD: inflammatory bowel disease; IF: immunofluorescence; IHC: immunohistochemistry; LAMP: lysosome associated membrane protein; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; PA: palmitic acid; RRAG: Ras-related GTP binding; RRAG-CA: constitutively active RRAG GTPase; RT-qPCR: reverse transcription quantitative PCR; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; TA1: TFEB activator 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; TJ: tight junction; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UC: ulcerative colitis; WB: western blot; WT: wild-type."
},
{
"quote": "UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.",
"source_id": "41886456",
"status": "PASS",
"error": "",
"abstract_text": "ID: 41886456\nTitle: UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.\nAbstract: UFMylation, a recently identified ubiquitin-like modification mediated by the E3 ligase UFL1, plays context-specific roles in cancers, but its substrates and functions in lung adenocarcinoma (LUAD) remain poorly defined. Here, we identify the AKT signaling repressor PHLDA3 as a substrate of UFL1 in LUAD. UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling. Tumor-associated PHLDA3 mutations F41L, E82G, and K106N impair its UFMylation and membrane translocation, resulting in AKT hyperactivation and enhanced tumor growth. In samples from patients with LUAD, UFL1 expression inversely correlates with phospho-AKT levels. Functionally, the UFL1-PHLDA3 axis inhibits LUAD progression in both cell line-based and patient-derived xenograft models. These findings define a tumor-suppressive UFMylation pathway that modulates AKT activity and provides a mechanistic rationale for targeting UFL1-PHLDA3 signaling in LUAD."
}
]
},
"displayText": "Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\n\n###[CLAIM EVALUATED AND ANSWER TO USER]\n\"Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.\"\n\nBased on the provided literature, this specific mechanism is not explicitly described. While the literature establishes that WDR44 promotes alpha-synuclein (\u03b1-SYN) aggregation at the lysosomal membrane and that PS-NPs exposure induces lysosomal dysfunction and \u03b1-SYN aggregation in various models, there is no direct evidence linking PS-NP presence to the recruitment of WDR44 to the lysosomal membrane. Consequently, while biologically plausible within the framework of PD research, the claim that PS-NPs specifically act as a scaffold for WDR44-driven \u03b1-SYN accumulation remains an unverified hypothesis lacking specific evidentiary support in the current source set.\n\n### [ABSTRACT & REWRITTEN CLAIM]\nThe hypothesis suggests that polystyrene nanoplastics (PS-NPs) function as a mechanical or biochemical scaffold that facilitates WDR44 enrichment at lysosomes, catalyzing alpha-synuclein aggregation. Current research confirms that WDR44 is a key adaptor protein that modulates early \u03b1-SYN oligomerization at the lysosomal membrane. Separately, PS-NPs are proven to enter cells, accumulate in lysosomes, impair lysosomal function, and trigger proteostasis imbalance, contributing to \u03b1-SYN pathology. However, a causative link between PS-NPs as a recruitment factor for WDR44 is not evidenced.\n\n### [INTRODUCTION & JUSTIFICATION]\nThe provided literature extensively documents two parallel processes: (1) The role of WDR44 in promoting \u03b1-SYN aggregation at the lysosomal interface and (2) the role of nanoplastics in disrupting lysosomal integrity, which in turn leads to protein aggregation and autophagy-lysosomal pathway (ALP) dysfunction. \n\nWDR44 is recognized as a key mediator that \"drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\" Concurrently, nanoplastics are identified as environmental pollutants that penetrate cellular compartments, where they \"induce lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\" Despite these observations, the literature does not support a specific model where nanoplastics directly modulate WDR44 recruitment. The potential for such a connection remains speculative and requires further experimental investigation to define if physical interaction exists between ingested particles and this specific regulatory protein.\n\n### [DISCUSSION: NOVEL & OVERLOOKED]\n* Lysosomal membrane permeabilization (LMP) is a central nexus in both neurodegeneration and nanoplastic-induced cellular toxicity.\n* WDR44 knockdown is documented to markedly reduce \u03b1-SYN aggregation, whereas its overexpression accelerates pathology, identifying it as a primary target for therapeutic intervention.\n* Nanoplastics can induce lysosomal iron efflux, facilitating pathways such as ferroptosis, which overlaps with the lysosomal-mitochondrial crosstalk seen in PD.\n* Cellular mechanisms for lysosome repair, such as ESCRT recruitment and TFG-mediated repair, are hindered by the proteinopathies that nanoplastics potentially amplify.\n* The \"body-first\" hypothesis of PD is supported by studies on the enteric nervous system, where nanoplastics induce \u03b1-SYN aggregation similar to pesticides.\n* In addition to proteinopathies, nanoplastics influence epigenetic reprogramming and cytoskeletal remodeling, adding layers of complexity beyond pure protein-folding models.\n* Lysosomal acidification is a major bottleneck; multiple compounds, including acidic nanoparticles and ginsenoside Rg1, show potential for restoring degradative function in PD models.\n* Small GTPases and their activation, such as those analyzed by the SAIYAN system, provide potential monitoring tools for the spatiotemporal activation of pathways impacted by both PD and plastic exposure.\n\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n1. ID: 41993512 - Application: WDR44 is characterized as a driver of \u03b1-SYN aggregation at the lysosome. Alignment: 5. Quote: *\"WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.\"*\n2. ID: 41643617 - Application: PS-NPs impair autophagic flux via lysosomal dysfunction. Alignment: 5. Quote: *\"PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\"*\n3. ID: 42165414 - Application: High-fat diet and palmitic acid lead to TFEB phosphorylation and hindered nuclear translocation. Alignment: 4. Quote: *\"This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.\"*\n4. ID: 41919495 - Application: Lysosomal integrity is a common denominator across neurodegeneration. Alignment: 4. Quote: *\"Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.\"*\n5. ID: 42203786 - Application: STING degradation by microautophagy is ESCRT-driven. Alignment: 4. Quote: *\"STING signalling is terminated by ESCRT-driven lysosomal microautophagy.\"*\n6. ID: 42215790 - Application: C9orf72 coordinates RAB8A-ESCRT-mediated lysosomal repair. Alignment: 4. Quote: *\"The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.\"*\n7. ID: 41886456 - Application: PHLDA3 UFMylation prevents AKT membrane recruitment. Alignment: 4. Quote: *\"UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.\"*\n8. ID: 42327061 - Application: ORP3 mediates lysosomal repair at ER-lysosome contact sites. Alignment: 4. Quote: *\"Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites\"*\n9. ID: 42477140 - Application: MDVs deliver MFF to lysosomes for budding-type fission. Alignment: 4. Quote: *\"mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.\"*\n10. ID: 41779229 - Application: SMAD3 palmitoylation regulates endomembrane recruitment. Alignment: 4. Quote: *\"SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I\"*\n11. ID: 42093006 - Application: ALP dysfunction is involved in PD pathogenesis via lysosomal exocytosis and trafficking. Alignment: 4. Quote: *\"mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.\"*\n12. ID: 41812834 - Application: Nanoplastics induce mitochondrial redox dysfunction and lipid droplet expansion. Alignment: 4. Quote: *\"PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines\"*\n13. ID: 41580402 - Application: Evidence for nanoplastics in PD development. Alignment: 4. Quote: *\"Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation\"*\n14. ID: 41957923 - Application: ENS damage by food contaminants links to neurodegeneration. Alignment: 4. Quote: *\"Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.\"*\n15. ID: 42325197 - Application: Aggrephagy requires stepwise aggregate degradation. Alignment: 4. Quote: *\"Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps\"*\n16. ID: 41980172 - Application: Microplastics induce mitochondrial GSDMD-N pore formation. Alignment: 4. Quote: *\"mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux\"*\n17. ID: 42162239 - Application: Atg18 positions Atg2 for lipid transfer. Alignment: 4. Quote: *\"the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux\"*\n18. ID: 42236937 - Application: LASER couples damage sensing to ESCRT assembly. Alignment: 4. Quote: *\"TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.\"*\n19. ID: 41707395 - Application: PS-NPs disrupt ovarian development via cytoskeletal remodeling. Alignment: 4. Quote: *\"PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications\"*\n20. ID: 41659462 - Application: PLC\u03b23 is recruited to the plasma membrane. Alignment: 4. Quote: *\"most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation\"*\n\n### [PROGRAMATICALLY MAPPED REFERENCES]\n[1]. ID: 41993512 - APA: Teixeira M, Sheta R, B\u00e9rard M, Insinna C, Mahul-Mellier AL et al. (2026). WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.. bioRxiv : the preprint server for biology. ID: 41993512.\n[2]. ID: 41643617 - APA: Yang G, Peng Y, Li J, Yang S, Li M et al. (2026). Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.. Journal of hazardous materials. ID: 41643617.\n[3]. ID: 41919495 - APA: De Tito S, Tooze SA (2026). Lysosomal homeostasis at the crossroads of neurodegeneration.. The Journal of clinical investigation. ID: 41919495.\n[4]. ID: 41957923 - APA: Ramos H, Ara\u00fajo AM, Ferreira IMPLVO, Faria MA (2026). Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?. Comprehensive reviews in food science and food safety. ID: 41957923.\n[5]. ID: 42215790 - APA: Li S, Xu S, Li F, Zhao Q, Zhang P et al. (2026). The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.. The EMBO journal. ID: 42215790.\n[6]. ID: 42327061 - APA: Bott CJ, Iwaniek MO, Casanova JE (2026). Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.. bioRxiv : the preprint server for biology. ID: 42327061.\n[7]. ID: 42477140 - APA: Luo Y, Yu J, Li Z, Li W, Jiang L et al. (2026). Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.. Nature cell biology. ID: 42477140.\n[8]. ID: 41779229 - APA: Xu Y, Ji S, Jiang P, Zhao Z, Zhou Q et al. (2026). Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.. Inflammation. ID: 41779229.\n[9]. ID: 42093006 - APA: Shimizu T, Isik S, Kamath N, Yue Z (2026). The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.. Translational neurodegeneration. ID: 42093006.\n[10]. ID: 41812834 - APA: Rathor P, Tiwari AK, Patel RP, Verma AK, Singh SP et al. (2026). Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.. Free radical biology & medicine. ID: 41812834.\n[11]. ID: 41580402 - APA: Lin L, Li J, Zhu S, Zhang Z, Li Z et al. (2026). Micro-nanoplastics and Parkinson's disease: evidence and perspectives.. NPJ Parkinson's disease. ID: 41580402.\n[12]. ID: 42325197 - APA: Hipp MS, Mauthe M (2026). Small bites for big problems: stepwise aggregate degradation by autophagy.. Biochemical Society transactions. ID: 42325197.\n[13]. ID: 41980172 - APA: Chen Y, Liu M, Hu J, Peng H, Lang L et al. (2026). Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.. Journal of agricultural and food chemistry. ID: 41980172.\n[14]. ID: 42162239 - APA: Ramirez SC, Shvarev D, Vargas Duarte P, Ahmed Y, Milach J et al. (2026). Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.. The EMBO journal. ID: 42162239.\n[15]. ID: 42236937 - APA: Goul CS, Jain A, Yitiz S, Soltani ZE, Yang S et al. (2026). LASER couples damage sensing to ESCRT assembly for lysosome repair.. Nature. ID: 42236937.\n[16]. ID: 41707395 - APA: Liu M, Wang S, Gao W, Zhang J, Zhang B et al. (2026). Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.. Journal of hazardous materials. ID: 41707395.\n[17]. ID: 41659462 - APA: Falzone ME, Banerjee P, MacKinnon R (2026). PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.. bioRxiv : the preprint server for biology. ID: 41659462.\n[18]. ID: 42203786 - APA: Shoji T, Shinojima A, Kishimoto T, Sato K, Ikegami N et al. (2026). A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.. Nature communications. ID: 42203786.\n[19]. ID: 42165414 - APA: He H, Guo X, Xu M, Tan Z, Tan C et al. (2026). High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.. Autophagy. ID: 42165414.\n[20]. ID: 41886456 - APA: Ma X, Wan R, Yang X, Tang J, Wen Y et al. (2026). UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.. Cell reports. ID: 41886456.\n",
"prompt": "CRITICAL INSTRUCTION: You MUST wrap your internal reasoning in ... tags at the very beginning of your response.\n\n=======================================================\nCONTEXT LITERATURE (STATIC CACHE):\nID: 42463431\nTitle: VPS35 Regulates Microglial Lipid Droplet Accumulation in Parkinson's Disease via Rab7.\nAbstract: Microglial dysfunction and aberrant lipid metabolism are emerging as key contributors to Parkinson's disease (PD) pathogenesis. However, the specific role and regulation of lipid droplets (LDs) within microglia remain poorly defined. In this study, we employed MPTP- and LPS-induced PD mouse models and an in\u00a0vitro system utilizing astrocyte-conditioned medium to model disease-relevant lipid stress and found enhanced LD accumulation in microglia. VPS35 expression was decreased in microglia, correlating with elevated microglial LD levels in PD mouse models. We then performed genetic manipulations (knockdown and overexpression) of VPS35, including the PD-associated D620N mutant, in primary microglia and assessed LD accumulation, phagocytic function, inflammatory responses, and integrated stress pathways. We showed that VPS35 knockdown exacerbated the accumulation of LDs in microglia. Conversely, VPS35 overexpression ameliorated LD formation, improved phagocytic function, and reduced inflammatory and integrated stress responses in microglia. The PD-related VPS35[D620N] mutation abolished these protective effects. We further found that VPS35 interacts with Rab7 to maintain lysosomal function, and the D620N mutation disrupts this interaction, leading to defective LD clearance. Our findings reveal VPS35 dysfunction as a key pathogenic mechanism in PD, where the D620N mutation disrupts microglial lipid handling to promote disease progression, thereby nominating VPS35 restoration as a promising therapeutic strategy.\n\nID: 42455619\nTitle: Clearance and secretion of \u03b1-synuclein by RTN3L-mediated endoplasmic reticulum autophagy.\nAbstract: The misfolding and aggregation of \u03b1-synuclein (\u03b1-syn), an abundant synaptic protein, leads to the pathogenesis of Parkinson's disease and related synucleinopathies. The cell-to-cell propagation of seeding-competent \u03b1-syn is initiated by unconventional protein secretion, yet the physiological pathway(s) underlying this process remain poorly defined. Here we show that \u03b1-syn secretion in human cells is mediated by Reticulon-3L (RTN3L)-dependent endoplasmic reticulum autophagy (ER-phagy), a conserved protein quality-control pathway that safeguards ER protein homeostasis. We also demonstrate that RTN3L cooperates with several autophagy regulators, including the ULK1 cofactor FIP200, to drive the delivery of \u03b1-syn into an acidic endolysosomal compartment. Increasing concentrations of \u03b1-syn disrupt ER-lysosome traffic and \u03b1-syn-containing vesicles appear to be rerouted to the cell surface. Consistent with this proposal, knockdown of vesicle associated SNAREs, that mediate fusion at the cell surface, disrupt \u03b1-syn secretion. These findings suggest that pathogenic \u03b1-syn secretion arises as a by-product of a physiological clearance mechanism, driven by the fusion of autophagosome-derived vesicles with the plasma membrane. Our results provide a conceptual framework for understanding how an intracellular proteostasis pathway, when mis-regulated, could contribute to the spread of neurodegenerative pathology.\n\nID: 42400323\nTitle: A PARK9 iPSC-Derived Dopaminergic Neuron Model Enables Drug Screening Targeting Autophagy-Lysosome Pathway Dysfunction in Parkinson's Disease.\nAbstract: Parkinson's disease (PD) is a neurodegenerative disease characterized by dopaminergic neuronal degeneration in the substantia nigra, in which lysosomal dysfunction and impaired autophagy-lysosome pathway activity are increasingly recognized as important pathogenic mechanisms. However, disease-modifying therapies targeting this pathway remain unavailable. Here, we generated induced pluripotent stem cells (iPSCs) from a PARK9 patient carrying an ATP13A2 mutation and established mutation-corrected isogenic control iPSCs. PARK9 iPSC-derived neurons recapitulated lysosomal dysfunction-associated cellular phenotypes, including impaired lysosomal acidification, reduced mature cathepsin D levels, CD63-positive vesicle accumulation, LC3B-positive autophagosome accumulation, cytoplasmic pSer129 \u03b1-synuclein accumulation, and increased cleaved caspase-3 signals. These phenotypes were ameliorated in mutation-corrected neurons, supporting the contribution of ATP13A2 dysfunction to these abnormalities. We then performed high-content imaging-based compound screening targeting LC3B-positive autophagosome accumulation in PARK9 neurons. A three-step workflow identified 19 candidate compounds that reduced autophagosome accumulation consistent with partial improvement of lysosome-dependent downstream autophagosome processing rather than simple suppression of autophagosome formation. Among these, paroxetine, Ro 25-6981, amisulpride, and PK11195 showed additional, compound-dependent effects on PARK9-associated phenotypes, including lysosomal acidification, CD63-positive vesicle accumulation, cytoplasmic pSer129 \u03b1-synuclein signals, and cleaved caspase-3 signals. These findings establish PARK9 iPSC-derived neurons as a useful model of lysosomal dysfunction-associated PD pathology and provide a practical screening platform for identifying candidate compounds that modulate autophagy-lysosome pathway-related cellular phenotypes.\n\nID: 42365211\nTitle: A new paradigm in Parkinson's disease: kidney-origin \u03b1-synuclein pathology driven by PKC signaling and aurothioglucose.\nAbstract: Protein Kinase C (PKC), a zinc-dependent signaling enzyme essential for cellular homeostasis, has recently emerged as a critical regulator of \u03b1-synuclein (\u03b1-Syn) dynamics beyond the central nervous system. Growing evidence suggests that PKC may contribute to \u03b1-Syn accumulation in kidney cells through multiple converging mechanisms, including direct phosphorylation of \u03b1-Syn, which promotes its aggregation, disruption of the autophagy-lysosome pathway leading to impaired protein clearance, and amplification of oxidative stress and inflammatory responses that enhance \u03b1-Syn toxicity. In a paradigm-shifting discovery, recent findings from Wuhan University indicate that Parkinson's disease (PD) pathology may originate in peripheral organs such as the kidneys rather than the brain. Abnormal \u03b1-Syn aggregates have been identified in renal tissues of affected individuals, and experimental models demonstrate that compromised kidney function facilitates the systemic spread of these toxic proteins to the brain, potentially initiating neurodegeneration. Notably, \u03b1-Syn accumulation has also been observed in patients with chronic kidney disease in the absence of neurological symptoms, suggesting a potential early reservoir function of the kidneys. In this context, aurothioglucose (ATG), a gold-based anti-inflammatory agent, emerges as a promising therapeutic candidate due to its ability to modulate PKC signaling, attenuate inflammation, and restore proteostatic balance. This review highlights a novel kidney-brain axis in PD pathogenesis and proposes PKC-targeted interventions, including ATG, as potential strategies for early disease modification.\n\nID: 42310725\nTitle: Targeting lysosomal pH restores mitochondrial quality control in GBA1-mutant Parkinson's disease.\nAbstract: Heterozygous mutations in the glucocerebrosidase gene (GBA1), which encodes the lysosomal enzyme \u03b2-glucocerebrosidase (GCase), are a genetic risk factor for Parkinson's disease (PD). The pathophysiological consequences of GBA1 mutations on dopaminergic neuronal function, especially their impact on lysosomal function, mitophagy, and mitochondrial bioenergetics, remain unclear. Fibroblasts and dopaminergic neurons generated from induced pluripotent stem cells (iPSCs) derived from patients with\u00a0GBA1-PD were used in the study. Live-cell imaging was performed to measure lysosomal acidification, protease activity, mitochondrial membrane potential, and mitophagy. Mitochondrial morphology and autophagic vesicles were examined using transmission electron microscopy. Oxygen consumption rate was measured by Seahorse assay. V-ATPase assembly was quantified using fluorescence lifetime imaging with F\u00f6rster resonance energy transfer (FLIM-FRET), and pharmacological interventions included rapamycin and acidic nanoparticles. GCase activity, lysosomal acidification, protease activity, mitophagy and mitochondrial bioenergetic function were all impaired in GBA1 mutant dopaminergic neurons. Mitochondria were fragmented, with reduced membrane potential and oxygen consumption. Mechanistic target of rapamycin complex 1 (MTORC1) was constitutively phosphorylated and FLIM-FRET measurements confirmed impairment of lysosomal V-ATPase assembly, which was reversed by rapamycin treatment. Rapamycin and lysosome-targeting acidic nanoparticles rescued lysosomal pH and restored mitophagy, mitochondrial membrane potential and mitochondrial oxidative phosphorylation complex level in the GBA1 mutant dopaminergic neurons. We revealed a novel mechanistic link between GBA1 mutations and mitochondrial dysfunction, as the disruption of V-ATPase assembly driven by MTORC1 activation impairs lysosomal acidification. This causes impairment of mitophagy, leading to mitochondrial dysfunction, undermining dopaminergic cell function and fate. Pharmacological intervention with rapamycin or acidic nanoparticles restores lysosomal pH and rescue mitochondrial function, representing a novel therapeutic approach for\u00a0GBA1-PD .\n\nID: 42284733\nTitle: VPS13C-mediated endoplasmic reticulum-lysosome tethering in neuronal stress responses.\nAbstract: Organelle contact sites are increasingly recognized as regulatory interfaces that coordinate lipid transfer, ion signaling, and metabolic adaptation. In neurons, communication among the endoplasmic reticulum (ER), lysosomes, and mitochondria is essential for cellular homeostasis. Recent studies have identified vacuolar protein sorting 13 homolog C (VPS13C), a lipid transport protein, as a key mediator of ER-lysosome tethering and as an important component of the response to lysosomal stress. Structural analyses show that VPS13 family proteins form elongated lipid transport channels that are proposed to facilitate phospholipid transfer between adjacent membranes. Following lysosomal damage, VPS13C is recruited to ER-lysosome contact interfaces, where it forms tethering bridges that may support membrane repair by enabling high-capacity lipid transfer from the ER to lysosomal membranes. Beyond membrane repair, these contact interfaces may also participate in broader organelle communication networks. ER-lysosome contacts can occur in proximity to ER-mitochondria junctions, potentially forming multi organelle signaling hubs that coordinate lipid redistribution, calcium signaling, and mitochondrial adaptation. These signals may influence downstream responses, including activation of TFEB and TFE3, which regulate lysosomal biogenesis and autophagy. Disruption of this contact site network has emerged as a potential contributor to Parkinson's disease. Loss of VPS13C function is associated with altered lysosomal homeostasis and intersects with pathogenic pathways involving \u03b1-synuclein aggregation, PINK1/Parkin-mediated mitophagy, and LRRK2 signaling. This review presents a framework in which ER-lysosome tethering is considered part of a staged cellular damage response linking membrane repair, metabolic coordination, and transcriptional adaptation.\n\nID: 42282839\nTitle: Synphilin-1 mitigates autophagy dysfusnction, modulates ubiquitinated protein aggregation, and promotes cell survival during proteotoxic stress.\nAbstract: The decline of cellular proteostasis is a hallmark of aging and key contributor to neurodegenerative diseases. Protein turnover is controlled by the ubiquitin-proteasome and autophagosome-lysosome systems, but how degradation is coordinated when one of these pathways is compromised is not well understood. To study the regulation of proteostasis, we utilized human fibroblasts with targeted knockouts of the cytoskeletal factors WHAMM and JMY, which control multiple steps in autophagy. We found that cells lacking both WHAMM and JMY accumulated numerous intense foci of ubiquitinated proteins when exposed to proteotoxic stress and relied on proteasomes to clear the foci when the stressor was removed. RNA-seq and immunoblotting revealed that WHAMM/JMY knockout cells increased their expression of Synphilin-1, an \u03b1-synuclein-interacting protein implicated in Parkinson's Disease. In WHAMM/JMY knockout cells that upregulated endogenous Synphilin-1, and in cell lines engineered to overexpress mCherry-Synphilin-1, ubiquitinated proteins were present in structures containing both Synphilin-1 and proteasomes. RNAi-mediated depletion of Synphilin-1 caused a buildup of ubiquitinated proteins and the ubiquitin-binding adaptor protein SQSTM1/p62, while decreasing cell survival in response to proteotoxic stress. These data suggest that Synphilin-1 plays a pro-survival role in cells with impaired autophagy and functions in the distribution of ubiquitinated cargo during proteasomal degradation.\n\nID: 42252285\nTitle: Lysine acetyltransferase 8-mediated histone acetylation, regulated by GBA1, is associated with lysosomal function related to \u03b1-Synuclein pathology.\nAbstract: Lysosomal defects are closely linked to Parkinson's disease (PD). Mutations in the GBA1 gene, encoding the lysosomal enzyme glucocerebrosidase (GCase), are major genetic risk factors for PD. GBA1 deficiency causes lysosomal dysfunction, leading to \u03b1-synuclein (\u03b1-syn) accumulation and PD progression. However, the underlying mechanisms remain unclear. In this study, we identified a novel GBA1-KAT8 regulatory pathway that controls lysosomal activity. GBA1 overexpression enhances lysosomal enzyme expression, regulates histone H4 acetylation at K16 via KAT8, and promotes lysosome-associated gene expression, highlighting an epigenetic mechanism in lysosomal biogenesis. Furthermore, GBA1 upregulated KAT8 expression, increased lysosomal enzyme levels, and decreased PFF-induced \u03b1-syn accumulation both in vitro and in vivo. The involvement of KAT8 as a critical acetyltransferase that modulates nuclear-lysosomal signaling pathways provides a mechanistic explanation for GBA1 deficiency-induced lysosomal dysfunction in association with PD pathology.\n\nID: 42250519\nTitle: Microplastics alter the toxicity of benzo[a]pyrene in a mangrove oyster: An integrated biomarker approach.\nAbstract: Microplastics (MPs) and Benzo[a]pyrene (BaP) are ubiquitous co-contaminants in marine environments, yet their combined ecotoxicological effects remain poorly understood. This study evaluated the isolated and interactive toxicity of alone linear low-density polyethylene (LLDPE) (0, 5, 50, 500\u202fmg\u202fL-1) and BaP (0, 3, 12, 21, 30\u202f\u03bcg\u202fL-1) in the mangrove oyster Crassostrea gasar, a key filter-feeding species highly vulnerable to particulate and hydrophobic contaminants. The concentrations of 5\u202fmg/L MPs and all BaP concentrations tested are environmentally relevant. Adult oysters were exposed for 7 days in a full factorial design, and biomarkers (Glutathione S-transferase, Glutathione Peroxidase, Reduced Glutathione, Lipid Peroxidation, DNA damage, Neutral Red Retention Time) were assessed in gills and hemolymph. Alone MPs alone induced oxidative and cytogenotoxic effects, confirming that even uncontaminated plastic particles can disrupt cellular homeostasis. Significant interactive effects between MPs and BaP were observed, particularly influencing oxidative stress and DNA integrity. GPx, GST, and GSH responses were associated with DNA damage at higher exposure levels. BaP increased lipid peroxidation, reducing lysosomal membrane stability, and this impairment was exacerbated under combined exposure. The integrated biomarker response index identified the combination of 30\u202f\u03bcg\u202fL-1 BaP and 500\u202fmg\u202fL-1 MP as the most hazardous scenario. The environmentally relevant MP concentration (5\u202fmg\u202fL-1) also produced significant effects when combined with BaP. These findings demonstrate that MPs modulate BaP toxicity and highlight the importance of assessing co-contaminant interactions in filter-feeding organisms. Although the highest concentration tested (500\u202fmg\u202fL-1) exceeds environmental levels, effects were also observed at environmentally relevant concentrations. The inclusion of elevated concentrations was intended to identify effect thresholds and underlying mechanisms, providing robust data for environmental risk assessment.\n\nID: 42248811\nTitle: Ginsenoside Rg1, a Natural Lysosomal Enhancer, Alleviates Parkinson's Disease Pathology via Cathepsin D-Dependent Regulation of \u03b1-Synuclein Homeostasis.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and \u03b1-synuclein (\u03b1-syn) aggregation, often linked to lysosomal dysfunction. Cathepsin D (CTSD), a lysosomal hydrolase essential for \u03b1-syn clearance, becomes functionally impaired when its maturation is disrupted, exacerbating proteostatic stress. This study investigated whether ginsenoside Rg1(Rg1) restores CTSD maturation and lysosomal function to mitigate PD pathology. MPTP-induced zebrafish and mouse PD models, as well as MPP+-treated SH-SY5Y cells, animals and cells were treated with Rg1 at different concentrations. Motor behavior, dopaminergic neuron survival, \u03b1-syn clearance, CTSD maturation, lysosomal activity, endoplasmic reticulum (ER) stress, oxidative stress, autophagic flux, and apoptosis were systematically evaluated. Rg1 improved locomotor performance and preserved dopaminergic neurons, promoted \u03b1-syn clearance, and enhanced CTSD maturation in lysosomes. These effects coincided with reduced ER and oxidative stress, normalized autophagic flux, and decreased apoptosis. Rg1 functions as a natural lysosomal enhancer, restoring lysosome-ER homeostasis and counteracting multiple pathogenic pathways in PD. The findings reveal a CTSD-dependent regulatory axis in \u03b1-syn homeostasis and highlight Rg1 as a promising multi-target therapeutic candidate for PD.\n\nID: 42231395\nTitle: Polymeric lysosome-targeting chimeras for extracellular \u03b1-synuclein degradation in Parkinson's disease.\nAbstract: Disease progression in Parkinson's disease has been driven by extracellular \u03b1-synuclein prion-like seeding throughout the course of the disease and therefore not just by the intracellular accumulation of the protein in isolated aggregates. Current therapies utilizing PROTACs cannot address the extra-cellular effects of \u03b1-synuclein spreading in this manner. This article proposes PolyTACs (Polymeric Lysosome-Targeting Chimeras) as hybrid antibody-polymer conjugates which use neuronal exofacial thiol groups produced because of DJ-1/GSH dysregulation to capture \u03b1-synuclein pathological conformers before they can be derepressed (seeded pathological aggregates) into the cytoplasm. The hybridity of these antibodies (oligomers and fibrils) combined with pyridyl disulfide linkages in the multi-valent polymer allows these compounds to circumvent LTR co-option, and to be trafficked to lysosomes via a non-clathrin pathway. The delivery route for these agents is intended to be via intra-nasal, thereby bypassing many of the issues associated with delivery through the BBB. Delivery to patients will be guided by thiol profiling in cerebrospinal fluid to assist in inclusion-exclusion criteria for patients in prodromal trials. With these developments, it is anticipated that this new class of agent may provide a modular framework adaptable to other proteinopathies such as tau and TDP-43, pending further validation.\n\nID: 42213153\nTitle: Biomarker Responses in the Marine Mussel Mytilus Edulis Indicate Significant Toxicological Effects of Polyethylene Microplastics.\nAbstract: This study investigated the short\u2011term effects of polyethylene microplastics (PE\u2011MPs) on the marine mussel Mytilus edulis using a suite of cellular and subcellular biomarkers. A total of 225 mussels were collected from Umluj, Saudi Arabia, a relatively unimpacted coastal area of the Red Sea, and experimentally exposed for 72\u00a0h to spherical PE\u2011MPs (50\u00a0\u03bcm diameter) at nominal concentrations of 5, 10, 20, and 60 particles L-1. Genotoxicity, oxidative status, and cellular integrity were assessed by comet assay, thiobarbituric acid\u2011reactive substances (TBARS), superoxide dismutase (SOD) activity, and lysosomal membrane stability (LMS). At 60 particles L-1, DNA strand breakage increased markedly in hemocytes (13.09%) and gill cells (12.21%) relative to controls (2.14%; p\u2009<\u20090.01). Lipid peroxidation was 1.28 nmol TBARS mg protein-1, and activity of gill SOD was decreased by 16.13% of control. LMS was significantly reduced from 134.4\u00a0min in controls to 53.2\u00a0min in the highest exposure (p\u2009<\u20090.01), suggesting impaired cellular homeostasis. Given the short exposure duration, these results are preliminary. They indicate that acute PE-MP exposure at the tested concentrations is associated with measurable genotoxicity, oxidative stress, and reduced lysosomal stability. Longer-term ecological implications remain to be investigated.\n\nID: 42185903\nTitle: Irisin-integrin \u03b1V/\u03b25 coupling of \u03b1-synuclein phagocytosis and clearance.\nAbstract: Parkinson's disease-associated cognitive impairment (PD-CI) is closely linked to \u03b1-synuclein (\u03b1-syn) accumulation and synaptic dysfunction, yet effective disease-modifying strategies remain limited. Irisin is an exercise-inducible myokine with neuroprotective potential, but its receptor mechanisms and its role in \u03b1-syn clearance in PD-CI are poorly defined. Here, we observed that aerobic exercise markedly increased circulating irisin levels, reduced serum \u03b1-syn levels, and improved cognitive performance in a cohort of 21 PD patients. In addition, irisin signals through integrin \u03b1V/\u03b25 to enhance microglial \u03b1-syn clearance, resulting in reduced \u03b1-syn burden and improved PD-CI. Mechanistically, irisin activates integrin \u03b1V/\u03b25-FAK axis to promotes microglial phagocytic uptake of \u03b1-syn, while concurrently stabilizing HMGB1 to facilitate autophagy-lysosome mediated degradation of internalized \u03b1-syn, thereby coupling phagocytic uptake to efficient degradation. In summary, these results highlight a dual-module irisin-integrin \u03b1V/\u03b25 mechanism that couples microglial phagocytosis and autophagy-lysosome clearance to reduce \u03b1-syn burden and ameliorate PD-CI.\n\nID: 42178909\nTitle: Membrane ATG8ylation in secretory autophagy.\nAbstract: Mammalian Atg8-family (ATG8) proteins are crucial for macroautophagic/autophagic degradation in the lysosome and facilitate non-degradative processes including multiple distinct forms of unconventional protein secretion. These secretion pathways, collectively termed secretory autophagy, depend upon ATG8 conjugated to membranes to both specify and traffic molecules for extracellular release. Here, we review the current understanding of how membrane ATG8ylation supports secretory autophagy, and propose a cell biological framework for classifying the growing repertoire of secretory autophagy pathways based on membrane ATG8ylation at discrete intracellular vesicular intermediates. Finally, we detail the emerging roles of these pathways in physiology and disease.Abbreviations: A\u03b2, amyloid-\u03b2; Acb1, acyl-coA-binding 1; ALS, amyotrophic lateral sclerosis; APP, amyloid beta precursor protein; APEX2, ascorbate peroxidase; ATG, autophagy related; AWOL, autophagosome-mediated exit without lysis; BafA1, bafilomycin A1; BirA*, mutant BirA biotin ligase; BMI, body-mass index; CASM, ATG8 conjugation at single membranes; DAMPs, danger/damage-associated molecular patterns; DBI, diazepam binding inhibitor, acyl-CoA binding protein; DSS, dextran sodium sulfate; ER, endoplasmic reticulum; ERGIC, endoplasmic reticulum intermediate compartment; ESCRT, endosomal complexes required for transport; EVs, extracellular vesicles; EVPs, extracellular vesicles and particles; HMGB1, high mobility group box 1; IDE, insulin degrading enzyme; IFNB, interferon beta; ILV, intralumenal vesicles; LANDO, LC3-associated endocytosis; LAP, LC3-associated phagocytosis; LIR, LC3 interacting region; LDELS, LC3-dependent EV loading and secretion; LLOMe, L-leucyl-L-leucine methyl ester hydrobromide; M2, influenza A virus matrix 2, MAD, migratory autolysosome disposal; miRNAs, microRNAs; M-MDSC, monocytic myeloid derived suppressor cells; MVEs, multivesicular endosomes; PAMPs, pathogen-associated molecular patterns; P-bodies, processing bodies; PE, phosphatidylethanolamine; PD, Parkinson disease; PS, phosphatidylserine; RBPs, RNA binding proteins; R-EV, RAB22A-induced extracellular vesicle; SLC2A1, solute carrier family 2 member 1; TFRC, transferrin receptor; TGN, trans-Golgi network; TMED10, transmembrane p24 trafficking protein 10; THU, TMED10-channeled unconventional secretion; SALI, secretory autophagy during lysosome inhibition; SCF, SKP1-CUL1-F-box; SNAREs, soluble NSF attachment protein receptors.\n\nID: 42168299\nTitle: Lysosome-related biomarkers in peripheral blood immune cells discriminate sepsis from SIRS.\nAbstract: This study aimed to screen lysosome-related genes that distinguish sepsis from Systemic Inflammatory Response Syndrome (SIRS), in order to provide potential targets for the differential diagnosis of sepsis and for lysosome-targeted therapeutic strategies. Peripheral blood samples were collected from 12 SIRS patients and 20 sepsis patients for RNA sequencing and differential expression analysis. Meanwhile, lysosome-related gene sets were obtained from the Gene Ontology database. The intersection was taken between the differentially expressed genes and the lysosomal gene sets. Subsequently, Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on these overlapping genes. Meta-analysis was used to screen for core genes, and their diagnostic efficacy was evaluated using Receiver Operating Characteristic (ROC) curves. Furthermore, single-cell RNA sequencing was performed to identify the immune cell types that predominantly express the core genes, facilitating the selection of appropriate cell models for subsequent experimental validation. Functional enrichment analysis revealed that these 21 overlapping genes were significantly enriched in biological pathways such as receptor metabolic process, autophagy, vacuolar transport, cellular catabolic process, and lysosomal transport. Meta-analysis identified four core genes: CD1C, RNASE6, and SNCA were significantly downregulated in the sepsis group, while DRAM1 was significantly upregulated. Diagnostic efficacy evaluation demonstrated that all four core genes possessed good discriminatory value, with AUC as follows: CD1C (0.758), DRAM1 (0.888), RNASE6 (0.737), and SNCA (0.765). Single-cell RNA sequencing analysis suggested that CD1C and RNASE6 are primarily expressed in circulating monocyte-macrophages and B cells, DRAM1 is mainly expressed in circulating monocyte-macrophages, and SNCA is predominantly expressed in circulating monocyte-macrophages and platelets. The four core genes identified in this study could serve as potential diagnostic biomarkers to distinguish sepsis from SIRS. Their expression is mainly enriched in circulating monocyte-macrophages in peripheral blood, providing new directions for future research.\n\nID: 42140967\nTitle: \u03b1-Synuclein aggregates induce mitochondrial damage and trigger innate immunity to drive neuron-microglia communication.\nAbstract: Tunneling nanotubes (TNTs) enable direct intercellular transfer of macromolecules, organelles, and pathogenic protein aggregates. While \u03b1-synuclein (\u03b1-Syn) aggregates are known to promote TNT formation, the underlying mechanisms remain poorly defined. Here, using human neuronal and microglial cell lines, as well as iPSC-derived dopaminergic neurons and microglia, we show that \u03b1-Syn aggregates induce severe mitochondrial damage, leading to cytosolic release of mitochondrial DNA (mtDNA) and activation of the cGAS-STING-NF-\u03baB-IRF3 pathway. This innate immune response drives actin cytoskeleton remodeling and the formation of TNT-like structures, promoting intercellular transfer of \u03b1-Syn from neurons to microglia. Additionally, neuronal cells transfer damaged mitochondria to microglia, where they undergo lysosome-mediated degradation. Neuron-to-microglia communication under \u03b1-Syn-induced stress also triggers a bystander inflammatory response in microglia, suggesting a neuroimmune activation. Our findings identify mitochondrial damage and STING-mediated inflammation as key drivers of TNT formation and \u03b1-Syn propagation, highlighting potential targets to modulate disease progression in Synucleinopathies.\n\nID: 42114425\nTitle: Life-cycle exposure to tris(2-butoxyethyl) phosphate at environmentally relevant concentrations induces progressive Parkinsonian-like neurodegeneration via lysosomal dysfunction in Caenorhabditis elegans.\nAbstract: Environmental contaminants are increasingly recognized as key risk factors for chronic diseases, including neurodegenerative disorders. Tris(2-butoxyethyl) phosphate (TBOEP) is a representative organophosphate ester that is widely detected in environmental matrices and human tissues, yet whether chronic exposure to environmentally relevant concentrations of TBOEP drives progressive neurodegenerative pathology remains unclear. Here, using Caenorhabditis elegans as a model organism, we performed a 20-day, time-resolved life-cycle exposure to environmentally relevant concentrations of TBOEP (50-5000\u202fng/L) to systematically assess chronic neurotoxicity. TBOEP exposure induced progressive, age-dependent neurodegenerative phenotypes. Early effects were characterized by selective impairment of locomotor performance starting at 50\u202fng/L, followed by broader systemic toxicity, including growth retardation, feeding deficits, and accelerated aging. Consistent with a Parkinson's disease-like trajectory, hallmark pathological features progressively worsened with exposure duration, including dopamine-dependent functional impairment, while \u03b1-synuclein aggregation and dopaminergic neuronal impairment were mainly observed at concentrations \u2265\u202f500\u202fng/L. Mechanistically, time-resolved transcriptomics identified the lysosomal pathway as a central target of TBOEP. Functional assays further confirmed that TBOEP significantly impaired lysosomal acidification. Pharmacological validation with the lysosomal chaperone ambroxol showed that improving lysosomal function mitigated TBOEP-induced neurotoxicity, supporting lysosomal dysfunction as a primary contributor to the observed pathology. Collectively, our findings identify TBOEP as a potential environmental risk factor for neurodegeneration, providing important insights that could inform further studies assessing the environmental health risks of organophosphate esters.\n\nID: 42112758\nTitle: Integrated clinical and computational data-based repurposing of econazole as a novel autophagic activator in ULK1-related Parkinson disease.\nAbstract: Parkinson disease (PD), the second most common neurodegenerative disorder, is pathologically linked to dysregulated autophagy, a conserved lysosomal degradation pathway. Current conventional PD therapies are often limited by significant side effects, underscoring the demand for alternative treatment strategies. Drug repurposing of FDA-approved compounds represents a promising approach to address this unmet clinical need. Here, by integrating clinical data analysis, we identified an association between autophagy impairment and specific PD patient subtypes, suggesting that ULK1-dependent autophagy activation may offer therapeutic benefit. Through systematic screening for autophagy induction and neuroprotective activity, we identified econazole, a known imidazole antifungal, as a promising candidate. Econazole exhibited robust therapeutic effects across multiple PD models, including MPTP-induced zebrafish and mouse models, as well as SNCAA53T mutant mouse models. Notably, its efficacy was dependent on functional autophagy, as autophagy inhibition abrogated its beneficial effects. Mechanistically, econazole activated ULK1, enhanced autolysosome formation, and promoted clearance of SNCA aggregates. Mouse brain microarray analysis indicated that econazole-activated ULK1 suppresses MAP3K12/DLK-MAPK8/JNK-MAPK9/JNK2-mediated neuronal apoptosis. Further phosphoproteomic profiling uncovered a novel ULK1-HSPA8/Hsc70 interaction that promotes LAMP1 and LAMP2 activation and enhances lysosomal function. This ULK1-HSPA8 complex additionally activated the BECN1 (beclin 1) complex to facilitate autophagosome formation. Together, our findings highlight a clinical data-guided drug repurposing approach that identifies econazole as a potent autophagy activator with therapeutic efficacy in ULK1-linked PD models, opening new avenues for PD treatment.Abbreviations: 3-MA: 3-methyladenine; ACTB: actin beta; ATG: autophagy related; AUC: area under the curve; BafA1: bafilomycin A1; BECN1: beclin 1; CMA: chaperone-mediated autophagy; DA: dopamine; DOPAC: 3,4-dihydroxyphenylacetic acid; Econ: econazole; GFP: green fluorescent protein; HEK-293T: human embryonic kidney 293T; HSPA8: heat shock protein 8 family A (Hsp70) member 8; HVA: homovanillic acid; JUN: Jun proto-oncogene, AP-1 transcription factor subunit; KSEA: kinase-substrate enrichment analysis; LAMP: lysosome associated membrane protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP2K: mitogen-activated protein kinase kinase; MAP3K12: mitogen-activated protein kinase kinase kinase 12; MAPK: mitogen-activated protein kinase; MPP+: 1-methyl-4-phenylpyridinium; MPTP: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; PD: Parkinson disease; RB1CC1: RB1 inducible coiled-coil 1; RFP: red fluorescent protein; RMSD: root mean square deviation; SEM: standard error of the mean; SNCA: synuclein alpha; SQSTM1: sequestosome 1; SYP: synaptophysin; TFEB: transcription factor EB; TH: tyrosine hydroxylase; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type.\n\nID: 42093006\nTitle: The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and the accumulation of misfolded \u03b1-synuclein, yet the underlying mechanisms remain incompletely understood. Over the past two decades, genetic discoveries have highlighted the convergence of multiple familial PD genes on the autophagy-lysosome pathway (ALP), a key cellular system responsible for the degradation and recycling of intracellular components. Recent studies have further revealed that components of the ALP not only mediate the clearance of \u03b1-synuclein aggregates but also, under certain pathological conditions, contribute to their propagation via lysosomal exocytosis or secretory autophagy. The precise functions of autophagy are highly context-dependent, with neuronal and glial cells exhibiting distinct ALP dynamics that shift with development, stress, and aging. In this review, we summarize current knowledge on the physiological regulation of autophagy in the brain and critically examine its involvement in PD pathogenesis, incorporating mechanistic insights from familial models and emerging evidence from sporadic PD. We also explore translational implications, focusing on efforts to identify ALP-related biomarkers in cerebrospinal fluid and urine, and on the therapeutic potential of modulating ALP activity. Although the causality between ALP dysfunction and PD remains elusive, mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking. Future research should aim to define cell type-specific ALP alterations, clarify the bidirectional interactions between \u03b1-synuclein and autophagic machinery, and develop in vivo tools to monitor autophagy activity and secretory signatures. A deeper understanding of these processes will be crucial for refining PD models, discovering robust fluid biomarkers, and designing targeted therapies capable of modifying disease trajectory.\n\nID: 42074107\nTitle: LRRK2 I1371V Mutation Drives Astrocytic Glucose Metabolism Failure and Induces Integrated ER-Mitochondria-Lysosome Dysfunction in Parkinson's Disease.\nAbstract: Although LRRK2 mutations modulate systemic glucose homeostasis and metabolic dysfunction precedes Parkinson's disease (PD) motor symptoms; the way in which pathogenic variants of LRRK2 disrupt astrocytic glucose metabolism and organellar homeostasis remains poorly understood. Here, we demonstrate that LRRK2-I1371V mutation causes profound metabolic and organellar dysfunction in LRRK2-I1371V PD-iPSC-derived astrocytes and U87 cells overexpressing I1371V variant. LRRK2-I1371V astrocytes exhibit significantly reduced GLUT1 expression and cell surface localization, resulting in impaired glucose uptake and decreased lactate production. This metabolic insufficiency correlates with cascading mitochondrial dysfunction, characterized by membrane depolarization, elevated reactive oxygen species, enhanced ubiquitination and reduced proteasomal activity. Reduced LAMP1/LAMP2 expression, impaired lysosomal acidification, and selective cathepsin D deficiency were observed. Accumulation of undegraded cargo was confirmed by transmission electron microscopy upon \u03b1-synuclein exposure. ER stress was evident by upregulation of GADD34/CHOP, increased phospho-PERK, and reduced nascent protein synthesis. Increased ER-mitochondrial contact via MAMs and enhanced STIM1-ORAI3 clustering reflect compensatory but ultimately insufficient responses to energy stress. Our results reveal that LRRK2-I1371V induces glucose uptake deficits, leading to energy depletion and integrated ER-mitochondria-lysosome dysfunction, thus indicating restoration of astrocytic metabolic capacity as a potential therapeutic strategy for LRRK2-associated PD.\n\nID: 42033266\nTitle: Lysosome-Acidifying Nanoparticles Rescue A30P \u03b1-Synuclein Induced Neuronal Death in Cellular and Drosophila Models of Parkinson's Disease.\nAbstract: Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting over 10 million people worldwide. It is characterized by the progressive loss of dopaminergic neurons in the substantia nigra and the accumulation of misfolded \u03b1-synuclein (\u03b1Syn) in intracellular inclusions known as Lewy bodies. Emerging evidence links \u03b1Syn accumulation to impaired lysosomal acidification and defective autophagy-lysosomal degradation, which are central to disease progression. To address this lysosomal dysfunction, we engineered a novel type of lysosome-targeted acidic nanoparticles (AcNPs) based on a biodegradable copolymer, poly(ethylene tetrafluorosuccinate-co-succinate) (PEFSU). These nanomaterials were developed to locally acidify impaired lysosomes and restore their degradative capacity. We evaluated their therapeutic potential in two familial PD models: SH-SY5Y neuroblastoma cells overexpressing A30P \u03b1Syn and A30P \u03b1Syn transgenic Drosophila melanogaster. In vitro, AcNPs effectively restored lysosomal pH, enhanced autophagic clearance of \u03b1Syn, improved mitochondrial function, and rescued A30P \u03b1Syn-induced cytotoxicity. In vivo, AcNPs treatment reduced \u03b1Syn burden, preserved dopaminergic neurons, and improved motor function in flies. This study demonstrates the first application of lysosome-acidifying polymeric nanoparticles in familial PD models and highlights the promise of rationally engineered pH-modulating nanomaterials as therapeutic agents for PD and other neurodegenerative diseases driven by lysosomal dysfunction and protein aggregation.\n\nID: 42012897\nTitle: Pathogenic variants in BORCS5 cause a spectrum of neurodevelopmental and neurodegenerative disorders with lysosomal dysfunction.\nAbstract: BORCS5 encodes a subunit of the BLOC-One-Related Complex (BORC), which is known to promote anterograde movement and fusion of lysosomes. We identified 16 individuals from 9 families with bi-allelic BORCS5 variants, revealing a spectrum of neurodevelopmental and neurodegenerative phenotypes. Carriers of homozygous protein-truncating variants (PTVs), resulting in complete loss of BORCS5, presented with prenatally lethal arthrogryposis multiplex congenita, brain malformations, and neuropathological evidence of neuroaxonal dystrophy. Individuals with missense or splice-site variants presented differently, with microcephaly, developmental epileptic encephalopathy, optic atrophy, spasticity, and progressive movement disorders. In this group, brain MRI showed diffuse hypomyelination, corpus callosum abnormalities, and progressive global cerebral atrophy, consistent with neurodegeneration. Borcs5 KO in zebrafish resulted in microcephaly, motor deficits, and increased seizure susceptibility, mirroring the patients' clinical presentation. At the cellular level, only BORCS5 PTVs, but not missense variants, led to perinuclear lysosomal clustering and impaired lysosomal axonal trafficking in induced pluripotent stem cell-derived forebrain neurons. However, PTVs and missense variants were associated with reduced lysosomal proteolysis and activity of lysosomal hydrolases glucocerebrosidase and cathepsin B, indicating lysosomal dysfunction. Our study reveals a role for BORCS5 in modulation of lysosomal function, in addition to its known role in lysosome movement and fusion, possibly underlying the diverse clinical manifestations in individuals with BORCS5-related disorders.\n\nID: 41997430\nTitle: Impaired autophagy from TRPV4 activation drives \u03b1-synuclein pathology in a Parkinson's disease model: A toxicological insight.\nAbstract: The environmental toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a prototypical agent for modeling Parkinson's disease (PD). Our previous study demonstrated that calcium channel transient receptor potential vanilloid 4 (TRPV4) mediates MPTP-induced endoplasmic reticulum (ER) stress and inflammation, leading to loss of dopamine neurons and movement disorder. Here, we investigated whether TRPV4 activation impairs clearance of pathological \u03b1-Synuclein (\u03b1-Syn) via the autophagy-lysosomal pathway (ALP), contributing to cognitive deficits in PD. We used C57BL/6J mice subjected to intracerebral injection of adeno-associated virus in substantia nigra to knockdown or overexpress TRPV4, followed by MPTP treatment. Novel object recognition and Morris water maze tests, immunohistochemistry, electron microscopy, and western blot were employed to assess the role of TRPV4 in modulating \u03b1-Syn via ALP. We found that targeting TRPV4 to counteract neurotoxicity improved cognitive dysfunction in PD mice. Mechanistically, MPTP-triggered toxic stress and TRPV4 overexpression induced accumulation of \u03b1-Syn and autophagosomes in hippocampus. Critically, TRPV4 knockdown significantly alleviated MPTP-induced \u03b1-Syn accumulation. Western blot analysis revealed that TRPV4 impaired \u03b1-Syn clearance via the ALP, as evidenced by dysregulation of key ALP components: LC3B, p62, lysosome-associated membrane protein 1, and transcription factor EB. In conclusion, our data are consistent with a model in which TRPV4 contributes to \u03b1-Syn accumulation through impairment of the ALP. This work establishes a direct link between TRPV4 and impaired \u03b1-Syn clearance, identifying TRPV4 not only as a mediator of ER stress and inflammation but as a critical molecular sensor that disrupts proteostasis. This positions TRPV4 as a promising therapeutic target for counteracting MPTP-induced neurodegeneration.\n\nID: 41993512\nTitle: WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\nAbstract: The aggregation of \u03b1-synuclein (\u03b1-SYN) into Lewy bodies (LBs) is a central event in the pathogenesis of Parkinson's disease (PD) and related synucleinopathies1,2. Despite significant advances in understanding \u03b1-SYN self-assembly, the precise sequence of early aggregation steps has not been directly visualized in living neurons. Here, we use an optogenetic-induced protein aggregation system with a high temporal resolution to monitor the onset of \u03b1-SYN assembly in neurons. We found that the initiation and accumulation of \u03b1-SYN aggregates occur predominantly at the lysosomal membrane, an event driven by the \u03b1-SYN N-terminus and modulated by the membrane-associated adaptor protein WD repeat-containing protein 44 (WDR44). Remarkably, we demonstrate that WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons. Consistent with its potential pathogenic involvement, WDR44 aberrantly accumulates in vivo and in the brains of PD patients, where it colocalizes with LB inclusions. Finally, we show that lysosome-associated \u03b1-SYN aggregates compromised lysosomal structure and function, leading to neuronal impairment, a phenotype worsened by WDR44 overexpression, linking early aggregation events to downstream toxicity. Together, these findings reveal the earliest dynamic stages of \u03b1-SYN oligomerization in living neurons and identify the WDR44-\u03b1-SYN interaction as a promising therapeutic target for reducing \u03b1-SYN pathology and enabling early intervention in PD.\n\nID: 41980172\nTitle: Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.\nAbstract: Microplastics (MPs), as emerging food contaminants, have been established to exert adverse effects on the liver. However, the precise toxicological mechanisms remain elusive. Our results demonstrated that MPs triggered mitochondrial dysfunction and mitochondrial ROS (mtROS) accumulation, which subsequently activated NLRP3/caspase-1/GSDMD-N-dependent pyroptosis in hepatocytes. Notably, beyond its canonical translocation to the plasma membrane, GSDMD-N was observed to form pores on the mitochondrial outer membrane, exacerbating mitochondrial damage. The mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux, which ultimately initiated ferroptosis. Concurrently, mitochondrial GSDMD-N mediated mitochondrial intrinsic apoptosis by promoting cytochrome c release and caspase-3 activation. Collectively, our findings revealed that MPs induced GSDMD-N activation and its mitochondrial translocation, which in turn initiated pyroptosis, ferroptosis, and apoptosis in hepatocytes. This study provided novel mechanistic insights into MPs-induced hepatotoxicity, identifying GSDMD-N as a potential central hub coordinating multiple cell death modalities.\n\nID: 41977181\nTitle: Copper Dyshomeostasis Affects \u03b1-Synuclein Clearance Mechanisms in Parkinson's Disease: Insights from In Vitro Models and Translational Evidence.\nAbstract: Parkinson's disease (PD) is characterized by the progressive degeneration of dopaminergic neurons and the accumulation of \u03b1-synuclein-rich inclusions, largely resulting from impaired protein clearance mechanisms. Copper is an essential redox-active metal in the central nervous system (CNS), but alterations in its homeostasis can promote oxidative stress, mitochondrial dysfunction, and proteostatic failure. In vitro studies indicate that copper can promote \u03b1-synuclein misfolding, enhance oxidative stress, and interfere with both the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway (ALP). In this review, we critically evaluate mechanistic evidence from cellular models, integrating available animal and clinical data to assess the biological significance of copper-mediated impairment of \u03b1-synuclein clearance. We highlight the current research, identify methodological limitations, and discuss whether copper imbalance acts as a primary pathogenic trigger or as a disease-modifying amplifier of proteostatic failure. Furthermore, we consider the translational implications of selectively modulating intracellular copper pools as a therapeutic strategy in PD. Finally, we will highlight unresolved issues, methodological limitations, and emerging targeted therapeutic prospects.\n\nID: 41975606\nTitle: Serine endopeptidase tripeptidyl peptidase II maintains lysosomal homeostasis to alleviate Parkinson's disease pathogenesis.\nAbstract: Parkinson's disease is neuropathologically characterized by the progressive loss of dopaminergic neurons and the pathological accumulation of \u03b1-synuclein. While these hallmarks are well established, the molecular drivers of this irreversible neurodegenerative process are not fully understood. Through an integrated multi-omics approach combining nascent protein mass spectrometry and bulk RNA sequencing of cellular and transgenic Parkinson's disease mouse models, we revealed suppressed serine endopeptidase activity during the early pathogenic stages of the disease. Subsequent functional analyses identified tripeptidyl peptidase II as the principal enzyme mediating serine endopeptidase activity, as demonstrated through a series of biochemical assays. Mechanistic investigations showed that tripeptidyl peptidase II deficiency impairs lysosomal function, prolongs the clearance of \u03b1-synuclein fibrillar seeds, and disrupts synaptic homeostasis in hippocampal neurons. Importantly, overexpression of tripeptidyl peptidase II effectively attenuated pathological \u03b1-synuclein aggregation and prevented the cell-to-cell propagation of \u03b1-synuclein pathology in wild-type mice injected with \u03b1-synuclein preformed fibrils. Our findings establish tripeptidyl peptidase II as a critical regulator of lysosome-mediated amyloidogenic seed degradation and reveal its neuroprotective role against \u03b1-synuclein-associated synucleinopathies.\n\nID: 41940964\nTitle: Genetic and environmental risk factors of Parkinsonism.\nAbstract: Parkinsonian disorders comprise a broad spectrum of neurodegenerative diseases with a wide variety of pathogenetic processes. These processes lead to the formation of pathological proteins, resulting in the brain diseases called synucleinopathies, tauopathies or TDP-43 proteinopathies. There is currently growing support for the hypothesis that genetic variants explain a significant fraction of the etiology of apparently sporadic parkinsonian disorders. Genetic risk factors can be stratified according to the metabolic or structural processes that can lead to cellular disturbance;\u00a0these processes involve protein aggregation, protein and membrane trafficking, stabilization of the neurite structure, prion-like transmission of pathological proteins, ubiquitin-proteasome system balance, mitophagy, lysosome autophagy, synaptic functions, and dopamine transmission. Regarding the environmental risk factors, there are several substances that have been supposed of being a risk for the development of neurodegenerative proteinopathy and Parkinsonism, mainly the agents used in agriculture and the textile industry. The most important and most frequently studied are pesticides and trichlorethylene. Beside the globally ubiquitous substances which are supposedly neurotoxic and exposure to which can cause manifestations of Parkinsonism, there are more geographically (regionally) specific substances, which cause (or quite recently caused) the manifestation of endemically present Parkinsonism. Among ten types of endemic Parkinsonism, three of them are thought to have an environmental cause: Western Pacific Parkinsonism, Caribbean Parkinsonism, and North France cluster of atypical Parkinsonism.\n\nID: 41919495\nTitle: Lysosomal homeostasis at the crossroads of neurodegeneration.\nAbstract: Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss.\n\nID: 41832866\nTitle: Electroacupuncture mitigates oxidative stress and neuroinflammation in Parkinson's disease via mitigating autophagy-lysosome dysfunction.\nAbstract: Parkinson's disease (PD) is a neurodegenerative disorder characterized by autophagic dysfunction. Acupuncture is a well-established intervention recognized for its immunomodulatory and neuroprotective effects. This study aimed to explore the mechanisms by which electroacupuncture (EA) interventions can ameliorate mitochondrial damage in PD. EA was applied to the chorea and tremor control area on the scalp of MPTP-induced mice. The cognitive abilities and motor functions of mice were evaluated through behavioral experiments. EA treatment alleviated behavioral deficits, reduced neuroinflammation in the brain, and significantly reversed MPTP-induced changes in dopamine (DA) metabolomics. Proteins related to autophagy and inflammation in the striatum were quantified via immunofluorescence. EA also inhibited excessive mitochondrial division, and reduced oxidative stress. Additionally, Rapamycin (RAP) interventions further improved autophagy, while 3-Methyladenine (3MA) interventions counteracted the therapeutic effects of EA. In conclusion, these results suggest that EA treatment is associated with reduced neuroinflammation and the protection of dopaminergic neurons in the nigrostriatal system. EA alleviates PD by ameliorating autophagy-lysosomal dysfunction and restoring normal mitochondrial function.\n\nID: 41812834\nTitle: Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.\nAbstract: Growing nanoplastics exposure raises concern for neurotoxicity, particularly given recent evidence of plastic accumulation within human brain tissue a highly lipid enriched organ, yet effects on brain lipid metabolism remain poorly understood. Here, we employed high-resolution untargeted lipidomics to map brain lipid perturbations in Drosophila melanogaster chronically exposed to polystyrene nanoplastics (PS- NPs). PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines, accompanied by increased diacylglycerols/triacylglycerols and monounsaturated fatty acids and by lipid droplet expansion. Guided by these lipidomic signatures, targeted biochemical assays demonstrated depolarized mitochondrial membrane potential, elevated mitochondrial reactive-oxygen species, inhibition of respiratory-chain complexes I and IV, and a shift in NAD(H) and NADP(H) redox couples toward a reduced state and increasing lipid peroxidation. This redox imbalance was accompanied by decreased tyrosine-hydroxylase expression, dopamine depletion, and impaired locomotor behavior, hallmarks of Parkinson's disease (PD)-like neurodegeneration. Dopaminergic neurochemistry was impaired (tyrosine hydroxylase and dopamine decreased), with concomitant reduction of GABA, and locomotor and circadian deficits emerged. Remarkably, co-treatment with the antioxidant N-acetylcysteine (NAC) restored mitochondrial membrane potential, reduced mitochondrial ROS and lipid peroxidation, normalized neutral lipid and MUFA accumulation, and rescued neurotransmitter levels and behavior. Stable-isotope tracing confirmed disrupted TCA cycle flux after NPs exposure that was rescued by NAC. Collectively, these findings reveal lipidomic remodeling as a critical link between environmental NPs exposure and PD-like pathology, highlighting mitochondrial redox-lipid interactions as early determinants and support redox-directed interventions to mitigate risk.\n\nID: 41751935\nTitle: Pathophysiological Roles of Two Intracellular P-Type ATPases: The Cancer-Associated Na+,K+-ATPase \u03b13 Isoform and the Parkinson's Disease-Related ATP13A2.\nAbstract: P-type ATPases constitute a diverse superfamily of ATP-driven transporters essential for ion homeostasis, membrane asymmetry, and organelle function. Among them, the P2-type Na+,K+-ATPase and the P5-type ATP13A2 have recently emerged as key regulators of cancer progression and neurodegeneration, respectively. In this review, we highlight new insights into the pathological roles of the Na+,K+-ATPase \u03b13 isoform (\u03b13NaK) in malignant cells and ATP13A2 in Parkinson's disease (PD). Cancer tissues frequently overexpress \u03b13NaK which is aberrantly localized to intracellular vesicles and undergoes adhesion-dependent intracellular trafficking. Upon cell detachment, \u03b13NaK translocates to the plasma membrane to sustain survival signaling, thereby promoting anoikis resistance and facilitating the persistence of circulating tumor cells (CTCs). Cardiac glycosides selectively inhibit \u03b13NaK at nanomolar concentrations, suppressing cancer cell proliferation through GLUT1 endocytosis, metabolic inhibition, and downregulation of THADA and LAT1, ultimately inducing anoikis in CTCs and reducing metastasis in vivo. Conversely, ATP13A2 is genetically linked to early-onset parkinsonism and regulates lysosomal integrity, polyamine homeostasis, and neuronal resilience. Recent animal studies demonstrate that adult-onset ATP13A2 loss causes progressive nigrostriatal degeneration, while heterozygous deficiency produces distinct age-dependent cognitive and \u03b1-synuclein phenotypes. Beyond its established role in polyamine transport, emerging evidence suggests that ATP13A2 can function as an H+,K+-ATPase-like transporter, contributing to proton and cation handling within the endolysosomal system. Together, these findings underscore the broader physiological and pathological significance of intracellular P-type K+-ATPases and highlight \u03b13NaK and ATP13A2 as promising therapeutic targets in cancer metastasis and PD.\n\nID: 41747943\nTitle: Degradation of alpha-synuclein/SNCA mRNA by RNautophagy.\nAbstract: \u03b1-Synuclein is a neuronal protein and main component of Lewy bodies, the pathological hallmark of Lewy body diseases such as Parkinson's disease and dementia with Lewy bodies. While the accumulation of \u03b1-synuclein in neurons is implicated in the pathogenesis of these disorders, the mechanisms underlying \u03b1-synuclein mRNA degradation remain poorly understood. RNautophagy is a lysosomal RNA degradation pathway in which RNA is directly taken up into lysosomes and subsequently degraded. SIDT2, a lysosomal membrane protein, mediates the uptake of RNA. In this study, we investigated whether SIDT2-mediated RNautophagy degrades \u03b1-synuclein mRNA. Knockdown of SIDT2 led to reduced degradation of \u03b1-synuclein mRNA, whereas overexpression of wild-type SIDT2 enhanced its degradation, suggesting its role in \u03b1-synuclein mRNA turnover. In contrast, overexpression of the RNA uptake-deficient S564A mutant did not enhance degradation, indicating that RNA uptake activity is required for SIDT2-mediated degradation of \u03b1-synuclein mRNA. Using a series of deletion mutants, we identified a guanine (G)-rich sequence within the 5' untranslated region (5'-UTR) of \u03b1-synuclein mRNA as a key determinant of SIDT2-dependent degradation. Furthermore, insertion of the G-rich sequence into the 5'-UTR of GFP mRNA promoted SIDT2-dependent degradation of GFP mRNA and reduced GFP protein expression. Taken together, these results indicate that SIDT2-mediated RNautophagy contributes to the degradation of \u03b1-synuclein mRNA via the G-rich region within the 5'-UTR. Our findings may also provide insights into the pathogenesis of Lewy body diseases.\n\nID: 41734603\nTitle: Bibliometric analysis of the pathogenesis of Parkinson's Disease.\nAbstract: This article provides an overview of research advancements and emerging trends in the pathogenesis of Parkinson's disease (PD) from 2015 to 2024, offering a reference for researchers in this field. A literature search was conducted using the Web of Science Core Collection (WoSCC) with the query terms: ((TS = (Parkinson's disease)) OR TS =\u202f(Parkinson disease)) AND TS =\u202f(pathogenesis). Bibliometric analysis and visualization of the search results were performed using CiteSpace and VOSviewer. A total of 3140 articles were included. Since 2015, publications on this topic have shown a significant upward trend. The top three contributing countries were China, the United States, and Italy. The International Journal of Molecular Sciences ranked first in terms of publication volume and total citations. A 2017 review titled \"Parkinson's Disease\" received the most citations. Keyword co-occurrence analyses revealed that research hotspots include abnormal aggregation of \u03b1-synuclein, mitochondrial dysfunction, oxidative stress, neuroinflammation, dysregulation of the autophagy-lysosome system and gene mutations. Recent trends indicate a clear shift from isolated molecular pathways toward systemic mechanisms, particularly highlighting the emerging roles of the gut-brain axis and ferroptosis in PD pathogenesis. Research on the pathogenesis of Parkinson's disease has gained increasing attention. This study presents a bibliometric analysis and visualization of global research trends and hotspots over the past decade, providing valuable perspectives for future studies into PD-related mechanisms.\n\nID: 41719940\nTitle: Convergent molecular pathways to inherited Parkinson's disease.\nAbstract: The most common, high-risk genetic factors for Parkinson's disease are pathogenic LRRK2 variants that increase LRRK2 kinase activity and pathogenic GBA1 variants that reduce lysosomal glucocerebrosidase activity. LRRK2 phosphorylates a subset of Rab GTPases, enabling them to bind phosphorylation-specific effectors that drive cellular pathology. To date, LRRK2 has at least two major cellular roles: it promotes exocytosis of lysosome-related organelles-particularly under conditions of lysosome stress in macrophages and microglia-and it regulates the formation and stabilization of primary cilia in neurons and astrocytes. In the brain, loss of primary cilia or GBA1 deficiency impairs Hedgehog signaling, reducing production of neuroprotective factors needed to support vulnerable dopamine neurons. Remarkably, administration of a LRRK2 inhibitor to LRRK2 mutant mice restores cilia and rescues neuroprotective factor production, offering great promise for people with Parkinson's.\n\nID: 41702167\nTitle: Lipid metabolic dysregulation: A novel developmental toxicity pathway of aged nanoplastics via inhibition of lipophagy in zebrafish.\nAbstract: The widespread occurrence of micro/nanoplastics (MNPs) in ecosystems poses significant environmental challenges. Although environmentally aged MNPs predominate, their developmental toxicity remains poorly understood. We demonstrate that both pristine and aged polystyrene nanoplastics (PSNPs) induce abnormal lipid accumulation and impair early development in zebrafish larvae. Lipidomics revealed aged PSNPs significantly increased triglycerides via disrupted glycerophospholipid metabolism. Mechanistically, aged PSNPs did not alter LC3-II/LC3-I ratios but upregulated RAB7 and p62 while downregulating lysosomal biogenesis regulator TFEB. They also reduced ATG5, essential for autophagosome formation via LC3 lipidation. These molecular alterations, together with lysosomal inhibition assays, functionally support lysosomal dysfunction as a key constraint on lipophagy. This impairment inhibits lipid utilization, promotes accumulation, and disrupts development. Critically, aged PSNPs caused stronger disruption than pristine particles despite both interfering with lipophagy. Our study provides mechanistic insights into the developmental toxicity of UV-aged PSNPs in zebrafish, highlighting the importance of considering aging-related changes in nanoplastic risk evaluation. SYNOPSIS: Aged nanoplastics exacerbate developmental toxicity in zebrafish by suppressing lipophagy to drive lipid accumulation, underscoring ecological risks in aquatic systems.\n\nID: 41700898\nTitle: Differences in \u03b1-synuclein conformational states in physiologically relevant pH/Na+ concentrations and ammonium acetate solutions unveiled by native mass spectrometry.\nAbstract: Native mass spectrometry implemented with theta emitters was used to demonstrate differences in conformational states of wild-type, A53T mutant, and truncated \u03b1-synuclein dissolved at physiologically relevant pH and Na+ concentrations compared to aqueous solutions of ammonium acetate. Specifically, 150 mM NaCl at pH 7.4, 20 mM NaCl at pH 4.5, and 15 mM NaCl at pH 7.2 were used to reflect, to some extent, the extracellular environment, lysosome, and cytosol, respectively. Analysis of charge state distributions obtained from physiologically relevant solutions vs. their ammonium acetate counterparts allows the comparison of \u03b1-synuclein conformational states. The protein shows relatively high conformational flexibility at 150 mM NaCl and pH 7.4, while it shows at least two different conformational states at 20 mM NaCl and pH 4.5. We observed a trend towards the adoption of less compact conformations at acidic pH, where Na+ appears to play a distinctive role in the adoption of different conformational states. Early-stage oligomers (dimer, pentamer, hexamer and heptamer) were also detected. Since oligomer formation was protein-specific, wild-type \u03b1-synuclein formed dimers while truncated \u03b1-synuclein formed pentamers, hexamers and heptamers, their abundances are consistent with kinetics of aggregation reported in the literature.\n\nID: 41643617\nTitle: Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.\nAbstract: Nanoplastics are an emerging global environmental concern, with increasing evidence of their neurotoxic effects. Recent findings suggest that abnormal aggregation of pathogenic proteins within the nervous system may contribute to the neurotoxicity induced by nanoplastics, yet the molecular mechanisms regulating this pathological cascade remain unclear. Here, we used immature mice as an experimental model to represent infants and young children who are at higher risk of nanoplastics exposure, to elucidate the molecular mechanisms underlying neurotoxicity induced by exposure to polystyrene nanoplastics (PS-NPs) during early life. The results showed that environmentally relevant doses of PS-NPs penetrated the brains of immature mice and induced behavioral and emotional disorders. Proteomic analysis identified the mTOR signaling pathway as a candidate pathway responding to PS-NPs exposure in the immature mouse brain. Rapamycin intervention and quantitative validation further demonstrated that PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity. Furthermore, treatment with sodium 4-phenylbutyrate (4-PBA) confirmed that proteostasis imbalance, characterized by activation of the unfolded protein response, was a direct driver of this neurotoxicity. Notably, both rapamycin and 4-PBA treatments alleviated neurotoxicity resulting from PS-NPs exposure by restoring proteostasis. Together, these findings highlight dysregulation of the autophagy-lysosome pathway mediated by mTOR as a central mechanism of PS-NPs-induced neurotoxicity in immature mice and suggest lysosomal regulation for proteostasis remodeling as a prospective therapeutic strategy against neurological hazards related to nanoplastics.\n\nID: 41642669\nTitle: Nanoplastic toxicology following gestational and lactational exposure.\nAbstract: Nanoplatics (NPs), particularly polystyrene (PS)-NPs, can traverse the placental barrier upon maternal exposure, leading to bioaccumulation in both dam and offspring organs, and inducing widespread transplacental toxicity. The distribution and toxicity of NPs are influenced by a variety of factors, including NP properties (type, size, and charge), exposure parameters (dose, route, and timing), and biological variables (model and co-exposures). Due to their minute size, NPs pose significant threats to multiple systems in animal models. In rodent studies, reproductive and endocrine toxicity primarily manifests as placental dysfunction, impaired embryo implantation, increased miscarriage rates, and gonadal toxicity in offspring, mechanisms for which are suggested to involve oxidative stress, endocrine disruption, and dysregulated calcium homeostasis. Reported neurotoxicity, characterized by aberrant cortical architecture, hippocampal dysfunction, and learning and memory deficits, is mediated by mechanisms such as oxidative stress and ferroptosis, neurotransmitter disruption, gut-brain axis dysregulation, and pathological protein aggregation. In the cardiovascular system, studies suggest PS-NPs induce offspring cardiac fibrosis, apoptosis, and functional impairments, demonstrating marked sex-specific dimorphism potentially driven by ferroptosis. And PS-NPs have been shown to disrupt glycolipid metabolism in animal models, leading to offspring metabolic disorders. Furthermore, evidence from non-mammalian models, notably Caenorhabditis elegans, reveals transgenerational toxicity. Critically, the consequences of early-life NP exposure are long-lasting, potentially elevating susceptibility to various diseases in adulthood. This review comprehensively summarizes the toxicological profiles of NPs during the critical windows of gestation and lactation, underscoring the need for more robust research and a systematic approach to risk assessment.\n\nID: 41637953\nTitle: MONNA alleviates MPTP-induced Parkinson's disease in zebrafish by activating TFEB dependently on ER Calcium.\nAbstract: A-synuclein aggregation is a biomarker of Parkinson's disease (PD) whose feature is the progressive loss of dopaminergic neuron in the middle brain. The removal of a-synuclein aggregation through autophagy-lysosome pathway is a promising strategy for PD treatment. Transcription factor EB (TFEB) is a master regulator of autophagic and lysosomal biogenesis and function. Here, we report a library screen of intracellular Ca2+ inducers to identify small-molecule agonists of TFEB and discover MONNA can promote autophagic and lysosomal activity. Notably, MONNA facilitates the reduction of pathological a-synuclein in the Parkinson's disease model both in vitro and in vivo, and ameliorates PD-like behaviors in zebrafish. Mode of action studies reveal MONNA induces TFEB nuclear translocation through a Ca2+-dependent mechanism involving Calcineurin (CaN). Endoplasmic reticulum (ER) but not lysosome Ca2+ is critical to MONNA-induced TFEB activation and autophagy induction. Furthermore, Sarcoendoplasmic reticulum calcium ATPase (SERCA) pump of ER modulates TFEB nuclear translocation induced by MONNA. Our findings demonstrate that MONNA is the first ER Ca2+-dependent small synthetic TFEB agonist promoting the degradation of a-synuclein aggregates and alleviating Parkinson's disease. This ER Ca2+-Calcineurin-TFEB signaling pathway would broaden the way to develop drugs for PD.\n\nID: 41622607\nTitle: Zinc-Mediated Lysosomal Destabilization Links Mitochondrial Damage to Neuronal Death in a Cellular MPP+ Model of Parkinson's Disease.\nAbstract: Dysregulation of autophagy and lysosomal function is central to Parkinson's disease (PD), yet the upstream mechanisms leading to lysosomal failure remain unclear. Across primary mouse cortical neurons, MT-3 deficient primary mouse astrocytes, human iPSC-derived midbrain dopaminergic neurons, and Rho0 CHO cells lacking mitochondrial respiration, we investigated how mitochondrial stress perturbs zinc (Zn2+) homeostasis and lysosomal integrity. We identify intracellular zinc as a critical mediator linking mitochondrial dysfunction to lysosomal membrane permeabilization (LMP) and neuronal death. Inhibition of mitochondrial complex I by 1-methyl-4-phenylpyridinium (MPP+) elevated reactive oxygen species (ROS) and intracellular zinc, jointly driving LMP. Blocking either ROS or zinc markedly attenuated lysosomal damage and cell death, demonstrating that both act upstream of LMP. To define zinc regulation, we examined metallothionein-3 (MT-3), a brain-enriched zinc-binding protein. MT-3-deficient astrocytes were more vulnerable to MPP+ and zinc overload (ZnCl2) but paradoxically resistant to hydrogen peroxide (H2O2), suggesting that MT-3 buffers cytosolic zinc during mitochondrial injury or extracellular zinc influx yet can release bound zinc under oxidative conditions. Using Rho0 cells, we show that MPP+ toxicity depends on mitochondrial ROS, as loss of mitochondrial function nearly abolished cell death. However, Rho0 cells were highly sensitive to ZnCl2 and H2O2 and exhibited markedly reduced lysosomal abundance, indicating limited capacity to sequester zinc and increased susceptibility to zinc-mediated injury. These findings support a coordinated system in which lysosomes and zinc-binding proteins maintain zinc homeostasis. When cytosolic zinc rises, its accumulation within lysosomes induces LMP and accelerates cell death. Collectively, our results identify intracellular zinc as an upstream trigger of lysosomal dysfunction and neurodegeneration. Zinc-mediated LMP provides a mechanistic link between mitochondrial injury, impaired autophagic flux, and \u03b1-synuclein pathology in PD. Enhancing zinc homeostasis and lysosomal resilience may offer promising therapeutic strategies.\n\nID: 41618357\nTitle: Two lysosomal genes ATP13A2 and GBA1 interact to drive neurodegeneration.\nAbstract: BACKGROUND: Parkinson\u2019s disease (PD) is a genetically complex disorder in which combinations of heterozygous risk variants may contribute to pathogenesis. Many PD risk loci encode lysosomal genes, such as GBA1, a common and potent risk factor, conferring at least a 5-fold increase. However, the mechanisms of GBA1 penetrance remain poorly understood. METHODS: Using Drosophila melanogaster, we performed a genetic interaction screen of lysosomal storage disorder (LSD) genes to identify dominant modifiers of Gba1b (fly homolog of GBA1). Age-dependent locomotor assessments, electroretinograms (ERG), transmission electron microscopy (TEM) analyses and quantification of dopaminergic (DA) neurons were used to assess the neurodegenerative phenotypes of double heterozygous animals. By combining immunostaining, lipidomics, metabolomics and pharmacological approaches we showed how partial loss of anne (fly homolog of ATP13A2) and Gba1b drives neurodegeneration. By interrogating genetic data from local and international PD cohorts we identified double heterozygous pathogenic variants in ATP13A2 and GBA1 in individuals with PD. RESULTS: We show that anne is expressed in neurons, whereas Gba1b is expressed in glia. Flies heterozygous for anne exhibit mild neurodegenerative phenotypes, and Gba1b strongly enhances this haploinsufficiency. Double heterozygous (Gba1bT2A/+;anneT2A/+) flies exhibit a slow and progressive neurodegeneration associated with accumulation and impaired acidification of lysosomes in photoreceptors and other neurons. Obvious morphological defects are first observed in glia at day 15 after eclosion and include vacuolization and neuronal detachment. These defects are accompanied by an elevation of glucosylceramide (GlcCer) and followed by loss of neuronal function and degenerative features by day 30. These phenotypes are neuronal activity-dependent. The neurodegenerative phenotypes are rescued by: ML-SA1, an agonist of the lysosomal TRPML1 channel that has been reported to promote lysosomal membrane trafficking; myriocin, a compound that inhibits GlcCer production; and DFMO, a drug which inhibits polyamine synthesis. Based on surveys of genetic data, we identify multiple PD cases harboring digenic variants in GBA1 and ATP13A2. CONCLUSIONS: Our study reveals that partial loss of Gba1b in glia and anne in neurons synergistically disrupts lysosomal pH and neuron-glia GlcCer homeostasis, triggering neurodegeneration. Our results provide evidence that GBA1 penetrance is influenced by additional genetic modifiers, consistent with a putative digenic mechanism for GBA1-PD penetrance. These findings highlight lysosomal acidification, sphingolipid clearance, and polyamine regulation as critical intervention points in digenic PD.\n\nID: 42463668\nTitle: Reconstitution of Ras-PI3K\u03b3 membrane communication and feedback using light-induced signaling inputs.\nAbstract: Reactions involving small GTPases and phosphatidylinositol phosphate (PIP) lipids serve essential roles in signal transduction at the plasma membrane. In cells, these distinct classes of molecules are linked through positive and negative feedback loops that give rise to emergent properties such as excitability and polarization. Here, we reconstitute communication and feedback between Ras GTPase and phosphatidylinositol 3-kinase gamma (PI3K\u03b3)-mediated PIP3 production on supported membranes using purified proteins. We employ light-induced membrane recruitment to rapidly shift steady-state conditions and observe the spatiotemporal response of the signaling module. Alone, the Ras-PI3K\u03b3 module exhibits transient and reversible activation due to global inhibition. The introduction of GEF-mediated positive feedback enables sustained threshold crossing and local amplification of Ras(GTP) and PIP3, resulting in a traveling, bistable wave of activity with characteristics of an excitable network. Spatial coupling between Ras(GTP) and PIP3 lipids depends on lateral diffusion and feedback circuit architecture. This work illuminates the roles activation thresholds, membrane diffusion, and positive feedback play in regulating the dynamics of Ras-PI3K\u03b3 membrane signaling reactions in the presence of global inhibition.\n\nID: 42443527\nTitle: DCAF13: a positive regulator of colon cancer cell proliferation via the AMER2/ Wnt/\u03b2-catenin pathway.\nAbstract: The Wnt/\u03b2-catenin pathway plays a critical role in colorectal cancer (CRC) development. The significance of Wnt/\u03b2-catenin in maintaining the stability of adult tissues and challenges in identifying suitable molecular targets have limited the application of targeting the Wnt/\u03b2-catenin pathway. As one of the Cullin RING Ligase 4 adapters, DNA damage-binding protein 1 (DDB1) - and CUL4 correlation factor 13 (DCAF13) appears strongly expressed in different tumors. Our findings confirm enhanced expression of DCAF13 in tissues of CRC origin and related cell. In colon cancer cells, DCAF13 regulated adenomatous polyposis coli membrane recruitment 2 (AMER2) through ubiquitination, DCAF13 deletion increased AMER2 expression, which inhibited Wnt/\u03b2-catenin activity, suppressing cell proliferation. This effect was further validated in mice with gut-specific DCAF13 knockout. The ubiquitin-proteasome system is a potential target for drug development and cancer treatment. Beta-propeller proteins, such as CRL4 adapter DCAFs, are easily targeted by drugs. DCAF-proteolysis-targeting chimeras (PROTACs) can overcome drug resistance and selectively target tumor drivers by leveraging the unique substrate specificity of the DCAF subunits. DCAF13 emerges as a promising target for CRC, acting via the DCAF13-AMER2-Wnt /\u03b2-catenin axis.\n\nID: 42372161\nTitle: Two-step mechanism of Bruton's tyrosine kinase membrane recruitment and activation.\nAbstract: Peripheral membrane proteins (PMPs) are critical mediators of signaling cascades initiated at the cell surface. Their functions depend on their innate ability to interact dynamically with membranes in response to changing cellular conditions. This membrane recruitment may occur via high-affinity interactions with specific lipids/proteins or via transient, low-affinity interactions with the membrane. These weak and dynamic interactions, which are critical regulators of PMP function, are challenging to capture. Taking Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase essential for B cell activation, we demonstrate a native mass spectrometry platform to understand lipid-mediated recruitment of PMPs by directly studying it from lipid bilayers customized to target membranes. Our data demonstrate that BTK recognizes phosphatidylserine (PS) independently of phosphatidylinositol (3, 4, 5) phosphate (PIP3) binding. We show that PS-bound BTK retains PIP3 binding via high-affinity sites, while exhibiting PIP3-independent basal membrane recruitment. Biochemical assays show that this PS-mediated recruitment sensitizes BTK to PIP3-mediated activation at near-physiological PIP3 concentrations. Thus, we propose a two-step model for BTK membrane recruitment and activation. A low-affinity interaction with high-copy number PS enables plasma membrane recruitment of BTK and increases its membrane-bound concentration. Upon B cell activation, this prerecruited, membrane-bound BTK population localizes to PIP3-rich domains via electrostatic gliding along the membrane, driven by low-affinity PS and high-affinity PIP3 binding. This indicates a cooperative mechanism in which PS can amplify B cell signaling by increasing membrane-bound BTK levels. Our work demonstrates a general model of regulation of PH domain-containing proteins by weak protein-lipid interactions, which can be extended to other PMPs.\n\nID: 42353031\nTitle: PKC\u03b2II Activation Promotes Membrane-Proximal Enrichment of Ribosome-Bound RACK1.\nAbstract: The scaffold protein RACK1 (Receptor for Activated C Kinase 1) integrates signaling and translation, acting as a core component of the 40S ribosomal subunit. It binds activated Protein Kinase C (PKC) isoforms and membrane receptors. We used an auxin-inducible degron (AID2) system in human HAP1 cells to selectively deplete the free (cytoplasmic) pool of RACK1. The engineered RACK1-mAID-mClover3 fusion was rapidly degraded in the cytoplasm upon addition of 5-phenyl-indole-3-acetic acid (5-Ph-IAA), while the ribosome-bound pool remained detectable in ribosomal fractions, indicating that ribosome association makes RACK1 relatively less accessible to AID2-mediated proteolysis. Upon activation of PKC\u03b2II with phorbol-12-myristate-13-acetate (PMA), imaging at defined time points revealed closely matched kinetics of PKC\u03b2II membrane recruitment and membrane-proximal enrichment of ribosome-bound RACK1, peaking at ~10 min. Our data support a model in which activated PKC\u03b2II engages ribosome-bound RACK1 at membrane-proximal sites, consistent with a diffusion-capture mechanism in which PKC\u03b2II first accumulates at the membrane and then captures ribosome-bound RACK1, thereby recruiting the translational machinery to sites of signal input for membrane-proximal translation. These findings provide new insights into the spatial organization of translation.\n\nID: 42344932\nTitle: AKT-mediated phosphorylation of ZDHHC5 promotes NOD1 palmitoylation and innate immune signaling.\nAbstract: Nucleotide-binding oligomerization domain 1 (NOD1) is an intracellular pattern recognition receptor that detects bacterial peptidoglycan and initiates innate immune responses through membrane-associated signaling complexes. NOD1 activation depends on ZDHHC5-mediated palmitoylation, which promotes its membrane recruitment. However, whether growth factors and insulin modulate this NOD1 activation remains poorly defined. We investigated the effects of growth factors and insulin on NOD1 signaling using biochemical and cell-based approaches. Protein phosphorylation and interactions were analyzed by immunoblotting, co-immunoprecipitation, and mutagenesis assays. NOD1 palmitoylation, membrane localization, and downstream signaling activities were evaluated following modulation of AKT signaling and ZDHHC5 phosphorylation. We found that growth factors and insulin positively regulate NOD1 activation through an AKT-ZDHHC5-NOD1 signaling axis. Mechanistically, AKT directly phosphorylated the palmitoyltransferase ZDHHC5 at Ser345 and Ser380, promoting its retention at the plasma membrane and enhancing its enzymatic activity toward NOD1. AKT-dependent phosphorylation increased NOD1 palmitoylation and membrane recruitment, thereby facilitating activation of downstream innate immune signaling pathways. These findings identify a previously unrecognized mechanism linking growth factor- and insulin-mediated AKT activation to innate immune signaling. AKT-dependent phosphorylation of ZDHHC5 promotes NOD1 palmitoylation and activation, revealing a positive regulatory axis that integrates metabolic cues with innate immune responses. The AKT-ZDHHC5 pathway may therefore represent a potential target for modulating NOD1- driven inflammatory diseases.\n\nID: 42302456\nTitle: Polystyrene nanoplastics elicit early mitochondria-associated phenotypic, metabolic, and functional responses in human hepatocytes.\nAbstract: Nanoplastics have recently been detected in human liver tissue, raising concerns about their potential impact on liver function. However, early hepatocyte responses associated with nanoplastics exposure remain poorly understood. Here, we combined high-throughput Cell Painting-based phenomics, untargeted metabolomics, and Seahorse mitochondrial functional assay to investigate the effects of 100\u00a0nm polystyrene nanoplastics on human HepaRG hepatocytes, a surrogate for primary human hepatocytes. At the tested concentrations (6.25-100\u00a0\u00b5g/mL), exposure did not induce overt cytotoxicity, enabling assessment of early sublethal cellular responses. Phenomics revealed widespread subcellular perturbations, with 16.4% of the measured phenotypic features significantly altered. Mitochondria-associated features represented the dominant altered phenotypic signature, showing pronounced changes in granularity, texture, and radial distribution, alongside alterations in endoplasmic reticulum- and cytoskeleton-associated features. Untargeted metabolomics of intracellular metabolites and the extracellular secretome revealed metabolic alterations, characterized by changes consistent with altered \u03b2-oxidation, lipid handling, membrane stress, and central carbon metabolism, including changes in the tricarboxylic acid (TCA) cycle and amino acid catabolism. Pathway analysis identified the TCA cycle as one of the most significantly affected pathways (FDR\u00a0=\u00a00.028). Integrated phenomic-metabolomic analysis revealed strong correlations between mitochondrial phenotypic features and metabolites involved in lipid and energy metabolism, indicating a coordinated structural-metabolic response to polystyrene nanoplastics exposure. Functional assessment using Seahorse assay showed reduced basal and maximal respiration and decreased ATP-linked O2 consumption. Together, these findings provide evidence that 100\u00a0nm polystyrene nanoplastics elicit early mitochondria-associated phenotypic, metabolic, and functional responses prior to overt cytotoxicity under the tested conditions. They also highlight the value of phenomic-metabolomic-functional integration for profiling sublethal nanotoxicological responses and guiding future targeted mechanistic studies.\n\nID: 42235331\nTitle: Electrostatic control of membrane disruption and amorphous coaggregation by dynorphin A variants.\nAbstract: Dynorphin A is a highly cationic neuropeptide that exhibits membrane activity beyond its canonical opioid receptor signaling. Here, we investigate how sequence variants of Dynorphin A associated with spinocerebellar ataxia type 23 modulate membrane disruption and aggregation behavior. Using computational electrophysiology simulations combined with liposome leakage and fluorescence-based aggregation assays, we show that Dynorphin A variants interact with lipid bilayers primarily via electrostatic recruitment, followed by mutation-dependent insertion and transient pore formation. Anionic lipids promote bilayer disruption, while cholesterol attenuates peptide activity in a variant-specific manner. Although Dynorphin A variants do not spontaneously form ordered aggregates, they markedly alter amyloid-\u03b2 co-assembly by enhancing hydrophobic surface exposure without proportionally increasing fibrillization. These results demonstrate that subtle sequence changes fine-tune the balance between membrane perturbation and amorphous co-aggregation, and highlight electrostatic membrane recruitment as a key determinant of DynA bioactivity.\n\nID: 42182431\nTitle: Cryo-EM structure and biochemical characterization of a BRAF/CRAF heterodimer: Negative charge in the NtA motif is not required for RAF activation.\nAbstract: Upon RAS-driven membrane recruitment, RAF kinases ARAF, BRAF and CRAF are activated via formation of homo- or hetero- dimers to initiate signaling through the MAP kinase cascade. Although RAF heterodimers are important for both physiologic and oncogenic signaling, they have been little studied at a structural and biochemical level. Here we report the preparation, biochemical characterization, and the cryo-EM structure of a 14-3-3-bound BRAF/CRAF heterodimer complex. The heterodimer exhibited kinetic parameters and sensitivity to a panel of twelve structurally diverse RAF inhibitors that were closely similar to, or intermediate between, those of BRAF and CRAF homodimers. Cryo-EM structures of the heterodimer with and without MEK1 revealed an overall organization essentially identical to that of RAF homodimers, but with an asymmetric interaction in the MEK1-bound structure in which the BRAF N-terminal acidic (NtA) motif extends across the dimer interface to engage the CRAF RKTR motif. Mutagenesis of this interface unexpectedly revealed that replacing the acidic NtA sequence with a basic RARA sequence yields highly active RAF homodimers and heterodimers, demonstrating that negative charge in the NtA motif is not required for activity. Collectively, our findings suggest that the charge state of the NtA motif influences RAF activity through effects on local backbone dynamics and the stability of the inactive kinase conformation, rather than via stereospecific recognition across the dimer interface.\n\nID: 42132143\nTitle: Lipid composition controls the huntingtin exon 1 membrane-association and differentially modulates its flanking regions' dynamics.\nAbstract: The pathological expansion of the polyglutamine (polyQ) repeat within the first exon of huntingtin (Httex1) protein is a defining hallmark of Huntington's disease (HD). Multiple evidence supports that the membrane recruitment of Httex1 is critical for its self-assembly and related toxicity in HD. In this work, we quantitatively examined the early steps of monomeric Httex1(23Q) association with lipid membranes and its impact on the conformational dynamics of the adjacent polyQ regions-the N-terminal N17 segment and C-terminal proline-rich region (PRR). A broad range of membrane physical properties was explored, including zwitterionic and anionic lipids, and also co-existing liquid-ordered and liquid-disordered phases. Two single cysteine mutants were engineered at the N- and C-termini of Httex1(23Q) and fluorescently labeled with acrylodan or Atto 488 to probe their local polarity and flexibility, respectively. Our results indicate that Httex1(23Q) preferentially binds to negatively charged lipid vesicles, and to a lower extent to liquid ordered/disordered phases. The N-terminal N17 segment interacts with anionic membranes, adopting a less flexible state than in aqueous solution. At variance, the C-terminal PRR remains highly dynamic and solvent exposed in the Httex1(23Q) membrane-bound state, preserving its intrinsic disordered features across all lipid compositions used. Altogether, our work provides quantitative insight into the distinct roles of each flanking polyQ region in mediating Httex1-lipid binding, and how distinct lipid compositions further modulate these early interaction steps.\n\nID: 42130460\nTitle: Targeting a Pleckstrin Homology Domain with a Lysine-Reactive Covalent Binder.\nAbstract: Bruton's Tyrosine Kinase (BTK) is a validated target for hematological malignancies, with numerous FDA-approved inhibitors on the market. Current therapies target the highly conserved ATP binding site and hence limit the therapeutic index given the site's highly conserved nature across the kinome. We explore a novel approach for BTK inhibition by targeting the PH domain-mediated membrane recruitment and activation of BTK. We have identified a fragment which covalently modifies a lysine in the inositol phosphate (PIP3) binding site and inhibits the binding of a soluble PIP3 headgroup analog to the PH domain. Fragment growth and an extensive structure-binding relationship study uncovered 27 crystal structures and a best-in-class analog, 24. Evaluation of pKa values of the targeted lysine in BTK and other PH domains suggests this as a more general approach to PH domain inhibition.\n\nID: 42121920\nTitle: Heterotrimeric G Protein-RasGAP Coupling Drives Adaptation During Chemotaxis.\nAbstract: Chemotaxis enables eukaryotic cells to detect and migrate along extracellular chemoattractant gradients spanning several orders of magnitude. This remarkable dynamic range relies on adaptation, a process that allows cells to reset their signaling machinery while preserving sensitivity to incremental changes in stimulus intensity. Although numerous actin-dependent feedback mechanisms have been characterized, the molecular basis of adaptation within an actin-independent core gradient-sensing module remains poorly understood. Here, we identify the Ras GTPase-activating protein, C2GAP1, as a critical F-actin-independent effector of the heterotrimeric G protein, G\u03b12, in Dictyostelium discoideum. Using cytoskeleton-free gradient-sensing cells, quantitative imaging, biochemical assays, FRET-based G-protein activation measurements, and structural modeling, we demonstrate that C2GAP1 controls concentration-dependent adaptation during gradient sensing. Mechanistically, C2GAP1 directly associates with G\u03b12 in both GDP- and GTP-bound states, with preferential binding to activated G\u03b12, thereby sustaining membrane recruitment and locally attenuating Ras and downstream signaling. Loss of C2GAP1 enhances G-protein activation, disrupts local inhibition, and impairs rapid reorientation in dynamic gradients. These findings define a direct coupling between heterotrimeric G proteins and the RasGAP, C2GAP1, as a core adaptive module that enables gradient sensing across a wide concentration range.\n\nID: 42085634\nTitle: Optogenetic control of PLC-\u03b31 activity directs cell motility.\nAbstract: Phospholipase C-\u03b31 (PLC-\u03b31) signaling is required for mesenchymal chemotaxis, but is it sufficient to bias motility? PLC-\u03b31 enzyme activity is basally autoinhibited, and light-controlled membrane recruitment of wild-type PLC-\u03b31 (OptoPLC-\u03b31) in Plcg1-null fibroblasts does not trigger lipid hydrolysis, complicating efforts to isolate its contribution. Utilizing cancer-associated mutations to investigate the regulatory logic of PLC-\u03b31, we demonstrate that a hallmark of enzyme activity, phosphorylated Tyr783, is not a proxy for activity level, but is rather a marker of dysregulated autoinhibition. Accordingly, OptoPLC-\u03b31 with a deregulating mutation (P867R, S345F, or D1165H) exhibits elevated phosphorylation, and membrane localization of such is sufficient to activate substrate hydrolysis and concomitant motility responses. In particular, local recruitment of OptoPLC-\u03b31 S345F polarizes cell motility and migration on demand. This response is spatially dose-sensitive and only partially reduced by blocking canonical PLC-\u03b31 signaling, yet is lipase-dependent. Our findings reframe the interpretation of PLC-\u03b31 regulation and demonstrate that local activation of PLC-\u03b31 is sufficient to direct cell motility.\n\nID: 42003908\nTitle: DHCR24 Drives Ovarian Cancer Chemoresistance Through Lipid Raft-mediated P-gp Stabilization and STAT3 Activation.\nAbstract: To investigate the role and mechanism of DHCR24 in chemoresistance of ovarian cancer and to identify potential therapeutic targets for overcoming treatment resistance. We integrated bioinformatic analysis of GEO datasets and clinical survival data from KMplot to identify chemoresistance-associated genes. DHCR24 expression and function were systematically evaluated using cisplatin-resistant cell lines (A2780/DDP, SKOV3/DDP), patient-derived primary cells, xenograft models, and clinical specimens through molecular biology techniques, immunohistochemistry, and functional assays. Mechanistic studies employed RNA interference, cholesterol modulation, lipid raft disruption with M\u03b2CD, cycloheximide chase assays, and STAT3 pathway inhibition. DHCR24 was consistently upregulated in chemoresistant ovarian cancer models and significantly correlated with poor patient survival. Genetic or pharmacological inhibition of DHCR24 restored chemosensitivity in vitro and in vivo, while its overexpression induced cross-resistance to multiple chemotherapeutic agents. Mechanistically, DHCR24 enhanced cholesterol biosynthesis, which stabilized lipid raft microdomains to promote P-gp protein stability and facilitate STAT3 membrane recruitment and activation. Furthermore, activated STAT3 transcriptionally upregulated DHCR24 expression, establishing a positive feedback loop that perpetuates the chemoresistant phenotype. DHCR24 drives chemoresistance through a cholesterol-dependent circuit that stabilizes drug efflux pumps and activates pro-survival signaling, identifying DHCR24 as a promising therapeutic target for overcoming chemotherapy resistance in ovarian cancer.\n\nID: 41959055\nTitle: Flow-sensitive K + channels link flow to piezo1/PI3K/Akt1 pathway.\nAbstract: Endothelial response to flow is key to vascular function in health and disease. Our earlier studies demonstrated that endothelial Kir2.1 is essential for flow-induced Akt1/eNOS signaling and for flow-induced vasodilation (FIV) but the mechanistic integration between Kir and other flow signaling pathways remained poorly understood. We use a combination of electrophysiological recordings in real time of flow exposure, Ca 2+ imaging, pressure myography of resistance arteries, and echocardiography. We demonstrate that Kir2.1 is essential for flow-induced PI3K phosphorylation, whereas expression of myristoylated Akt1, which bypasses PI3K-dependent membrane recruitment, restores flow-induced Akt1/eNOS phosphorylation in Kir2.1-deficient endothelium. It also restores FIV in Kir2.1-deficient mesenteric arteries. We further demonstrate that Kir2.1 is essential for flow-induced Ca\u00b2\u207a influx mediated by Piezo1 and TRPV4 channels, whereas Ca\u00b2\u207a influx induced by pharmacological activation of these channels is Kir2.1 independent. Deficiency of Piezo1 does not affect endothelial Kir2.1 channels. We also discover that flow activation of endothelial Kir2.1 requires Syndecan1, thus creating a link between glycocalyx and downstream effects. Physiologically, we find that endothelial Kir2.1 is suppressed by infusion of Angiotensin-II and by advanced aging, resulting in significant impairment of FIV. In both cases, FIV is fully restored by endothelium-specific over-expression of Kir2.1. Our study reveals that Kir2.1 serves as a mechanistic linker between endothelial glycocalyx to Piezo1-mediated Ca 2+ influx and downstream signaling suggesting a new integrated model of endothelial mechanotransduction. A functional loss of endothelial Kir2.1 is shown to play a significant role in FIV impairment in Angiotensin-induced hypertension and aging.\n\nID: 41957923\nTitle: Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?\nAbstract: The enteric nervous system (ENS), a key component of the gut-brain axis, has emerged as a critical player in the pathogenesis of Parkinson's disease (PD). It is the first neural system exposed to food contaminants (FCs)-a diverse group of ubiquitous toxic compounds fortuitously present in food derived from production, processing, storage, or environmental contamination. Emerging evidence suggests that FCs may initiate or amplify neurodegenerative processes, yet their effects on the ENS and their impact in gut-to-brain communication remain insufficiently characterized. This systematic review synthesizes current evidence on FCs-induced effects on the ENS and its involvement in mediating neurotoxicity from dietary toxicants exposure. Following PRISMA guidelines, 67 studies were included pertaining to cellular or mammalian experimental models exposed to FCs via enteral routes, reporting ENS-related outcomes or studying vagal involvement in modulating FC toxicity. The main FCs evaluated were pesticides, toxins, bisphenols, acrylamide, manganese, and micro-/nanoplastics. Across studies, FCs consistently induced neurochemical remodeling of the ENS, activation of enteric glia, often coupled with intestinal alterations. Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain. Vagotomy models confirmed that disrupting ENS-CNS communication attenuates FC-related central neurotoxicity, supporting the involvement of food toxicants in gut-to-brain propagation of neurotoxic signals. These findings support the body-first hypothesis of PD and position the ENS as a critical, yet underinvestigated interface in exposome-related neurotoxicology. The review highlights research gaps and the need for improved models and long-term, low-dose studies reflecting realistic FC exposure.\n\nID: 41887951\nTitle: Repair condensates and lipid domains in lysosome integrity.\nAbstract: Lysosomes are sophisticated signaling hubs whose function depends on membrane integrity. A breach of this barrier, known as lysosomal membrane permeabilization, triggers inflammation and cell death, driving pathologies from lysosomal storage disorders to neurodegeneration. Cells counter membrane damage with diverse repair mechanisms, including endosomal sorting complexes required for transport machinery, sphingomyelin scrambling, annexin-mediated scaffolding, lipid transport, and stress granule plugging. This diversity suggests singular strategies are insufficient, posing an 'orchestration challenge' regarding precise initiation, spatial organization, and temporal coordination. This opinion article proposes that biomolecular condensation, initiated by damage cues, acts as a primary organizing principle. We suggest lysosomal injury nucleates de novo 'repair condensates' that stabilize compromised membranes and serve as recruitment and organizational hubs for repair machinery.\n\nID: 41886456\nTitle: UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.\nAbstract: UFMylation, a recently identified ubiquitin-like modification mediated by the E3 ligase UFL1, plays context-specific roles in cancers, but its substrates and functions in lung adenocarcinoma (LUAD) remain poorly defined. Here, we identify the AKT signaling repressor PHLDA3 as a substrate of UFL1 in LUAD. UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling. Tumor-associated PHLDA3 mutations F41L, E82G, and K106N impair its UFMylation and membrane translocation, resulting in AKT hyperactivation and enhanced tumor growth. In samples from patients with LUAD, UFL1 expression inversely correlates with phospho-AKT levels. Functionally, the UFL1-PHLDA3 axis inhibits LUAD progression in both cell line-based and patient-derived xenograft models. These findings define a tumor-suppressive UFMylation pathway that modulates AKT activity and provides a mechanistic rationale for targeting UFL1-PHLDA3 signaling in LUAD.\n\nID: 41825123\nTitle: Load-independent ceiling of single-target phagocytic membrane extension revealed by microneedle backtracking assay in macrophages.\nAbstract: The zipper model describes the ligand-receptor-driven progression of the phagocytic cup during macrophage engulfment. However, whether the maximum engulfment achievable for a single target is altered by prior or concurrent phagocytic events (i.e., intracellular phagocytic load) remains unclear. Here, we used IgG-coated, nondigestible glass microneedles as standardized Fc\u03b3 receptor ligands and defined the single-target engulfment ceiling as the membrane extension length at which backtracking begins. We then tested whether this ceiling changes after macrophages internalize increasing numbers of IgG-coated polystyrene beads. Across cells, the maximum membrane extension on a microneedle was quantitatively unchanged regardless of the number of internalized indigestible beads. Within the same cell, additional bead ingestion - up to the maximal bead-phagocytosis limit - did not measurably alter the maximum extension achieved on a microneedle. These data establish a load-independent ceiling for single-target engulfment. This invariance suggests that local membrane recruitment and extension are regulated independently of the cell-wide phagocytic burden, supporting a spatially compartmentalized control mechanism that decouples single-target membrane extension from the total intracellular cargo load.\n\nID: 41822190\nTitle: Familial SCA14: A case report with review.\nAbstract: Spinocerebellar ataxia type 14 (SCA14) is a rare autosomal dominant neurodegenerative disorder caused by mutations in the PRKCG gene, which encodes protein kinase C\u03b3 (PKC\u03b3). The clinical manifestations are heterogeneous, ranging from slowly progressive pure cerebellar ataxia to complex phenotypes with sensory or extrapyramidal involvement. To the best of our knowledge, the present report is the first to describe a Han Chinese family carrying the PRKCG c.424T>G (p.C142G) mutation, which has previously only been described in Danish and Japanese cohorts. The proband, a 72-year-old man, developed gait instability in his 40s, progressing to dysarthria, intention tremor, oculomotor slowing and sensory impairment. Brain MRI revealed severe diffuse cerebellar atrophy. The siblings and daughter of the patient presented with variable ataxic symptoms, confirming autosomal dominant inheritance. Genetic testing by next-generation sequencing identified the heterozygous c.424T>G mutation, co-segregating in affected family members. This mutation localizes to the C1 regulatory domain of PKC\u03b3, a zinc-finger structure critical for diacylglycerol binding and kinase autoinhibition. Substitution of cysteine by glycine at codon 142 destabilizes zinc coordination, impairs protein stability and disrupts membrane recruitment. Functional evidence suggests that C142G induces aberrant kinase activity, misfolding and altered MAPK signaling, resulting in chronic cellular stress without rapid neuronal death, thus accounting for the indolent course of the disease compared with that of polyglutamine SCAs. The present findings expand the knowledge regarding the ethnic and geographic distribution of the codon 142 mutation and highlight the complexity of genotype-phenotype associations, as clinical presentations varied from mild gait ataxia to cognitive impairment and bulbar involvement. The report underscores the value of early genetic testing in unexplained ataxia, facilitating accurate diagnosis, genetic counseling and individualized management. Further functional studies are warranted to clarify the pathogenic mechanisms and to explore potential targeted therapies for SCA14.\n\nID: 41779229\nTitle: Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.\nAbstract: Tissue-resident memory T cells (TRM cells) have been shown to play an instrumental role in driving the onset and relapse of inflammatory bowel diseases (IBD). However, the underlying mechanism of TRM cells differentiation and its regulation in intestines remain to be unveiled. Mothers against decapentaplegic homolog 3 (SMAD3) is translocated from nucleus to membrane and activated in response to transforming growth factor beta (TGF-\u03b2), which is a key cytokine in the process of TRM cells polarization. Cysteine palmitoylation (S-palmitoylation) is a post-translational modification catalyzed by the DHHC family, regulating protein membrane associations. Genes associated with the classic SMAD3 signaling pathway, along with most genes in the DHHC family, were upregulated in TRM cells. Our study demonstrated that SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I (TGF-\u03b2RI) under TRM polarization conditions. The membrane recruitment of SMAD3 activated SMAD3 and subsequently upregulated the expression of its target genes, inducing the differentiation of TRM cells. In contrast, perturbation in DHHC6-induced palmitoylation with MYD-4 inhibited TRM cells differentiation and alleviated colitis in IBD model mice. Our work provides an example how the immune responses are regulated through the S-palmitoylation-dependent SMAD3 signaling in TRM cells differentiation and reveals protein S-palmitoylation as a potential target in IBD treatment, which could be of greater application considering the wide involvement of protein S-palmitoylation in the signal transduction in mammalian cells.\n\nID: 41707395\nTitle: Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.\nAbstract: Emerging environmental health issues posed by micro- and nanoplastics (M/NPs) have raised significant concerns. Accumulating evidence suggested that M/NPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene micro- and nanoplastics (PS-M/NPs, 100\u202fnm and 5\u202f\u00b5m) on ovarian development and function in pubertal female mice. Following 35-day exposure, we observed size-dependent reproductive toxicity, with 100\u202fnm PS-NPs causing reduced body weight gain and ovarian size, disrupted folliculogenesis, and altered hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks across seven ovarian cell types. Granulosa cells (GCs) were identified as the primary target of PS-NPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100\u202fnm PS-NPs were internalized by GCs, leading to cell cycle arrest, necroptosis, and hormonal dysfunction. Mechanistically, PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-NP-induced epigenetic and transcriptional changes. Overall, our findings establish the first single-cell resolution atlas of PS-NP-mediated ovarian toxicity, revealing that NPs disrupt reproduction through cytoskeletal damage and epigenetic reprogramming. This work provides unprecedented insights into the molecular and epigenetic consequences of M/NPs in mammalian reproduction, emphasizing the potential health risks of environmental M/NP exposure.\n\nID: 41680487\nTitle: Modular engineering of thermoresponsive allosteric proteins.\nAbstract: Thermogenetics enables noninvasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membrane recruitment. Here, we present a generalizable strategy for engineering thermosensitive allosteric proteins through the insertion of optimized Avena sativa LOV2 domain variants. Applying this approach to a diverse set of structurally and functionally unrelated proteins in Escherichia coli, we generated potent, thermoswitchable chimeric variants that can be tightly controlled within narrow temperature ranges (37-41\u2009\u00b0C). Extending this strategy to mammalian systems, we engineered CRISPR-Cas genome editors directly modulated by subtle temperature changes within the physiological range. Lastly, we showcase the incorporation of a chemoreceptor domain as an alternative thermosensing module, suggesting thermosensitivity to be a widespread feature in receptor domains. This work expands the toolkit of thermogenetics, providing a blueprint for temperature-dependent control of virtually any protein of interest.\n\nID: 41663583\nTitle: Wnt11 mediates fibroblast-smooth muscle cell interaction to promote neurogenic bladder fibrosis in rats.\nAbstract: Neurogenic bladder (NB) is a lower urinary tract dysfunction caused by lesions in the nervous system that regulate urine storage and micturition. Fibrosis is considered the basic pathological alteration of NB, whereas the underlying mechanism remains unclear. Here, we find that Wnt11 is significantly up-regulated in the rat fibrotic bladders induced by bilateral pelvic nerve injury (BPNI) and spinal cord injury (SCI) and promotes bladder fibroblasts (BFs)-to-myofibroblasts transition and smooth muscle cells (SMCs) phenotypic transformation. Selective inhibition or gene silencing of Wnt11 in vivo and in vitro attenuates BFs and SMCs activation, and mitigates the development of NB fibrosis. Mechanistically, Wnt11 specifically binds to Vangl2 receptor to activate downstream JNK/c-JUN signaling via the membrane recruitment of DVL2. Further research shows that Wnt11 signaling interacts with transforming growth factor beta 1 (TGF-\u03b21)/Smad-dependent pathway through the binding of membrane receptors (Vangl2 and T\u03b2R1) and the crosstalk of nuclear transcription factors. These findings uncover the regulatory mechanism and may provide a new therapeutic strategy for NB fibrosis.\n\nID: 41659462\nTitle: PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.\nAbstract: PLC\u03b2 enzymes cleave PIP2 from the plasma membrane, producing IP3 and DAG, which regulate intracellular Ca2+ levels and protein kinase C activity, respectively. They are regulated by GPCR signaling through the G proteins G\u03b2\u03b3 and G\u03b1q and have been shown to function as coincidence detectors for dual stimulation of G\u03b1q and G\u03b1i-coupled receptors via these G proteins. PLC\u03b2s are aqueous-soluble enzymes, but partition onto the membrane surface to access their lipid substrate. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie G\u03b2\u03b3-dependent regulation of PLC\u03b2 enzymes. Using macrophages as a model system, where PLC\u03b2 signaling is essential for responses to infection and tissue injury, we investigated the contribution of G\u03b2\u03b3-dependent regulation and membrane recruitment of PLC\u03b2 in the context of endogenous signaling. By measuring Ca2+ mobilization, we demonstrate that both G\u03b1i and G\u03b1q-coupled receptors independently stimulate PLC\u03b2 activity, illustrating that G\u03b2\u03b3 alone is sufficient to activate PLC\u03b2 in certain contexts. Using total internal reflection and stimulated emission depletion microscopy, we demonstrate that most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation by both G\u03b1i and G\u03b1q-coupled receptors, illustrating that both G\u03b2\u03b3 and G\u03b1q recruit PLC\u03b2 to the plasma membrane. These results support an updated model for G protein-dependent regulation of PLC\u03b2 enzymes, where G\u03b2\u03b3-induced regulation in the absence of G\u03b1q is context dependent and dictated by the local concentration of receptor, G proteins, and PLC\u03b2. PLC\u03b2 enzymes are critical mediators of signal transduction with roles in neuronal, cardiac, and immunological signaling. Despite this importance, many aspects of their function and regulation remain poorly understood. PLC\u03b2s are aqueous soluble but must partition onto the membrane surface to access their lipid substrate, which enables regulation at the partitioning step, the catalytic step, or both. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie the PLC\u03b2 regulation by one effector, G\u03b2\u03b3. Using macrophages as a model system for physiological signaling, we demonstrate that G\u03b2\u03b3 is capable of independently activating PLC\u03b2 via membrane recruitment under the conditions of endogenous signaling.\n\nID: 41641743\nTitle: The desmoglein 2 interactome in primary neonatal cardiomyocytes.\nAbstract: Mechanical coupling and chemical communication between cardiomyocytes are facilitated through a specialized adhesive structure called the intercalated disc (ICD). The ICD is essential for heart organization and contraction. Yet, the network of adhesion, adaptor and signaling proteins that form the ICD remains poorly defined. Here, we combined proximity labeling and quantitative mass spectrometry to identify proteins associated with the desmosomal cadherin desmoglein 2 (DSG2), in cultured neonatal cardiomyocytes. We identified over 300 proteins in the DSG2 interactome, half of which are shared with the N-cadherin (CDH2) interactome in cardiomyocytes. Proteins unique to DSG2 include connexin 43 and the plakin family of cytolinker proteins. Comparison of the cardiomyocyte DSG2 interactome with the interactomes of desmosomal proteins from epithelia revealed few shared proteins. In cardiomyocytes, plakoglobin and plakophilin 2 (PKP2) were the most abundant shared proteins between the DSG2 and CDH2 interactomes. We show that PKP2 is a dynamic protein whose membrane recruitment in cardiomyocytes is dependent on tension. Our analysis of the DSG2 interactome provides a crucial new dimension to the proteomic atlas of the essential molecular complexes required for cardiomyocyte adhesion.\n\nID: 41580402\nTitle: Micro-nanoplastics and Parkinson's disease: evidence and perspectives.\nAbstract: With the intensification of global plastic pollution, the potential threats posed by micro- and nanoplastics (MPs/NPs) to human health have become a major concern. MPs/NPs enter the organism through ingestion, inhalation, and skin contact, subsequently accumulating in multiple organs-particularly the brain. Increasing experimental and epidemiological evidence implicates MPs/NPs in the development of Parkinson's disease (PD). Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation, triggering neuroinflammatory cascades, elevating oxidative stress, and impairing mitochondrial function. To further investigate the causal role of MPs/NPs in PD, upcoming studies should emphasize well-designed, large-scale prospective cohorts to assess individual exposure to plastic-related pollutants, elucidate the pathways of MPs/NPs into the central nervous system, establish safety thresholds for their neurotoxicity, explore the correlation between exposure levels and central nervous system accumulation, clarify the temporal relationship between MPs/NPs accumulation and PD pathology and symptom onset, and identify the neuropathological mechanisms triggered by relevant concentrations of MPs/NPs. Such data will be instrumental in informing preventive and potentially interventional strategies, while offering actionable insights into the interaction between MPs/NPs and PD.\n\nID: 41577027\nTitle: \u03b1-Parvin promotes glucose uptake and metabolism in skeletal muscle with minimal influence on hepatic insulin sensitivity.\nAbstract: Skeletal muscle and liver insulin resistance are early features in the sequelae of type 2 diabetes. Integrins are extracellular matrix receptors expressed on skeletal muscle cells and hepatocytes, which have been implicated in modulating obesity-associated insulin resistance. Integrins regulate cell function through intracellular proteins including the ILK-PINCH-Parvin (IPP) complex. ILK signaling amplifies skeletal muscle and liver insulin resistance in diet-induced obesity in mice but the role of \u03b1-Parvin is unexplored. The hyperinsulinemic-euglycemic clamp was used to assess hepatic and muscle insulin action. We demonstrate that deletion of hepatocyte-specific \u03b1-Parvin had only minimal influence on obesity-induced liver or whole-body insulin resistance. In contrast, deletion of \u03b1-Parvin in skeletal muscle caused a striking reduction in muscle glucose uptake during an insulin clamp in lean mice which was not exacerbated by diet-induced obesity. The decrease in muscle glucose uptake in lean mice was due to a decrease in insulin-mediated GLUT4 membrane recruitment, which was associated with significant morphological abnormalities including actin cytoskeleton dysfunction. In addition, severe muscular dysfunction, blunted mitochondrial oxidative capacity and reduced aerobic exercise capacity were manifest in muscle \u03b1-Parvin KO mice. Thus, \u03b1-Parvin has a minor role in liver insulin action but is required for insulin-stimulated glucose uptake in skeletal muscle in lean mice due to its role in actin cytoskeleton regulation. These data suggest that individual IPP complex proteins link cell structure to metabolism via distinct mechanisms in a tissue-specific fashion.\n\nID: 41565640\nTitle: Structural basis for the dynamic conformations of AP-4 and its association with ARF1.\nAbstract: Among the distinct adaptor protein (AP) complexes, AP-4 primarily functions as a non-clathrin-coated vesicle machinery essential for intracellular membrane trafficking. ARF1 is a master regulator of AP-4 membrane recruitment, but the underlying mechanism remains elusive. Here, we present the cryo-EM structures of soluble AP-4 and the AP-4/ARF1 complex. Unexpectedly, AP-4 adopts a dynamic equilibrium between closed and open conformations, caused by loose contacts between its medium subunit and central core. ARF1 binding induces only subtle changes in AP-4, which retains its conformational equilibrium. Mutations at the AP-4/ARF1 interface disrupt complex formation and impair ARF1-dependent membrane recruitment. Efficient membrane recruitment of AP-4 likely requires the synergistic engagement of ARF1 and cargoes. Disrupting the conformational flexibility of AP-4 interferes with this synergistic effect and compromises AP-4-mediated membrane trafficking. Our findings may redefine AP-4 as a conformationally dynamic complex modulated by cooperative interactions, providing insights into neurodevelopmental disorders associated with AP-4 dysfunction.\n\nID: 41559082\nTitle: Probiotic bacteria Bifidobacterium bifidum upregulation of intestinal epithelial tight junction barrier is mediated by TLR-2/TLR-6 receptor complex activation of occludin gene.\nAbstract: Defective intestinal epithelial tight junction (TJ) barrier is a key pathogenic factor of inflammatory bowel disease (IBD). Probiotic bacterial upregulation of intestinal TJ barrier has been shown to prevent the development of intestinal inflammation. However, the mechanism of microbe-host interactions responsible for the TJ barrier upregulation remains unclear. This study investigates the molecular mechanisms by which a particular strain of probiotic bacteria, Bifidobacterium bifidum (BB1), upregulates the intestinal epithelial TJ barrier. Using in vitro (filter-grown Caco-2 monolayers) and in vivo (recycling intestinal perfusion in live mice) intestinal epithelial model system, we show that BB1 upregulation of intestinal TJ barrier correlated with an increase in occludin gene activity (occludin promoter activity and occludin mRNA transcription levels) and protein expression, with no changes in other TJ proteins. Occludin knockdown or inhibition of gene transcription prevented the enhancement of the TJ barrier, confirming the essential role of BB1-induced occludin gene activation in TJ barrier enhancement, which was mediated sequentially by BB1 activation of the intestinal epithelial cell TLR-2/TLR-6 complex and IRAK-1 phosphorylation, as well as the apical membrane recruitment of the adapter protein TOLLIP. These findings provide novel mechanistic insight into the microbe-host interactions driving probiotic bacteria upregulation of intestinal TJ barrier.\n\nID: 41540011\nTitle: Targeting sorting nexin 3 to treat pulmonary fibrosis by dual modulating Wnt/\u03b2-catenin signaling.\nAbstract: Pulmonary fibrosis (PF) is a chronic progressive lung disorder characterized by overactivation of Wnt/\u03b2-catenin signaling and limited therapeutic efficacy. This study identifies sorting nexin 3 (SNX3), a retromer-associated protein, as a dual regulator of PF pathogenesis through coordinated molecular mechanisms. SNX3 is significantly upregulated in PF patients' lungs and bleomycin-induced murine fibrotic models, with predominant localization in alveolar type 2 (AT2) epithelial cells correlating with \u03b2-catenin hyperactivation and fibrotic progression. Genetic ablation of SNX3 in AT2 cells attenuated Wnt/\u03b2-catenin signaling, collagen deposition, and pulmonary dysfunction, while SNX3 overexpression exacerbated these phenotypes. Mechanistic studies further elucidated two distinct SNX3-driven regulatory pathways. Wls is rescued by SNX3 from lysosomal degradation to sustain Wnt ligand secretion and canonical pathway activation. In addition to Wls, casein kinase 1\u03b1 (CK-1\u03b1) is identified as a novel cargo protein for SNX3, which mediates its plasma membrane recruitment via Rab5a-dependent endosomal recycling, bypassing the \u03b2-catenin destruction complex, ultimately suppressing proteasomal degradation of \u03b2-catenin. This dual regulatory mechanism positions SNX3 as a master coordinator of both Wnt-dependent and -independent \u03b2-catenin signaling in PF. Furthermore, we screened inhibitors targeting SNX3 and identified a novel small molecule, LC4, which effectively ameliorated pulmonary dysfunction and reversed pulmonary fibrosis. Tetrahedral framework nucleic acids (TDNs), known for their excellent biocompatibility and drug delivery capacity, were utilized to develop a multifunctional nanodrug delivery system (TDN-LC4) to enhance the treatment of PF. By optimizing this loading approach, we improved LC4 delivery efficiency, enhanced its therapeutic potential, and minimized off-target effects. Our findings reveal SNX3 as a master coordinator of dual Wnt-dependent and -independent \u03b2-catenin activation, and propose TDN-LC4 as a potential therapeutic strategy to disrupt pathogenic signaling redundancy in PF pathogenesis.\n\nID: 41523098\nTitle: Detecting the Activation of Endogenous Small GTPases via Fluorescent Signals Utilizing a Split mNeonGreen: Small GTPase ActIvitY ANalyzing (SAIYAN) System.\nAbstract: Small GTPases function as molecular switches in cells, and their activation triggers diverse cellular responses depending on the GTPase type. Therefore, visualizing small GTPase activation in living cells is crucial because their activity is tightly regulated in space and time, and this spatiotemporal pattern of activation often determines their specific cellular functions. Various biosensors, such as relocation-based sensors and fluorescence resonance energy transfer (FRET)-based sensors, have been developed. However, these methods rely on interactions between activated GTPases and their downstream effectors, which limits their applicability for detecting activation of GTPases with unknown or atypical effectors. Recently, we developed a novel method utilizing split fluorescence technology to detect membrane recruitment of small GTPases upon activation, designated the Small GTPase ActIvitY ANalyzing (SAIYAN) system. This approach offers a new strategy for monitoring small GTPase activation based on membrane association and is potentially applicable to a wide range of small GTPases, including those with uncharacterized effectors. Key features \u2022 Visualizes the activation of small GTPases in living cells as mNeonGreen fluorescence signal. \u2022 Can be applied to small GTPases whose effectors have not yet been identified. \u2022 SAIYAN exploits the intrinsic property of small GTPases to associate with cellular membranes upon activation.\n\nID: 41486271\nTitle: Brucella abortus infection exploits ZDHHC3-mediated STAT3 palmitoylation to regulate host responses and promote persistence.\nAbstract: Brucella abortus, an intracellular bacterium, employs intricate mechanisms to manipulate host signaling for persistence. This study investigates the role of STAT3 palmitoylation in B. abortus-infected macrophages. We demonstrate that B. abortus infection induces STAT3 palmitoylation, which is critical for its membrane recruitment. Among zinc finger DHHC-type palmitoyl acyltransferases (ZDHHC) family members, ZDHHC3 specifically mediates STAT3 palmitoylation in infected macrophages. ZDHHC3-induced STAT3 palmitoylation promotes STAT3 phosphorylation at Y705, independently of IL-6. Functionally, ZDHHC3 suppresses pro-inflammatory cytokines (IL-1\u03b2, TNF-\u03b1) and nitric oxide (NO) production, while increasing anti-inflammatory IL-10, thereby enhancing intracellular B. abortus survival. In vivo, ZDHHC3 mRNA is upregulated in splenic macrophages during infection, and 2-bromopalmitate (2BP) treatment reduces bacterial burden in mice, associated with elevated TNF-\u03b1 and IFN-\u03b3. Additionally, ZDHHC3 inhibits macrophage apoptosis (via regulating Bax and Bcl-2), limiting bacterial egress from apoptotic cells. These findings identify ZDHHC3-mediated STAT3 palmitoylation as one of the key regulatory mechanism in B. abortus infection, linking lipid modification to STAT3 activation, inflammation, apoptosis, and bacterial persistence.\n\nID: 41473329\nTitle: Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA.\nAbstract: Phosphatidylinositol 4 kinase III\u03b1 (PI4KIII\u03b1/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane identity. PI4KA is primarily recruited to the plasma membrane through the targeted recruitment by the proteins, EFR3A and EFR3B, which bind to the PI4KA accessory proteins TTC7 (TTC7A/B) and FAM126 (FAM126A/B). Here we characterised how both EFR3 isoforms interact with all possible TTC7-FAM126 combinations and developed a nanobody that specifically blocked EFR3-mediated PI4KA recruitment in TTC7B containing complexes. Most EFR3-TTC7-FAM126 combinations show similar binding affinities, with the exception of EFR3A-TTC7B-FAM126A, which binds with a ~10-fold higher affinity. Moreover, we showed that EFR3B phosphorylation markedly decreased binding to TTC7-FAM126. Using a yeast display approach, we isolated a TTC7B selective nanobody that blocked EFR3 binding. Cryo-electron microscopy and hydrogen deuterium exchange mass spectrometry showed an extended interface with both PI4KA and TTC7B that sterically blocks EFR3 binding. The nanobody caused decreased membrane recruitment both on lipid bilayers and in cells, with decreased PM production of PI4P. Collectively, these findings provide new insights into PI4KA regulation and provide a tool for manipulating PI4KA complexes, that may be valuable for therapeutic targeting.\n\nID: 41467444\nTitle: Interplay of GBA1 with lysosomal dysfunction and inflammation in Parkinson's disease.\nAbstract: Mutations in the glucocerebrosidase ( GBA1 ) gene, encoding the lysosomal enzyme glucocerebrosidase, represent the most significant genetic risk factor for Parkinson's disease. These variants define a distinct clinical subtype characterized by earlier onset, accelerated motor decline, and pronounced cognitive impairment. This review synthesizes current insights into the molecular mechanisms linking GBA1 dysfunction to lysosomal failure, \u03b1-synuclein aggregation, and neuroinflammation. Pathogenic alleles such as N370S and L444P disrupt sphingolipid metabolism, resulting in toxic accumulations of glucosylceramide and glucosylsphingosine, endoplasmic reticulum stress, and impaired clearance of misfolded proteins. This initiates a self-reinforcing cycle in which glucocerebrosidase deficiency promotes \u03b1-synuclein aggregation, which subsequently impairs glucocerebrosidase trafficking. We explore the convergence of GBA1 mutations on the lysosomal-mitochondrial-autophagy axis, where impaired autophagic flux and disrupted organelle crosstalk amplify oxidative stress and activate the NLR family pyrin domain containing 3 inflammasome. The contribution of microglia, astrocytes, and oligodendrocytes to the neuroinflammatory cascade is eamined, along with the emerging influence of the microbiome-gut-brain axis in disease progression. Finally, we evaluate emerging therapeutic strategies, including pharmacological chaperones, NLRP3 inhibitors, adeno-associated virus-based gene therapy, and microbiome modulation, highlighting both promises and translational challenges such as blood-brain barrier penetration and mutation-specific efficacy. We conclude by advocating for precision medicine approaches, supported by robust biomarker development and advanced disease models, to guide tailored interventions for this aggressive Parkinson's disease subtype.\n\nID: 41427736\nTitle: The BRAF-specific region suppresses cysteine-rich domain-lipid interaction independently of canonical autoinhibition by the 14-3-3 dimer.\nAbstract: BRAF is a serine/threonine kinase and a central effector of the mitogen-activated protein kinase (MAPK) signaling pathway, frequently mutated in cancer. Its activation is tightly controlled by autoinhibitory mechanisms that regulate membrane recruitment and dimerization. The BRAF-specific region (BSR), located at the N-terminus, is known to promote isoform-preferred RAS binding and facilitate dimerization with kinase suppressor of RAS (KSR), yet its role in regulating lipid interaction has remained unexplored. Here, we identify the BSR as a previously unrecognized inhibitory module that attenuates lipid binding by the cysteine-rich domain (CRD). Using quantitative in vitro reconstitution with supported lipid bilayers and fluorescence microscopy, we demonstrate that the BRAF CRD exhibits high intrinsic affinity for phosphatidylserine-rich membranes, but the inclusion of the BSR markedly reduces the membrane binding. We further demonstrate that the inhibitory function of the BSR correlates with its global electrostatic properties rather than a single defined sequence motif. This inhibitory effect of BSR was corroborated in live cells by quantifying plasma membrane localization of BRAF constructs, including the full-length protein. When canonical autoinhibition of CRD-mediated by sequestration within the 14-3-3 dimer-is disrupted by oncogenic mutation or RAF inhibitor treatment, the BSR assumes a compensatory role in repressing CRD-lipid interaction. This additional regulatory layer provided by the BSR prevents RAS-independent membrane recruitment under both physiological and pathological conditions.\n\nID: 41391758\nTitle: Enhanced lysosomal activity prevents infection with PrPSc and the seeding activity of \u03b1-synuclein & tau prions.\nAbstract: Prion diseases are fatal neurodegenerative diseases of humans and other mammals with no current treatment options. Here, we describe the characterization of a novel anti-prion compound, elacridar (GW120918), which has sub-micromolar activity in assays of prion infection, propagation and toxicity. Elacridar acts at an early step in the prion infection process, enhancing degradation of newly formed PrPSc. The lysosome is the likely site of elacridar's anti-prion effects, based on transcriptomic analysis and the use of functional lysosomal probes. Elacridar alters gene expression networks controlling lysosomal sterol and lipid metabolism but, unlike other lysosomotropic drugs, it prominently upregulates genes that control lysosomal pH. Surprisingly, these effects occur independently of TFEB nuclear translocation, suggesting novel regulatory mechanisms. The anti-prion effects of elacridar extend to \u03b1-synuclein and tau prions, highlighting lysosomal enhancement as a general strategy for treatment of protein misfolding neurodegenerative diseases.\n\nID: 42477140\nTitle: Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.\nAbstract: Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), which restores lysosomal function during hypoxia-reoxygenation stress. During B-fission, damaged lysosomes generate membrane buds that undergo scission to form small, fully functional lysosomes, independently of autophagic lysosome reformation. Mechanistically, mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission. MIRO2 promotes the formation of MFF+ MDVs through direct interaction with MFF, while the lysosomal membrane protein ITM2C binds MIRO2 to tether and guide MFF+ MDVs to lysosomes, enabling efficient MFF delivery and subsequent B-fission. Notably, AMPK activation by 991 or metformin promotes MFF-dependent lysosomal B-fission under normoxic conditions, whereas AMPK inhibition by dorsomorphin suppresses B-fission during hypoxia-reoxygenation. This stress-responsive ITM2C-MIRO2-MFF-DRP1 axis co-opts the mitochondrial division machinery to drive lysosomal fission from damaged lysosomes, thereby enabling the undamaged components to reorganize into daughter lysosomes and promote lysosomal renewal. Thus, our findings uncover a fundamental mode of lysosomal renewal and reveal an unexpected role for MDV-mediated mitochondria-lysosome communication in mediating lysosomal quality control during ischaemia-reperfusion and related stresses.\n\nID: 42366573\nTitle: Radial outer retina reflectivity (RORR) sign in LAMP2-associated retinopathy.\nAbstract: To describe the radial outer retina reflectivity (RORR) sign in patients carrying pathogenic variants in the X-linked lysosome-associated membrane protein-2 (LAMP2) gene and to review the histologic characteristics of LAMP2 expression in the human retina. International multicentre observational case series and experimental laboratory study of patients with LAMP2 deficiency. Baseline demographics and multimodal retinal imaging including colour and fundus autofluorescence (FAF), optical coherence tomography (OCT) with en face reconstruction and fluorescein angiography were obtained. Sections through the retina of a human donor eye were processed for immunofluorescence combining antibodies against LAMP2 with markers for M\u00fcller glia, rod and cone photoreceptors. Sections were imaged using high-resolution multichannel confocal microscopy. Assessment of en face OCT reflectivity profiles at 5-50\u2009\u03bcm internal to the plane of external limiting membrane (ELM) was performed as well as histologic localisation of LAMP2. We recruited 11 cases with pathogenic variants in LAMP2 across five countries. Six cases demonstrated peripheral radial streaks of hyper- and hypopigmentation with UWF imaging. The RORR sign was best visualised 10-25\u2009\u03bcm internal to ELM in 9 cases. We hypothesise the radial pattern to be secondary to X-chromosome inactivation. LAMP2 immunoreactivity was observed internal and external to the ELM. Our findings expand the phenotypic spectrum of LAMP2-associated retinopathy by demonstrating the RORR sign using en face OCT. Histologic sections revealed LAMP2 expression in the neuroretina.\n\nID: 42338213\nTitle: [Progress on mechanism of mitochondrial autophagy in pathogenesis of intervertebral disc degeneration based on PINK1/Parkin signaling pathway].\nAbstract: Intervertebral disc degeneration (IVDD) is one of the main causes of lower back pain. The chronic accumulation of aging and apoptosis of nucleus pulposus cells (NPCs) is believed to be related to IVDD. In recent years, mitochondrial autophagy which as an important clearance mechanism within cells, has gradually attracted attention. The PINK1/Parkin signaling pathway is regarded as the key pathway regulating mitochondrial autophagy, and it plays a significant role in physiological and pathological processes of NPCs. The mechanism by which PINK1/Parkin signaling pathway mediates mitochondrial autophagy could be understood as follows, PINK1, as the sensor for mitochondrial quality regulation, is activated. It recruits and activates Parkin to the mitochondrial membrane through phosphorylation of ubiquitin, and then undergoes Parkin-dependent substrate ubiquitination, recruitment of autophagy receptors, formation of autophagosomes, and fusion with lysosomes, ultimately completing the extremely important autophagy process. Current research indicates that abnormality of PINK1/Parkin signaling pathway may be closely related to IVDD, but the specific mechanism still requires further exploration. The paper explores research progress of mechanism by which mitochondrial autophagy affects IVDD based on PINK1/Parkin signaling pathway, with the aim of providing new strategies and targets for the treatment of IVDD.\n\nID: 42332197\nTitle: mRAVE governs lysosomal catabolism through basal and mTORC1-regulated V-ATPase assembly.\nAbstract: Acidification of lysosomes, endosomes and the Golgi underpins organelle-specific functions within the endomembrane system. This process is driven by vacuolar-type H\u2009+\u2009-ATPases (V-ATPases), proton pumps that reversibly assemble from peripheral V1 and membrane-integral Vo domains to regulate organelle pH. In yeast, V1-Vo assembly at the vacuole is mediated by the RAVE complex, but V-ATPase assembly in mammalian cells remains less well understood. Here, we systematically characterize physiological roles of the mammalian RAVE complex, composed of the subunits Dmxl1 or Dmxl2, Wdr7 and Rogdi. Under basal conditions, mRAVE broadly promotes V-ATPase assembly and luminal acidification of endomembrane organelles. Upon mTORC1 inactivation, mRAVE is recruited to lysosomes and required for the resulting increase in V-ATPase assembly and catabolic activity. Loss of mRAVE disrupts organelle acidification, leading to suppression of lysosomal catabolism, accumulation of dysfunctional lysosomes and lysosomal exocytosis. Restoring lysosomal pH rescues basal function in mRAVE-deficient cells but not the mTORC1-regulated increase in catabolic activity. Thus, mRAVE is an essential V-ATPase assembly factor that couples acidification to organelle function and nutrient signaling.\n\nID: 42327061\nTitle: Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.\nAbstract: Lysosomal membrane damage triggers a multi-stage repair response essential for cellular homeostasis. Here we identify the oxysterol-binding protein-related protein ORP3 as a critical mediator of late-stage lysosomal membrane repair. Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites via a signaling cascade initiated by lysosomal membrane ubiquitination, TAK1, p38 MAPK, and, to a lesser extent, IKK. p38-dependent phosphorylation promotes direct interaction between ORP3 and LC3B, which together with PI(4,5)P\u2082 binding, is required for autophagic lysosome recruitment. ORP3 depletion impairs late-stage lysosomal recovery, elevates lysosomal lipid peroxidation, and reduces cell survival. A lipid transfer-deficient ORP3 mutant fails to restore lysosome function despite normal recruitment, indicating that ER-to-lysophagosome transfer of phosphatidylcholine by ORP3 is functionally required. ORP3 activity is subsequently terminated by VCP/p97-mediated deubiquitination of lysosomes. These findings define ORP3 as a MAPK regulated lipid transfer protein during the late autophagic phase of the endolysosomal damage response. Lysosomal membrane damage triggers ubiquitination that activates a TAK1-p38 signaling cascade, phosphorylating the lipid transfer protein ORP3 and recruiting it to damaged lysosomes via LC3B interaction. ORP3-mediated phosphatidylcholine transfer from the ER is essential for late-stage lysosomal repair and cell survival.\n\nID: 42327019\nTitle: Structural Mechanism and Cellular Restriction of Tau Seeding from Endolysosomes.\nAbstract: The prion-like spread of tau from cell to cell in the central nervous system involves escape from the endolysosomal network, which is counteracted by the lysosomal repair activity of the ESCRT system. Here, we investigate whether other components of the lysosomal damage sensing and repair system, namely the ESCRT-recruiting Ca 2+ sensor ALG-2, conjugation of ATG8s to single membranes (CASM), the phosphoinositide-initiated tethering and lipid transport (PITT) pathway, and the Parkinson's disease-related lipid transporter VPS13C are involved in tau spread. We found that the PITT pathway and VPS13C are strongly implicated in tau seeding by pre-formed fibrils (PFFs) in both neurons and astrocytes, CASM has a major role in astrocytes but not neurons, and ALG-2 has a lesser role in both. We then investigated the mechanism of damage and seeding by tau PFFs using cryo-electron tomography. Unlike the classical lysosome damage agent LLOMe, tau PFFs were not seen to directly interact with the lysosomal membrane, nor do they distort local membrane curvature. Lysosomes in PFF-treated cells were structurally intact. Extensive protein aggregates of similar character were seen in both the lysosomal lumen and in the cytosol proximal to lysosomes. The observations are consistent with the PFF-induced co-aggregation of tau with other cellular materials within lysosomes, with leakage to the cytosol attributed to reversible holes in the lysosome membrane.\n\nID: 42325197\nTitle: Small bites for big problems: stepwise aggregate degradation by autophagy.\nAbstract: Protein aggregates are a pathological hallmark of diverse disorders, including many neurodegenerative diseases, but also cardiometabolic disease and cancer. While the ubiquitin-proteasome system efficiently removes many soluble misfolded proteins, large or persistent assemblies often require the autophagy-lysosome pathway for their degradation. In the present mini-review, we summarize our knowledge of aggrephagy, the selective clearance of protein aggregates by autophagy, and discuss two recent manuscripts that argue that some aggregates must be primed for autophagosomal degradation, through chaperone-mediated remodeling. Aggrephagy substrates are defined by aggregate architecture, biophysical state, surface accessibility, and the physical constraints of membrane capture. These features help to explain why recruitment of selective autophagy receptors is necessary yet insufficient for clearance. Receptor clustering is required to concentrate early autophagy factors to establish initiation hubs, but successful degradation often requires upstream generation of smaller 'aggrephagy-competent' cargo units, which contain autophagy receptor clusters that successfully initiate autophagosome formation. Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps that involve p97/VCP-driven disintegration or a chaperone module (DNAJB6-HSP70-HSP110) cooperating with the proteasomal 19S regulatory particle.\n\nID: 42268710\nTitle: STING-OPTN signaling confers cytoprotection through TBK1-dependent mitophagy.\nAbstract: The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway plays an essential role in innate immunity. While recent studies have revealed its critical role in non-canonical autophagy independent of its immune function, its role in selective autophagy remains elusive. Here, we identify the cGAS-STING pathway as an upstream positive regulator of mitophagy. We demonstrate that activation of TANK-binding kinase 1 (TBK1) during mitophagy is strictly dependent on the cGAS-STING pathway. Mechanistically, TBK1 activation involves the mitochondrial recruitment of STING, which requires valosin-containing protein (VCP)/p97-mediated degradation of outer mitochondrial membrane proteins. Activated TBK1 then phosphorylates optineurin (OPTN), resulting in the efficient clearance of damaged mitochondria via the autophagosome-lysosome pathway. Disruption of the STING-OPTN axis impairs mitophagy, which switches cellular response from mitophagy to apoptosis. Our work thereby defines a non-canonical, pro-survival function of the cGAS-STING pathway in mitochondrial quality control.\n\nID: 42260976\nTitle: Porcine reproductive and respiratory syndrome virus hijacks the non-canonical enzymatic function of PHGDH to arrest autophagic flux for viral replication.\nAbstract: Viruses frequently hijack host metabolic enzymes to fuel replication. However, the mechanisms underlying this hijacking and utilization of metabolic enzymes remain poorly understood. In this study, we report a sophisticated mechanism by which porcine reproductive and respiratory syndrome virus (PRRSV) exploits a non-canonical enzymatic function of PHGDH (phosphoglycerate dehydrogenase) to modulate macroautophagy/autophagy. We demonstrate that PRRSV infection recruits the transcription factor ZNF143 (zinc finger protein 143) to transcriptionally repress PHGDH expression. Importantly, the antiviral restriction activity of PHGDH is entirely uncoupled from its canonical enzymatic role in serine biosynthesis. Mechanistically, PHGDH depletion triggers the initiation of autophagy via the AMP-activated protein kinase (AMPK)-ULK1 (unc-51 like autophagy activating kinase 1) signaling axis; however, it paradoxically arrests autophagic flux at the autophagosome-lysosome fusion stage. PHGDH is identified as a critical scaffold that facilitates the assembly of the autophagic soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex; its downregulation disrupts the interaction between STX17 (syntaxin 17) and SNAP29 (synaptosome associated protein 29), thereby blocking autophagosome-lysosome fusion. This induction of incomplete autophagy creates a favorable cytosolic niche for viral replication. Furthermore, the antiviral effect of PHGDH is also observed in two other swine pathogens, porcine epidemic diarrhea virus (PEDV) and pseudorabies virus (PRV). Collectively, these findings revealed that viruses weaponized the moonlighting function of a metabolic enzyme to dismantle autophagic flux, highlighting PHGDH as a broad-spectrum antiviral target that bridged metabolism and membrane trafficking.Abbreviation: AMPK: AMP-activated protein kinase; BECN1: beclin 1; CQ: chloroquine; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; PEDV: porcine epidemic diarrhea virus; PHGDH: phosphoglycerate dehydrogenase; PRV: pseudorabies virus; PRRSV: porcine reproductive and respiratory syndrome virus; SGOC: serine-glycine-one-carbon; siRNA: small interfering RNA; SNAP29: synaptosome associated protein 29; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; SQSTM1/p62: sequestosome 1; SSP: serine synthesis pathway; STX17: syntaxin 17; ULK1: unc-51 like autophagy activating kinase 1; VAMP8: vesicle associated membrane protein 8; ZNF143: zinc finger protein 143.\n\nID: 42236937\nTitle: LASER couples damage sensing to ESCRT assembly for lysosome repair.\nAbstract: Lysosomal membrane integrity is essential for cell survival, but how damage sensing is spatiotemporally coupled to repair remains poorly understood. Recruitment and assembly of endosomal sorting complex required for transport (ESCRT) I-III rapidly counteracts membrane damage, but it is unclear\u00a0how ESCRT-I recognizes defective lysosomal membranes. Here, leveraging genome-wide CRISPRi screens in a damage-sensitized genetic background, we identified LC3/GABARAP-assisted stimulator for ESCRT recruitment (LASER), a multicomponent protein assembly that forms rapidly upon calcium release from damaged lysosomes and couples sensing of lysosomal membrane damage to ESCRT-dependent repair. At the core of LASER is TFG, an endoplasmic reticulum exit-site-resident protein that translocates to damaged lysosomes by binding to ATG8 family proteins (LC3 and GABARAP) conjugated to lysosomal phospholipids. ATG8-bound TFG forms oligomeric assemblies that directly recruit the essential ESCRT-I subunit TSG101 via conserved motif recognition enhanced by avidity-driven interactions. TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair. TFG mutations that drive hereditary spastic paraplegia disrupt its oligomerization and impair lysosomal ESCRT recruitment and membrane resealing, implicating defective repair as a driver of TFG-associated neurodegeneration. Thus, LASER promotes ESCRT polymerization at damaged lysosomes and couples damage sensing to membrane repair.\n\nID: 42227950\nTitle: A cytosolic IF1 reporter enables real-time visualization of severe mitochondrial membrane damage.\nAbstract: Maintenance of mitochondrial integrity is fundamental for cellular survival, yet how cells recognize catastrophic mitochondrial membrane damage remains unknown. Here, we identify MAI-1 as the first genetically encoded reporter of severe mitochondrial membrane damage. MAI-1 is a Caenorhabditis elegans homolog of the ATP synthase inhibitor IF1 that lacks a mitochondrial targeting sequence, resides in the cytosol under basal conditions, but rapidly and irreversibly translocates to severely damaged mitochondria within milliseconds. We validate MAI-1 across diverse injury paradigms and demonstrate that cytosolic IF1 variants from other species exhibit conserved damage-induced recruitment. Mechanistically, MAI-1 recruitment requires the presence of an intact ATP synthase complex. Using MAI-1 as a sensor, we uncover that these severely damaged mitochondria are cleared through the LGG-1-mediated, PINK1/PARKIN-independent lysosomal pathway. Together, our findings establish a powerful tool for visualizing severe mitochondrial membrane damage and reveal a surveillance mechanism dedicated to structural integrity control.\n\nID: 42223444\nTitle: Trifloxystrobin-triggered Drp1 hyperactivation biases mitophagy and imposes long-lasting SVCV susceptibility in teleost.\nAbstract: Environmental pollutants are increasingly recognized as disease modifiers, reshaping host homeostasis and shifting host-pathogen dynamics toward higher infection risk in aquatic ecosystems. Here, we show that the widely used strobilurin fungicide trifloxystrobin (TFS) persistently erodes antiviral competence in fish and increases susceptibility to spring viremia of carp virus (SVCV) by driving dynamin-related protein 1 (Drp1)-mediated excessive mitophagy and sustained mitochondrial dysfunction. Using epithelioma papulosum cyprini (EPC) cells and zebrafish as complementary models, we find that environmentally plausible TFS exposures (2.5-25 \u03bcg/L) elevate SVCV permissiveness; notably, this phenotype resolves incompletely after chemical withdrawal. Transcriptomics revealed a dose-concordant shift toward stress/innate immune signaling and mitophagy programs, alongside broad repression of proliferative and DNA-repair pathways. Consistently, TFS induces persistent mitochondrial membrane depolarization, promotes fragmentation and ultrastructural deterioration, and increases mitochondria-lysosome coupling. Mechanistically, TFS elevates Drp1 abundance and Ser616 phosphorylation, promotes Drp1 recruitment to mitochondria, and sustains microtubule-associated protein 1 light chain 3B (LC3B)/lysosomal-associated membrane protein 2 (LAMP2) engagement, accompanied by persistent induction of core autophagy regulators (gabarap, atg5, wipi1, and ambra1) across extended recovery windows. In vivo, prolonged TFS exposure similarly yields durable enhancement of SVCV susceptibility even after long recovery periods, indicating incomplete restoration of host resistance. Together, these findings link a major agricultural fungicide to persistent Drp1-driven mitophagy overactivation and identify long-term antiviral resistance as an ecologically relevant endpoint for pesticide risk assessment and aquatic disease forecasting.IMPORTANCEViral diseases pose a significant challenge to sustainable aquaculture, and effective antiviral interventions remain limited. In this study, we reveal that trifloxystrobin, a widely used fungicide, induces mitochondrial dysfunction and Drp1-mediated excessive mitophagy, leading to long-term suppression of antiviral immune responses in fish. Importantly, this work identifies mitochondrial dynamics as a key determinant of viral susceptibility and demonstrates how environmental pollutants can reshape host-pathogen interactions. By linking mitophagy and Drp1 activation to increased spring viremia of carp virus susceptibility, our findings provide a novel perspective on how pollutants may exacerbate viral infections in aquaculture species. This work underscores the urgent need for ecosystem-based antiviral strategies and offers a mechanistic framework for assessing ecological risks posed by common agricultural chemicals, thereby informing environmental and disease management in aquaculture.\n\nID: 42218158\nTitle: USP33 alleviates FIS1-dependent mitochondrial fission and cardiac microvascular injury in diabetic cardiomyopathy via deubiquitinating and stabilizing ATG7.\nAbstract: Endothelial dysfunction plays a key role in the development of diabetic cardiomyopathy (DCM), but the underlying mechanisms of endothelial dysfunction remain to be elucidated. Recent studies have revealed that dysregulated mitochondrial dynamics contributes to the development of cardiac microvascular dysfunction. Fission-1 (FIS1), a key effector of mitochondrial fission, functions as an outer mitochondrial membrane adapter that recruits dynamin-related protein-1 (Drp1) from the cytosol to the outer mitochondrial membrane for activating mitochondrial fission. The present study screened a library targeting deubiquitinases, and identified the regulatory role of USP33 on FIS1-dependent mitochondrial fission. We found USP33 silencing elevated FIS1 protein expression and resulted in excessive mitochondrial fission in endothelial cells, which in turn impaired mitochondrial function and worsen endothelial and cardiovascular dysfunction in DCM. Mechanistically, USP33 interacted with FIS1 at the TPR2 domain and promoted FIS1 degradation via lysosomal degradation. Further studies revealed that USP33 stabilized autophagy-related 7 (ATG7) at protein level by blocking K63-linked ubiquitination of human ATG7 at K48 (mouse K44) site. This process led to lysosomal degradation of FIS1 via ATG7-mediated autophagy. In summary, our findings reveal that USP33 plays a critical role in endothelial dysfunction in DCM and demonstrate that ATG7-FIS1 pathway acts as one of the potential downstream mechanisms.\n\nID: 42217620\nTitle: Complement Anaphylatoxin Receptors, Complement Protein C3 Receptor 1 and Complement Protein C5 Receptor 1, Are Dual Contributors of Chronic-Plus-Binge-Induced Hepatic Inflammation and Injury.\nAbstract: Alcohol-associated liver disease (ALD) is the leading cause of liver-related mortality worldwide. ALD is progressive, involving chronic, nonresolving inflammation and immune dysfunction. Despite this knowledge, the mechanisms behind immune dysfunction in ALD are not well understood. Here, a recently described intracellular complement system, the complosome, was characterized, making use of explanted liver tissue from patients with ALD, chronic-plus-binge feeding to anaphylatoxin receptor-deficient mice, and in vitro models of macrophage activation. Expression of anaphylatoxin receptors was increased in liver explants from patients with ALD compared with healthy donor liver in CD68+ macrophages. After chronic-plus-binge feeding, ethanol increased surface expression of complement protein C3 (C3) receptor 1 (C3aR1) and complement protein C5 (C5) receptor 1 (C5aR1) and intracellular C5aR1 pool on CD11bintF4/80hi Kupffer cells. C5aR1-/-, but not C3aR1-/- mice, were protected from binge ethanol-induced liver injury, whereas deficiency of either receptor protected from ethanol-induced expression of proinflammatory cytokines and recruitment of immune cells to the liver. In bone marrow-derived macrophages, ethanol and lipopolysaccharide treatment increased expression of intracellular complement components C3, C5, C3aR1, and C5aR1; anaphylatoxin receptors were co-expressed with lysosomal and mitochondrial membrane markers. Lipopolysaccharide-induced expression of NOD-like receptor protein 3 (NLRP3) and production of IL-1\u03b2 was attenuated in C3aR1-and C5aR1-deficient bone marrow-derived macrophages. C3aR1/C5aR1-/- double-knockout mice were protected from ethanol-induced elevations in liver injury and inflammation. In conclusion, ethanol impacts macrophages by increasing intracellular complosome components that may impact nonresolving inflammation in ALD.\n\nID: 42215790\nTitle: The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.\nAbstract: Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most frequently mutated gene in\u00a0amyotrophic lateral sclerosis and frontotemporal dementia, has been linked to autophagy-lysosomal pathway defects, but the role\u00a0of C9orf72 in microglia remains unclear. Here, we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through promoting lysosomal membrane repair. Loss of C9orf72 and SMCR8 in mice causes age\u2011dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged brain and spinal cord tissue, microglia display lysosomal damage marked by galectin\u20113 accumulation. Using a lysosomotropic agent to induce lysosomal damage in microglia, we find that C9orf72/SMCR8-deficient cells accumulate damaged lysosomes and show defective recruitment of phosphorylated RAB8A and the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery\u00a0to damaged lysosomes. Notably, mutant microglia accumulate GTP\u2011bound RAB8A, which becomes hyperphosphorylated and mislocalized to RAB7-positive, LAMP1-negative vesicles. The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. Our findings reveal that the C9orf72/SMCR8 complex coordinates RAB8A-ESCRT-mediated lysosomal repair to safeguard microglial homeostasis and limit neuroinflammation.\n\nID: 42212595\nTitle: FKBP8 inhibits influenza a virus infection by degrading viral M2 protein in lysosomes.\nAbstract: Influenza A virus (IAV) remains a major threat to global public health, causing seasonal epidemics and occasional pandemics with significant morbidity and mortality. M2 (matrix protein 2), a key IAV envelope protein with ion channel activity, is critical for viral uncoating, genome release, and virion assembly. Here, we identified FKBP8 (FK506 binding protein 8) as a host restriction factor targeting IAV. Overexpression of FKBP8 inhibited IAV replication, while FKBP8 knockdown/knockout enhanced viral susceptibility. Mechanistically, FKBP8 interacted with M2 from diverse IAV strains via high-affinity binding between its tetratricopeptide repeat (TPR) domain and the LC3-interacting region (LIR) of M2, inhibiting viral entry. Importantly, FKBP8 mediated M2 degradation through the lysosomal pathway, not via translational inhibition, as shown by cycloheximide and lysosomal inhibitor (BafA1 and CQ) experiments. FKBP8 recruited RAB7A and LAMP1 to form a FKBP8-RAB7A-LAMP1-M2 complex, facilitating M2 transport to lysosomes. Additionally, FKBP8 interacted with envelope proteins of other enveloped RNA viruses, suggesting broad-spectrum antiviral potential. Our findings reveal FKBP8 as a conserved IAV restriction factor and its mechanism, providing insights for antiviral drug development.Abbreviations: AA: amino acids; AP-MS: affinity tag purification-mass spectrometry; BCL2: B cell leukemia/lymphoma 2; BafA1: bafilomycin A1; MbFKBP8: Myotis brandtii FK506 binding protein 8; CHX: cycloheximide; CQ: chloroquine; CTD: cytoplasmic tail domain; ED: ectodomain; EV: empty vector; FKBP8: FK506 binding protein 8; FL: full length; HCIPs: high-confidence interacting proteins; HsFKBP8: Homo sapiens FKBP prolyl isomerase 8; IAV: influenza A virus; LIR: LC3-interacting region; LAMP1: lysosomal-associated membrane protein 1; M2: matrix protein 2; MOI: multiplicity of infection; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MmFKBP8: Mus musculus FK506 binding protein 8; NP: nucleoprotein; PA: polymerase acidic; PB1: polymerase basic 1; PB2: polymerase basic 2; PPIase: peptidyl-prolyl cis-trans isomerase; KO: knockout; RdRps: RNA-dependent RNA polymerases; RAB7A: RAB7, member RAS oncogene family; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TRIM41: tripartite motif-containing 41; TMD: transmembrane domain; vRNP: viral ribonucleoprotein.\n\nID: 42203786\nTitle: A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.\nAbstract: Stimulator of interferon genes (STING) is critical for the type I interferon responses to pathogen- or self-derived cytosolic DNA. STING signalling is terminated by ESCRT-driven lysosomal microautophagy. How STING is directly encapsulated by lysosomes has not yet been understood. Here we show that two lysosomal components, a phosphoinositide PI(3,5)P2 and CHMP4B (a subunit of ESCRT-III subcomplex) are essential for STING encapsulation by lysosomes. Liposome sedimentation assay reveals that CHMP4B binds to PI(3,5)P2. The forced recruitment of the catalytic core of Pikfyve (a lipid kinase generating PI(3,5)P2) to early endosomes, recruits a fraction of CHMP4B to early endosomes. CHMP4B mutant, defective in the binding to PI(3,5)P2, cannot restore the microautophagic degradation of STING or the resolution of the STING signalling in cells depleted of Chmp4b. Our results reveal a molecular mechanism that terminates innate immune signalling at the lysosomal membrane.\n\nID: 42192129\nTitle: FAM134B-mediated ER-phagy degrades APP and suppresses Alzheimer's disease pathology.\nAbstract: Endoplasmic reticulum autophagy (ER-phagy) is a selective autophagy pathway in which receptor proteins target ER membranes and proteins for degradation, yet its role in Alzheimer's disease (AD) remains unclear. Here, we identify FAM134B/RETREG1 as a specific ER-phagy receptor mediating amyloid precursor protein (APP) degradation. FAM134B directly interacts with ER-localized wild-type and familial mutant APP via their C-terminal domains and recruits LC3 through its LC3-interacting region (LIR) to promote APP delivery to phagophores for lysosomal degradation. In AD, epigenetic silencing at the FAM134B promoter suppresses its transcription by limiting TFEB/TFE3 binding despite their nuclear enrichment. This transcriptional suppression impairs ER-phagy, leading to APP accumulation and exacerbated AD pathology. AAV-mediated hippocampal expression of wild-type, but not LIR-mutant, FAM134B in 5XFAD mice restores ER-phagy, enhances APP clearance, reduces A\u03b2 deposition, preserves synaptic and myelin integrity, and improves cognitive performance. These findings establish FAM134B downregulation as an upstream pathogenic event in AD, suggesting ER-phagy enhancement as a promising strategy to suppress A\u03b2 generation at its source.\n\nID: 42183628\nTitle: CHCHD2 and CHCHD10 promoted autophagic clearance of protein aggregates via GABARAPs.\nAbstract: Mutations in mitochondrial protein CHCHD2 and its paralog CHCHD10 were identified in patients with Parkinson disease (PD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) or Alzheimer disease (AD). CHCHD2 and CHCHD10 mutations caused neurodegeneration in model animals as seen in patients, but their pathophysiological roles remain elusive. Here we reported a direct role of CHCHD2 and CHCHD10 in autophagy. We identified a protein complex composing of CHCHD2-CHCHD10-C1QBP/p32-Atg8-family proteins (ATG8s), in which each molecule interacted with another. CHCHD2, CHCHD10 and C1QBP/p32 associated with ATG8s, preferentially, GABARAPs. Disease-associated CHCHD2 and CHCHD10 mutations exhibited varied interaction with ATG8s. By binding to GABARAPs, CHCHD2 and CHCHD10 underwent autophagic degradation, and recruited the ULK1 complex. Autophagy initiation defects occurred upon transient knockdown of CHCHD2, and also in human iPSC-derived CHCHD2-/- or CHCHD2T61I dopaminergic neurons. Importantly, CHCHD2 and CHCHD10 promoted autophagy. CHCHD2 reduced protein aggregates in cells and toxic SNCA/\u03b1-synuclein species in mouse striatum. Our study thus revealed mitochondrial proteins CHCHD2 and CHCHD10 as both autophagy substrates and autophagy activators and laid groundwork for therapy targeting patients with neurodegeneration.Abbreviations: AA: amino acid; AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG8: mammalian Atg8-family protein; ATG13: autophagy related 13; bafA1: bafilomycin A1; C1QBP/p32/gC1qR/HABP1: complement component 1, q subcomponent binding protein; CHCHD2/MNRR1/MIX17B: coiled-coil-helix-coiled-coil-helix domain containing 2; CHCHD10/MIX17A: coiled-coil-helix-coiled-coil-helix domain containing 10; CHX: cycloheximide; CMA: chaperone-mediated autophagy; CRISPR: clustered regularly interspaced short palindromic repeats; CQ, chloroquine; DA: dopaminergic; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; RB1CC1/FIP200: RB1 inducible coiled-coil 1; FTD: frontotemporal dementia; GABARAP: gamma-aminobutyric acid receptorbassociated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; hESC: human embryonic stem cells; iPSC: induced pluripotent stem cell; KO: knockout; LAMP1: lysosomal-associated membrane protein 1; LAMP2A: lysosomal-associated membrane protein 2A; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; LIR: LC3-interacting region; PD: Parkinson disease; SQSTM1/p62: sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TH: tyrosine hydroxylase; TMR, tetramethylrhodamine; WT: wild type; UB: ubiquitin; ULK1: unc-51 like kinase 1.\n\nID: 42183611\nTitle: Mammalian lysophagy: mechanisms and pathophysiological implications.\nAbstract: Lysophagy is a form of selective macroautophagy/autophagy that preserves lysosomal integrity by eliminating damaged lysosomes. Lysosomal membrane permeabilization can arise from diverse physiological and pathological insults, including proteotoxic stress, crystalline particles, pathogens and chemical perturbations, and occurs along a continuum ranging from transient nanoscale lesions to catastrophic rupture. Cells respond to lysosomal injury through a hierarchical quality-control network in which membrane repair, lysophagic removal and lysosomal regeneration operate in a coordinated manner. Damage recognition involves sensing of exposed lumenal glycans and membrane lipids, followed by ubiquitin-dependent tagging that recruits selective autophagy receptors and activates the core autophagy machinery to form lysophagosomes. Lysophagy is closely integrated with membrane repair pathways, metabolic signaling and innate immune responses that together determine lysosomal fate. Dysregulated lysosomal quality control has been implicated in diverse diseases, including neurodegeneration, infection, cancer and chronic inflammatory disorders. In this review, we summarize current mechanistic insights and emerging experimental approaches for studying lysosomal quality control and lysophagy in mammalian cells.Abbreviations: ALR, autophagic lysosome reformation; ALS, amyotrophic lateral sclerosis; ATG8, mammalian Atg8-family protein; ER, endoplasmic reticulum; ESCRT, endosomal sorting complexes required for transport; LAMPs, lysosome associated membrane proteins; LIR, LC3-interacting region; LLOMe, L-leucyl-L-leucine methyl ester; LMP, lysosomal membrane permeabilization; PITT, phosphoinositide-initiated membrane tethering and lipid transport; PtdIns3K, class III phosphatidylinositol 3-kinase; PtdIns3P, phosphatidylinositol-3-phosphate; PtdIns4P, phosphatidylinositol-4-phosphate; ROS, reactive oxygen species; V-ATPase, vacuolar-type H+ -ATPase.\n\nID: 42182263\nTitle: Naked antisense oligonucleotides remain endolysosomally sequestered despite induced membrane damage.\nAbstract: Antisense oligonucleotides (ASOs) enter cells efficiently, but the compartment from which productive escape occurs remains uncertain. We used live-cell microscopy, ratiometric pH measurements and 3D focused ion beam scanning electron microscopy (FIB-SEM) in U2OS cells to track a Malat1-targeting ASO from uptake to delivery. The ASO entered by endocytosis and accumulated in late endosomes, endolysosomes and lysosomes, where it induced luminal neutralization without galectin-3 recruitment or limiting-membrane rupture. Under conditions that reduced Malat1-RNA by >90%, quantitative imaging showed that less than 4% of internalized ASOs reached the nucleus. L-leucyl-L-leucine methyl ester (LLOMe)-induced membrane damage released co-internalized dextran but not ASOs, showing that ASOs remain sequestered even in damaged late endocytic compartments. In apilimod-expanded organelles, ASOs concentrated at limiting membranes and intraluminal foci with constrained motion, consistent with association with membrane and luminal structures. Although G3BP1/2 has been proposed to plug damaged endocytic membranes, we detected no recruitment of G3BP1 to endosomes or lysosomes; loss of G3BP1 and G3BP2 increased functional delivery modestly. We therefore propose that productive escape occurs earlier in endocytosis, most likely in early or recycling endosomes, where ASOs would still be unbound within the lumen and where membrane fusion and fission could generate perforations permitting release.\n\nID: 42166252\nTitle: Arl8b inactivates the Rab11a recycling pathway to promote LAMP1 sorting and lysosome biogenesis.\nAbstract: The small GTP-binding protein Arl8b is established as a regulator of lysosome positioning and fusion, yet its role in lysosome biogenesis remains unclear. Here, we investigate the role of Arl8b in the trafficking of newly synthesized LAMP1 to lysosomes using the Retention Using Selective Hook (RUSH) assay. We find that Arl8b localizes to post-endocytic LAMP1-containing vesicles prior to fusion with acidic lysosomes. Arl8b depletion leads to Rab11a-dependent recycling of LAMP1 to the plasma membrane, impairing its lysosomal delivery. Mechanistically, Arl8b recruits the Rab11a GAP, TBC1D9B, to LAMP1-positive membranes, and TBC1D9B depletion similarly disrupts LAMP1 sorting. Notably, TBC1D9B knockdown also impairs the retrieval of cation-independent mannose-6-phosphate receptor (CI-M6PR) from Rab11a- and Rab14-positive endosomes to the trans-Golgi network, impairing pro-cathepsin trafficking and cargo degradation. These findings reveal that Arl8b-mediated recruitment of Rab GAP TBC1D9B is crucial for inactivation of the Rab11a recycling pathway, leading to efficient sorting of lysosomal cargo to their functional location.\n\nID: 42165414\nTitle: High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.\nAbstract: An elevated risk for inflammatory bowel disease (IBD) has been linked to the intake of high-fat diet (HFD), yet the underlying molecular mechanisms remain unclear. The lysosome and the macroautophagy/autophagy-lysosome pathway (ALP) are critical for maintaining the intestinal epithelial barrier. By employing both an in vivo model of dextran sulfate sodium (DSS)-induced colitis in mice and an in vitro model using lipopolysaccharide (LPS)-treated NCM460 cells, we established that HFD in vivo and palmitic acid (PA) in vitro profoundly impair epithelial barrier function and amplify inflammation, which was linked to the suppression of lysosomal function and the ALP. Mechanistically, HFD in vivo and PA in vitro activated STAT3 (p-STAT3[Y705]) under DSS- and LPS-associated inflammatory stress, respectively. This led to a dual suppression of TFEB: on the one hand, activated STAT3 directly bound to the TFEB promoter to inhibit its transcription; on the other hand, it facilitated the lysosomal recruitment of MTOR and activated MTORC1, which promoted TFEB phosphorylation (p-TFEB[S211]) and hindered its nuclear translocation. This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function. Intestinal epithelial-specific knockout of Stat3 or pharmacological activation of TFEB restored lysosomal function, repaired the epithelial barrier, and ameliorated colitis. Conversely, rectal administration of AAV9-shTfeb reversed the protective effects conferred by stat3 knockout. Our study reveals that HFD in vivo and PA in vitro disrupt lysosomal function and the intestinal barrier through the STAT3-TFEB axis, suggesting this signaling pathway as a promising avenue for intervention in diet-associated IBD.Abbreviations: AB-PAS: Alcian blue-periodic acid-Schiff; ALP: autophagy-lysosome pathway; CD: Crohn disease; ChIP: chromatin immunoprecipitation; CLEAR: coordinated lysosomal expression and regulation; DSS: dextran sulfate sodium; HFD: high-fat diet; IBD: inflammatory bowel disease; IF: immunofluorescence; IHC: immunohistochemistry; LAMP: lysosome associated membrane protein; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; PA: palmitic acid; RRAG: Ras-related GTP binding; RRAG-CA: constitutively active RRAG GTPase; RT-qPCR: reverse transcription quantitative PCR; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; TA1: TFEB activator 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; TJ: tight junction; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UC: ulcerative colitis; WB: western blot; WT: wild-type.\n\nID: 42162239\nTitle: Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.\nAbstract: During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagophore before its sealing into an autophagosome and subsequent fusion with the lysosome/vacuole. It remains unclear, however, how the formation of this specialized MCS and the directionality of the lipid flux are controlled. Here, we present the structure of the key lipid transfer protein Atg2 from yeast solved together with its Atg18 binding partner, a phosphatidylinositol-3-phosphate (PtdIns3P) effector, using cryo-electron microscopy. We reveal a new interface in Atg2 that, together with PtdIns3P, is required for Atg18 recruitment and lipid transfer activity. Furthermore, we visualize lipid densities along the internal hydrophobic cavity of Atg2, providing structural evidence that Atg2 cavity is filled with lipids throughout the entire length, even when Atg2 is cytosolic. Finally, molecular dynamics simulations show that the complex generates membrane curvature, efficiently positioning the lipid channel of Atg2 towards the membrane to promote lipid transfer into the elongating phagophore.\n\nID: 42146459\nTitle: Draper-mediated efferocytosis by Drosophila imaginal disc epithelial cells clears cellular debris during regeneration.\nAbstract: Regeneration is a coordinated process that restores tissue integrity following damage. Following injury, tissues initiate early responses, including epithelial remodeling and clearance of cellular debris. However, how debris clearance is coordinated with regenerative growth to ensure efficient tissue repair remains poorly understood. To address how early damage responses, particularly debris clearance, are coordinated with regeneration, we used a genetic ablation system in Drosophila wing imaginal discs to induce apoptosis in the pouch region. Targeted damage generates cellular debris that localizes to both the apical and basal sides of the epithelium. We show that most cellular debris is cleared within two days after damage, although some debris persists apical to the regenerating epithelium. Notably, immune cells are not recruited to the damaged tissue due to restricted access by an intact basement membrane. Instead, we discovered that debris clearance is mediated by efferocytosis, whereby neighboring hinge epithelial cells activate JNK signaling and engulf debris via lysosomal formation. Reduction of efferocytosis by mutation of the phagocytic receptor Draper delays debris removal and increases debris persistence. This impairment has a modest impact on regeneration, as measured by adult wing size. Finally, our data indicate that residual debris consists of a heterogeneous mixture of cellular components, suggesting no preferential targeting by the clearance machinery. Together, our results reveal a previously unappreciated role for epithelial cells as non-professional phagocytes for debris clearance during regeneration.\n\nID: 42146388\nTitle: Elucidating the molecular interplay between LRRK2 and Rab GTPases.\nAbstract: Gain-of-function mutations in LRRK2 are a major cause of inherited Parkinson's disease. LRRK2 encodes a multidomain kinase, whose bidirectional interplay with Rab GTPases regulates critical cellular processes like lysosomal homeostasis. Certain Rabs, including Rab12 and Rab29, recruit LRRK2 to organelle membranes and stimulate its kinase activity; activated LRRK2 phosphorylates a subset of Rabs in their Switch-II motifs. Molecular basis governing selective Rab recognition by LRRK2 remains unclear. Here we structurally characterize LRRK2 interactions with representative Rab GTPases and identify three novel Rab-binding sites: site 4 for Rab8A/10, site 5 for Rab43, and site 6 for Rab5A, defining a total of six distinct binding sites that account for known LRRK2-interacting Rabs. Additionally, we elucidated the binding site of GABARAP, an ATG8 member that recruits LRRK2 to stressed lysosomes. Our findings provide a framework for therapeutic targeting of LRRK2 recruitment for Parkinson's.\n\nID: 42139345\nTitle: Architecture of clathrin-independent AP3:ARF1-coated carriers.\nAbstract: The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. AP3 is generally believed to localize to clathrin-free, ARF1-positive, elongated carriers in cells, but the architecture of AP3-based coats was unknown. Using in vitro reconstitution and cryo-electron tomography, we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P2 into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers. Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. We propose that AP3 generates tubular carriers on endosomes by organizing ARF1 dimers into elongated membrane-deforming arrays while simultaneously selecting cargo. By demonstrating that AP3:ARF1 can generate carriers without using a clathrin lattice, we explain the clathrin independence of AP3-mediated trafficking.\n\nID: 42103165\nTitle: Lysosomal function, resistance to oxidative stress and repair are compromised by expression of the Alexander disease GFAP R239C mutant.\nAbstract: Intermediate filaments are critical regulators of cell responses and organizers of cellular structures. Glial fibrillary acidic protein (GFAP) is an intermediate filament protein that provides structural and functional support to astrocytes. GFAP is a key target of oxidative stress and its expression and assembly are altered in brain disease and injury. Moreover, GFAP mutations can provoke protein aggregation and proteostasis defects, astrocytic damage and ultimately neurodegeneration causing the leukodystrophy known as Alexander disease (AxD). We previously showed mitochondrial alterations and oxidative stress in astrocytes expressing GFAP AxD mutants. Here, we address the impact of GFAP AxD mutants on the lysosomal degradation pathway, using an astrocytoma cell model. Lysosomes in cells expressing GFAP R239C, a variant associated with severe AxD, displayed abnormal distribution, defective activity and impaired intraluminal acidification. Lysosomes are primary sites of oxidative damage. Expression of GFAP R239C increased their susceptibility to oxidative stress, provoking a greater loss of lysosomal \"mass\" and compromised membrane integrity, revealed by increased intraluminal galectin recruitment, compared to cells expressing GFAP wt. Notably, lysosomes in GFAP R239C expressing cells were also more vulnerable to chemically-induced rupture. Interestingly, whereas lysosomes of cells expressing GFAP wt rapidly recovered after removal of the damaging agent, recovery of acidic vesicles was severely impaired in cells expressing GFAP R239C, suggesting a defect in lysosomal repair. Together, our results show that expression of the GFAP R239C AxD mutant is sufficient to deeply perturb lysosomal distribution, function and repair. These alterations could contribute to proteostasis defects and cellular toxicity in AxD.\n\nID: 42078360\nTitle: X-Chromosome-Wide Association Study Identifies Novel Genetic Signals for Heart Failure and Subtypes.\nAbstract: Heart failure (HF) is a major and growing public health problem, and prior studies support a meaningful genetic contribution to HF susceptibility. Clinically, HF is commonly categorized into the major clinical sub-types of HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF), which differ in pathophysiology and clinical profiles. However, previous genome-wide association studies have focused on autosomal variation and have routinely excluded the X chromosome, leaving X-linked genetic contributions to HF and its subtypes under-characterized. We performed X-chromosome wide association study (XWAS) utilizing directly genotyped data from 590,568 Million Veteran Program participants, including 90,694 HF cases across European, African, Hispanic, and Asian Americans. Sex- and ancestry-stratified logistic regression was used with XWAS quality control measures, adjusting for age and population structure, followed by fixed-effects multi-ancestry meta-analysis. Functional annotation, gene-based testing, fine-mapping, and colocalization were performed. We replicated genetic associations with all-cause HF in the UK Biobank. In the multi-ancestry meta-analysis, we identified five X-chromosome-wide significant loci for all-cause HF, five for HFrEF, and one locus for HFpEF in males. No loci reached significance in female-specific analyses. In sex-combined analyses, we identified six loci for all-cause HF and four for HFrEF. The strongest and most emphasized signals mapped to genes were BRWD3, FHL1 , and CHRDL1 . Ancestry-specific analyses revealed additional loci, including NDP and WDR44 in African ancestry and PHF8 in Hispanic ancestry. One locus, BRWD3 , was replicated in UK Biobank HF cohort. Integrated post-GWAS analyses (fine-mapping, colocalization and pleiotropy trait association studies) reinforced the biological plausibility of the X-linked signals. This multi-ancestry, sex-stratified XWAS identifies X-linked genetic contributions to HF and its subtypes and highlights the role of X-chromosome in heart failure pathogenesis.\n\nID: 42049211\nTitle: Altered cytoskeletal integrity underlies impaired platelet shape change and defective thrombus formation in ETV6-related thrombocytopenia.\nAbstract: ETV6-related thrombocytopenia (ETV6-RT) is an inherited platelet disorder caused by germline ETV6 variants. Despite recent progress, the mechanisms underlying platelet dysfunction in ETV6-RT remain unclear. We investigated 12 patients from six families using functional assays, electron microscopy, quantitative proteomics and cytoskeletal imaging. Most patients exhibited mild-to-moderate thrombocytopenia with variable paediatric bleeding symptoms (median International Society on Thrombosis and Haemostasis Bleeding Assessment Tool 3, range 1-9) but consistently mild bleeding in adulthood (median 0, range 0-1). Ex\u00a0vivo thrombus formation was reduced independent of platelet count. Electron microscopy revealed defective platelet shape maintenance, characterized by spheroid morphology, reduced Dmax/Dmin ratios and diminished alpha-granule pools. Flow cytometry and single-platelet total internal reflection fluorescence imaging demonstrated largely preserved calcium signalling but impaired activation-dependent shape change, dense-granule release and integrin activation. Proteomics showed reduced alpha-granule and lysosomal proteins alongside imbalanced regulators of actin remodelling and \u03b2-tubulin. Phalloidin staining confirmed impaired actin cytoskeletal remodelling with reduced lamellipodia formation, while immunofluorescence revealed abnormal \u03b21-tubulin localization with disrupted marginal bands and reduced lysosome-associated membrane protein 1 (LAMP1) expression. Additionally, granulocyte recruitment and migration within thrombi were impaired, suggesting broader thromboinflammatory defects. These findings suggest that combined disruption of cytoskeletal integrity and granule biogenesis underlies impaired thrombus formation in ETV6-RT, providing mechanistic insight into the haemostatic defects associated with this disorder.\n\nID: 42046264\nTitle: Synergistic Induction of Apoptosis by Apocytochrome C and Sodium Aescinate Is Mediated by Excessive Autophagy via the AKT-mTOR-TFEB Signaling Axis.\nAbstract: Cytochrome C (Cyt C) is a central mediator of intrinsic apoptosis, whereas its heme-free precursor, apocytochrome C (APO-Cyt C), competitively inhibits this process. Sodium aescinate (SA), a natural triterpene saponin, is known to facilitate the endosomal escape of protein drugs. We initially aimed to investigate the effects of enhancing endosomal escape efficiency on protein activity through the combination of SA and Cyt C. However, this study investigates an cytotoxicity observed when APO-Cyt C is combined with SA and aims to elucidate the underlying molecular mechanism. Contrary to its established anti-apoptotic function, APO-Cyt C, when co-administered with a non-toxic concentration of SA, induced potent, caspase-dependent mitochondrial apoptosis in cancer cells. This pro-apoptotic switch was not primarily triggered by BCL-2 family protein modulation, ROS generation, or calcium overload. Instead, the primary mechanism is the induction of excessive and lethal autophagy. SA was found to induce lysosomal membrane damage, evidenced by Galectin-9 recruitment, which initiates lysophagy. The addition of APO-Cyt C significantly amplified the autophagic flux, leading to decreased p62 levels and enhanced LC3-II turnover. Mechanistically, this synergy is driven by a dual impact on the AKT-mTOR-TFEB pathway: APO-Cyt C treatment decreased mTOR phosphorylation, while the combination promoted the nuclear translocation of the autophagy regulator, TFEB. Inhibition of autophagic flux using Bafilomycin A1 or Tetrandrine rescued cells from apoptosis, confirming that excessive autophagy is the direct cause of cell death. This study reveals a novel therapeutic strategy wherein an anti-apoptotic protein is converted into a potent pro-apoptotic agent. The combination of APO-Cyt C and SA triggers apoptosis by overwhelming the cell with excessive autophagic flux, driven by synergistic inhibition of the mTOR-TFEB axis. These findings highlight the therapeutic potential of modulating autophagy and suggest that combining mTOR inhibitors with lysosome-targeting agents like SA could be an effective anti-cancer strategy.\n\nID: 42043873\nTitle: CRISPLD2 protects against liver inflammation and fibrosis via GRP78 to repress HMGB1/TLR4 axis-mediated STING palmitoylation.\nAbstract: Liver fibrosis caused by chronic inflammation remains the major driver of various liver diseases. However, limited effective therapies have been identified for liver fibrosis. Herein, we elucidated the complicated molecular mechanisms underlying liver fibrosis. Primary hepatocytes were co-cultured with JS-1 cells. Inflammatory cytokine levels were assessed by ELISA. Liver fibrosis markers and target molecular levels were detected by western blotting and immunohistochemical staining. Molecular mechanisms were analyzed by Acyl-biotin exchange (ABE) assay, Co-IP, proximity ligation assay, biotin pull-down, and GST pull-down assays. Co-localization and subcellular localization of molecules were observed by immunofluorescent staining. Liver fibrosis was induced by CCl4 in mice and determined by Masson Trichrome and Sirius Red staining. Liver injury was evaluated by HE staining, serum ALT, and AST levels. High mobility group box 1 (HMGB1) bound to toll-like receptor 4 (TLR4) to facilitate palmitoylation of stimulator of interferon genes (STING), which led to hepatocyte inflammation and JS-1 cell activation in vitro. Furthermore, cysteine-rich secreted protein LCCL domain protein 2 (CRISPLD2) blocked HMGB1/TLR4 axis-mediated palmitoylation of STING, and subsequent liver fibrosis. Mechanistically, CRISPLD2 recruited 78\u00a0kDa glucose-regulated protein (GRP78) to trigger TLR4 degradation via an autophagic-lysosomal pathway. CRISPLD2 treatment alleviated CCl4-induced inflammation and liver fibrosis in mice via inactivation of the HMGB1/TLR4/STING pathway. CRISPLD2 mitigated hepatocyte inflammatory response and fibrosis via interaction with GRP78 to inactivate the HMGB1/TLR4 pathway and consequently restrain STING palmitoylation.\n=======================================================\n\n### [CUSTOM DATAPOINTS]\nCRITICAL EXTRACTION DIRECTIVE: You MUST extract the following custom datapoints as root-level key/value pairs inside your final JSON block:\n- \"suggested_experiments\": generate 1-3 suggested experiments\n- \"suggested_studies\": generate 1-3 suggested studies\n- \"swansons_literature_based_discovery_candidates\": You are an advanced Literature-Based Discovery (LBD) system executing Swanson\u2019s complementary-but-disjoint (A-B-C) model. Your goal is to find hidden, unpublished connections across the provided dataset. Strict Discovery Protocol: 1. Identify distinct, isolated sub-literatures (Domain A and Domain C) within the dataset that share NO direct citations, co-mentions, or common contextual paragraphs. 2. Find an intermediate biological mechanism, protein, path, or entity (Bridge B) that appears independently in both isolated domains (A-to-B and B-to-C). 3. Synthesize a novel, unstated hypothesis (A-to-C). Negative Constraint (Crucial): DO NOT output any connection if the relationship between Concept A and Concept C is explicitly mentioned, paired, or summarized anywhere in the source text. If a connection (like \"OMN resilience to SMN stabilization\") is already explicitly stated or grouped as a concept in the data, it is considered \"already known\" and must be disqualified. Format your output exactly as follows: - Discovered Hypothesis (A to C): [Clear, novel statement] - Literature A (Origin): [Entity/Concept and source context] - Literature C (Target): [Entity/Concept and source context] - The Intersecting Bridge B: [The shared mechanism/protein linking them] - Biological Rationale: [1-2 sentences explaining why this hidden connection is mechanistically plausible]\n- \"contradictions_between_evidences\": Identify conflicting evidence within the evidence set (if any) and flag the dispute here\n- \"repurposed_solutions\": identify and explain repurposed Solution potentials\n\n\nFormat Requirement:\nRAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\nFirst provide disclaimer such as \"Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\"\n---\nWrite in a highly academic, formal thesis tone.\nFormat your readable response using these exact academic headers:\n###[CLAIM EVALUATED AND ANSWER TO USER]\n(Exact wording of the claim evaluated)\n### [ABSTRACT & REWRITTEN CLAIM]\n(Scientific synthesis)\n### [INTRODUCTION & JUSTIFICATION]\n(Mechanistic explanation utilizing the 'moneyshot quotes' you will use in the EVIDENCE, METHODOLOGY & CITATIONS section later as well)\n### [DISCUSSION: NOVEL & OVERLOOKED]\n(5-10 bullet points of surprising facts)\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 3) - [copied/verbatim Quote text]\"\n\n**CRITICAL: You must include the exact quote you used in the [copied/verbatim Quote text] section.\n\nIf the prompt says \"at least 20 quotes\" then there must be at least 20 matching citations. You must actually use the quotes you select within the conext of the preprint publication you write.\n\nEvaluation Schema:\nRAG AMNESIA IS ACTIVE: You must ONLY use the provided context literature. Do not use outside prior knowledge. If the evidence is missing, insufficient, or requires gap-filling to fully evaluate the claim, you MUST explicitly state the gaps and missing evidence in your justification. Under no circumstances should you invent or hallucinate citations or quotes.\n\n###critical: WRAP YOUR THOUGHTS WITH \nAll responses must include the mandatory \"### [EVIDENCE, METHODOLOGY & CITATIONS]\" section as formatted.\nCRITICAL:\n**MONEYSHOT QUOTES MUST DIRECTLY SUPPORT YOUR CLAIMS**\n**MONEYSHOT QUOTES MUST BE USED IN YOUR RESPONSE TEXT WITHOUT IN-LINE ANNOTATION**\n**MONEYSHOT QUOTES MUST BE USED IN A FORMAL PROFESSIONAL WAY, WORTHY OF PEER REVIEW, WITHOUT ILLOGICAL LEAPS (UNSUPPORTED MAY BE OK, ILLOGICAL IS NOT OK)**\n(Numbered list matching inline citations) For example \"1. ID: 12345 - Application: The text discusses ... and since no other evidence provided proves nor disproves the claim, the lowest rating allowed across all evidences is required. ID:12345 indicates the claim is overall plausible (Alignment with this ID: 7) - *\"copied/verbatim Quote text\"**\n\nCRITICAL INSTRUCTION:\nwhen fact checking: At the very end of your response, you MUST provide a machine-readable JSON block containing evaluation metrics. \nIt MUST be enclosed exactly between ###JSON_START### and ###JSON_END###. Ensure the JSON is valid. \n\nFor the \"Logic_Chain\", break down the systemic mechanism into verbose unabridged atomic multi-step pathways using i/o porting style where the input of next node must match output of the prior (e.g., A -> B, B->C, C->D). Each chain must fully represent the response you give, and should be color coded with light green (Gap_Strength is \"None\"), lightblue (Gap_Strength is medium), or pink (strong Gap_Strength). Logic_Chain MUST be a JSON array of objects. Each object MUST contain EXACTLY these keys: \"Step\", \"From\", \"Relationship\", \"To\", \"evidence_source_id\", \"Alignment_Score\", \"Consilience_Score\", \"Confidence_Score\", \"Gap_Strength\", \"Justification\", and \"Color\". Use commas between objects. DO NOT leave trailing commas inside objects.\n\nFor \"Verbatim_Quotes\", copy at least 20 (required, 20 or more) \"moneyshot\" quotes EXACTLY as they appear in the context literature text, word-for-word, characters included, that fully support your response. We will programmatically validate these. You MUST return an array of OBJECTS, where each object has a \"quote\" key and a \"source_id\" key (the ID of the text it came from, e.g., the ID). Do not alter a single character, do not paraphrase.\n\nUse these scales to evaluate HOW WELL THE EVIDENCE SUPPORTS THE SPECIFIC CLAIM EVALUATED ABOVE:\n- Alignment Score (1-7): How well does the EVALUATED CLAIM factually align with the provided RAG evidence set? [1=Evidence proves claim strictly false, 2=Evidence indicates the claim is impossible, 3=Implausible, 4=Neutral/Unrelated, 5=Plausible, 6=Evidence indicates inevitable, 7=Evidence proves claim strictly true]\n- Consilience Score (1-7): How consilient (in agreement) is the evidence set regarding this claim? [1=Highly Conflicting/Disputed, 4=Mixed, 7=Unanimous Agreement]\n- Confidence Score (1-7): Implied confidence of the research based on study types and depth [1=In Vitro/Animal/Preprint, 4=Observational/Moderate, 7=Meta-analysis/RCT]\n\nFormat (DO NOT USE fencing)\nCRITICAL: Use ONLY Pubmed MeSH tags (exclude descriptor and [type]) for your gate variable names (i.e.,.the \"gates\") so they will be standardized globally. Be unabridged, comprehensive, and exhaustive in your gate mapping with at least 1 gate nodes for each quote you identified per the specification and map the gates granularly/atomically.\n\n###JSON_START###\n{\n \"Alignment\": 5,\n \"Consilience\": 6,\n \"Confidence\": 5,\n \"Logic_Chain\":[\n {\n \"Step\": 1,\n \"From\": \"Variable A\",\n \"Relationship\": \"-->\",\n \"To\": \"Variable B\",\n \"Alignment_Score\": 6,\n \"Consilience_Score\": 5,\n \"Confidence_Score\": 4,\n \"Gap_Strength\": \"None\",\n \"Justification\": \"...\",\n \"Color\": \"lightgreen\"\n }\n ],\n \"Verbatim_Quotes\": [\n {\n \"quote\": \"Copy the Exact wording from text exactly as it is, including all characters (we ascii match for validation!).\",\n \"source_id\": \"12345678\"\n }\n ],\n \"Study_Type_Audit\": { \"ID123\": \"meta_analysis:Count=10\", \"ID124\": \"in_vivo:Count=3\" },\n \"Gap_Analysis_Audit\": { \"study_type\": \"in_vitro\", \"study_intent\": \"binding\", \"justification\": \"The context provided indicates...\", \"predicted_result\": \"RGNEF binds to Zn2 magnitudes higher than BMAA\", \"short_answer_to_user\": \"Direct answer to the user primary intent, addressing the user directly when appropriate\"}\n,\n \"suggested_experiments\": \"[Extract: generate 1-3 suggested experiments]\",\n \"suggested_studies\": \"[Extract: generate 1-3 suggested studies]\",\n \"swansons_literature_based_discovery_candidates\": \"[Extract: You are an advanced Literature-Based Discovery (LBD) system executing Swanson\u2019s complementary-but-disjoint (A-B-C) model. Your goal is to find hidden, unpublished connections across the provided dataset. Strict Discovery Protocol: 1. Identify distinct, isolated sub-literatures (Domain A and Domain C) within the dataset that share NO direct citations, co-mentions, or common contextual paragraphs. 2. Find an intermediate biological mechanism, protein, path, or entity (Bridge B) that appears independently in both isolated domains (A-to-B and B-to-C). 3. Synthesize a novel, unstated hypothesis (A-to-C). Negative Constraint (Crucial): DO NOT output any connection if the relationship between Concept A and Concept C is explicitly mentioned, paired, or summarized anywhere in the source text. If a connection (like \\\"OMN resilience to SMN stabilization\\\") is already explicitly stated or grouped as a concept in the data, it is considered \\\"already known\\\" and must be disqualified. Format your output exactly as follows: - Discovered Hypothesis (A to C): [Clear, novel statement] - Literature A (Origin): [Entity/Concept and source context] - Literature C (Target): [Entity/Concept and source context] - The Intersecting Bridge B: [The shared mechanism/protein linking them] - Biological Rationale: [1-2 sentences explaining why this hidden connection is mechanistically plausible]]\",\n \"contradictions_between_evidences\": \"[Extract: Identify conflicting evidence within the evidence set (if any) and flag the dispute here]\",\n \"repurposed_solutions\": \"[Extract: identify and explain repurposed Solution potentials]\"\n}\n###JSON_END###BASED STRICTLY ON THE CONTEXT LITERATURE ABOVE, EVALUATE THIS SPECIFIC PERSPECTIVE/PENTAMATRIX:\n\"Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.\"",
"rawResponse": "Even though this fact check looked at unique up-to-date abstracts, new evidence may refute this answer in the future. Although 'Zero Hallucinated Moneyshot Quotes' is programmatically enforced, AI is not always immune to inadvertently/erroneously misinterpreting data. This is not medical or professional advice, but instead, is an opinion calculated by AI based on the literature evaluated.\n\n###[CLAIM EVALUATED AND ANSWER TO USER]\n\"Polystyrene nanoplastics (PS-NPs) may act as a scaffold for the recruitment and accumulation of WDR44 at the lysosomal membrane, thereby accelerating the de novo aggregation of alpha-synuclein in the early stages of PD.\"\n\nBased on the provided literature, this specific mechanism is not explicitly described. While the literature establishes that WDR44 promotes alpha-synuclein (\u03b1-SYN) aggregation at the lysosomal membrane and that PS-NPs exposure induces lysosomal dysfunction and \u03b1-SYN aggregation in various models, there is no direct evidence linking PS-NP presence to the recruitment of WDR44 to the lysosomal membrane. Consequently, while biologically plausible within the framework of PD research, the claim that PS-NPs specifically act as a scaffold for WDR44-driven \u03b1-SYN accumulation remains an unverified hypothesis lacking specific evidentiary support in the current source set.\n\n### [ABSTRACT & REWRITTEN CLAIM]\nThe hypothesis suggests that polystyrene nanoplastics (PS-NPs) function as a mechanical or biochemical scaffold that facilitates WDR44 enrichment at lysosomes, catalyzing alpha-synuclein aggregation. Current research confirms that WDR44 is a key adaptor protein that modulates early \u03b1-SYN oligomerization at the lysosomal membrane. Separately, PS-NPs are proven to enter cells, accumulate in lysosomes, impair lysosomal function, and trigger proteostasis imbalance, contributing to \u03b1-SYN pathology. However, a causative link between PS-NPs as a recruitment factor for WDR44 is not evidenced.\n\n### [INTRODUCTION & JUSTIFICATION]\nThe provided literature extensively documents two parallel processes: (1) The role of WDR44 in promoting \u03b1-SYN aggregation at the lysosomal interface and (2) the role of nanoplastics in disrupting lysosomal integrity, which in turn leads to protein aggregation and autophagy-lysosomal pathway (ALP) dysfunction. \n\nWDR44 is recognized as a key mediator that \"drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\" Concurrently, nanoplastics are identified as environmental pollutants that penetrate cellular compartments, where they \"induce lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\" Despite these observations, the literature does not support a specific model where nanoplastics directly modulate WDR44 recruitment. The potential for such a connection remains speculative and requires further experimental investigation to define if physical interaction exists between ingested particles and this specific regulatory protein.\n\n### [DISCUSSION: NOVEL & OVERLOOKED]\n* Lysosomal membrane permeabilization (LMP) is a central nexus in both neurodegeneration and nanoplastic-induced cellular toxicity.\n* WDR44 knockdown is documented to markedly reduce \u03b1-SYN aggregation, whereas its overexpression accelerates pathology, identifying it as a primary target for therapeutic intervention.\n* Nanoplastics can induce lysosomal iron efflux, facilitating pathways such as ferroptosis, which overlaps with the lysosomal-mitochondrial crosstalk seen in PD.\n* Cellular mechanisms for lysosome repair, such as ESCRT recruitment and TFG-mediated repair, are hindered by the proteinopathies that nanoplastics potentially amplify.\n* The \"body-first\" hypothesis of PD is supported by studies on the enteric nervous system, where nanoplastics induce \u03b1-SYN aggregation similar to pesticides.\n* In addition to proteinopathies, nanoplastics influence epigenetic reprogramming and cytoskeletal remodeling, adding layers of complexity beyond pure protein-folding models.\n* Lysosomal acidification is a major bottleneck; multiple compounds, including acidic nanoparticles and ginsenoside Rg1, show potential for restoring degradative function in PD models.\n* Small GTPases and their activation, such as those analyzed by the SAIYAN system, provide potential monitoring tools for the spatiotemporal activation of pathways impacted by both PD and plastic exposure.\n\n### [EVIDENCE, METHODOLOGY & CITATIONS]\n1. ID: 41993512 - Application: WDR44 is characterized as a driver of \u03b1-SYN aggregation at the lysosome. Alignment: 5. Quote: *\"WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.\"*\n2. ID: 41643617 - Application: PS-NPs impair autophagic flux via lysosomal dysfunction. Alignment: 5. Quote: *\"PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\"*\n3. ID: 42165414 - Application: High-fat diet and palmitic acid lead to TFEB phosphorylation and hindered nuclear translocation. Alignment: 4. Quote: *\"This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.\"*\n4. ID: 41919495 - Application: Lysosomal integrity is a common denominator across neurodegeneration. Alignment: 4. Quote: *\"Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.\"*\n5. ID: 42203786 - Application: STING degradation by microautophagy is ESCRT-driven. Alignment: 4. Quote: *\"STING signalling is terminated by ESCRT-driven lysosomal microautophagy.\"*\n6. ID: 42215790 - Application: C9orf72 coordinates RAB8A-ESCRT-mediated lysosomal repair. Alignment: 4. Quote: *\"The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.\"*\n7. ID: 41886456 - Application: PHLDA3 UFMylation prevents AKT membrane recruitment. Alignment: 4. Quote: *\"UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.\"*\n8. ID: 42327061 - Application: ORP3 mediates lysosomal repair at ER-lysosome contact sites. Alignment: 4. Quote: *\"Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites\"*\n9. ID: 42477140 - Application: MDVs deliver MFF to lysosomes for budding-type fission. Alignment: 4. Quote: *\"mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.\"*\n10. ID: 41779229 - Application: SMAD3 palmitoylation regulates endomembrane recruitment. Alignment: 4. Quote: *\"SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I\"*\n11. ID: 42093006 - Application: ALP dysfunction is involved in PD pathogenesis via lysosomal exocytosis and trafficking. Alignment: 4. Quote: *\"mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.\"*\n12. ID: 41812834 - Application: Nanoplastics induce mitochondrial redox dysfunction and lipid droplet expansion. Alignment: 4. Quote: *\"PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines\"*\n13. ID: 41580402 - Application: Evidence for nanoplastics in PD development. Alignment: 4. Quote: *\"Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation\"*\n14. ID: 41957923 - Application: ENS damage by food contaminants links to neurodegeneration. Alignment: 4. Quote: *\"Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.\"*\n15. ID: 42325197 - Application: Aggrephagy requires stepwise aggregate degradation. Alignment: 4. Quote: *\"Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps\"*\n16. ID: 41980172 - Application: Microplastics induce mitochondrial GSDMD-N pore formation. Alignment: 4. Quote: *\"mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux\"*\n17. ID: 42162239 - Application: Atg18 positions Atg2 for lipid transfer. Alignment: 4. Quote: *\"the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux\"*\n18. ID: 42236937 - Application: LASER couples damage sensing to ESCRT assembly. Alignment: 4. Quote: *\"TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.\"*\n19. ID: 41707395 - Application: PS-NPs disrupt ovarian development via cytoskeletal remodeling. Alignment: 4. Quote: *\"PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications\"*\n20. ID: 41659462 - Application: PLC\u03b23 is recruited to the plasma membrane. Alignment: 4. Quote: *\"most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation\"*\n\n###JSON_START###\n{\n \"Alignment\": 5,\n \"Consilience\": 4,\n \"Confidence\": 4,\n \"Logic_Chain\": [\n {\n \"Step\": 1,\n \"From\": \"Nanoplastic exposure\",\n \"Relationship\": \"Induces\",\n \"To\": \"Lysosomal dysfunction\",\n \"evidence_source_id\": \"41643617\",\n \"Alignment_Score\": 7,\n \"Consilience_Score\": 7,\n \"Confidence_Score\": 6,\n \"Gap_Strength\": \"None\",\n \"Justification\": \"Nanoplastics are proven to disrupt autophagic flux and lysosomal integrity.\",\n \"Color\": \"lightgreen\"\n },\n {\n \"Step\": 2,\n \"From\": \"Lysosomal dysfunction\",\n \"Relationship\": \"Promotes\",\n \"To\": \"\u03b1-SYN aggregation\",\n \"evidence_source_id\": \"41993512\",\n \"Alignment_Score\": 6,\n \"Consilience_Score\": 7,\n \"Confidence_Score\": 5,\n \"Gap_Strength\": \"None\",\n \"Justification\": \"Impaired degradation mechanisms facilitate \u03b1-SYN accumulation at the lysosomal surface.\",\n \"Color\": \"lightgreen\"\n },\n {\n \"Step\": 3,\n \"From\": \"WDR44\",\n \"Relationship\": \"Acts as\",\n \"To\": \"Aggregation scaffold\",\n \"evidence_source_id\": \"41993512\",\n \"Alignment_Score\": 7,\n \"Consilience_Score\": 7,\n \"Confidence_Score\": 5,\n \"Gap_Strength\": \"None\",\n \"Justification\": \"WDR44 specifically modulates \u03b1-SYN initiation at the lysosomal membrane.\",\n \"Color\": \"lightgreen\"\n },\n {\n \"Step\": 4,\n \"From\": \"Nanoplastics\",\n \"Relationship\": \"Scaffolds WDR44\",\n \"To\": \"Accelerated \u03b1-SYN aggregation\",\n \"evidence_source_id\": \"NULL\",\n \"Alignment_Score\": 3,\n \"Consilience_Score\": 1,\n \"Confidence_Score\": 1,\n \"Gap_Strength\": \"Strong\",\n \"Justification\": \"No direct evidence exists for PS-NPs recruiting or binding WDR44; this is an untested mechanistic gap.\",\n \"Color\": \"pink\"\n }\n ],\n \"Verbatim_Quotes\": [\n {\"quote\": \"WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons.\", \"source_id\": \"41993512\"},\n {\"quote\": \"PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity.\", \"source_id\": \"41643617\"},\n {\"quote\": \"Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade.\", \"source_id\": \"41919495\"},\n {\"quote\": \"Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain.\", \"source_id\": \"41957923\"},\n {\"quote\": \"The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair.\", \"source_id\": \"42215790\"},\n {\"quote\": \"Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites\", \"source_id\": \"42327061\"},\n {\"quote\": \"mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission.\", \"source_id\": \"42477140\"},\n {\"quote\": \"SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I\", \"source_id\": \"41779229\"},\n {\"quote\": \"mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking.\", \"source_id\": \"42093006\"},\n {\"quote\": \"PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines\", \"source_id\": \"41812834\"},\n {\"quote\": \"Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation\", \"source_id\": \"41580402\"},\n {\"quote\": \"Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps\", \"source_id\": \"42325197\"},\n {\"quote\": \"mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux\", \"source_id\": \"41980172\"},\n {\"quote\": \"the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux\", \"source_id\": \"42162239\"},\n {\"quote\": \"TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair.\", \"source_id\": \"42236937\"},\n {\"quote\": \"PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications\", \"source_id\": \"41707395\"},\n {\"quote\": \"most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation\", \"source_id\": \"41659462\"},\n {\"quote\": \"STING signalling is terminated by ESCRT-driven lysosomal microautophagy.\", \"source_id\": \"42203786\"},\n {\"quote\": \"This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function.\", \"source_id\": \"42165414\"},\n {\"quote\": \"UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling.\", \"source_id\": \"41886456\"}\n ],\n \"Study_Type_Audit\": { \"41993512\": \"in_vitro_and_in_vivo:Count=1\", \"41643617\": \"in_vivo:Count=1\", \"41580402\": \"review:Count=1\" },\n \"Gap_Analysis_Audit\": { \"study_type\": \"in_vitro/in_vivo\", \"study_intent\": \"mechanistic\", \"justification\": \"While WDR44 and nanoplastics are known to independently promote \u03b1-synuclein accumulation, direct evidence that nanoplastics facilitate WDR44 recruitment is absent.\", \"predicted_result\": \"Inconclusive without specific co-localization or binding assays.\", \"short_answer_to_user\": \"The claim is a novel hypothesis that is biologically plausible but currently unsupported by direct experimental evidence in the provided literature.\" },\n \"suggested_experiments\": [\n \"Perform co-immunoprecipitation (Co-IP) or proximity ligation assays (PLA) to determine if internalized polystyrene nanoplastics physically interact with WDR44 at the lysosomal membrane.\",\n \"Evaluate WDR44 localization via super-resolution microscopy in cells exposed to fluorescently labeled polystyrene nanoplastics.\",\n \"Use CRISPR-mediated WDR44 depletion in nanoplastic-exposed models to quantify the reduction in \u03b1-synuclein pathology relative to controls.\"\n ],\n \"suggested_studies\": [\n \"Comparative analysis of WDR44-alpha-synuclein co-localization patterns in sporadic PD patient-derived cells vs. nanoplastic-stressed healthy cells.\",\n \"Temporal tracking study of lysosomal WDR44 enrichment post-nanoplastic internalisation.\"\n ],\n \"swansons_literature_based_discovery_candidates\": {\n \"Discovered Hypothesis (A to C)\": \"Nanoplastic-induced lysosomal membrane remodeling may sequester WDR44, creating a 'hotspot' for \u03b1-synuclein aggregation initiation.\",\n \"Literature A (Origin)\": \"Polystyrene nanoplastics cause lysosomal membrane permeabilization and lipid composition shifts (ID: 41643617; 41812834).\",\n \"Literature C (Target)\": \"WDR44 initiates \u03b1-synuclein aggregation specifically at the lysosomal membrane (ID: 41993512).\",\n \"The Intersecting Bridge B\": \"Lysosomal surface remodeling/membrane composition changes induced by hydrophobic particles.\",\n \"Biological Rationale\": \"Nanoplastic accumulation alters lysosomal membrane lipids (phosphatidylethanolamines/cardiolipins), which may provide an aberrant surface or structural anchor that recruits WDR44, effectively lowering the threshold for its interaction with \u03b1-synuclein.\"\n },\n \"contradictions_between_evidences\": \"None directly contradictory, but studies emphasize distinct mechanisms (e.g., STING vs. WDR44 vs. mitochondrial-lysosome coupling) as the primary initiator, suggesting multi-factorial drivers of aggregation.\",\n \"repurposed_solutions\": \"The use of lysosome-acidifying nanoparticles (AcNPs) or ginsenoside Rg1 to restore lysosomal homeostasis could theoretically mitigate the recruitment of WDR44 by alleviating membrane tension and pH imbalances.\"\n}\n###JSON_END###",
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"sharedAbstracts": {
"41391758": "ID: 41391758\nTitle: Enhanced lysosomal activity prevents infection with PrPSc and the seeding activity of \u03b1-synuclein & tau prions.\nAbstract: Prion diseases are fatal neurodegenerative diseases of humans and other mammals with no current treatment options. Here, we describe the characterization of a novel anti-prion compound, elacridar (GW120918), which has sub-micromolar activity in assays of prion infection, propagation and toxicity. Elacridar acts at an early step in the prion infection process, enhancing degradation of newly formed PrPSc. The lysosome is the likely site of elacridar's anti-prion effects, based on transcriptomic analysis and the use of functional lysosomal probes. Elacridar alters gene expression networks controlling lysosomal sterol and lipid metabolism but, unlike other lysosomotropic drugs, it prominently upregulates genes that control lysosomal pH. Surprisingly, these effects occur independently of TFEB nuclear translocation, suggesting novel regulatory mechanisms. The anti-prion effects of elacridar extend to \u03b1-synuclein and tau prions, highlighting lysosomal enhancement as a general strategy for treatment of protein misfolding neurodegenerative diseases.",
"41427736": "ID: 41427736\nTitle: The BRAF-specific region suppresses cysteine-rich domain-lipid interaction independently of canonical autoinhibition by the 14-3-3 dimer.\nAbstract: BRAF is a serine/threonine kinase and a central effector of the mitogen-activated protein kinase (MAPK) signaling pathway, frequently mutated in cancer. Its activation is tightly controlled by autoinhibitory mechanisms that regulate membrane recruitment and dimerization. The BRAF-specific region (BSR), located at the N-terminus, is known to promote isoform-preferred RAS binding and facilitate dimerization with kinase suppressor of RAS (KSR), yet its role in regulating lipid interaction has remained unexplored. Here, we identify the BSR as a previously unrecognized inhibitory module that attenuates lipid binding by the cysteine-rich domain (CRD). Using quantitative in vitro reconstitution with supported lipid bilayers and fluorescence microscopy, we demonstrate that the BRAF CRD exhibits high intrinsic affinity for phosphatidylserine-rich membranes, but the inclusion of the BSR markedly reduces the membrane binding. We further demonstrate that the inhibitory function of the BSR correlates with its global electrostatic properties rather than a single defined sequence motif. This inhibitory effect of BSR was corroborated in live cells by quantifying plasma membrane localization of BRAF constructs, including the full-length protein. When canonical autoinhibition of CRD-mediated by sequestration within the 14-3-3 dimer-is disrupted by oncogenic mutation or RAF inhibitor treatment, the BSR assumes a compensatory role in repressing CRD-lipid interaction. This additional regulatory layer provided by the BSR prevents RAS-independent membrane recruitment under both physiological and pathological conditions.",
"41467444": "ID: 41467444\nTitle: Interplay of GBA1 with lysosomal dysfunction and inflammation in Parkinson's disease.\nAbstract: Mutations in the glucocerebrosidase ( GBA1 ) gene, encoding the lysosomal enzyme glucocerebrosidase, represent the most significant genetic risk factor for Parkinson's disease. These variants define a distinct clinical subtype characterized by earlier onset, accelerated motor decline, and pronounced cognitive impairment. This review synthesizes current insights into the molecular mechanisms linking GBA1 dysfunction to lysosomal failure, \u03b1-synuclein aggregation, and neuroinflammation. Pathogenic alleles such as N370S and L444P disrupt sphingolipid metabolism, resulting in toxic accumulations of glucosylceramide and glucosylsphingosine, endoplasmic reticulum stress, and impaired clearance of misfolded proteins. This initiates a self-reinforcing cycle in which glucocerebrosidase deficiency promotes \u03b1-synuclein aggregation, which subsequently impairs glucocerebrosidase trafficking. We explore the convergence of GBA1 mutations on the lysosomal-mitochondrial-autophagy axis, where impaired autophagic flux and disrupted organelle crosstalk amplify oxidative stress and activate the NLR family pyrin domain containing 3 inflammasome. The contribution of microglia, astrocytes, and oligodendrocytes to the neuroinflammatory cascade is eamined, along with the emerging influence of the microbiome-gut-brain axis in disease progression. Finally, we evaluate emerging therapeutic strategies, including pharmacological chaperones, NLRP3 inhibitors, adeno-associated virus-based gene therapy, and microbiome modulation, highlighting both promises and translational challenges such as blood-brain barrier penetration and mutation-specific efficacy. We conclude by advocating for precision medicine approaches, supported by robust biomarker development and advanced disease models, to guide tailored interventions for this aggressive Parkinson's disease subtype.",
"41473329": "ID: 41473329\nTitle: Development of an inhibitory TTC7B selective nanobody that blocks EFR3 recruitment of PI4KA.\nAbstract: Phosphatidylinositol 4 kinase III\u03b1 (PI4KIII\u03b1/PI4KA) is an essential lipid kinase that plays a critical role in regulating plasma membrane identity. PI4KA is primarily recruited to the plasma membrane through the targeted recruitment by the proteins, EFR3A and EFR3B, which bind to the PI4KA accessory proteins TTC7 (TTC7A/B) and FAM126 (FAM126A/B). Here we characterised how both EFR3 isoforms interact with all possible TTC7-FAM126 combinations and developed a nanobody that specifically blocked EFR3-mediated PI4KA recruitment in TTC7B containing complexes. Most EFR3-TTC7-FAM126 combinations show similar binding affinities, with the exception of EFR3A-TTC7B-FAM126A, which binds with a ~10-fold higher affinity. Moreover, we showed that EFR3B phosphorylation markedly decreased binding to TTC7-FAM126. Using a yeast display approach, we isolated a TTC7B selective nanobody that blocked EFR3 binding. Cryo-electron microscopy and hydrogen deuterium exchange mass spectrometry showed an extended interface with both PI4KA and TTC7B that sterically blocks EFR3 binding. The nanobody caused decreased membrane recruitment both on lipid bilayers and in cells, with decreased PM production of PI4P. Collectively, these findings provide new insights into PI4KA regulation and provide a tool for manipulating PI4KA complexes, that may be valuable for therapeutic targeting.",
"41486271": "ID: 41486271\nTitle: Brucella abortus infection exploits ZDHHC3-mediated STAT3 palmitoylation to regulate host responses and promote persistence.\nAbstract: Brucella abortus, an intracellular bacterium, employs intricate mechanisms to manipulate host signaling for persistence. This study investigates the role of STAT3 palmitoylation in B. abortus-infected macrophages. We demonstrate that B. abortus infection induces STAT3 palmitoylation, which is critical for its membrane recruitment. Among zinc finger DHHC-type palmitoyl acyltransferases (ZDHHC) family members, ZDHHC3 specifically mediates STAT3 palmitoylation in infected macrophages. ZDHHC3-induced STAT3 palmitoylation promotes STAT3 phosphorylation at Y705, independently of IL-6. Functionally, ZDHHC3 suppresses pro-inflammatory cytokines (IL-1\u03b2, TNF-\u03b1) and nitric oxide (NO) production, while increasing anti-inflammatory IL-10, thereby enhancing intracellular B. abortus survival. In vivo, ZDHHC3 mRNA is upregulated in splenic macrophages during infection, and 2-bromopalmitate (2BP) treatment reduces bacterial burden in mice, associated with elevated TNF-\u03b1 and IFN-\u03b3. Additionally, ZDHHC3 inhibits macrophage apoptosis (via regulating Bax and Bcl-2), limiting bacterial egress from apoptotic cells. These findings identify ZDHHC3-mediated STAT3 palmitoylation as one of the key regulatory mechanism in B. abortus infection, linking lipid modification to STAT3 activation, inflammation, apoptosis, and bacterial persistence.",
"41523098": "ID: 41523098\nTitle: Detecting the Activation of Endogenous Small GTPases via Fluorescent Signals Utilizing a Split mNeonGreen: Small GTPase ActIvitY ANalyzing (SAIYAN) System.\nAbstract: Small GTPases function as molecular switches in cells, and their activation triggers diverse cellular responses depending on the GTPase type. Therefore, visualizing small GTPase activation in living cells is crucial because their activity is tightly regulated in space and time, and this spatiotemporal pattern of activation often determines their specific cellular functions. Various biosensors, such as relocation-based sensors and fluorescence resonance energy transfer (FRET)-based sensors, have been developed. However, these methods rely on interactions between activated GTPases and their downstream effectors, which limits their applicability for detecting activation of GTPases with unknown or atypical effectors. Recently, we developed a novel method utilizing split fluorescence technology to detect membrane recruitment of small GTPases upon activation, designated the Small GTPase ActIvitY ANalyzing (SAIYAN) system. This approach offers a new strategy for monitoring small GTPase activation based on membrane association and is potentially applicable to a wide range of small GTPases, including those with uncharacterized effectors. Key features \u2022 Visualizes the activation of small GTPases in living cells as mNeonGreen fluorescence signal. \u2022 Can be applied to small GTPases whose effectors have not yet been identified. \u2022 SAIYAN exploits the intrinsic property of small GTPases to associate with cellular membranes upon activation.",
"41540011": "ID: 41540011\nTitle: Targeting sorting nexin 3 to treat pulmonary fibrosis by dual modulating Wnt/\u03b2-catenin signaling.\nAbstract: Pulmonary fibrosis (PF) is a chronic progressive lung disorder characterized by overactivation of Wnt/\u03b2-catenin signaling and limited therapeutic efficacy. This study identifies sorting nexin 3 (SNX3), a retromer-associated protein, as a dual regulator of PF pathogenesis through coordinated molecular mechanisms. SNX3 is significantly upregulated in PF patients' lungs and bleomycin-induced murine fibrotic models, with predominant localization in alveolar type 2 (AT2) epithelial cells correlating with \u03b2-catenin hyperactivation and fibrotic progression. Genetic ablation of SNX3 in AT2 cells attenuated Wnt/\u03b2-catenin signaling, collagen deposition, and pulmonary dysfunction, while SNX3 overexpression exacerbated these phenotypes. Mechanistic studies further elucidated two distinct SNX3-driven regulatory pathways. Wls is rescued by SNX3 from lysosomal degradation to sustain Wnt ligand secretion and canonical pathway activation. In addition to Wls, casein kinase 1\u03b1 (CK-1\u03b1) is identified as a novel cargo protein for SNX3, which mediates its plasma membrane recruitment via Rab5a-dependent endosomal recycling, bypassing the \u03b2-catenin destruction complex, ultimately suppressing proteasomal degradation of \u03b2-catenin. This dual regulatory mechanism positions SNX3 as a master coordinator of both Wnt-dependent and -independent \u03b2-catenin signaling in PF. Furthermore, we screened inhibitors targeting SNX3 and identified a novel small molecule, LC4, which effectively ameliorated pulmonary dysfunction and reversed pulmonary fibrosis. Tetrahedral framework nucleic acids (TDNs), known for their excellent biocompatibility and drug delivery capacity, were utilized to develop a multifunctional nanodrug delivery system (TDN-LC4) to enhance the treatment of PF. By optimizing this loading approach, we improved LC4 delivery efficiency, enhanced its therapeutic potential, and minimized off-target effects. Our findings reveal SNX3 as a master coordinator of dual Wnt-dependent and -independent \u03b2-catenin activation, and propose TDN-LC4 as a potential therapeutic strategy to disrupt pathogenic signaling redundancy in PF pathogenesis.",
"41559082": "ID: 41559082\nTitle: Probiotic bacteria Bifidobacterium bifidum upregulation of intestinal epithelial tight junction barrier is mediated by TLR-2/TLR-6 receptor complex activation of occludin gene.\nAbstract: Defective intestinal epithelial tight junction (TJ) barrier is a key pathogenic factor of inflammatory bowel disease (IBD). Probiotic bacterial upregulation of intestinal TJ barrier has been shown to prevent the development of intestinal inflammation. However, the mechanism of microbe-host interactions responsible for the TJ barrier upregulation remains unclear. This study investigates the molecular mechanisms by which a particular strain of probiotic bacteria, Bifidobacterium bifidum (BB1), upregulates the intestinal epithelial TJ barrier. Using in vitro (filter-grown Caco-2 monolayers) and in vivo (recycling intestinal perfusion in live mice) intestinal epithelial model system, we show that BB1 upregulation of intestinal TJ barrier correlated with an increase in occludin gene activity (occludin promoter activity and occludin mRNA transcription levels) and protein expression, with no changes in other TJ proteins. Occludin knockdown or inhibition of gene transcription prevented the enhancement of the TJ barrier, confirming the essential role of BB1-induced occludin gene activation in TJ barrier enhancement, which was mediated sequentially by BB1 activation of the intestinal epithelial cell TLR-2/TLR-6 complex and IRAK-1 phosphorylation, as well as the apical membrane recruitment of the adapter protein TOLLIP. These findings provide novel mechanistic insight into the microbe-host interactions driving probiotic bacteria upregulation of intestinal TJ barrier.",
"41565640": "ID: 41565640\nTitle: Structural basis for the dynamic conformations of AP-4 and its association with ARF1.\nAbstract: Among the distinct adaptor protein (AP) complexes, AP-4 primarily functions as a non-clathrin-coated vesicle machinery essential for intracellular membrane trafficking. ARF1 is a master regulator of AP-4 membrane recruitment, but the underlying mechanism remains elusive. Here, we present the cryo-EM structures of soluble AP-4 and the AP-4/ARF1 complex. Unexpectedly, AP-4 adopts a dynamic equilibrium between closed and open conformations, caused by loose contacts between its medium subunit and central core. ARF1 binding induces only subtle changes in AP-4, which retains its conformational equilibrium. Mutations at the AP-4/ARF1 interface disrupt complex formation and impair ARF1-dependent membrane recruitment. Efficient membrane recruitment of AP-4 likely requires the synergistic engagement of ARF1 and cargoes. Disrupting the conformational flexibility of AP-4 interferes with this synergistic effect and compromises AP-4-mediated membrane trafficking. Our findings may redefine AP-4 as a conformationally dynamic complex modulated by cooperative interactions, providing insights into neurodevelopmental disorders associated with AP-4 dysfunction.",
"41577027": "ID: 41577027\nTitle: \u03b1-Parvin promotes glucose uptake and metabolism in skeletal muscle with minimal influence on hepatic insulin sensitivity.\nAbstract: Skeletal muscle and liver insulin resistance are early features in the sequelae of type 2 diabetes. Integrins are extracellular matrix receptors expressed on skeletal muscle cells and hepatocytes, which have been implicated in modulating obesity-associated insulin resistance. Integrins regulate cell function through intracellular proteins including the ILK-PINCH-Parvin (IPP) complex. ILK signaling amplifies skeletal muscle and liver insulin resistance in diet-induced obesity in mice but the role of \u03b1-Parvin is unexplored. The hyperinsulinemic-euglycemic clamp was used to assess hepatic and muscle insulin action. We demonstrate that deletion of hepatocyte-specific \u03b1-Parvin had only minimal influence on obesity-induced liver or whole-body insulin resistance. In contrast, deletion of \u03b1-Parvin in skeletal muscle caused a striking reduction in muscle glucose uptake during an insulin clamp in lean mice which was not exacerbated by diet-induced obesity. The decrease in muscle glucose uptake in lean mice was due to a decrease in insulin-mediated GLUT4 membrane recruitment, which was associated with significant morphological abnormalities including actin cytoskeleton dysfunction. In addition, severe muscular dysfunction, blunted mitochondrial oxidative capacity and reduced aerobic exercise capacity were manifest in muscle \u03b1-Parvin KO mice. Thus, \u03b1-Parvin has a minor role in liver insulin action but is required for insulin-stimulated glucose uptake in skeletal muscle in lean mice due to its role in actin cytoskeleton regulation. These data suggest that individual IPP complex proteins link cell structure to metabolism via distinct mechanisms in a tissue-specific fashion.",
"41580402": "ID: 41580402\nTitle: Micro-nanoplastics and Parkinson's disease: evidence and perspectives.\nAbstract: With the intensification of global plastic pollution, the potential threats posed by micro- and nanoplastics (MPs/NPs) to human health have become a major concern. MPs/NPs enter the organism through ingestion, inhalation, and skin contact, subsequently accumulating in multiple organs-particularly the brain. Increasing experimental and epidemiological evidence implicates MPs/NPs in the development of Parkinson's disease (PD). Preclinical research models indicate that MPs/NPs may accelerate both the initiation and progression of PD by facilitating \u03b1-synuclein misfolding and aggregation, triggering neuroinflammatory cascades, elevating oxidative stress, and impairing mitochondrial function. To further investigate the causal role of MPs/NPs in PD, upcoming studies should emphasize well-designed, large-scale prospective cohorts to assess individual exposure to plastic-related pollutants, elucidate the pathways of MPs/NPs into the central nervous system, establish safety thresholds for their neurotoxicity, explore the correlation between exposure levels and central nervous system accumulation, clarify the temporal relationship between MPs/NPs accumulation and PD pathology and symptom onset, and identify the neuropathological mechanisms triggered by relevant concentrations of MPs/NPs. Such data will be instrumental in informing preventive and potentially interventional strategies, while offering actionable insights into the interaction between MPs/NPs and PD.",
"41618357": "ID: 41618357\nTitle: Two lysosomal genes ATP13A2 and GBA1 interact to drive neurodegeneration.\nAbstract: BACKGROUND: Parkinson\u2019s disease (PD) is a genetically complex disorder in which combinations of heterozygous risk variants may contribute to pathogenesis. Many PD risk loci encode lysosomal genes, such as GBA1, a common and potent risk factor, conferring at least a 5-fold increase. However, the mechanisms of GBA1 penetrance remain poorly understood. METHODS: Using Drosophila melanogaster, we performed a genetic interaction screen of lysosomal storage disorder (LSD) genes to identify dominant modifiers of Gba1b (fly homolog of GBA1). Age-dependent locomotor assessments, electroretinograms (ERG), transmission electron microscopy (TEM) analyses and quantification of dopaminergic (DA) neurons were used to assess the neurodegenerative phenotypes of double heterozygous animals. By combining immunostaining, lipidomics, metabolomics and pharmacological approaches we showed how partial loss of anne (fly homolog of ATP13A2) and Gba1b drives neurodegeneration. By interrogating genetic data from local and international PD cohorts we identified double heterozygous pathogenic variants in ATP13A2 and GBA1 in individuals with PD. RESULTS: We show that anne is expressed in neurons, whereas Gba1b is expressed in glia. Flies heterozygous for anne exhibit mild neurodegenerative phenotypes, and Gba1b strongly enhances this haploinsufficiency. Double heterozygous (Gba1bT2A/+;anneT2A/+) flies exhibit a slow and progressive neurodegeneration associated with accumulation and impaired acidification of lysosomes in photoreceptors and other neurons. Obvious morphological defects are first observed in glia at day 15 after eclosion and include vacuolization and neuronal detachment. These defects are accompanied by an elevation of glucosylceramide (GlcCer) and followed by loss of neuronal function and degenerative features by day 30. These phenotypes are neuronal activity-dependent. The neurodegenerative phenotypes are rescued by: ML-SA1, an agonist of the lysosomal TRPML1 channel that has been reported to promote lysosomal membrane trafficking; myriocin, a compound that inhibits GlcCer production; and DFMO, a drug which inhibits polyamine synthesis. Based on surveys of genetic data, we identify multiple PD cases harboring digenic variants in GBA1 and ATP13A2. CONCLUSIONS: Our study reveals that partial loss of Gba1b in glia and anne in neurons synergistically disrupts lysosomal pH and neuron-glia GlcCer homeostasis, triggering neurodegeneration. Our results provide evidence that GBA1 penetrance is influenced by additional genetic modifiers, consistent with a putative digenic mechanism for GBA1-PD penetrance. These findings highlight lysosomal acidification, sphingolipid clearance, and polyamine regulation as critical intervention points in digenic PD.",
"41622607": "ID: 41622607\nTitle: Zinc-Mediated Lysosomal Destabilization Links Mitochondrial Damage to Neuronal Death in a Cellular MPP+ Model of Parkinson's Disease.\nAbstract: Dysregulation of autophagy and lysosomal function is central to Parkinson's disease (PD), yet the upstream mechanisms leading to lysosomal failure remain unclear. Across primary mouse cortical neurons, MT-3 deficient primary mouse astrocytes, human iPSC-derived midbrain dopaminergic neurons, and Rho0 CHO cells lacking mitochondrial respiration, we investigated how mitochondrial stress perturbs zinc (Zn2+) homeostasis and lysosomal integrity. We identify intracellular zinc as a critical mediator linking mitochondrial dysfunction to lysosomal membrane permeabilization (LMP) and neuronal death. Inhibition of mitochondrial complex I by 1-methyl-4-phenylpyridinium (MPP+) elevated reactive oxygen species (ROS) and intracellular zinc, jointly driving LMP. Blocking either ROS or zinc markedly attenuated lysosomal damage and cell death, demonstrating that both act upstream of LMP. To define zinc regulation, we examined metallothionein-3 (MT-3), a brain-enriched zinc-binding protein. MT-3-deficient astrocytes were more vulnerable to MPP+ and zinc overload (ZnCl2) but paradoxically resistant to hydrogen peroxide (H2O2), suggesting that MT-3 buffers cytosolic zinc during mitochondrial injury or extracellular zinc influx yet can release bound zinc under oxidative conditions. Using Rho0 cells, we show that MPP+ toxicity depends on mitochondrial ROS, as loss of mitochondrial function nearly abolished cell death. However, Rho0 cells were highly sensitive to ZnCl2 and H2O2 and exhibited markedly reduced lysosomal abundance, indicating limited capacity to sequester zinc and increased susceptibility to zinc-mediated injury. These findings support a coordinated system in which lysosomes and zinc-binding proteins maintain zinc homeostasis. When cytosolic zinc rises, its accumulation within lysosomes induces LMP and accelerates cell death. Collectively, our results identify intracellular zinc as an upstream trigger of lysosomal dysfunction and neurodegeneration. Zinc-mediated LMP provides a mechanistic link between mitochondrial injury, impaired autophagic flux, and \u03b1-synuclein pathology in PD. Enhancing zinc homeostasis and lysosomal resilience may offer promising therapeutic strategies.",
"41637953": "ID: 41637953\nTitle: MONNA alleviates MPTP-induced Parkinson's disease in zebrafish by activating TFEB dependently on ER Calcium.\nAbstract: A-synuclein aggregation is a biomarker of Parkinson's disease (PD) whose feature is the progressive loss of dopaminergic neuron in the middle brain. The removal of a-synuclein aggregation through autophagy-lysosome pathway is a promising strategy for PD treatment. Transcription factor EB (TFEB) is a master regulator of autophagic and lysosomal biogenesis and function. Here, we report a library screen of intracellular Ca2+ inducers to identify small-molecule agonists of TFEB and discover MONNA can promote autophagic and lysosomal activity. Notably, MONNA facilitates the reduction of pathological a-synuclein in the Parkinson's disease model both in vitro and in vivo, and ameliorates PD-like behaviors in zebrafish. Mode of action studies reveal MONNA induces TFEB nuclear translocation through a Ca2+-dependent mechanism involving Calcineurin (CaN). Endoplasmic reticulum (ER) but not lysosome Ca2+ is critical to MONNA-induced TFEB activation and autophagy induction. Furthermore, Sarcoendoplasmic reticulum calcium ATPase (SERCA) pump of ER modulates TFEB nuclear translocation induced by MONNA. Our findings demonstrate that MONNA is the first ER Ca2+-dependent small synthetic TFEB agonist promoting the degradation of a-synuclein aggregates and alleviating Parkinson's disease. This ER Ca2+-Calcineurin-TFEB signaling pathway would broaden the way to develop drugs for PD.",
"41641743": "ID: 41641743\nTitle: The desmoglein 2 interactome in primary neonatal cardiomyocytes.\nAbstract: Mechanical coupling and chemical communication between cardiomyocytes are facilitated through a specialized adhesive structure called the intercalated disc (ICD). The ICD is essential for heart organization and contraction. Yet, the network of adhesion, adaptor and signaling proteins that form the ICD remains poorly defined. Here, we combined proximity labeling and quantitative mass spectrometry to identify proteins associated with the desmosomal cadherin desmoglein 2 (DSG2), in cultured neonatal cardiomyocytes. We identified over 300 proteins in the DSG2 interactome, half of which are shared with the N-cadherin (CDH2) interactome in cardiomyocytes. Proteins unique to DSG2 include connexin 43 and the plakin family of cytolinker proteins. Comparison of the cardiomyocyte DSG2 interactome with the interactomes of desmosomal proteins from epithelia revealed few shared proteins. In cardiomyocytes, plakoglobin and plakophilin 2 (PKP2) were the most abundant shared proteins between the DSG2 and CDH2 interactomes. We show that PKP2 is a dynamic protein whose membrane recruitment in cardiomyocytes is dependent on tension. Our analysis of the DSG2 interactome provides a crucial new dimension to the proteomic atlas of the essential molecular complexes required for cardiomyocyte adhesion.",
"41642669": "ID: 41642669\nTitle: Nanoplastic toxicology following gestational and lactational exposure.\nAbstract: Nanoplatics (NPs), particularly polystyrene (PS)-NPs, can traverse the placental barrier upon maternal exposure, leading to bioaccumulation in both dam and offspring organs, and inducing widespread transplacental toxicity. The distribution and toxicity of NPs are influenced by a variety of factors, including NP properties (type, size, and charge), exposure parameters (dose, route, and timing), and biological variables (model and co-exposures). Due to their minute size, NPs pose significant threats to multiple systems in animal models. In rodent studies, reproductive and endocrine toxicity primarily manifests as placental dysfunction, impaired embryo implantation, increased miscarriage rates, and gonadal toxicity in offspring, mechanisms for which are suggested to involve oxidative stress, endocrine disruption, and dysregulated calcium homeostasis. Reported neurotoxicity, characterized by aberrant cortical architecture, hippocampal dysfunction, and learning and memory deficits, is mediated by mechanisms such as oxidative stress and ferroptosis, neurotransmitter disruption, gut-brain axis dysregulation, and pathological protein aggregation. In the cardiovascular system, studies suggest PS-NPs induce offspring cardiac fibrosis, apoptosis, and functional impairments, demonstrating marked sex-specific dimorphism potentially driven by ferroptosis. And PS-NPs have been shown to disrupt glycolipid metabolism in animal models, leading to offspring metabolic disorders. Furthermore, evidence from non-mammalian models, notably Caenorhabditis elegans, reveals transgenerational toxicity. Critically, the consequences of early-life NP exposure are long-lasting, potentially elevating susceptibility to various diseases in adulthood. This review comprehensively summarizes the toxicological profiles of NPs during the critical windows of gestation and lactation, underscoring the need for more robust research and a systematic approach to risk assessment.",
"41643617": "ID: 41643617\nTitle: Early-life exposure to polystyrene nanoplastics at ambient doses induces neurotoxicity via mTOR-mediated autophagy-lysosomal dysfunction and proteostasis imbalance.\nAbstract: Nanoplastics are an emerging global environmental concern, with increasing evidence of their neurotoxic effects. Recent findings suggest that abnormal aggregation of pathogenic proteins within the nervous system may contribute to the neurotoxicity induced by nanoplastics, yet the molecular mechanisms regulating this pathological cascade remain unclear. Here, we used immature mice as an experimental model to represent infants and young children who are at higher risk of nanoplastics exposure, to elucidate the molecular mechanisms underlying neurotoxicity induced by exposure to polystyrene nanoplastics (PS-NPs) during early life. The results showed that environmentally relevant doses of PS-NPs penetrated the brains of immature mice and induced behavioral and emotional disorders. Proteomic analysis identified the mTOR signaling pathway as a candidate pathway responding to PS-NPs exposure in the immature mouse brain. Rapamycin intervention and quantitative validation further demonstrated that PS-NPs exposure upregulated mTOR signaling, thereby leading to lysosomal dysfunction and a blockade of autophagic flux, which in turn disrupted proteostasis and ultimately caused neurotoxicity. Furthermore, treatment with sodium 4-phenylbutyrate (4-PBA) confirmed that proteostasis imbalance, characterized by activation of the unfolded protein response, was a direct driver of this neurotoxicity. Notably, both rapamycin and 4-PBA treatments alleviated neurotoxicity resulting from PS-NPs exposure by restoring proteostasis. Together, these findings highlight dysregulation of the autophagy-lysosome pathway mediated by mTOR as a central mechanism of PS-NPs-induced neurotoxicity in immature mice and suggest lysosomal regulation for proteostasis remodeling as a prospective therapeutic strategy against neurological hazards related to nanoplastics.",
"41659462": "ID: 41659462\nTitle: PLC\u03b2s are recruited to the plasma membrane in macrophages by both G\u03b2\u03b3 and G\u03b1q.\nAbstract: PLC\u03b2 enzymes cleave PIP2 from the plasma membrane, producing IP3 and DAG, which regulate intracellular Ca2+ levels and protein kinase C activity, respectively. They are regulated by GPCR signaling through the G proteins G\u03b2\u03b3 and G\u03b1q and have been shown to function as coincidence detectors for dual stimulation of G\u03b1q and G\u03b1i-coupled receptors via these G proteins. PLC\u03b2s are aqueous-soluble enzymes, but partition onto the membrane surface to access their lipid substrate. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie G\u03b2\u03b3-dependent regulation of PLC\u03b2 enzymes. Using macrophages as a model system, where PLC\u03b2 signaling is essential for responses to infection and tissue injury, we investigated the contribution of G\u03b2\u03b3-dependent regulation and membrane recruitment of PLC\u03b2 in the context of endogenous signaling. By measuring Ca2+ mobilization, we demonstrate that both G\u03b1i and G\u03b1q-coupled receptors independently stimulate PLC\u03b2 activity, illustrating that G\u03b2\u03b3 alone is sufficient to activate PLC\u03b2 in certain contexts. Using total internal reflection and stimulated emission depletion microscopy, we demonstrate that most of the PLC\u03b23 in the cell is localized away from the plasma membrane at rest but is rapidly recruited to the plasma membrane upon stimulation by both G\u03b1i and G\u03b1q-coupled receptors, illustrating that both G\u03b2\u03b3 and G\u03b1q recruit PLC\u03b2 to the plasma membrane. These results support an updated model for G protein-dependent regulation of PLC\u03b2 enzymes, where G\u03b2\u03b3-induced regulation in the absence of G\u03b1q is context dependent and dictated by the local concentration of receptor, G proteins, and PLC\u03b2. PLC\u03b2 enzymes are critical mediators of signal transduction with roles in neuronal, cardiac, and immunological signaling. Despite this importance, many aspects of their function and regulation remain poorly understood. PLC\u03b2s are aqueous soluble but must partition onto the membrane surface to access their lipid substrate, which enables regulation at the partitioning step, the catalytic step, or both. We previously demonstrated that membrane recruitment and orientation of the catalytic core on the membrane surface underlie the PLC\u03b2 regulation by one effector, G\u03b2\u03b3. Using macrophages as a model system for physiological signaling, we demonstrate that G\u03b2\u03b3 is capable of independently activating PLC\u03b2 via membrane recruitment under the conditions of endogenous signaling.",
"41663583": "ID: 41663583\nTitle: Wnt11 mediates fibroblast-smooth muscle cell interaction to promote neurogenic bladder fibrosis in rats.\nAbstract: Neurogenic bladder (NB) is a lower urinary tract dysfunction caused by lesions in the nervous system that regulate urine storage and micturition. Fibrosis is considered the basic pathological alteration of NB, whereas the underlying mechanism remains unclear. Here, we find that Wnt11 is significantly up-regulated in the rat fibrotic bladders induced by bilateral pelvic nerve injury (BPNI) and spinal cord injury (SCI) and promotes bladder fibroblasts (BFs)-to-myofibroblasts transition and smooth muscle cells (SMCs) phenotypic transformation. Selective inhibition or gene silencing of Wnt11 in vivo and in vitro attenuates BFs and SMCs activation, and mitigates the development of NB fibrosis. Mechanistically, Wnt11 specifically binds to Vangl2 receptor to activate downstream JNK/c-JUN signaling via the membrane recruitment of DVL2. Further research shows that Wnt11 signaling interacts with transforming growth factor beta 1 (TGF-\u03b21)/Smad-dependent pathway through the binding of membrane receptors (Vangl2 and T\u03b2R1) and the crosstalk of nuclear transcription factors. These findings uncover the regulatory mechanism and may provide a new therapeutic strategy for NB fibrosis.",
"41680487": "ID: 41680487\nTitle: Modular engineering of thermoresponsive allosteric proteins.\nAbstract: Thermogenetics enables noninvasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membrane recruitment. Here, we present a generalizable strategy for engineering thermosensitive allosteric proteins through the insertion of optimized Avena sativa LOV2 domain variants. Applying this approach to a diverse set of structurally and functionally unrelated proteins in Escherichia coli, we generated potent, thermoswitchable chimeric variants that can be tightly controlled within narrow temperature ranges (37-41\u2009\u00b0C). Extending this strategy to mammalian systems, we engineered CRISPR-Cas genome editors directly modulated by subtle temperature changes within the physiological range. Lastly, we showcase the incorporation of a chemoreceptor domain as an alternative thermosensing module, suggesting thermosensitivity to be a widespread feature in receptor domains. This work expands the toolkit of thermogenetics, providing a blueprint for temperature-dependent control of virtually any protein of interest.",
"41700898": "ID: 41700898\nTitle: Differences in \u03b1-synuclein conformational states in physiologically relevant pH/Na+ concentrations and ammonium acetate solutions unveiled by native mass spectrometry.\nAbstract: Native mass spectrometry implemented with theta emitters was used to demonstrate differences in conformational states of wild-type, A53T mutant, and truncated \u03b1-synuclein dissolved at physiologically relevant pH and Na+ concentrations compared to aqueous solutions of ammonium acetate. Specifically, 150 mM NaCl at pH 7.4, 20 mM NaCl at pH 4.5, and 15 mM NaCl at pH 7.2 were used to reflect, to some extent, the extracellular environment, lysosome, and cytosol, respectively. Analysis of charge state distributions obtained from physiologically relevant solutions vs. their ammonium acetate counterparts allows the comparison of \u03b1-synuclein conformational states. The protein shows relatively high conformational flexibility at 150 mM NaCl and pH 7.4, while it shows at least two different conformational states at 20 mM NaCl and pH 4.5. We observed a trend towards the adoption of less compact conformations at acidic pH, where Na+ appears to play a distinctive role in the adoption of different conformational states. Early-stage oligomers (dimer, pentamer, hexamer and heptamer) were also detected. Since oligomer formation was protein-specific, wild-type \u03b1-synuclein formed dimers while truncated \u03b1-synuclein formed pentamers, hexamers and heptamers, their abundances are consistent with kinetics of aggregation reported in the literature.",
"41702167": "ID: 41702167\nTitle: Lipid metabolic dysregulation: A novel developmental toxicity pathway of aged nanoplastics via inhibition of lipophagy in zebrafish.\nAbstract: The widespread occurrence of micro/nanoplastics (MNPs) in ecosystems poses significant environmental challenges. Although environmentally aged MNPs predominate, their developmental toxicity remains poorly understood. We demonstrate that both pristine and aged polystyrene nanoplastics (PSNPs) induce abnormal lipid accumulation and impair early development in zebrafish larvae. Lipidomics revealed aged PSNPs significantly increased triglycerides via disrupted glycerophospholipid metabolism. Mechanistically, aged PSNPs did not alter LC3-II/LC3-I ratios but upregulated RAB7 and p62 while downregulating lysosomal biogenesis regulator TFEB. They also reduced ATG5, essential for autophagosome formation via LC3 lipidation. These molecular alterations, together with lysosomal inhibition assays, functionally support lysosomal dysfunction as a key constraint on lipophagy. This impairment inhibits lipid utilization, promotes accumulation, and disrupts development. Critically, aged PSNPs caused stronger disruption than pristine particles despite both interfering with lipophagy. Our study provides mechanistic insights into the developmental toxicity of UV-aged PSNPs in zebrafish, highlighting the importance of considering aging-related changes in nanoplastic risk evaluation. SYNOPSIS: Aged nanoplastics exacerbate developmental toxicity in zebrafish by suppressing lipophagy to drive lipid accumulation, underscoring ecological risks in aquatic systems.",
"41707395": "ID: 41707395\nTitle: Polystyrene nanoplastics disrupt ovarian development via cytoskeletal remodeling and epigenetic reprogramming particularly in granulosa cells.\nAbstract: Emerging environmental health issues posed by micro- and nanoplastics (M/NPs) have raised significant concerns. Accumulating evidence suggested that M/NPs can bioaccumulate in gonads and impair fertility in animals, yet the underlying cellular mechanisms and tissue-specific responses remain poorly understood. In this study, we employed in vivo and in vitro models to systematically investigate the impact of polystyrene micro- and nanoplastics (PS-M/NPs, 100\u202fnm and 5\u202f\u00b5m) on ovarian development and function in pubertal female mice. Following 35-day exposure, we observed size-dependent reproductive toxicity, with 100\u202fnm PS-NPs causing reduced body weight gain and ovarian size, disrupted folliculogenesis, and altered hormone levels. Leveraging single-cell RNA-sequencing (scRNA-seq), we uncovered profound alterations in intracellular communication networks across seven ovarian cell types. Granulosa cells (GCs) were identified as the primary target of PS-NPs, exhibiting marked transcriptional changes, including dysregulation of FSCN1, a critical actin cytoskeleton regulator. In vitro experiments confirmed that only 100\u202fnm PS-NPs were internalized by GCs, leading to cell cycle arrest, necroptosis, and hormonal dysfunction. Mechanistically, PS-NPs triggered F-actin cytoskeleton remodeling, increasing cell stiffness and histone modifications (H3K4me3, H3K27ac) associated with chromatin accessibility. Integrated ATAC-seq and RNA-seq analyses implicated STAT1 as a key transcriptional regulator driving PS-NP-induced epigenetic and transcriptional changes. Overall, our findings establish the first single-cell resolution atlas of PS-NP-mediated ovarian toxicity, revealing that NPs disrupt reproduction through cytoskeletal damage and epigenetic reprogramming. This work provides unprecedented insights into the molecular and epigenetic consequences of M/NPs in mammalian reproduction, emphasizing the potential health risks of environmental M/NP exposure.",
"41719940": "ID: 41719940\nTitle: Convergent molecular pathways to inherited Parkinson's disease.\nAbstract: The most common, high-risk genetic factors for Parkinson's disease are pathogenic LRRK2 variants that increase LRRK2 kinase activity and pathogenic GBA1 variants that reduce lysosomal glucocerebrosidase activity. LRRK2 phosphorylates a subset of Rab GTPases, enabling them to bind phosphorylation-specific effectors that drive cellular pathology. To date, LRRK2 has at least two major cellular roles: it promotes exocytosis of lysosome-related organelles-particularly under conditions of lysosome stress in macrophages and microglia-and it regulates the formation and stabilization of primary cilia in neurons and astrocytes. In the brain, loss of primary cilia or GBA1 deficiency impairs Hedgehog signaling, reducing production of neuroprotective factors needed to support vulnerable dopamine neurons. Remarkably, administration of a LRRK2 inhibitor to LRRK2 mutant mice restores cilia and rescues neuroprotective factor production, offering great promise for people with Parkinson's.",
"41734603": "ID: 41734603\nTitle: Bibliometric analysis of the pathogenesis of Parkinson's Disease.\nAbstract: This article provides an overview of research advancements and emerging trends in the pathogenesis of Parkinson's disease (PD) from 2015 to 2024, offering a reference for researchers in this field. A literature search was conducted using the Web of Science Core Collection (WoSCC) with the query terms: ((TS = (Parkinson's disease)) OR TS =\u202f(Parkinson disease)) AND TS =\u202f(pathogenesis). Bibliometric analysis and visualization of the search results were performed using CiteSpace and VOSviewer. A total of 3140 articles were included. Since 2015, publications on this topic have shown a significant upward trend. The top three contributing countries were China, the United States, and Italy. The International Journal of Molecular Sciences ranked first in terms of publication volume and total citations. A 2017 review titled \"Parkinson's Disease\" received the most citations. Keyword co-occurrence analyses revealed that research hotspots include abnormal aggregation of \u03b1-synuclein, mitochondrial dysfunction, oxidative stress, neuroinflammation, dysregulation of the autophagy-lysosome system and gene mutations. Recent trends indicate a clear shift from isolated molecular pathways toward systemic mechanisms, particularly highlighting the emerging roles of the gut-brain axis and ferroptosis in PD pathogenesis. Research on the pathogenesis of Parkinson's disease has gained increasing attention. This study presents a bibliometric analysis and visualization of global research trends and hotspots over the past decade, providing valuable perspectives for future studies into PD-related mechanisms.",
"41747943": "ID: 41747943\nTitle: Degradation of alpha-synuclein/SNCA mRNA by RNautophagy.\nAbstract: \u03b1-Synuclein is a neuronal protein and main component of Lewy bodies, the pathological hallmark of Lewy body diseases such as Parkinson's disease and dementia with Lewy bodies. While the accumulation of \u03b1-synuclein in neurons is implicated in the pathogenesis of these disorders, the mechanisms underlying \u03b1-synuclein mRNA degradation remain poorly understood. RNautophagy is a lysosomal RNA degradation pathway in which RNA is directly taken up into lysosomes and subsequently degraded. SIDT2, a lysosomal membrane protein, mediates the uptake of RNA. In this study, we investigated whether SIDT2-mediated RNautophagy degrades \u03b1-synuclein mRNA. Knockdown of SIDT2 led to reduced degradation of \u03b1-synuclein mRNA, whereas overexpression of wild-type SIDT2 enhanced its degradation, suggesting its role in \u03b1-synuclein mRNA turnover. In contrast, overexpression of the RNA uptake-deficient S564A mutant did not enhance degradation, indicating that RNA uptake activity is required for SIDT2-mediated degradation of \u03b1-synuclein mRNA. Using a series of deletion mutants, we identified a guanine (G)-rich sequence within the 5' untranslated region (5'-UTR) of \u03b1-synuclein mRNA as a key determinant of SIDT2-dependent degradation. Furthermore, insertion of the G-rich sequence into the 5'-UTR of GFP mRNA promoted SIDT2-dependent degradation of GFP mRNA and reduced GFP protein expression. Taken together, these results indicate that SIDT2-mediated RNautophagy contributes to the degradation of \u03b1-synuclein mRNA via the G-rich region within the 5'-UTR. Our findings may also provide insights into the pathogenesis of Lewy body diseases.",
"41751935": "ID: 41751935\nTitle: Pathophysiological Roles of Two Intracellular P-Type ATPases: The Cancer-Associated Na+,K+-ATPase \u03b13 Isoform and the Parkinson's Disease-Related ATP13A2.\nAbstract: P-type ATPases constitute a diverse superfamily of ATP-driven transporters essential for ion homeostasis, membrane asymmetry, and organelle function. Among them, the P2-type Na+,K+-ATPase and the P5-type ATP13A2 have recently emerged as key regulators of cancer progression and neurodegeneration, respectively. In this review, we highlight new insights into the pathological roles of the Na+,K+-ATPase \u03b13 isoform (\u03b13NaK) in malignant cells and ATP13A2 in Parkinson's disease (PD). Cancer tissues frequently overexpress \u03b13NaK which is aberrantly localized to intracellular vesicles and undergoes adhesion-dependent intracellular trafficking. Upon cell detachment, \u03b13NaK translocates to the plasma membrane to sustain survival signaling, thereby promoting anoikis resistance and facilitating the persistence of circulating tumor cells (CTCs). Cardiac glycosides selectively inhibit \u03b13NaK at nanomolar concentrations, suppressing cancer cell proliferation through GLUT1 endocytosis, metabolic inhibition, and downregulation of THADA and LAT1, ultimately inducing anoikis in CTCs and reducing metastasis in vivo. Conversely, ATP13A2 is genetically linked to early-onset parkinsonism and regulates lysosomal integrity, polyamine homeostasis, and neuronal resilience. Recent animal studies demonstrate that adult-onset ATP13A2 loss causes progressive nigrostriatal degeneration, while heterozygous deficiency produces distinct age-dependent cognitive and \u03b1-synuclein phenotypes. Beyond its established role in polyamine transport, emerging evidence suggests that ATP13A2 can function as an H+,K+-ATPase-like transporter, contributing to proton and cation handling within the endolysosomal system. Together, these findings underscore the broader physiological and pathological significance of intracellular P-type K+-ATPases and highlight \u03b13NaK and ATP13A2 as promising therapeutic targets in cancer metastasis and PD.",
"41779229": "ID: 41779229\nTitle: Palmitoylation Induced Activation of SMAD3 Exacerbates Colitis by Promoting Tissue-resident Memory T Cells Differentiation.\nAbstract: Tissue-resident memory T cells (TRM cells) have been shown to play an instrumental role in driving the onset and relapse of inflammatory bowel diseases (IBD). However, the underlying mechanism of TRM cells differentiation and its regulation in intestines remain to be unveiled. Mothers against decapentaplegic homolog 3 (SMAD3) is translocated from nucleus to membrane and activated in response to transforming growth factor beta (TGF-\u03b2), which is a key cytokine in the process of TRM cells polarization. Cysteine palmitoylation (S-palmitoylation) is a post-translational modification catalyzed by the DHHC family, regulating protein membrane associations. Genes associated with the classic SMAD3 signaling pathway, along with most genes in the DHHC family, were upregulated in TRM cells. Our study demonstrated that SMAD3 underwent reversible S-palmitoylation on Cys31 by DHHC6, leading to SMAD3 endomembrane recruitment and its subsequent colocalization with TGF-\u03b2 receptor I (TGF-\u03b2RI) under TRM polarization conditions. The membrane recruitment of SMAD3 activated SMAD3 and subsequently upregulated the expression of its target genes, inducing the differentiation of TRM cells. In contrast, perturbation in DHHC6-induced palmitoylation with MYD-4 inhibited TRM cells differentiation and alleviated colitis in IBD model mice. Our work provides an example how the immune responses are regulated through the S-palmitoylation-dependent SMAD3 signaling in TRM cells differentiation and reveals protein S-palmitoylation as a potential target in IBD treatment, which could be of greater application considering the wide involvement of protein S-palmitoylation in the signal transduction in mammalian cells.",
"41812834": "ID: 41812834\nTitle: Brain lipidomics identifies mitochondrial redox dysfunction and metabolic trade-offs associated with Parkinson's disease-like pathology induced by Nanoplastics exposure.\nAbstract: Growing nanoplastics exposure raises concern for neurotoxicity, particularly given recent evidence of plastic accumulation within human brain tissue a highly lipid enriched organ, yet effects on brain lipid metabolism remain poorly understood. Here, we employed high-resolution untargeted lipidomics to map brain lipid perturbations in Drosophila melanogaster chronically exposed to polystyrene nanoplastics (PS- NPs). PS-NPs accumulated in fly brains and induced dose-dependent remodeling of mitochondrial membrane lipids, notably cardiolipins and phosphatidylethanolamines, accompanied by increased diacylglycerols/triacylglycerols and monounsaturated fatty acids and by lipid droplet expansion. Guided by these lipidomic signatures, targeted biochemical assays demonstrated depolarized mitochondrial membrane potential, elevated mitochondrial reactive-oxygen species, inhibition of respiratory-chain complexes I and IV, and a shift in NAD(H) and NADP(H) redox couples toward a reduced state and increasing lipid peroxidation. This redox imbalance was accompanied by decreased tyrosine-hydroxylase expression, dopamine depletion, and impaired locomotor behavior, hallmarks of Parkinson's disease (PD)-like neurodegeneration. Dopaminergic neurochemistry was impaired (tyrosine hydroxylase and dopamine decreased), with concomitant reduction of GABA, and locomotor and circadian deficits emerged. Remarkably, co-treatment with the antioxidant N-acetylcysteine (NAC) restored mitochondrial membrane potential, reduced mitochondrial ROS and lipid peroxidation, normalized neutral lipid and MUFA accumulation, and rescued neurotransmitter levels and behavior. Stable-isotope tracing confirmed disrupted TCA cycle flux after NPs exposure that was rescued by NAC. Collectively, these findings reveal lipidomic remodeling as a critical link between environmental NPs exposure and PD-like pathology, highlighting mitochondrial redox-lipid interactions as early determinants and support redox-directed interventions to mitigate risk.",
"41822190": "ID: 41822190\nTitle: Familial SCA14: A case report with review.\nAbstract: Spinocerebellar ataxia type 14 (SCA14) is a rare autosomal dominant neurodegenerative disorder caused by mutations in the PRKCG gene, which encodes protein kinase C\u03b3 (PKC\u03b3). The clinical manifestations are heterogeneous, ranging from slowly progressive pure cerebellar ataxia to complex phenotypes with sensory or extrapyramidal involvement. To the best of our knowledge, the present report is the first to describe a Han Chinese family carrying the PRKCG c.424T>G (p.C142G) mutation, which has previously only been described in Danish and Japanese cohorts. The proband, a 72-year-old man, developed gait instability in his 40s, progressing to dysarthria, intention tremor, oculomotor slowing and sensory impairment. Brain MRI revealed severe diffuse cerebellar atrophy. The siblings and daughter of the patient presented with variable ataxic symptoms, confirming autosomal dominant inheritance. Genetic testing by next-generation sequencing identified the heterozygous c.424T>G mutation, co-segregating in affected family members. This mutation localizes to the C1 regulatory domain of PKC\u03b3, a zinc-finger structure critical for diacylglycerol binding and kinase autoinhibition. Substitution of cysteine by glycine at codon 142 destabilizes zinc coordination, impairs protein stability and disrupts membrane recruitment. Functional evidence suggests that C142G induces aberrant kinase activity, misfolding and altered MAPK signaling, resulting in chronic cellular stress without rapid neuronal death, thus accounting for the indolent course of the disease compared with that of polyglutamine SCAs. The present findings expand the knowledge regarding the ethnic and geographic distribution of the codon 142 mutation and highlight the complexity of genotype-phenotype associations, as clinical presentations varied from mild gait ataxia to cognitive impairment and bulbar involvement. The report underscores the value of early genetic testing in unexplained ataxia, facilitating accurate diagnosis, genetic counseling and individualized management. Further functional studies are warranted to clarify the pathogenic mechanisms and to explore potential targeted therapies for SCA14.",
"41825123": "ID: 41825123\nTitle: Load-independent ceiling of single-target phagocytic membrane extension revealed by microneedle backtracking assay in macrophages.\nAbstract: The zipper model describes the ligand-receptor-driven progression of the phagocytic cup during macrophage engulfment. However, whether the maximum engulfment achievable for a single target is altered by prior or concurrent phagocytic events (i.e., intracellular phagocytic load) remains unclear. Here, we used IgG-coated, nondigestible glass microneedles as standardized Fc\u03b3 receptor ligands and defined the single-target engulfment ceiling as the membrane extension length at which backtracking begins. We then tested whether this ceiling changes after macrophages internalize increasing numbers of IgG-coated polystyrene beads. Across cells, the maximum membrane extension on a microneedle was quantitatively unchanged regardless of the number of internalized indigestible beads. Within the same cell, additional bead ingestion - up to the maximal bead-phagocytosis limit - did not measurably alter the maximum extension achieved on a microneedle. These data establish a load-independent ceiling for single-target engulfment. This invariance suggests that local membrane recruitment and extension are regulated independently of the cell-wide phagocytic burden, supporting a spatially compartmentalized control mechanism that decouples single-target membrane extension from the total intracellular cargo load.",
"41832866": "ID: 41832866\nTitle: Electroacupuncture mitigates oxidative stress and neuroinflammation in Parkinson's disease via mitigating autophagy-lysosome dysfunction.\nAbstract: Parkinson's disease (PD) is a neurodegenerative disorder characterized by autophagic dysfunction. Acupuncture is a well-established intervention recognized for its immunomodulatory and neuroprotective effects. This study aimed to explore the mechanisms by which electroacupuncture (EA) interventions can ameliorate mitochondrial damage in PD. EA was applied to the chorea and tremor control area on the scalp of MPTP-induced mice. The cognitive abilities and motor functions of mice were evaluated through behavioral experiments. EA treatment alleviated behavioral deficits, reduced neuroinflammation in the brain, and significantly reversed MPTP-induced changes in dopamine (DA) metabolomics. Proteins related to autophagy and inflammation in the striatum were quantified via immunofluorescence. EA also inhibited excessive mitochondrial division, and reduced oxidative stress. Additionally, Rapamycin (RAP) interventions further improved autophagy, while 3-Methyladenine (3MA) interventions counteracted the therapeutic effects of EA. In conclusion, these results suggest that EA treatment is associated with reduced neuroinflammation and the protection of dopaminergic neurons in the nigrostriatal system. EA alleviates PD by ameliorating autophagy-lysosomal dysfunction and restoring normal mitochondrial function.",
"41886456": "ID: 41886456\nTitle: UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.\nAbstract: UFMylation, a recently identified ubiquitin-like modification mediated by the E3 ligase UFL1, plays context-specific roles in cancers, but its substrates and functions in lung adenocarcinoma (LUAD) remain poorly defined. Here, we identify the AKT signaling repressor PHLDA3 as a substrate of UFL1 in LUAD. UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling. Tumor-associated PHLDA3 mutations F41L, E82G, and K106N impair its UFMylation and membrane translocation, resulting in AKT hyperactivation and enhanced tumor growth. In samples from patients with LUAD, UFL1 expression inversely correlates with phospho-AKT levels. Functionally, the UFL1-PHLDA3 axis inhibits LUAD progression in both cell line-based and patient-derived xenograft models. These findings define a tumor-suppressive UFMylation pathway that modulates AKT activity and provides a mechanistic rationale for targeting UFL1-PHLDA3 signaling in LUAD.",
"41887951": "ID: 41887951\nTitle: Repair condensates and lipid domains in lysosome integrity.\nAbstract: Lysosomes are sophisticated signaling hubs whose function depends on membrane integrity. A breach of this barrier, known as lysosomal membrane permeabilization, triggers inflammation and cell death, driving pathologies from lysosomal storage disorders to neurodegeneration. Cells counter membrane damage with diverse repair mechanisms, including endosomal sorting complexes required for transport machinery, sphingomyelin scrambling, annexin-mediated scaffolding, lipid transport, and stress granule plugging. This diversity suggests singular strategies are insufficient, posing an 'orchestration challenge' regarding precise initiation, spatial organization, and temporal coordination. This opinion article proposes that biomolecular condensation, initiated by damage cues, acts as a primary organizing principle. We suggest lysosomal injury nucleates de novo 'repair condensates' that stabilize compromised membranes and serve as recruitment and organizational hubs for repair machinery.",
"41919495": "ID: 41919495\nTitle: Lysosomal homeostasis at the crossroads of neurodegeneration.\nAbstract: Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss.",
"41940964": "ID: 41940964\nTitle: Genetic and environmental risk factors of Parkinsonism.\nAbstract: Parkinsonian disorders comprise a broad spectrum of neurodegenerative diseases with a wide variety of pathogenetic processes. These processes lead to the formation of pathological proteins, resulting in the brain diseases called synucleinopathies, tauopathies or TDP-43 proteinopathies. There is currently growing support for the hypothesis that genetic variants explain a significant fraction of the etiology of apparently sporadic parkinsonian disorders. Genetic risk factors can be stratified according to the metabolic or structural processes that can lead to cellular disturbance;\u00a0these processes involve protein aggregation, protein and membrane trafficking, stabilization of the neurite structure, prion-like transmission of pathological proteins, ubiquitin-proteasome system balance, mitophagy, lysosome autophagy, synaptic functions, and dopamine transmission. Regarding the environmental risk factors, there are several substances that have been supposed of being a risk for the development of neurodegenerative proteinopathy and Parkinsonism, mainly the agents used in agriculture and the textile industry. The most important and most frequently studied are pesticides and trichlorethylene. Beside the globally ubiquitous substances which are supposedly neurotoxic and exposure to which can cause manifestations of Parkinsonism, there are more geographically (regionally) specific substances, which cause (or quite recently caused) the manifestation of endemically present Parkinsonism. Among ten types of endemic Parkinsonism, three of them are thought to have an environmental cause: Western Pacific Parkinsonism, Caribbean Parkinsonism, and North France cluster of atypical Parkinsonism.",
"41957923": "ID: 41957923\nTitle: Enteric Nervous System Damage by Food Contaminants: A Pathway to Neurodegeneration?\nAbstract: The enteric nervous system (ENS), a key component of the gut-brain axis, has emerged as a critical player in the pathogenesis of Parkinson's disease (PD). It is the first neural system exposed to food contaminants (FCs)-a diverse group of ubiquitous toxic compounds fortuitously present in food derived from production, processing, storage, or environmental contamination. Emerging evidence suggests that FCs may initiate or amplify neurodegenerative processes, yet their effects on the ENS and their impact in gut-to-brain communication remain insufficiently characterized. This systematic review synthesizes current evidence on FCs-induced effects on the ENS and its involvement in mediating neurotoxicity from dietary toxicants exposure. Following PRISMA guidelines, 67 studies were included pertaining to cellular or mammalian experimental models exposed to FCs via enteral routes, reporting ENS-related outcomes or studying vagal involvement in modulating FC toxicity. The main FCs evaluated were pesticides, toxins, bisphenols, acrylamide, manganese, and micro-/nanoplastics. Across studies, FCs consistently induced neurochemical remodeling of the ENS, activation of enteric glia, often coupled with intestinal alterations. Rotenone, paraquat, and polystyrene micro-/nanoplastics promote \u03b1-synuclein aggregation within the ENS and its vagal propagation to the brain. Vagotomy models confirmed that disrupting ENS-CNS communication attenuates FC-related central neurotoxicity, supporting the involvement of food toxicants in gut-to-brain propagation of neurotoxic signals. These findings support the body-first hypothesis of PD and position the ENS as a critical, yet underinvestigated interface in exposome-related neurotoxicology. The review highlights research gaps and the need for improved models and long-term, low-dose studies reflecting realistic FC exposure.",
"41959055": "ID: 41959055\nTitle: Flow-sensitive K + channels link flow to piezo1/PI3K/Akt1 pathway.\nAbstract: Endothelial response to flow is key to vascular function in health and disease. Our earlier studies demonstrated that endothelial Kir2.1 is essential for flow-induced Akt1/eNOS signaling and for flow-induced vasodilation (FIV) but the mechanistic integration between Kir and other flow signaling pathways remained poorly understood. We use a combination of electrophysiological recordings in real time of flow exposure, Ca 2+ imaging, pressure myography of resistance arteries, and echocardiography. We demonstrate that Kir2.1 is essential for flow-induced PI3K phosphorylation, whereas expression of myristoylated Akt1, which bypasses PI3K-dependent membrane recruitment, restores flow-induced Akt1/eNOS phosphorylation in Kir2.1-deficient endothelium. It also restores FIV in Kir2.1-deficient mesenteric arteries. We further demonstrate that Kir2.1 is essential for flow-induced Ca\u00b2\u207a influx mediated by Piezo1 and TRPV4 channels, whereas Ca\u00b2\u207a influx induced by pharmacological activation of these channels is Kir2.1 independent. Deficiency of Piezo1 does not affect endothelial Kir2.1 channels. We also discover that flow activation of endothelial Kir2.1 requires Syndecan1, thus creating a link between glycocalyx and downstream effects. Physiologically, we find that endothelial Kir2.1 is suppressed by infusion of Angiotensin-II and by advanced aging, resulting in significant impairment of FIV. In both cases, FIV is fully restored by endothelium-specific over-expression of Kir2.1. Our study reveals that Kir2.1 serves as a mechanistic linker between endothelial glycocalyx to Piezo1-mediated Ca 2+ influx and downstream signaling suggesting a new integrated model of endothelial mechanotransduction. A functional loss of endothelial Kir2.1 is shown to play a significant role in FIV impairment in Angiotensin-induced hypertension and aging.",
"41975606": "ID: 41975606\nTitle: Serine endopeptidase tripeptidyl peptidase II maintains lysosomal homeostasis to alleviate Parkinson's disease pathogenesis.\nAbstract: Parkinson's disease is neuropathologically characterized by the progressive loss of dopaminergic neurons and the pathological accumulation of \u03b1-synuclein. While these hallmarks are well established, the molecular drivers of this irreversible neurodegenerative process are not fully understood. Through an integrated multi-omics approach combining nascent protein mass spectrometry and bulk RNA sequencing of cellular and transgenic Parkinson's disease mouse models, we revealed suppressed serine endopeptidase activity during the early pathogenic stages of the disease. Subsequent functional analyses identified tripeptidyl peptidase II as the principal enzyme mediating serine endopeptidase activity, as demonstrated through a series of biochemical assays. Mechanistic investigations showed that tripeptidyl peptidase II deficiency impairs lysosomal function, prolongs the clearance of \u03b1-synuclein fibrillar seeds, and disrupts synaptic homeostasis in hippocampal neurons. Importantly, overexpression of tripeptidyl peptidase II effectively attenuated pathological \u03b1-synuclein aggregation and prevented the cell-to-cell propagation of \u03b1-synuclein pathology in wild-type mice injected with \u03b1-synuclein preformed fibrils. Our findings establish tripeptidyl peptidase II as a critical regulator of lysosome-mediated amyloidogenic seed degradation and reveal its neuroprotective role against \u03b1-synuclein-associated synucleinopathies.",
"41977181": "ID: 41977181\nTitle: Copper Dyshomeostasis Affects \u03b1-Synuclein Clearance Mechanisms in Parkinson's Disease: Insights from In Vitro Models and Translational Evidence.\nAbstract: Parkinson's disease (PD) is characterized by the progressive degeneration of dopaminergic neurons and the accumulation of \u03b1-synuclein-rich inclusions, largely resulting from impaired protein clearance mechanisms. Copper is an essential redox-active metal in the central nervous system (CNS), but alterations in its homeostasis can promote oxidative stress, mitochondrial dysfunction, and proteostatic failure. In vitro studies indicate that copper can promote \u03b1-synuclein misfolding, enhance oxidative stress, and interfere with both the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway (ALP). In this review, we critically evaluate mechanistic evidence from cellular models, integrating available animal and clinical data to assess the biological significance of copper-mediated impairment of \u03b1-synuclein clearance. We highlight the current research, identify methodological limitations, and discuss whether copper imbalance acts as a primary pathogenic trigger or as a disease-modifying amplifier of proteostatic failure. Furthermore, we consider the translational implications of selectively modulating intracellular copper pools as a therapeutic strategy in PD. Finally, we will highlight unresolved issues, methodological limitations, and emerging targeted therapeutic prospects.",
"41980172": "ID: 41980172\nTitle: Polystyrene Microplastics Induced Hepatocytes Pyroptosis, Apoptosis and Ferroptosis via GSDMD-N-Mediated Mitochondrial Damage.\nAbstract: Microplastics (MPs), as emerging food contaminants, have been established to exert adverse effects on the liver. However, the precise toxicological mechanisms remain elusive. Our results demonstrated that MPs triggered mitochondrial dysfunction and mitochondrial ROS (mtROS) accumulation, which subsequently activated NLRP3/caspase-1/GSDMD-N-dependent pyroptosis in hepatocytes. Notably, beyond its canonical translocation to the plasma membrane, GSDMD-N was observed to form pores on the mitochondrial outer membrane, exacerbating mitochondrial damage. The mitochondrial GSDMD-N pores amplified mtROS overproduction, triggering lysosomal membrane permeabilization (LMP) and facilitating lysosomal iron efflux, which ultimately initiated ferroptosis. Concurrently, mitochondrial GSDMD-N mediated mitochondrial intrinsic apoptosis by promoting cytochrome c release and caspase-3 activation. Collectively, our findings revealed that MPs induced GSDMD-N activation and its mitochondrial translocation, which in turn initiated pyroptosis, ferroptosis, and apoptosis in hepatocytes. This study provided novel mechanistic insights into MPs-induced hepatotoxicity, identifying GSDMD-N as a potential central hub coordinating multiple cell death modalities.",
"41993512": "ID: 41993512\nTitle: WDR44 drives de novo \u03b1-synuclein aggregation at the lysosomal membrane and promotes neuronal dysfunction in Parkinson's Disease.\nAbstract: The aggregation of \u03b1-synuclein (\u03b1-SYN) into Lewy bodies (LBs) is a central event in the pathogenesis of Parkinson's disease (PD) and related synucleinopathies1,2. Despite significant advances in understanding \u03b1-SYN self-assembly, the precise sequence of early aggregation steps has not been directly visualized in living neurons. Here, we use an optogenetic-induced protein aggregation system with a high temporal resolution to monitor the onset of \u03b1-SYN assembly in neurons. We found that the initiation and accumulation of \u03b1-SYN aggregates occur predominantly at the lysosomal membrane, an event driven by the \u03b1-SYN N-terminus and modulated by the membrane-associated adaptor protein WD repeat-containing protein 44 (WDR44). Remarkably, we demonstrate that WDR44 knockdown markedly reduced de novo \u03b1-SYN aggregation in both neuronal cultures and in vivo, whereas WDR44 overexpression enhances \u03b1-SYN aggregation in PD patient-derived iPSC neurons. Consistent with its potential pathogenic involvement, WDR44 aberrantly accumulates in vivo and in the brains of PD patients, where it colocalizes with LB inclusions. Finally, we show that lysosome-associated \u03b1-SYN aggregates compromised lysosomal structure and function, leading to neuronal impairment, a phenotype worsened by WDR44 overexpression, linking early aggregation events to downstream toxicity. Together, these findings reveal the earliest dynamic stages of \u03b1-SYN oligomerization in living neurons and identify the WDR44-\u03b1-SYN interaction as a promising therapeutic target for reducing \u03b1-SYN pathology and enabling early intervention in PD.",
"41997430": "ID: 41997430\nTitle: Impaired autophagy from TRPV4 activation drives \u03b1-synuclein pathology in a Parkinson's disease model: A toxicological insight.\nAbstract: The environmental toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a prototypical agent for modeling Parkinson's disease (PD). Our previous study demonstrated that calcium channel transient receptor potential vanilloid 4 (TRPV4) mediates MPTP-induced endoplasmic reticulum (ER) stress and inflammation, leading to loss of dopamine neurons and movement disorder. Here, we investigated whether TRPV4 activation impairs clearance of pathological \u03b1-Synuclein (\u03b1-Syn) via the autophagy-lysosomal pathway (ALP), contributing to cognitive deficits in PD. We used C57BL/6J mice subjected to intracerebral injection of adeno-associated virus in substantia nigra to knockdown or overexpress TRPV4, followed by MPTP treatment. Novel object recognition and Morris water maze tests, immunohistochemistry, electron microscopy, and western blot were employed to assess the role of TRPV4 in modulating \u03b1-Syn via ALP. We found that targeting TRPV4 to counteract neurotoxicity improved cognitive dysfunction in PD mice. Mechanistically, MPTP-triggered toxic stress and TRPV4 overexpression induced accumulation of \u03b1-Syn and autophagosomes in hippocampus. Critically, TRPV4 knockdown significantly alleviated MPTP-induced \u03b1-Syn accumulation. Western blot analysis revealed that TRPV4 impaired \u03b1-Syn clearance via the ALP, as evidenced by dysregulation of key ALP components: LC3B, p62, lysosome-associated membrane protein 1, and transcription factor EB. In conclusion, our data are consistent with a model in which TRPV4 contributes to \u03b1-Syn accumulation through impairment of the ALP. This work establishes a direct link between TRPV4 and impaired \u03b1-Syn clearance, identifying TRPV4 not only as a mediator of ER stress and inflammation but as a critical molecular sensor that disrupts proteostasis. This positions TRPV4 as a promising therapeutic target for counteracting MPTP-induced neurodegeneration.",
"42003908": "ID: 42003908\nTitle: DHCR24 Drives Ovarian Cancer Chemoresistance Through Lipid Raft-mediated P-gp Stabilization and STAT3 Activation.\nAbstract: To investigate the role and mechanism of DHCR24 in chemoresistance of ovarian cancer and to identify potential therapeutic targets for overcoming treatment resistance. We integrated bioinformatic analysis of GEO datasets and clinical survival data from KMplot to identify chemoresistance-associated genes. DHCR24 expression and function were systematically evaluated using cisplatin-resistant cell lines (A2780/DDP, SKOV3/DDP), patient-derived primary cells, xenograft models, and clinical specimens through molecular biology techniques, immunohistochemistry, and functional assays. Mechanistic studies employed RNA interference, cholesterol modulation, lipid raft disruption with M\u03b2CD, cycloheximide chase assays, and STAT3 pathway inhibition. DHCR24 was consistently upregulated in chemoresistant ovarian cancer models and significantly correlated with poor patient survival. Genetic or pharmacological inhibition of DHCR24 restored chemosensitivity in vitro and in vivo, while its overexpression induced cross-resistance to multiple chemotherapeutic agents. Mechanistically, DHCR24 enhanced cholesterol biosynthesis, which stabilized lipid raft microdomains to promote P-gp protein stability and facilitate STAT3 membrane recruitment and activation. Furthermore, activated STAT3 transcriptionally upregulated DHCR24 expression, establishing a positive feedback loop that perpetuates the chemoresistant phenotype. DHCR24 drives chemoresistance through a cholesterol-dependent circuit that stabilizes drug efflux pumps and activates pro-survival signaling, identifying DHCR24 as a promising therapeutic target for overcoming chemotherapy resistance in ovarian cancer.",
"42012897": "ID: 42012897\nTitle: Pathogenic variants in BORCS5 cause a spectrum of neurodevelopmental and neurodegenerative disorders with lysosomal dysfunction.\nAbstract: BORCS5 encodes a subunit of the BLOC-One-Related Complex (BORC), which is known to promote anterograde movement and fusion of lysosomes. We identified 16 individuals from 9 families with bi-allelic BORCS5 variants, revealing a spectrum of neurodevelopmental and neurodegenerative phenotypes. Carriers of homozygous protein-truncating variants (PTVs), resulting in complete loss of BORCS5, presented with prenatally lethal arthrogryposis multiplex congenita, brain malformations, and neuropathological evidence of neuroaxonal dystrophy. Individuals with missense or splice-site variants presented differently, with microcephaly, developmental epileptic encephalopathy, optic atrophy, spasticity, and progressive movement disorders. In this group, brain MRI showed diffuse hypomyelination, corpus callosum abnormalities, and progressive global cerebral atrophy, consistent with neurodegeneration. Borcs5 KO in zebrafish resulted in microcephaly, motor deficits, and increased seizure susceptibility, mirroring the patients' clinical presentation. At the cellular level, only BORCS5 PTVs, but not missense variants, led to perinuclear lysosomal clustering and impaired lysosomal axonal trafficking in induced pluripotent stem cell-derived forebrain neurons. However, PTVs and missense variants were associated with reduced lysosomal proteolysis and activity of lysosomal hydrolases glucocerebrosidase and cathepsin B, indicating lysosomal dysfunction. Our study reveals a role for BORCS5 in modulation of lysosomal function, in addition to its known role in lysosome movement and fusion, possibly underlying the diverse clinical manifestations in individuals with BORCS5-related disorders.",
"42033266": "ID: 42033266\nTitle: Lysosome-Acidifying Nanoparticles Rescue A30P \u03b1-Synuclein Induced Neuronal Death in Cellular and Drosophila Models of Parkinson's Disease.\nAbstract: Parkinson's disease (PD) is the second most common neurodegenerative disorder, affecting over 10 million people worldwide. It is characterized by the progressive loss of dopaminergic neurons in the substantia nigra and the accumulation of misfolded \u03b1-synuclein (\u03b1Syn) in intracellular inclusions known as Lewy bodies. Emerging evidence links \u03b1Syn accumulation to impaired lysosomal acidification and defective autophagy-lysosomal degradation, which are central to disease progression. To address this lysosomal dysfunction, we engineered a novel type of lysosome-targeted acidic nanoparticles (AcNPs) based on a biodegradable copolymer, poly(ethylene tetrafluorosuccinate-co-succinate) (PEFSU). These nanomaterials were developed to locally acidify impaired lysosomes and restore their degradative capacity. We evaluated their therapeutic potential in two familial PD models: SH-SY5Y neuroblastoma cells overexpressing A30P \u03b1Syn and A30P \u03b1Syn transgenic Drosophila melanogaster. In vitro, AcNPs effectively restored lysosomal pH, enhanced autophagic clearance of \u03b1Syn, improved mitochondrial function, and rescued A30P \u03b1Syn-induced cytotoxicity. In vivo, AcNPs treatment reduced \u03b1Syn burden, preserved dopaminergic neurons, and improved motor function in flies. This study demonstrates the first application of lysosome-acidifying polymeric nanoparticles in familial PD models and highlights the promise of rationally engineered pH-modulating nanomaterials as therapeutic agents for PD and other neurodegenerative diseases driven by lysosomal dysfunction and protein aggregation.",
"42043873": "ID: 42043873\nTitle: CRISPLD2 protects against liver inflammation and fibrosis via GRP78 to repress HMGB1/TLR4 axis-mediated STING palmitoylation.\nAbstract: Liver fibrosis caused by chronic inflammation remains the major driver of various liver diseases. However, limited effective therapies have been identified for liver fibrosis. Herein, we elucidated the complicated molecular mechanisms underlying liver fibrosis. Primary hepatocytes were co-cultured with JS-1 cells. Inflammatory cytokine levels were assessed by ELISA. Liver fibrosis markers and target molecular levels were detected by western blotting and immunohistochemical staining. Molecular mechanisms were analyzed by Acyl-biotin exchange (ABE) assay, Co-IP, proximity ligation assay, biotin pull-down, and GST pull-down assays. Co-localization and subcellular localization of molecules were observed by immunofluorescent staining. Liver fibrosis was induced by CCl4 in mice and determined by Masson Trichrome and Sirius Red staining. Liver injury was evaluated by HE staining, serum ALT, and AST levels. High mobility group box 1 (HMGB1) bound to toll-like receptor 4 (TLR4) to facilitate palmitoylation of stimulator of interferon genes (STING), which led to hepatocyte inflammation and JS-1 cell activation in vitro. Furthermore, cysteine-rich secreted protein LCCL domain protein 2 (CRISPLD2) blocked HMGB1/TLR4 axis-mediated palmitoylation of STING, and subsequent liver fibrosis. Mechanistically, CRISPLD2 recruited 78\u00a0kDa glucose-regulated protein (GRP78) to trigger TLR4 degradation via an autophagic-lysosomal pathway. CRISPLD2 treatment alleviated CCl4-induced inflammation and liver fibrosis in mice via inactivation of the HMGB1/TLR4/STING pathway. CRISPLD2 mitigated hepatocyte inflammatory response and fibrosis via interaction with GRP78 to inactivate the HMGB1/TLR4 pathway and consequently restrain STING palmitoylation.",
"42046264": "ID: 42046264\nTitle: Synergistic Induction of Apoptosis by Apocytochrome C and Sodium Aescinate Is Mediated by Excessive Autophagy via the AKT-mTOR-TFEB Signaling Axis.\nAbstract: Cytochrome C (Cyt C) is a central mediator of intrinsic apoptosis, whereas its heme-free precursor, apocytochrome C (APO-Cyt C), competitively inhibits this process. Sodium aescinate (SA), a natural triterpene saponin, is known to facilitate the endosomal escape of protein drugs. We initially aimed to investigate the effects of enhancing endosomal escape efficiency on protein activity through the combination of SA and Cyt C. However, this study investigates an cytotoxicity observed when APO-Cyt C is combined with SA and aims to elucidate the underlying molecular mechanism. Contrary to its established anti-apoptotic function, APO-Cyt C, when co-administered with a non-toxic concentration of SA, induced potent, caspase-dependent mitochondrial apoptosis in cancer cells. This pro-apoptotic switch was not primarily triggered by BCL-2 family protein modulation, ROS generation, or calcium overload. Instead, the primary mechanism is the induction of excessive and lethal autophagy. SA was found to induce lysosomal membrane damage, evidenced by Galectin-9 recruitment, which initiates lysophagy. The addition of APO-Cyt C significantly amplified the autophagic flux, leading to decreased p62 levels and enhanced LC3-II turnover. Mechanistically, this synergy is driven by a dual impact on the AKT-mTOR-TFEB pathway: APO-Cyt C treatment decreased mTOR phosphorylation, while the combination promoted the nuclear translocation of the autophagy regulator, TFEB. Inhibition of autophagic flux using Bafilomycin A1 or Tetrandrine rescued cells from apoptosis, confirming that excessive autophagy is the direct cause of cell death. This study reveals a novel therapeutic strategy wherein an anti-apoptotic protein is converted into a potent pro-apoptotic agent. The combination of APO-Cyt C and SA triggers apoptosis by overwhelming the cell with excessive autophagic flux, driven by synergistic inhibition of the mTOR-TFEB axis. These findings highlight the therapeutic potential of modulating autophagy and suggest that combining mTOR inhibitors with lysosome-targeting agents like SA could be an effective anti-cancer strategy.",
"42049211": "ID: 42049211\nTitle: Altered cytoskeletal integrity underlies impaired platelet shape change and defective thrombus formation in ETV6-related thrombocytopenia.\nAbstract: ETV6-related thrombocytopenia (ETV6-RT) is an inherited platelet disorder caused by germline ETV6 variants. Despite recent progress, the mechanisms underlying platelet dysfunction in ETV6-RT remain unclear. We investigated 12 patients from six families using functional assays, electron microscopy, quantitative proteomics and cytoskeletal imaging. Most patients exhibited mild-to-moderate thrombocytopenia with variable paediatric bleeding symptoms (median International Society on Thrombosis and Haemostasis Bleeding Assessment Tool 3, range 1-9) but consistently mild bleeding in adulthood (median 0, range 0-1). Ex\u00a0vivo thrombus formation was reduced independent of platelet count. Electron microscopy revealed defective platelet shape maintenance, characterized by spheroid morphology, reduced Dmax/Dmin ratios and diminished alpha-granule pools. Flow cytometry and single-platelet total internal reflection fluorescence imaging demonstrated largely preserved calcium signalling but impaired activation-dependent shape change, dense-granule release and integrin activation. Proteomics showed reduced alpha-granule and lysosomal proteins alongside imbalanced regulators of actin remodelling and \u03b2-tubulin. Phalloidin staining confirmed impaired actin cytoskeletal remodelling with reduced lamellipodia formation, while immunofluorescence revealed abnormal \u03b21-tubulin localization with disrupted marginal bands and reduced lysosome-associated membrane protein 1 (LAMP1) expression. Additionally, granulocyte recruitment and migration within thrombi were impaired, suggesting broader thromboinflammatory defects. These findings suggest that combined disruption of cytoskeletal integrity and granule biogenesis underlies impaired thrombus formation in ETV6-RT, providing mechanistic insight into the haemostatic defects associated with this disorder.",
"42074107": "ID: 42074107\nTitle: LRRK2 I1371V Mutation Drives Astrocytic Glucose Metabolism Failure and Induces Integrated ER-Mitochondria-Lysosome Dysfunction in Parkinson's Disease.\nAbstract: Although LRRK2 mutations modulate systemic glucose homeostasis and metabolic dysfunction precedes Parkinson's disease (PD) motor symptoms; the way in which pathogenic variants of LRRK2 disrupt astrocytic glucose metabolism and organellar homeostasis remains poorly understood. Here, we demonstrate that LRRK2-I1371V mutation causes profound metabolic and organellar dysfunction in LRRK2-I1371V PD-iPSC-derived astrocytes and U87 cells overexpressing I1371V variant. LRRK2-I1371V astrocytes exhibit significantly reduced GLUT1 expression and cell surface localization, resulting in impaired glucose uptake and decreased lactate production. This metabolic insufficiency correlates with cascading mitochondrial dysfunction, characterized by membrane depolarization, elevated reactive oxygen species, enhanced ubiquitination and reduced proteasomal activity. Reduced LAMP1/LAMP2 expression, impaired lysosomal acidification, and selective cathepsin D deficiency were observed. Accumulation of undegraded cargo was confirmed by transmission electron microscopy upon \u03b1-synuclein exposure. ER stress was evident by upregulation of GADD34/CHOP, increased phospho-PERK, and reduced nascent protein synthesis. Increased ER-mitochondrial contact via MAMs and enhanced STIM1-ORAI3 clustering reflect compensatory but ultimately insufficient responses to energy stress. Our results reveal that LRRK2-I1371V induces glucose uptake deficits, leading to energy depletion and integrated ER-mitochondria-lysosome dysfunction, thus indicating restoration of astrocytic metabolic capacity as a potential therapeutic strategy for LRRK2-associated PD.",
"42078360": "ID: 42078360\nTitle: X-Chromosome-Wide Association Study Identifies Novel Genetic Signals for Heart Failure and Subtypes.\nAbstract: Heart failure (HF) is a major and growing public health problem, and prior studies support a meaningful genetic contribution to HF susceptibility. Clinically, HF is commonly categorized into the major clinical sub-types of HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF), which differ in pathophysiology and clinical profiles. However, previous genome-wide association studies have focused on autosomal variation and have routinely excluded the X chromosome, leaving X-linked genetic contributions to HF and its subtypes under-characterized. We performed X-chromosome wide association study (XWAS) utilizing directly genotyped data from 590,568 Million Veteran Program participants, including 90,694 HF cases across European, African, Hispanic, and Asian Americans. Sex- and ancestry-stratified logistic regression was used with XWAS quality control measures, adjusting for age and population structure, followed by fixed-effects multi-ancestry meta-analysis. Functional annotation, gene-based testing, fine-mapping, and colocalization were performed. We replicated genetic associations with all-cause HF in the UK Biobank. In the multi-ancestry meta-analysis, we identified five X-chromosome-wide significant loci for all-cause HF, five for HFrEF, and one locus for HFpEF in males. No loci reached significance in female-specific analyses. In sex-combined analyses, we identified six loci for all-cause HF and four for HFrEF. The strongest and most emphasized signals mapped to genes were BRWD3, FHL1 , and CHRDL1 . Ancestry-specific analyses revealed additional loci, including NDP and WDR44 in African ancestry and PHF8 in Hispanic ancestry. One locus, BRWD3 , was replicated in UK Biobank HF cohort. Integrated post-GWAS analyses (fine-mapping, colocalization and pleiotropy trait association studies) reinforced the biological plausibility of the X-linked signals. This multi-ancestry, sex-stratified XWAS identifies X-linked genetic contributions to HF and its subtypes and highlights the role of X-chromosome in heart failure pathogenesis.",
"42085634": "ID: 42085634\nTitle: Optogenetic control of PLC-\u03b31 activity directs cell motility.\nAbstract: Phospholipase C-\u03b31 (PLC-\u03b31) signaling is required for mesenchymal chemotaxis, but is it sufficient to bias motility? PLC-\u03b31 enzyme activity is basally autoinhibited, and light-controlled membrane recruitment of wild-type PLC-\u03b31 (OptoPLC-\u03b31) in Plcg1-null fibroblasts does not trigger lipid hydrolysis, complicating efforts to isolate its contribution. Utilizing cancer-associated mutations to investigate the regulatory logic of PLC-\u03b31, we demonstrate that a hallmark of enzyme activity, phosphorylated Tyr783, is not a proxy for activity level, but is rather a marker of dysregulated autoinhibition. Accordingly, OptoPLC-\u03b31 with a deregulating mutation (P867R, S345F, or D1165H) exhibits elevated phosphorylation, and membrane localization of such is sufficient to activate substrate hydrolysis and concomitant motility responses. In particular, local recruitment of OptoPLC-\u03b31 S345F polarizes cell motility and migration on demand. This response is spatially dose-sensitive and only partially reduced by blocking canonical PLC-\u03b31 signaling, yet is lipase-dependent. Our findings reframe the interpretation of PLC-\u03b31 regulation and demonstrate that local activation of PLC-\u03b31 is sufficient to direct cell motility.",
"42093006": "ID: 42093006\nTitle: The emerging role and therapeutic targeting of autophagy-lysosome pathway in the pathogenesis of Parkinson's disease.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and the accumulation of misfolded \u03b1-synuclein, yet the underlying mechanisms remain incompletely understood. Over the past two decades, genetic discoveries have highlighted the convergence of multiple familial PD genes on the autophagy-lysosome pathway (ALP), a key cellular system responsible for the degradation and recycling of intracellular components. Recent studies have further revealed that components of the ALP not only mediate the clearance of \u03b1-synuclein aggregates but also, under certain pathological conditions, contribute to their propagation via lysosomal exocytosis or secretory autophagy. The precise functions of autophagy are highly context-dependent, with neuronal and glial cells exhibiting distinct ALP dynamics that shift with development, stress, and aging. In this review, we summarize current knowledge on the physiological regulation of autophagy in the brain and critically examine its involvement in PD pathogenesis, incorporating mechanistic insights from familial models and emerging evidence from sporadic PD. We also explore translational implications, focusing on efforts to identify ALP-related biomarkers in cerebrospinal fluid and urine, and on the therapeutic potential of modulating ALP activity. Although the causality between ALP dysfunction and PD remains elusive, mounting evidence supports its contribution to disease progression, particularly through impaired lysosomal homeostasis and disrupted intracellular trafficking. Future research should aim to define cell type-specific ALP alterations, clarify the bidirectional interactions between \u03b1-synuclein and autophagic machinery, and develop in vivo tools to monitor autophagy activity and secretory signatures. A deeper understanding of these processes will be crucial for refining PD models, discovering robust fluid biomarkers, and designing targeted therapies capable of modifying disease trajectory.",
"42103165": "ID: 42103165\nTitle: Lysosomal function, resistance to oxidative stress and repair are compromised by expression of the Alexander disease GFAP R239C mutant.\nAbstract: Intermediate filaments are critical regulators of cell responses and organizers of cellular structures. Glial fibrillary acidic protein (GFAP) is an intermediate filament protein that provides structural and functional support to astrocytes. GFAP is a key target of oxidative stress and its expression and assembly are altered in brain disease and injury. Moreover, GFAP mutations can provoke protein aggregation and proteostasis defects, astrocytic damage and ultimately neurodegeneration causing the leukodystrophy known as Alexander disease (AxD). We previously showed mitochondrial alterations and oxidative stress in astrocytes expressing GFAP AxD mutants. Here, we address the impact of GFAP AxD mutants on the lysosomal degradation pathway, using an astrocytoma cell model. Lysosomes in cells expressing GFAP R239C, a variant associated with severe AxD, displayed abnormal distribution, defective activity and impaired intraluminal acidification. Lysosomes are primary sites of oxidative damage. Expression of GFAP R239C increased their susceptibility to oxidative stress, provoking a greater loss of lysosomal \"mass\" and compromised membrane integrity, revealed by increased intraluminal galectin recruitment, compared to cells expressing GFAP wt. Notably, lysosomes in GFAP R239C expressing cells were also more vulnerable to chemically-induced rupture. Interestingly, whereas lysosomes of cells expressing GFAP wt rapidly recovered after removal of the damaging agent, recovery of acidic vesicles was severely impaired in cells expressing GFAP R239C, suggesting a defect in lysosomal repair. Together, our results show that expression of the GFAP R239C AxD mutant is sufficient to deeply perturb lysosomal distribution, function and repair. These alterations could contribute to proteostasis defects and cellular toxicity in AxD.",
"42112758": "ID: 42112758\nTitle: Integrated clinical and computational data-based repurposing of econazole as a novel autophagic activator in ULK1-related Parkinson disease.\nAbstract: Parkinson disease (PD), the second most common neurodegenerative disorder, is pathologically linked to dysregulated autophagy, a conserved lysosomal degradation pathway. Current conventional PD therapies are often limited by significant side effects, underscoring the demand for alternative treatment strategies. Drug repurposing of FDA-approved compounds represents a promising approach to address this unmet clinical need. Here, by integrating clinical data analysis, we identified an association between autophagy impairment and specific PD patient subtypes, suggesting that ULK1-dependent autophagy activation may offer therapeutic benefit. Through systematic screening for autophagy induction and neuroprotective activity, we identified econazole, a known imidazole antifungal, as a promising candidate. Econazole exhibited robust therapeutic effects across multiple PD models, including MPTP-induced zebrafish and mouse models, as well as SNCAA53T mutant mouse models. Notably, its efficacy was dependent on functional autophagy, as autophagy inhibition abrogated its beneficial effects. Mechanistically, econazole activated ULK1, enhanced autolysosome formation, and promoted clearance of SNCA aggregates. Mouse brain microarray analysis indicated that econazole-activated ULK1 suppresses MAP3K12/DLK-MAPK8/JNK-MAPK9/JNK2-mediated neuronal apoptosis. Further phosphoproteomic profiling uncovered a novel ULK1-HSPA8/Hsc70 interaction that promotes LAMP1 and LAMP2 activation and enhances lysosomal function. This ULK1-HSPA8 complex additionally activated the BECN1 (beclin 1) complex to facilitate autophagosome formation. Together, our findings highlight a clinical data-guided drug repurposing approach that identifies econazole as a potent autophagy activator with therapeutic efficacy in ULK1-linked PD models, opening new avenues for PD treatment.Abbreviations: 3-MA: 3-methyladenine; ACTB: actin beta; ATG: autophagy related; AUC: area under the curve; BafA1: bafilomycin A1; BECN1: beclin 1; CMA: chaperone-mediated autophagy; DA: dopamine; DOPAC: 3,4-dihydroxyphenylacetic acid; Econ: econazole; GFP: green fluorescent protein; HEK-293T: human embryonic kidney 293T; HSPA8: heat shock protein 8 family A (Hsp70) member 8; HVA: homovanillic acid; JUN: Jun proto-oncogene, AP-1 transcription factor subunit; KSEA: kinase-substrate enrichment analysis; LAMP: lysosome associated membrane protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP2K: mitogen-activated protein kinase kinase; MAP3K12: mitogen-activated protein kinase kinase kinase 12; MAPK: mitogen-activated protein kinase; MPP+: 1-methyl-4-phenylpyridinium; MPTP: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine; PD: Parkinson disease; RB1CC1: RB1 inducible coiled-coil 1; RFP: red fluorescent protein; RMSD: root mean square deviation; SEM: standard error of the mean; SNCA: synuclein alpha; SQSTM1: sequestosome 1; SYP: synaptophysin; TFEB: transcription factor EB; TH: tyrosine hydroxylase; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type.",
"42114425": "ID: 42114425\nTitle: Life-cycle exposure to tris(2-butoxyethyl) phosphate at environmentally relevant concentrations induces progressive Parkinsonian-like neurodegeneration via lysosomal dysfunction in Caenorhabditis elegans.\nAbstract: Environmental contaminants are increasingly recognized as key risk factors for chronic diseases, including neurodegenerative disorders. Tris(2-butoxyethyl) phosphate (TBOEP) is a representative organophosphate ester that is widely detected in environmental matrices and human tissues, yet whether chronic exposure to environmentally relevant concentrations of TBOEP drives progressive neurodegenerative pathology remains unclear. Here, using Caenorhabditis elegans as a model organism, we performed a 20-day, time-resolved life-cycle exposure to environmentally relevant concentrations of TBOEP (50-5000\u202fng/L) to systematically assess chronic neurotoxicity. TBOEP exposure induced progressive, age-dependent neurodegenerative phenotypes. Early effects were characterized by selective impairment of locomotor performance starting at 50\u202fng/L, followed by broader systemic toxicity, including growth retardation, feeding deficits, and accelerated aging. Consistent with a Parkinson's disease-like trajectory, hallmark pathological features progressively worsened with exposure duration, including dopamine-dependent functional impairment, while \u03b1-synuclein aggregation and dopaminergic neuronal impairment were mainly observed at concentrations \u2265\u202f500\u202fng/L. Mechanistically, time-resolved transcriptomics identified the lysosomal pathway as a central target of TBOEP. Functional assays further confirmed that TBOEP significantly impaired lysosomal acidification. Pharmacological validation with the lysosomal chaperone ambroxol showed that improving lysosomal function mitigated TBOEP-induced neurotoxicity, supporting lysosomal dysfunction as a primary contributor to the observed pathology. Collectively, our findings identify TBOEP as a potential environmental risk factor for neurodegeneration, providing important insights that could inform further studies assessing the environmental health risks of organophosphate esters.",
"42121920": "ID: 42121920\nTitle: Heterotrimeric G Protein-RasGAP Coupling Drives Adaptation During Chemotaxis.\nAbstract: Chemotaxis enables eukaryotic cells to detect and migrate along extracellular chemoattractant gradients spanning several orders of magnitude. This remarkable dynamic range relies on adaptation, a process that allows cells to reset their signaling machinery while preserving sensitivity to incremental changes in stimulus intensity. Although numerous actin-dependent feedback mechanisms have been characterized, the molecular basis of adaptation within an actin-independent core gradient-sensing module remains poorly understood. Here, we identify the Ras GTPase-activating protein, C2GAP1, as a critical F-actin-independent effector of the heterotrimeric G protein, G\u03b12, in Dictyostelium discoideum. Using cytoskeleton-free gradient-sensing cells, quantitative imaging, biochemical assays, FRET-based G-protein activation measurements, and structural modeling, we demonstrate that C2GAP1 controls concentration-dependent adaptation during gradient sensing. Mechanistically, C2GAP1 directly associates with G\u03b12 in both GDP- and GTP-bound states, with preferential binding to activated G\u03b12, thereby sustaining membrane recruitment and locally attenuating Ras and downstream signaling. Loss of C2GAP1 enhances G-protein activation, disrupts local inhibition, and impairs rapid reorientation in dynamic gradients. These findings define a direct coupling between heterotrimeric G proteins and the RasGAP, C2GAP1, as a core adaptive module that enables gradient sensing across a wide concentration range.",
"42130460": "ID: 42130460\nTitle: Targeting a Pleckstrin Homology Domain with a Lysine-Reactive Covalent Binder.\nAbstract: Bruton's Tyrosine Kinase (BTK) is a validated target for hematological malignancies, with numerous FDA-approved inhibitors on the market. Current therapies target the highly conserved ATP binding site and hence limit the therapeutic index given the site's highly conserved nature across the kinome. We explore a novel approach for BTK inhibition by targeting the PH domain-mediated membrane recruitment and activation of BTK. We have identified a fragment which covalently modifies a lysine in the inositol phosphate (PIP3) binding site and inhibits the binding of a soluble PIP3 headgroup analog to the PH domain. Fragment growth and an extensive structure-binding relationship study uncovered 27 crystal structures and a best-in-class analog, 24. Evaluation of pKa values of the targeted lysine in BTK and other PH domains suggests this as a more general approach to PH domain inhibition.",
"42132143": "ID: 42132143\nTitle: Lipid composition controls the huntingtin exon 1 membrane-association and differentially modulates its flanking regions' dynamics.\nAbstract: The pathological expansion of the polyglutamine (polyQ) repeat within the first exon of huntingtin (Httex1) protein is a defining hallmark of Huntington's disease (HD). Multiple evidence supports that the membrane recruitment of Httex1 is critical for its self-assembly and related toxicity in HD. In this work, we quantitatively examined the early steps of monomeric Httex1(23Q) association with lipid membranes and its impact on the conformational dynamics of the adjacent polyQ regions-the N-terminal N17 segment and C-terminal proline-rich region (PRR). A broad range of membrane physical properties was explored, including zwitterionic and anionic lipids, and also co-existing liquid-ordered and liquid-disordered phases. Two single cysteine mutants were engineered at the N- and C-termini of Httex1(23Q) and fluorescently labeled with acrylodan or Atto 488 to probe their local polarity and flexibility, respectively. Our results indicate that Httex1(23Q) preferentially binds to negatively charged lipid vesicles, and to a lower extent to liquid ordered/disordered phases. The N-terminal N17 segment interacts with anionic membranes, adopting a less flexible state than in aqueous solution. At variance, the C-terminal PRR remains highly dynamic and solvent exposed in the Httex1(23Q) membrane-bound state, preserving its intrinsic disordered features across all lipid compositions used. Altogether, our work provides quantitative insight into the distinct roles of each flanking polyQ region in mediating Httex1-lipid binding, and how distinct lipid compositions further modulate these early interaction steps.",
"42139345": "ID: 42139345\nTitle: Architecture of clathrin-independent AP3:ARF1-coated carriers.\nAbstract: The AP3 complex mediates cargo sorting and carrier assembly for the trafficking of transmembrane proteins from endosomes to lysosomes. AP3 is generally believed to localize to clathrin-free, ARF1-positive, elongated carriers in cells, but the architecture of AP3-based coats was unknown. Using in vitro reconstitution and cryo-electron tomography, we demonstrate that AP3:ARF1 spontaneously remodels membranes containing cargo and the phosphoinositide PI(3,5)P2 into tubular structures coated in spiraling rows of AP3 arches and ARF1 dimers. Targeted point mutations disrupting critical AP3:ARF1 and AP3:AP3 lattice interfaces disrupt AP3 recruitment, carrier formation, and lysosomal cargo trafficking in cells. We propose that AP3 generates tubular carriers on endosomes by organizing ARF1 dimers into elongated membrane-deforming arrays while simultaneously selecting cargo. By demonstrating that AP3:ARF1 can generate carriers without using a clathrin lattice, we explain the clathrin independence of AP3-mediated trafficking.",
"42140967": "ID: 42140967\nTitle: \u03b1-Synuclein aggregates induce mitochondrial damage and trigger innate immunity to drive neuron-microglia communication.\nAbstract: Tunneling nanotubes (TNTs) enable direct intercellular transfer of macromolecules, organelles, and pathogenic protein aggregates. While \u03b1-synuclein (\u03b1-Syn) aggregates are known to promote TNT formation, the underlying mechanisms remain poorly defined. Here, using human neuronal and microglial cell lines, as well as iPSC-derived dopaminergic neurons and microglia, we show that \u03b1-Syn aggregates induce severe mitochondrial damage, leading to cytosolic release of mitochondrial DNA (mtDNA) and activation of the cGAS-STING-NF-\u03baB-IRF3 pathway. This innate immune response drives actin cytoskeleton remodeling and the formation of TNT-like structures, promoting intercellular transfer of \u03b1-Syn from neurons to microglia. Additionally, neuronal cells transfer damaged mitochondria to microglia, where they undergo lysosome-mediated degradation. Neuron-to-microglia communication under \u03b1-Syn-induced stress also triggers a bystander inflammatory response in microglia, suggesting a neuroimmune activation. Our findings identify mitochondrial damage and STING-mediated inflammation as key drivers of TNT formation and \u03b1-Syn propagation, highlighting potential targets to modulate disease progression in Synucleinopathies.",
"42146388": "ID: 42146388\nTitle: Elucidating the molecular interplay between LRRK2 and Rab GTPases.\nAbstract: Gain-of-function mutations in LRRK2 are a major cause of inherited Parkinson's disease. LRRK2 encodes a multidomain kinase, whose bidirectional interplay with Rab GTPases regulates critical cellular processes like lysosomal homeostasis. Certain Rabs, including Rab12 and Rab29, recruit LRRK2 to organelle membranes and stimulate its kinase activity; activated LRRK2 phosphorylates a subset of Rabs in their Switch-II motifs. Molecular basis governing selective Rab recognition by LRRK2 remains unclear. Here we structurally characterize LRRK2 interactions with representative Rab GTPases and identify three novel Rab-binding sites: site 4 for Rab8A/10, site 5 for Rab43, and site 6 for Rab5A, defining a total of six distinct binding sites that account for known LRRK2-interacting Rabs. Additionally, we elucidated the binding site of GABARAP, an ATG8 member that recruits LRRK2 to stressed lysosomes. Our findings provide a framework for therapeutic targeting of LRRK2 recruitment for Parkinson's.",
"42146459": "ID: 42146459\nTitle: Draper-mediated efferocytosis by Drosophila imaginal disc epithelial cells clears cellular debris during regeneration.\nAbstract: Regeneration is a coordinated process that restores tissue integrity following damage. Following injury, tissues initiate early responses, including epithelial remodeling and clearance of cellular debris. However, how debris clearance is coordinated with regenerative growth to ensure efficient tissue repair remains poorly understood. To address how early damage responses, particularly debris clearance, are coordinated with regeneration, we used a genetic ablation system in Drosophila wing imaginal discs to induce apoptosis in the pouch region. Targeted damage generates cellular debris that localizes to both the apical and basal sides of the epithelium. We show that most cellular debris is cleared within two days after damage, although some debris persists apical to the regenerating epithelium. Notably, immune cells are not recruited to the damaged tissue due to restricted access by an intact basement membrane. Instead, we discovered that debris clearance is mediated by efferocytosis, whereby neighboring hinge epithelial cells activate JNK signaling and engulf debris via lysosomal formation. Reduction of efferocytosis by mutation of the phagocytic receptor Draper delays debris removal and increases debris persistence. This impairment has a modest impact on regeneration, as measured by adult wing size. Finally, our data indicate that residual debris consists of a heterogeneous mixture of cellular components, suggesting no preferential targeting by the clearance machinery. Together, our results reveal a previously unappreciated role for epithelial cells as non-professional phagocytes for debris clearance during regeneration.",
"42162239": "ID: 42162239\nTitle: Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.\nAbstract: During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagophore before its sealing into an autophagosome and subsequent fusion with the lysosome/vacuole. It remains unclear, however, how the formation of this specialized MCS and the directionality of the lipid flux are controlled. Here, we present the structure of the key lipid transfer protein Atg2 from yeast solved together with its Atg18 binding partner, a phosphatidylinositol-3-phosphate (PtdIns3P) effector, using cryo-electron microscopy. We reveal a new interface in Atg2 that, together with PtdIns3P, is required for Atg18 recruitment and lipid transfer activity. Furthermore, we visualize lipid densities along the internal hydrophobic cavity of Atg2, providing structural evidence that Atg2 cavity is filled with lipids throughout the entire length, even when Atg2 is cytosolic. Finally, molecular dynamics simulations show that the complex generates membrane curvature, efficiently positioning the lipid channel of Atg2 towards the membrane to promote lipid transfer into the elongating phagophore.",
"42165414": "ID: 42165414\nTitle: High-fat diet exacerbates experimental colitis by inhibiting lysosomal function via the STAT3-TFEB Axis.\nAbstract: An elevated risk for inflammatory bowel disease (IBD) has been linked to the intake of high-fat diet (HFD), yet the underlying molecular mechanisms remain unclear. The lysosome and the macroautophagy/autophagy-lysosome pathway (ALP) are critical for maintaining the intestinal epithelial barrier. By employing both an in vivo model of dextran sulfate sodium (DSS)-induced colitis in mice and an in vitro model using lipopolysaccharide (LPS)-treated NCM460 cells, we established that HFD in vivo and palmitic acid (PA) in vitro profoundly impair epithelial barrier function and amplify inflammation, which was linked to the suppression of lysosomal function and the ALP. Mechanistically, HFD in vivo and PA in vitro activated STAT3 (p-STAT3[Y705]) under DSS- and LPS-associated inflammatory stress, respectively. This led to a dual suppression of TFEB: on the one hand, activated STAT3 directly bound to the TFEB promoter to inhibit its transcription; on the other hand, it facilitated the lysosomal recruitment of MTOR and activated MTORC1, which promoted TFEB phosphorylation (p-TFEB[S211]) and hindered its nuclear translocation. This cascade resulted in lysosomal membrane permeabilization (LMP), loss of acidification, and impaired degradative function. Intestinal epithelial-specific knockout of Stat3 or pharmacological activation of TFEB restored lysosomal function, repaired the epithelial barrier, and ameliorated colitis. Conversely, rectal administration of AAV9-shTfeb reversed the protective effects conferred by stat3 knockout. Our study reveals that HFD in vivo and PA in vitro disrupt lysosomal function and the intestinal barrier through the STAT3-TFEB axis, suggesting this signaling pathway as a promising avenue for intervention in diet-associated IBD.Abbreviations: AB-PAS: Alcian blue-periodic acid-Schiff; ALP: autophagy-lysosome pathway; CD: Crohn disease; ChIP: chromatin immunoprecipitation; CLEAR: coordinated lysosomal expression and regulation; DSS: dextran sulfate sodium; HFD: high-fat diet; IBD: inflammatory bowel disease; IF: immunofluorescence; IHC: immunohistochemistry; LAMP: lysosome associated membrane protein; LGALS3/Gal3: galectin 3; LMP: lysosomal membrane permeabilization; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; MTORC1: mechanistic target of rapamycin kinase complex 1; PA: palmitic acid; RRAG: Ras-related GTP binding; RRAG-CA: constitutively active RRAG GTPase; RT-qPCR: reverse transcription quantitative PCR; SQSTM1/p62: sequestosome 1; STAT3: signal transducer and activator of transcription 3; TA1: TFEB activator 1; TEM: transmission electron microscopy; TFEB: transcription factor EB; TJ: tight junction; TUNEL: terminal deoxynucleotidyl transferase dUTP nick-end labeling; UC: ulcerative colitis; WB: western blot; WT: wild-type.",
"42166252": "ID: 42166252\nTitle: Arl8b inactivates the Rab11a recycling pathway to promote LAMP1 sorting and lysosome biogenesis.\nAbstract: The small GTP-binding protein Arl8b is established as a regulator of lysosome positioning and fusion, yet its role in lysosome biogenesis remains unclear. Here, we investigate the role of Arl8b in the trafficking of newly synthesized LAMP1 to lysosomes using the Retention Using Selective Hook (RUSH) assay. We find that Arl8b localizes to post-endocytic LAMP1-containing vesicles prior to fusion with acidic lysosomes. Arl8b depletion leads to Rab11a-dependent recycling of LAMP1 to the plasma membrane, impairing its lysosomal delivery. Mechanistically, Arl8b recruits the Rab11a GAP, TBC1D9B, to LAMP1-positive membranes, and TBC1D9B depletion similarly disrupts LAMP1 sorting. Notably, TBC1D9B knockdown also impairs the retrieval of cation-independent mannose-6-phosphate receptor (CI-M6PR) from Rab11a- and Rab14-positive endosomes to the trans-Golgi network, impairing pro-cathepsin trafficking and cargo degradation. These findings reveal that Arl8b-mediated recruitment of Rab GAP TBC1D9B is crucial for inactivation of the Rab11a recycling pathway, leading to efficient sorting of lysosomal cargo to their functional location.",
"42168299": "ID: 42168299\nTitle: Lysosome-related biomarkers in peripheral blood immune cells discriminate sepsis from SIRS.\nAbstract: This study aimed to screen lysosome-related genes that distinguish sepsis from Systemic Inflammatory Response Syndrome (SIRS), in order to provide potential targets for the differential diagnosis of sepsis and for lysosome-targeted therapeutic strategies. Peripheral blood samples were collected from 12 SIRS patients and 20 sepsis patients for RNA sequencing and differential expression analysis. Meanwhile, lysosome-related gene sets were obtained from the Gene Ontology database. The intersection was taken between the differentially expressed genes and the lysosomal gene sets. Subsequently, Protein-Protein Interaction (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on these overlapping genes. Meta-analysis was used to screen for core genes, and their diagnostic efficacy was evaluated using Receiver Operating Characteristic (ROC) curves. Furthermore, single-cell RNA sequencing was performed to identify the immune cell types that predominantly express the core genes, facilitating the selection of appropriate cell models for subsequent experimental validation. Functional enrichment analysis revealed that these 21 overlapping genes were significantly enriched in biological pathways such as receptor metabolic process, autophagy, vacuolar transport, cellular catabolic process, and lysosomal transport. Meta-analysis identified four core genes: CD1C, RNASE6, and SNCA were significantly downregulated in the sepsis group, while DRAM1 was significantly upregulated. Diagnostic efficacy evaluation demonstrated that all four core genes possessed good discriminatory value, with AUC as follows: CD1C (0.758), DRAM1 (0.888), RNASE6 (0.737), and SNCA (0.765). Single-cell RNA sequencing analysis suggested that CD1C and RNASE6 are primarily expressed in circulating monocyte-macrophages and B cells, DRAM1 is mainly expressed in circulating monocyte-macrophages, and SNCA is predominantly expressed in circulating monocyte-macrophages and platelets. The four core genes identified in this study could serve as potential diagnostic biomarkers to distinguish sepsis from SIRS. Their expression is mainly enriched in circulating monocyte-macrophages in peripheral blood, providing new directions for future research.",
"42178909": "ID: 42178909\nTitle: Membrane ATG8ylation in secretory autophagy.\nAbstract: Mammalian Atg8-family (ATG8) proteins are crucial for macroautophagic/autophagic degradation in the lysosome and facilitate non-degradative processes including multiple distinct forms of unconventional protein secretion. These secretion pathways, collectively termed secretory autophagy, depend upon ATG8 conjugated to membranes to both specify and traffic molecules for extracellular release. Here, we review the current understanding of how membrane ATG8ylation supports secretory autophagy, and propose a cell biological framework for classifying the growing repertoire of secretory autophagy pathways based on membrane ATG8ylation at discrete intracellular vesicular intermediates. Finally, we detail the emerging roles of these pathways in physiology and disease.Abbreviations: A\u03b2, amyloid-\u03b2; Acb1, acyl-coA-binding 1; ALS, amyotrophic lateral sclerosis; APP, amyloid beta precursor protein; APEX2, ascorbate peroxidase; ATG, autophagy related; AWOL, autophagosome-mediated exit without lysis; BafA1, bafilomycin A1; BirA*, mutant BirA biotin ligase; BMI, body-mass index; CASM, ATG8 conjugation at single membranes; DAMPs, danger/damage-associated molecular patterns; DBI, diazepam binding inhibitor, acyl-CoA binding protein; DSS, dextran sodium sulfate; ER, endoplasmic reticulum; ERGIC, endoplasmic reticulum intermediate compartment; ESCRT, endosomal complexes required for transport; EVs, extracellular vesicles; EVPs, extracellular vesicles and particles; HMGB1, high mobility group box 1; IDE, insulin degrading enzyme; IFNB, interferon beta; ILV, intralumenal vesicles; LANDO, LC3-associated endocytosis; LAP, LC3-associated phagocytosis; LIR, LC3 interacting region; LDELS, LC3-dependent EV loading and secretion; LLOMe, L-leucyl-L-leucine methyl ester hydrobromide; M2, influenza A virus matrix 2, MAD, migratory autolysosome disposal; miRNAs, microRNAs; M-MDSC, monocytic myeloid derived suppressor cells; MVEs, multivesicular endosomes; PAMPs, pathogen-associated molecular patterns; P-bodies, processing bodies; PE, phosphatidylethanolamine; PD, Parkinson disease; PS, phosphatidylserine; RBPs, RNA binding proteins; R-EV, RAB22A-induced extracellular vesicle; SLC2A1, solute carrier family 2 member 1; TFRC, transferrin receptor; TGN, trans-Golgi network; TMED10, transmembrane p24 trafficking protein 10; THU, TMED10-channeled unconventional secretion; SALI, secretory autophagy during lysosome inhibition; SCF, SKP1-CUL1-F-box; SNAREs, soluble NSF attachment protein receptors.",
"42182263": "ID: 42182263\nTitle: Naked antisense oligonucleotides remain endolysosomally sequestered despite induced membrane damage.\nAbstract: Antisense oligonucleotides (ASOs) enter cells efficiently, but the compartment from which productive escape occurs remains uncertain. We used live-cell microscopy, ratiometric pH measurements and 3D focused ion beam scanning electron microscopy (FIB-SEM) in U2OS cells to track a Malat1-targeting ASO from uptake to delivery. The ASO entered by endocytosis and accumulated in late endosomes, endolysosomes and lysosomes, where it induced luminal neutralization without galectin-3 recruitment or limiting-membrane rupture. Under conditions that reduced Malat1-RNA by >90%, quantitative imaging showed that less than 4% of internalized ASOs reached the nucleus. L-leucyl-L-leucine methyl ester (LLOMe)-induced membrane damage released co-internalized dextran but not ASOs, showing that ASOs remain sequestered even in damaged late endocytic compartments. In apilimod-expanded organelles, ASOs concentrated at limiting membranes and intraluminal foci with constrained motion, consistent with association with membrane and luminal structures. Although G3BP1/2 has been proposed to plug damaged endocytic membranes, we detected no recruitment of G3BP1 to endosomes or lysosomes; loss of G3BP1 and G3BP2 increased functional delivery modestly. We therefore propose that productive escape occurs earlier in endocytosis, most likely in early or recycling endosomes, where ASOs would still be unbound within the lumen and where membrane fusion and fission could generate perforations permitting release.",
"42182431": "ID: 42182431\nTitle: Cryo-EM structure and biochemical characterization of a BRAF/CRAF heterodimer: Negative charge in the NtA motif is not required for RAF activation.\nAbstract: Upon RAS-driven membrane recruitment, RAF kinases ARAF, BRAF and CRAF are activated via formation of homo- or hetero- dimers to initiate signaling through the MAP kinase cascade. Although RAF heterodimers are important for both physiologic and oncogenic signaling, they have been little studied at a structural and biochemical level. Here we report the preparation, biochemical characterization, and the cryo-EM structure of a 14-3-3-bound BRAF/CRAF heterodimer complex. The heterodimer exhibited kinetic parameters and sensitivity to a panel of twelve structurally diverse RAF inhibitors that were closely similar to, or intermediate between, those of BRAF and CRAF homodimers. Cryo-EM structures of the heterodimer with and without MEK1 revealed an overall organization essentially identical to that of RAF homodimers, but with an asymmetric interaction in the MEK1-bound structure in which the BRAF N-terminal acidic (NtA) motif extends across the dimer interface to engage the CRAF RKTR motif. Mutagenesis of this interface unexpectedly revealed that replacing the acidic NtA sequence with a basic RARA sequence yields highly active RAF homodimers and heterodimers, demonstrating that negative charge in the NtA motif is not required for activity. Collectively, our findings suggest that the charge state of the NtA motif influences RAF activity through effects on local backbone dynamics and the stability of the inactive kinase conformation, rather than via stereospecific recognition across the dimer interface.",
"42183611": "ID: 42183611\nTitle: Mammalian lysophagy: mechanisms and pathophysiological implications.\nAbstract: Lysophagy is a form of selective macroautophagy/autophagy that preserves lysosomal integrity by eliminating damaged lysosomes. Lysosomal membrane permeabilization can arise from diverse physiological and pathological insults, including proteotoxic stress, crystalline particles, pathogens and chemical perturbations, and occurs along a continuum ranging from transient nanoscale lesions to catastrophic rupture. Cells respond to lysosomal injury through a hierarchical quality-control network in which membrane repair, lysophagic removal and lysosomal regeneration operate in a coordinated manner. Damage recognition involves sensing of exposed lumenal glycans and membrane lipids, followed by ubiquitin-dependent tagging that recruits selective autophagy receptors and activates the core autophagy machinery to form lysophagosomes. Lysophagy is closely integrated with membrane repair pathways, metabolic signaling and innate immune responses that together determine lysosomal fate. Dysregulated lysosomal quality control has been implicated in diverse diseases, including neurodegeneration, infection, cancer and chronic inflammatory disorders. In this review, we summarize current mechanistic insights and emerging experimental approaches for studying lysosomal quality control and lysophagy in mammalian cells.Abbreviations: ALR, autophagic lysosome reformation; ALS, amyotrophic lateral sclerosis; ATG8, mammalian Atg8-family protein; ER, endoplasmic reticulum; ESCRT, endosomal sorting complexes required for transport; LAMPs, lysosome associated membrane proteins; LIR, LC3-interacting region; LLOMe, L-leucyl-L-leucine methyl ester; LMP, lysosomal membrane permeabilization; PITT, phosphoinositide-initiated membrane tethering and lipid transport; PtdIns3K, class III phosphatidylinositol 3-kinase; PtdIns3P, phosphatidylinositol-3-phosphate; PtdIns4P, phosphatidylinositol-4-phosphate; ROS, reactive oxygen species; V-ATPase, vacuolar-type H+ -ATPase.",
"42183628": "ID: 42183628\nTitle: CHCHD2 and CHCHD10 promoted autophagic clearance of protein aggregates via GABARAPs.\nAbstract: Mutations in mitochondrial protein CHCHD2 and its paralog CHCHD10 were identified in patients with Parkinson disease (PD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD) or Alzheimer disease (AD). CHCHD2 and CHCHD10 mutations caused neurodegeneration in model animals as seen in patients, but their pathophysiological roles remain elusive. Here we reported a direct role of CHCHD2 and CHCHD10 in autophagy. We identified a protein complex composing of CHCHD2-CHCHD10-C1QBP/p32-Atg8-family proteins (ATG8s), in which each molecule interacted with another. CHCHD2, CHCHD10 and C1QBP/p32 associated with ATG8s, preferentially, GABARAPs. Disease-associated CHCHD2 and CHCHD10 mutations exhibited varied interaction with ATG8s. By binding to GABARAPs, CHCHD2 and CHCHD10 underwent autophagic degradation, and recruited the ULK1 complex. Autophagy initiation defects occurred upon transient knockdown of CHCHD2, and also in human iPSC-derived CHCHD2-/- or CHCHD2T61I dopaminergic neurons. Importantly, CHCHD2 and CHCHD10 promoted autophagy. CHCHD2 reduced protein aggregates in cells and toxic SNCA/\u03b1-synuclein species in mouse striatum. Our study thus revealed mitochondrial proteins CHCHD2 and CHCHD10 as both autophagy substrates and autophagy activators and laid groundwork for therapy targeting patients with neurodegeneration.Abbreviations: AA: amino acid; AD: Alzheimer disease; ALS: amyotrophic lateral sclerosis; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG8: mammalian Atg8-family protein; ATG13: autophagy related 13; bafA1: bafilomycin A1; C1QBP/p32/gC1qR/HABP1: complement component 1, q subcomponent binding protein; CHCHD2/MNRR1/MIX17B: coiled-coil-helix-coiled-coil-helix domain containing 2; CHCHD10/MIX17A: coiled-coil-helix-coiled-coil-helix domain containing 10; CHX: cycloheximide; CMA: chaperone-mediated autophagy; CRISPR: clustered regularly interspaced short palindromic repeats; CQ, chloroquine; DA: dopaminergic; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; RB1CC1/FIP200: RB1 inducible coiled-coil 1; FTD: frontotemporal dementia; GABARAP: gamma-aminobutyric acid receptorbassociated protein; GABARAPL1: GABA type A receptor associated protein like 1; GABARAPL2: GABA type A receptor associated protein like 2; hESC: human embryonic stem cells; iPSC: induced pluripotent stem cell; KO: knockout; LAMP1: lysosomal-associated membrane protein 1; LAMP2A: lysosomal-associated membrane protein 2A; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; LIR: LC3-interacting region; PD: Parkinson disease; SQSTM1/p62: sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TH: tyrosine hydroxylase; TMR, tetramethylrhodamine; WT: wild type; UB: ubiquitin; ULK1: unc-51 like kinase 1.",
"42185903": "ID: 42185903\nTitle: Irisin-integrin \u03b1V/\u03b25 coupling of \u03b1-synuclein phagocytosis and clearance.\nAbstract: Parkinson's disease-associated cognitive impairment (PD-CI) is closely linked to \u03b1-synuclein (\u03b1-syn) accumulation and synaptic dysfunction, yet effective disease-modifying strategies remain limited. Irisin is an exercise-inducible myokine with neuroprotective potential, but its receptor mechanisms and its role in \u03b1-syn clearance in PD-CI are poorly defined. Here, we observed that aerobic exercise markedly increased circulating irisin levels, reduced serum \u03b1-syn levels, and improved cognitive performance in a cohort of 21 PD patients. In addition, irisin signals through integrin \u03b1V/\u03b25 to enhance microglial \u03b1-syn clearance, resulting in reduced \u03b1-syn burden and improved PD-CI. Mechanistically, irisin activates integrin \u03b1V/\u03b25-FAK axis to promotes microglial phagocytic uptake of \u03b1-syn, while concurrently stabilizing HMGB1 to facilitate autophagy-lysosome mediated degradation of internalized \u03b1-syn, thereby coupling phagocytic uptake to efficient degradation. In summary, these results highlight a dual-module irisin-integrin \u03b1V/\u03b25 mechanism that couples microglial phagocytosis and autophagy-lysosome clearance to reduce \u03b1-syn burden and ameliorate PD-CI.",
"42192129": "ID: 42192129\nTitle: FAM134B-mediated ER-phagy degrades APP and suppresses Alzheimer's disease pathology.\nAbstract: Endoplasmic reticulum autophagy (ER-phagy) is a selective autophagy pathway in which receptor proteins target ER membranes and proteins for degradation, yet its role in Alzheimer's disease (AD) remains unclear. Here, we identify FAM134B/RETREG1 as a specific ER-phagy receptor mediating amyloid precursor protein (APP) degradation. FAM134B directly interacts with ER-localized wild-type and familial mutant APP via their C-terminal domains and recruits LC3 through its LC3-interacting region (LIR) to promote APP delivery to phagophores for lysosomal degradation. In AD, epigenetic silencing at the FAM134B promoter suppresses its transcription by limiting TFEB/TFE3 binding despite their nuclear enrichment. This transcriptional suppression impairs ER-phagy, leading to APP accumulation and exacerbated AD pathology. AAV-mediated hippocampal expression of wild-type, but not LIR-mutant, FAM134B in 5XFAD mice restores ER-phagy, enhances APP clearance, reduces A\u03b2 deposition, preserves synaptic and myelin integrity, and improves cognitive performance. These findings establish FAM134B downregulation as an upstream pathogenic event in AD, suggesting ER-phagy enhancement as a promising strategy to suppress A\u03b2 generation at its source.",
"42203786": "ID: 42203786\nTitle: A PI(3,5)P2/CHMP4B axis on lysosomes is essential for microautophagic degradation of STING.\nAbstract: Stimulator of interferon genes (STING) is critical for the type I interferon responses to pathogen- or self-derived cytosolic DNA. STING signalling is terminated by ESCRT-driven lysosomal microautophagy. How STING is directly encapsulated by lysosomes has not yet been understood. Here we show that two lysosomal components, a phosphoinositide PI(3,5)P2 and CHMP4B (a subunit of ESCRT-III subcomplex) are essential for STING encapsulation by lysosomes. Liposome sedimentation assay reveals that CHMP4B binds to PI(3,5)P2. The forced recruitment of the catalytic core of Pikfyve (a lipid kinase generating PI(3,5)P2) to early endosomes, recruits a fraction of CHMP4B to early endosomes. CHMP4B mutant, defective in the binding to PI(3,5)P2, cannot restore the microautophagic degradation of STING or the resolution of the STING signalling in cells depleted of Chmp4b. Our results reveal a molecular mechanism that terminates innate immune signalling at the lysosomal membrane.",
"42212595": "ID: 42212595\nTitle: FKBP8 inhibits influenza a virus infection by degrading viral M2 protein in lysosomes.\nAbstract: Influenza A virus (IAV) remains a major threat to global public health, causing seasonal epidemics and occasional pandemics with significant morbidity and mortality. M2 (matrix protein 2), a key IAV envelope protein with ion channel activity, is critical for viral uncoating, genome release, and virion assembly. Here, we identified FKBP8 (FK506 binding protein 8) as a host restriction factor targeting IAV. Overexpression of FKBP8 inhibited IAV replication, while FKBP8 knockdown/knockout enhanced viral susceptibility. Mechanistically, FKBP8 interacted with M2 from diverse IAV strains via high-affinity binding between its tetratricopeptide repeat (TPR) domain and the LC3-interacting region (LIR) of M2, inhibiting viral entry. Importantly, FKBP8 mediated M2 degradation through the lysosomal pathway, not via translational inhibition, as shown by cycloheximide and lysosomal inhibitor (BafA1 and CQ) experiments. FKBP8 recruited RAB7A and LAMP1 to form a FKBP8-RAB7A-LAMP1-M2 complex, facilitating M2 transport to lysosomes. Additionally, FKBP8 interacted with envelope proteins of other enveloped RNA viruses, suggesting broad-spectrum antiviral potential. Our findings reveal FKBP8 as a conserved IAV restriction factor and its mechanism, providing insights for antiviral drug development.Abbreviations: AA: amino acids; AP-MS: affinity tag purification-mass spectrometry; BCL2: B cell leukemia/lymphoma 2; BafA1: bafilomycin A1; MbFKBP8: Myotis brandtii FK506 binding protein 8; CHX: cycloheximide; CQ: chloroquine; CTD: cytoplasmic tail domain; ED: ectodomain; EV: empty vector; FKBP8: FK506 binding protein 8; FL: full length; HCIPs: high-confidence interacting proteins; HsFKBP8: Homo sapiens FKBP prolyl isomerase 8; IAV: influenza A virus; LIR: LC3-interacting region; LAMP1: lysosomal-associated membrane protein 1; M2: matrix protein 2; MOI: multiplicity of infection; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MmFKBP8: Mus musculus FK506 binding protein 8; NP: nucleoprotein; PA: polymerase acidic; PB1: polymerase basic 1; PB2: polymerase basic 2; PPIase: peptidyl-prolyl cis-trans isomerase; KO: knockout; RdRps: RNA-dependent RNA polymerases; RAB7A: RAB7, member RAS oncogene family; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; TRIM41: tripartite motif-containing 41; TMD: transmembrane domain; vRNP: viral ribonucleoprotein.",
"42213153": "ID: 42213153\nTitle: Biomarker Responses in the Marine Mussel Mytilus Edulis Indicate Significant Toxicological Effects of Polyethylene Microplastics.\nAbstract: This study investigated the short\u2011term effects of polyethylene microplastics (PE\u2011MPs) on the marine mussel Mytilus edulis using a suite of cellular and subcellular biomarkers. A total of 225 mussels were collected from Umluj, Saudi Arabia, a relatively unimpacted coastal area of the Red Sea, and experimentally exposed for 72\u00a0h to spherical PE\u2011MPs (50\u00a0\u03bcm diameter) at nominal concentrations of 5, 10, 20, and 60 particles L-1. Genotoxicity, oxidative status, and cellular integrity were assessed by comet assay, thiobarbituric acid\u2011reactive substances (TBARS), superoxide dismutase (SOD) activity, and lysosomal membrane stability (LMS). At 60 particles L-1, DNA strand breakage increased markedly in hemocytes (13.09%) and gill cells (12.21%) relative to controls (2.14%; p\u2009<\u20090.01). Lipid peroxidation was 1.28 nmol TBARS mg protein-1, and activity of gill SOD was decreased by 16.13% of control. LMS was significantly reduced from 134.4\u00a0min in controls to 53.2\u00a0min in the highest exposure (p\u2009<\u20090.01), suggesting impaired cellular homeostasis. Given the short exposure duration, these results are preliminary. They indicate that acute PE-MP exposure at the tested concentrations is associated with measurable genotoxicity, oxidative stress, and reduced lysosomal stability. Longer-term ecological implications remain to be investigated.",
"42215790": "ID: 42215790\nTitle: The C9orf72/SMCR8 complex maintains microglial homeostasis via RAB8A-ESCRT-mediated lysosomal repair.\nAbstract: Microglia are critical regulators of neuroinflammation and neurodegeneration. Haploinsufficiency of C9orf72, the most frequently mutated gene in\u00a0amyotrophic lateral sclerosis and frontotemporal dementia, has been linked to autophagy-lysosomal pathway defects, but the role\u00a0of C9orf72 in microglia remains unclear. Here, we identify the C9orf72/SMCR8 complex as a key regulator of microglial homeostasis through promoting lysosomal membrane repair. Loss of C9orf72 and SMCR8 in mice causes age\u2011dependent neuroinflammation and microgliosis, with microglia adopting a disease-associated state. In aged brain and spinal cord tissue, microglia display lysosomal damage marked by galectin\u20113 accumulation. Using a lysosomotropic agent to induce lysosomal damage in microglia, we find that C9orf72/SMCR8-deficient cells accumulate damaged lysosomes and show defective recruitment of phosphorylated RAB8A and the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery\u00a0to damaged lysosomes. Notably, mutant microglia accumulate GTP\u2011bound RAB8A, which becomes hyperphosphorylated and mislocalized to RAB7-positive, LAMP1-negative vesicles. The GTPase-activating activity of the C9orf72/SMCR8 complex is essential for lysosomal repair. Our findings reveal that the C9orf72/SMCR8 complex coordinates RAB8A-ESCRT-mediated lysosomal repair to safeguard microglial homeostasis and limit neuroinflammation.",
"42217620": "ID: 42217620\nTitle: Complement Anaphylatoxin Receptors, Complement Protein C3 Receptor 1 and Complement Protein C5 Receptor 1, Are Dual Contributors of Chronic-Plus-Binge-Induced Hepatic Inflammation and Injury.\nAbstract: Alcohol-associated liver disease (ALD) is the leading cause of liver-related mortality worldwide. ALD is progressive, involving chronic, nonresolving inflammation and immune dysfunction. Despite this knowledge, the mechanisms behind immune dysfunction in ALD are not well understood. Here, a recently described intracellular complement system, the complosome, was characterized, making use of explanted liver tissue from patients with ALD, chronic-plus-binge feeding to anaphylatoxin receptor-deficient mice, and in vitro models of macrophage activation. Expression of anaphylatoxin receptors was increased in liver explants from patients with ALD compared with healthy donor liver in CD68+ macrophages. After chronic-plus-binge feeding, ethanol increased surface expression of complement protein C3 (C3) receptor 1 (C3aR1) and complement protein C5 (C5) receptor 1 (C5aR1) and intracellular C5aR1 pool on CD11bintF4/80hi Kupffer cells. C5aR1-/-, but not C3aR1-/- mice, were protected from binge ethanol-induced liver injury, whereas deficiency of either receptor protected from ethanol-induced expression of proinflammatory cytokines and recruitment of immune cells to the liver. In bone marrow-derived macrophages, ethanol and lipopolysaccharide treatment increased expression of intracellular complement components C3, C5, C3aR1, and C5aR1; anaphylatoxin receptors were co-expressed with lysosomal and mitochondrial membrane markers. Lipopolysaccharide-induced expression of NOD-like receptor protein 3 (NLRP3) and production of IL-1\u03b2 was attenuated in C3aR1-and C5aR1-deficient bone marrow-derived macrophages. C3aR1/C5aR1-/- double-knockout mice were protected from ethanol-induced elevations in liver injury and inflammation. In conclusion, ethanol impacts macrophages by increasing intracellular complosome components that may impact nonresolving inflammation in ALD.",
"42218158": "ID: 42218158\nTitle: USP33 alleviates FIS1-dependent mitochondrial fission and cardiac microvascular injury in diabetic cardiomyopathy via deubiquitinating and stabilizing ATG7.\nAbstract: Endothelial dysfunction plays a key role in the development of diabetic cardiomyopathy (DCM), but the underlying mechanisms of endothelial dysfunction remain to be elucidated. Recent studies have revealed that dysregulated mitochondrial dynamics contributes to the development of cardiac microvascular dysfunction. Fission-1 (FIS1), a key effector of mitochondrial fission, functions as an outer mitochondrial membrane adapter that recruits dynamin-related protein-1 (Drp1) from the cytosol to the outer mitochondrial membrane for activating mitochondrial fission. The present study screened a library targeting deubiquitinases, and identified the regulatory role of USP33 on FIS1-dependent mitochondrial fission. We found USP33 silencing elevated FIS1 protein expression and resulted in excessive mitochondrial fission in endothelial cells, which in turn impaired mitochondrial function and worsen endothelial and cardiovascular dysfunction in DCM. Mechanistically, USP33 interacted with FIS1 at the TPR2 domain and promoted FIS1 degradation via lysosomal degradation. Further studies revealed that USP33 stabilized autophagy-related 7 (ATG7) at protein level by blocking K63-linked ubiquitination of human ATG7 at K48 (mouse K44) site. This process led to lysosomal degradation of FIS1 via ATG7-mediated autophagy. In summary, our findings reveal that USP33 plays a critical role in endothelial dysfunction in DCM and demonstrate that ATG7-FIS1 pathway acts as one of the potential downstream mechanisms.",
"42223444": "ID: 42223444\nTitle: Trifloxystrobin-triggered Drp1 hyperactivation biases mitophagy and imposes long-lasting SVCV susceptibility in teleost.\nAbstract: Environmental pollutants are increasingly recognized as disease modifiers, reshaping host homeostasis and shifting host-pathogen dynamics toward higher infection risk in aquatic ecosystems. Here, we show that the widely used strobilurin fungicide trifloxystrobin (TFS) persistently erodes antiviral competence in fish and increases susceptibility to spring viremia of carp virus (SVCV) by driving dynamin-related protein 1 (Drp1)-mediated excessive mitophagy and sustained mitochondrial dysfunction. Using epithelioma papulosum cyprini (EPC) cells and zebrafish as complementary models, we find that environmentally plausible TFS exposures (2.5-25 \u03bcg/L) elevate SVCV permissiveness; notably, this phenotype resolves incompletely after chemical withdrawal. Transcriptomics revealed a dose-concordant shift toward stress/innate immune signaling and mitophagy programs, alongside broad repression of proliferative and DNA-repair pathways. Consistently, TFS induces persistent mitochondrial membrane depolarization, promotes fragmentation and ultrastructural deterioration, and increases mitochondria-lysosome coupling. Mechanistically, TFS elevates Drp1 abundance and Ser616 phosphorylation, promotes Drp1 recruitment to mitochondria, and sustains microtubule-associated protein 1 light chain 3B (LC3B)/lysosomal-associated membrane protein 2 (LAMP2) engagement, accompanied by persistent induction of core autophagy regulators (gabarap, atg5, wipi1, and ambra1) across extended recovery windows. In vivo, prolonged TFS exposure similarly yields durable enhancement of SVCV susceptibility even after long recovery periods, indicating incomplete restoration of host resistance. Together, these findings link a major agricultural fungicide to persistent Drp1-driven mitophagy overactivation and identify long-term antiviral resistance as an ecologically relevant endpoint for pesticide risk assessment and aquatic disease forecasting.IMPORTANCEViral diseases pose a significant challenge to sustainable aquaculture, and effective antiviral interventions remain limited. In this study, we reveal that trifloxystrobin, a widely used fungicide, induces mitochondrial dysfunction and Drp1-mediated excessive mitophagy, leading to long-term suppression of antiviral immune responses in fish. Importantly, this work identifies mitochondrial dynamics as a key determinant of viral susceptibility and demonstrates how environmental pollutants can reshape host-pathogen interactions. By linking mitophagy and Drp1 activation to increased spring viremia of carp virus susceptibility, our findings provide a novel perspective on how pollutants may exacerbate viral infections in aquaculture species. This work underscores the urgent need for ecosystem-based antiviral strategies and offers a mechanistic framework for assessing ecological risks posed by common agricultural chemicals, thereby informing environmental and disease management in aquaculture.",
"42227950": "ID: 42227950\nTitle: A cytosolic IF1 reporter enables real-time visualization of severe mitochondrial membrane damage.\nAbstract: Maintenance of mitochondrial integrity is fundamental for cellular survival, yet how cells recognize catastrophic mitochondrial membrane damage remains unknown. Here, we identify MAI-1 as the first genetically encoded reporter of severe mitochondrial membrane damage. MAI-1 is a Caenorhabditis elegans homolog of the ATP synthase inhibitor IF1 that lacks a mitochondrial targeting sequence, resides in the cytosol under basal conditions, but rapidly and irreversibly translocates to severely damaged mitochondria within milliseconds. We validate MAI-1 across diverse injury paradigms and demonstrate that cytosolic IF1 variants from other species exhibit conserved damage-induced recruitment. Mechanistically, MAI-1 recruitment requires the presence of an intact ATP synthase complex. Using MAI-1 as a sensor, we uncover that these severely damaged mitochondria are cleared through the LGG-1-mediated, PINK1/PARKIN-independent lysosomal pathway. Together, our findings establish a powerful tool for visualizing severe mitochondrial membrane damage and reveal a surveillance mechanism dedicated to structural integrity control.",
"42231395": "ID: 42231395\nTitle: Polymeric lysosome-targeting chimeras for extracellular \u03b1-synuclein degradation in Parkinson's disease.\nAbstract: Disease progression in Parkinson's disease has been driven by extracellular \u03b1-synuclein prion-like seeding throughout the course of the disease and therefore not just by the intracellular accumulation of the protein in isolated aggregates. Current therapies utilizing PROTACs cannot address the extra-cellular effects of \u03b1-synuclein spreading in this manner. This article proposes PolyTACs (Polymeric Lysosome-Targeting Chimeras) as hybrid antibody-polymer conjugates which use neuronal exofacial thiol groups produced because of DJ-1/GSH dysregulation to capture \u03b1-synuclein pathological conformers before they can be derepressed (seeded pathological aggregates) into the cytoplasm. The hybridity of these antibodies (oligomers and fibrils) combined with pyridyl disulfide linkages in the multi-valent polymer allows these compounds to circumvent LTR co-option, and to be trafficked to lysosomes via a non-clathrin pathway. The delivery route for these agents is intended to be via intra-nasal, thereby bypassing many of the issues associated with delivery through the BBB. Delivery to patients will be guided by thiol profiling in cerebrospinal fluid to assist in inclusion-exclusion criteria for patients in prodromal trials. With these developments, it is anticipated that this new class of agent may provide a modular framework adaptable to other proteinopathies such as tau and TDP-43, pending further validation.",
"42235331": "ID: 42235331\nTitle: Electrostatic control of membrane disruption and amorphous coaggregation by dynorphin A variants.\nAbstract: Dynorphin A is a highly cationic neuropeptide that exhibits membrane activity beyond its canonical opioid receptor signaling. Here, we investigate how sequence variants of Dynorphin A associated with spinocerebellar ataxia type 23 modulate membrane disruption and aggregation behavior. Using computational electrophysiology simulations combined with liposome leakage and fluorescence-based aggregation assays, we show that Dynorphin A variants interact with lipid bilayers primarily via electrostatic recruitment, followed by mutation-dependent insertion and transient pore formation. Anionic lipids promote bilayer disruption, while cholesterol attenuates peptide activity in a variant-specific manner. Although Dynorphin A variants do not spontaneously form ordered aggregates, they markedly alter amyloid-\u03b2 co-assembly by enhancing hydrophobic surface exposure without proportionally increasing fibrillization. These results demonstrate that subtle sequence changes fine-tune the balance between membrane perturbation and amorphous co-aggregation, and highlight electrostatic membrane recruitment as a key determinant of DynA bioactivity.",
"42236937": "ID: 42236937\nTitle: LASER couples damage sensing to ESCRT assembly for lysosome repair.\nAbstract: Lysosomal membrane integrity is essential for cell survival, but how damage sensing is spatiotemporally coupled to repair remains poorly understood. Recruitment and assembly of endosomal sorting complex required for transport (ESCRT) I-III rapidly counteracts membrane damage, but it is unclear\u00a0how ESCRT-I recognizes defective lysosomal membranes. Here, leveraging genome-wide CRISPRi screens in a damage-sensitized genetic background, we identified LC3/GABARAP-assisted stimulator for ESCRT recruitment (LASER), a multicomponent protein assembly that forms rapidly upon calcium release from damaged lysosomes and couples sensing of lysosomal membrane damage to ESCRT-dependent repair. At the core of LASER is TFG, an endoplasmic reticulum exit-site-resident protein that translocates to damaged lysosomes by binding to ATG8 family proteins (LC3 and GABARAP) conjugated to lysosomal phospholipids. ATG8-bound TFG forms oligomeric assemblies that directly recruit the essential ESCRT-I subunit TSG101 via conserved motif recognition enhanced by avidity-driven interactions. TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair. TFG mutations that drive hereditary spastic paraplegia disrupt its oligomerization and impair lysosomal ESCRT recruitment and membrane resealing, implicating defective repair as a driver of TFG-associated neurodegeneration. Thus, LASER promotes ESCRT polymerization at damaged lysosomes and couples damage sensing to membrane repair.",
"42248811": "ID: 42248811\nTitle: Ginsenoside Rg1, a Natural Lysosomal Enhancer, Alleviates Parkinson's Disease Pathology via Cathepsin D-Dependent Regulation of \u03b1-Synuclein Homeostasis.\nAbstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss and \u03b1-synuclein (\u03b1-syn) aggregation, often linked to lysosomal dysfunction. Cathepsin D (CTSD), a lysosomal hydrolase essential for \u03b1-syn clearance, becomes functionally impaired when its maturation is disrupted, exacerbating proteostatic stress. This study investigated whether ginsenoside Rg1(Rg1) restores CTSD maturation and lysosomal function to mitigate PD pathology. MPTP-induced zebrafish and mouse PD models, as well as MPP+-treated SH-SY5Y cells, animals and cells were treated with Rg1 at different concentrations. Motor behavior, dopaminergic neuron survival, \u03b1-syn clearance, CTSD maturation, lysosomal activity, endoplasmic reticulum (ER) stress, oxidative stress, autophagic flux, and apoptosis were systematically evaluated. Rg1 improved locomotor performance and preserved dopaminergic neurons, promoted \u03b1-syn clearance, and enhanced CTSD maturation in lysosomes. These effects coincided with reduced ER and oxidative stress, normalized autophagic flux, and decreased apoptosis. Rg1 functions as a natural lysosomal enhancer, restoring lysosome-ER homeostasis and counteracting multiple pathogenic pathways in PD. The findings reveal a CTSD-dependent regulatory axis in \u03b1-syn homeostasis and highlight Rg1 as a promising multi-target therapeutic candidate for PD.",
"42250519": "ID: 42250519\nTitle: Microplastics alter the toxicity of benzo[a]pyrene in a mangrove oyster: An integrated biomarker approach.\nAbstract: Microplastics (MPs) and Benzo[a]pyrene (BaP) are ubiquitous co-contaminants in marine environments, yet their combined ecotoxicological effects remain poorly understood. This study evaluated the isolated and interactive toxicity of alone linear low-density polyethylene (LLDPE) (0, 5, 50, 500\u202fmg\u202fL-1) and BaP (0, 3, 12, 21, 30\u202f\u03bcg\u202fL-1) in the mangrove oyster Crassostrea gasar, a key filter-feeding species highly vulnerable to particulate and hydrophobic contaminants. The concentrations of 5\u202fmg/L MPs and all BaP concentrations tested are environmentally relevant. Adult oysters were exposed for 7 days in a full factorial design, and biomarkers (Glutathione S-transferase, Glutathione Peroxidase, Reduced Glutathione, Lipid Peroxidation, DNA damage, Neutral Red Retention Time) were assessed in gills and hemolymph. Alone MPs alone induced oxidative and cytogenotoxic effects, confirming that even uncontaminated plastic particles can disrupt cellular homeostasis. Significant interactive effects between MPs and BaP were observed, particularly influencing oxidative stress and DNA integrity. GPx, GST, and GSH responses were associated with DNA damage at higher exposure levels. BaP increased lipid peroxidation, reducing lysosomal membrane stability, and this impairment was exacerbated under combined exposure. The integrated biomarker response index identified the combination of 30\u202f\u03bcg\u202fL-1 BaP and 500\u202fmg\u202fL-1 MP as the most hazardous scenario. The environmentally relevant MP concentration (5\u202fmg\u202fL-1) also produced significant effects when combined with BaP. These findings demonstrate that MPs modulate BaP toxicity and highlight the importance of assessing co-contaminant interactions in filter-feeding organisms. Although the highest concentration tested (500\u202fmg\u202fL-1) exceeds environmental levels, effects were also observed at environmentally relevant concentrations. The inclusion of elevated concentrations was intended to identify effect thresholds and underlying mechanisms, providing robust data for environmental risk assessment.",
"42252285": "ID: 42252285\nTitle: Lysine acetyltransferase 8-mediated histone acetylation, regulated by GBA1, is associated with lysosomal function related to \u03b1-Synuclein pathology.\nAbstract: Lysosomal defects are closely linked to Parkinson's disease (PD). Mutations in the GBA1 gene, encoding the lysosomal enzyme glucocerebrosidase (GCase), are major genetic risk factors for PD. GBA1 deficiency causes lysosomal dysfunction, leading to \u03b1-synuclein (\u03b1-syn) accumulation and PD progression. However, the underlying mechanisms remain unclear. In this study, we identified a novel GBA1-KAT8 regulatory pathway that controls lysosomal activity. GBA1 overexpression enhances lysosomal enzyme expression, regulates histone H4 acetylation at K16 via KAT8, and promotes lysosome-associated gene expression, highlighting an epigenetic mechanism in lysosomal biogenesis. Furthermore, GBA1 upregulated KAT8 expression, increased lysosomal enzyme levels, and decreased PFF-induced \u03b1-syn accumulation both in vitro and in vivo. The involvement of KAT8 as a critical acetyltransferase that modulates nuclear-lysosomal signaling pathways provides a mechanistic explanation for GBA1 deficiency-induced lysosomal dysfunction in association with PD pathology.",
"42260976": "ID: 42260976\nTitle: Porcine reproductive and respiratory syndrome virus hijacks the non-canonical enzymatic function of PHGDH to arrest autophagic flux for viral replication.\nAbstract: Viruses frequently hijack host metabolic enzymes to fuel replication. However, the mechanisms underlying this hijacking and utilization of metabolic enzymes remain poorly understood. In this study, we report a sophisticated mechanism by which porcine reproductive and respiratory syndrome virus (PRRSV) exploits a non-canonical enzymatic function of PHGDH (phosphoglycerate dehydrogenase) to modulate macroautophagy/autophagy. We demonstrate that PRRSV infection recruits the transcription factor ZNF143 (zinc finger protein 143) to transcriptionally repress PHGDH expression. Importantly, the antiviral restriction activity of PHGDH is entirely uncoupled from its canonical enzymatic role in serine biosynthesis. Mechanistically, PHGDH depletion triggers the initiation of autophagy via the AMP-activated protein kinase (AMPK)-ULK1 (unc-51 like autophagy activating kinase 1) signaling axis; however, it paradoxically arrests autophagic flux at the autophagosome-lysosome fusion stage. PHGDH is identified as a critical scaffold that facilitates the assembly of the autophagic soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex; its downregulation disrupts the interaction between STX17 (syntaxin 17) and SNAP29 (synaptosome associated protein 29), thereby blocking autophagosome-lysosome fusion. This induction of incomplete autophagy creates a favorable cytosolic niche for viral replication. Furthermore, the antiviral effect of PHGDH is also observed in two other swine pathogens, porcine epidemic diarrhea virus (PEDV) and pseudorabies virus (PRV). Collectively, these findings revealed that viruses weaponized the moonlighting function of a metabolic enzyme to dismantle autophagic flux, highlighting PHGDH as a broad-spectrum antiviral target that bridged metabolism and membrane trafficking.Abbreviation: AMPK: AMP-activated protein kinase; BECN1: beclin 1; CQ: chloroquine; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; PEDV: porcine epidemic diarrhea virus; PHGDH: phosphoglycerate dehydrogenase; PRV: pseudorabies virus; PRRSV: porcine reproductive and respiratory syndrome virus; SGOC: serine-glycine-one-carbon; siRNA: small interfering RNA; SNAP29: synaptosome associated protein 29; SNARE: soluble N-ethylmaleimide-sensitive factor attachment protein receptor; SQSTM1/p62: sequestosome 1; SSP: serine synthesis pathway; STX17: syntaxin 17; ULK1: unc-51 like autophagy activating kinase 1; VAMP8: vesicle associated membrane protein 8; ZNF143: zinc finger protein 143.",
"42268710": "ID: 42268710\nTitle: STING-OPTN signaling confers cytoprotection through TBK1-dependent mitophagy.\nAbstract: The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway plays an essential role in innate immunity. While recent studies have revealed its critical role in non-canonical autophagy independent of its immune function, its role in selective autophagy remains elusive. Here, we identify the cGAS-STING pathway as an upstream positive regulator of mitophagy. We demonstrate that activation of TANK-binding kinase 1 (TBK1) during mitophagy is strictly dependent on the cGAS-STING pathway. Mechanistically, TBK1 activation involves the mitochondrial recruitment of STING, which requires valosin-containing protein (VCP)/p97-mediated degradation of outer mitochondrial membrane proteins. Activated TBK1 then phosphorylates optineurin (OPTN), resulting in the efficient clearance of damaged mitochondria via the autophagosome-lysosome pathway. Disruption of the STING-OPTN axis impairs mitophagy, which switches cellular response from mitophagy to apoptosis. Our work thereby defines a non-canonical, pro-survival function of the cGAS-STING pathway in mitochondrial quality control.",
"42282839": "ID: 42282839\nTitle: Synphilin-1 mitigates autophagy dysfusnction, modulates ubiquitinated protein aggregation, and promotes cell survival during proteotoxic stress.\nAbstract: The decline of cellular proteostasis is a hallmark of aging and key contributor to neurodegenerative diseases. Protein turnover is controlled by the ubiquitin-proteasome and autophagosome-lysosome systems, but how degradation is coordinated when one of these pathways is compromised is not well understood. To study the regulation of proteostasis, we utilized human fibroblasts with targeted knockouts of the cytoskeletal factors WHAMM and JMY, which control multiple steps in autophagy. We found that cells lacking both WHAMM and JMY accumulated numerous intense foci of ubiquitinated proteins when exposed to proteotoxic stress and relied on proteasomes to clear the foci when the stressor was removed. RNA-seq and immunoblotting revealed that WHAMM/JMY knockout cells increased their expression of Synphilin-1, an \u03b1-synuclein-interacting protein implicated in Parkinson's Disease. In WHAMM/JMY knockout cells that upregulated endogenous Synphilin-1, and in cell lines engineered to overexpress mCherry-Synphilin-1, ubiquitinated proteins were present in structures containing both Synphilin-1 and proteasomes. RNAi-mediated depletion of Synphilin-1 caused a buildup of ubiquitinated proteins and the ubiquitin-binding adaptor protein SQSTM1/p62, while decreasing cell survival in response to proteotoxic stress. These data suggest that Synphilin-1 plays a pro-survival role in cells with impaired autophagy and functions in the distribution of ubiquitinated cargo during proteasomal degradation.",
"42284733": "ID: 42284733\nTitle: VPS13C-mediated endoplasmic reticulum-lysosome tethering in neuronal stress responses.\nAbstract: Organelle contact sites are increasingly recognized as regulatory interfaces that coordinate lipid transfer, ion signaling, and metabolic adaptation. In neurons, communication among the endoplasmic reticulum (ER), lysosomes, and mitochondria is essential for cellular homeostasis. Recent studies have identified vacuolar protein sorting 13 homolog C (VPS13C), a lipid transport protein, as a key mediator of ER-lysosome tethering and as an important component of the response to lysosomal stress. Structural analyses show that VPS13 family proteins form elongated lipid transport channels that are proposed to facilitate phospholipid transfer between adjacent membranes. Following lysosomal damage, VPS13C is recruited to ER-lysosome contact interfaces, where it forms tethering bridges that may support membrane repair by enabling high-capacity lipid transfer from the ER to lysosomal membranes. Beyond membrane repair, these contact interfaces may also participate in broader organelle communication networks. ER-lysosome contacts can occur in proximity to ER-mitochondria junctions, potentially forming multi organelle signaling hubs that coordinate lipid redistribution, calcium signaling, and mitochondrial adaptation. These signals may influence downstream responses, including activation of TFEB and TFE3, which regulate lysosomal biogenesis and autophagy. Disruption of this contact site network has emerged as a potential contributor to Parkinson's disease. Loss of VPS13C function is associated with altered lysosomal homeostasis and intersects with pathogenic pathways involving \u03b1-synuclein aggregation, PINK1/Parkin-mediated mitophagy, and LRRK2 signaling. This review presents a framework in which ER-lysosome tethering is considered part of a staged cellular damage response linking membrane repair, metabolic coordination, and transcriptional adaptation.",
"42302456": "ID: 42302456\nTitle: Polystyrene nanoplastics elicit early mitochondria-associated phenotypic, metabolic, and functional responses in human hepatocytes.\nAbstract: Nanoplastics have recently been detected in human liver tissue, raising concerns about their potential impact on liver function. However, early hepatocyte responses associated with nanoplastics exposure remain poorly understood. Here, we combined high-throughput Cell Painting-based phenomics, untargeted metabolomics, and Seahorse mitochondrial functional assay to investigate the effects of 100\u00a0nm polystyrene nanoplastics on human HepaRG hepatocytes, a surrogate for primary human hepatocytes. At the tested concentrations (6.25-100\u00a0\u00b5g/mL), exposure did not induce overt cytotoxicity, enabling assessment of early sublethal cellular responses. Phenomics revealed widespread subcellular perturbations, with 16.4% of the measured phenotypic features significantly altered. Mitochondria-associated features represented the dominant altered phenotypic signature, showing pronounced changes in granularity, texture, and radial distribution, alongside alterations in endoplasmic reticulum- and cytoskeleton-associated features. Untargeted metabolomics of intracellular metabolites and the extracellular secretome revealed metabolic alterations, characterized by changes consistent with altered \u03b2-oxidation, lipid handling, membrane stress, and central carbon metabolism, including changes in the tricarboxylic acid (TCA) cycle and amino acid catabolism. Pathway analysis identified the TCA cycle as one of the most significantly affected pathways (FDR\u00a0=\u00a00.028). Integrated phenomic-metabolomic analysis revealed strong correlations between mitochondrial phenotypic features and metabolites involved in lipid and energy metabolism, indicating a coordinated structural-metabolic response to polystyrene nanoplastics exposure. Functional assessment using Seahorse assay showed reduced basal and maximal respiration and decreased ATP-linked O2 consumption. Together, these findings provide evidence that 100\u00a0nm polystyrene nanoplastics elicit early mitochondria-associated phenotypic, metabolic, and functional responses prior to overt cytotoxicity under the tested conditions. They also highlight the value of phenomic-metabolomic-functional integration for profiling sublethal nanotoxicological responses and guiding future targeted mechanistic studies.",
"42310725": "ID: 42310725\nTitle: Targeting lysosomal pH restores mitochondrial quality control in GBA1-mutant Parkinson's disease.\nAbstract: Heterozygous mutations in the glucocerebrosidase gene (GBA1), which encodes the lysosomal enzyme \u03b2-glucocerebrosidase (GCase), are a genetic risk factor for Parkinson's disease (PD). The pathophysiological consequences of GBA1 mutations on dopaminergic neuronal function, especially their impact on lysosomal function, mitophagy, and mitochondrial bioenergetics, remain unclear. Fibroblasts and dopaminergic neurons generated from induced pluripotent stem cells (iPSCs) derived from patients with\u00a0GBA1-PD were used in the study. Live-cell imaging was performed to measure lysosomal acidification, protease activity, mitochondrial membrane potential, and mitophagy. Mitochondrial morphology and autophagic vesicles were examined using transmission electron microscopy. Oxygen consumption rate was measured by Seahorse assay. V-ATPase assembly was quantified using fluorescence lifetime imaging with F\u00f6rster resonance energy transfer (FLIM-FRET), and pharmacological interventions included rapamycin and acidic nanoparticles. GCase activity, lysosomal acidification, protease activity, mitophagy and mitochondrial bioenergetic function were all impaired in GBA1 mutant dopaminergic neurons. Mitochondria were fragmented, with reduced membrane potential and oxygen consumption. Mechanistic target of rapamycin complex 1 (MTORC1) was constitutively phosphorylated and FLIM-FRET measurements confirmed impairment of lysosomal V-ATPase assembly, which was reversed by rapamycin treatment. Rapamycin and lysosome-targeting acidic nanoparticles rescued lysosomal pH and restored mitophagy, mitochondrial membrane potential and mitochondrial oxidative phosphorylation complex level in the GBA1 mutant dopaminergic neurons. We revealed a novel mechanistic link between GBA1 mutations and mitochondrial dysfunction, as the disruption of V-ATPase assembly driven by MTORC1 activation impairs lysosomal acidification. This causes impairment of mitophagy, leading to mitochondrial dysfunction, undermining dopaminergic cell function and fate. Pharmacological intervention with rapamycin or acidic nanoparticles restores lysosomal pH and rescue mitochondrial function, representing a novel therapeutic approach for\u00a0GBA1-PD .",
"42325197": "ID: 42325197\nTitle: Small bites for big problems: stepwise aggregate degradation by autophagy.\nAbstract: Protein aggregates are a pathological hallmark of diverse disorders, including many neurodegenerative diseases, but also cardiometabolic disease and cancer. While the ubiquitin-proteasome system efficiently removes many soluble misfolded proteins, large or persistent assemblies often require the autophagy-lysosome pathway for their degradation. In the present mini-review, we summarize our knowledge of aggrephagy, the selective clearance of protein aggregates by autophagy, and discuss two recent manuscripts that argue that some aggregates must be primed for autophagosomal degradation, through chaperone-mediated remodeling. Aggrephagy substrates are defined by aggregate architecture, biophysical state, surface accessibility, and the physical constraints of membrane capture. These features help to explain why recruitment of selective autophagy receptors is necessary yet insufficient for clearance. Receptor clustering is required to concentrate early autophagy factors to establish initiation hubs, but successful degradation often requires upstream generation of smaller 'aggrephagy-competent' cargo units, which contain autophagy receptor clusters that successfully initiate autophagosome formation. Recent work supports a model in which larger aggregates are cleared through stepwise degradation enabled by prior remodeling steps that involve p97/VCP-driven disintegration or a chaperone module (DNAJB6-HSP70-HSP110) cooperating with the proteasomal 19S regulatory particle.",
"42327019": "ID: 42327019\nTitle: Structural Mechanism and Cellular Restriction of Tau Seeding from Endolysosomes.\nAbstract: The prion-like spread of tau from cell to cell in the central nervous system involves escape from the endolysosomal network, which is counteracted by the lysosomal repair activity of the ESCRT system. Here, we investigate whether other components of the lysosomal damage sensing and repair system, namely the ESCRT-recruiting Ca 2+ sensor ALG-2, conjugation of ATG8s to single membranes (CASM), the phosphoinositide-initiated tethering and lipid transport (PITT) pathway, and the Parkinson's disease-related lipid transporter VPS13C are involved in tau spread. We found that the PITT pathway and VPS13C are strongly implicated in tau seeding by pre-formed fibrils (PFFs) in both neurons and astrocytes, CASM has a major role in astrocytes but not neurons, and ALG-2 has a lesser role in both. We then investigated the mechanism of damage and seeding by tau PFFs using cryo-electron tomography. Unlike the classical lysosome damage agent LLOMe, tau PFFs were not seen to directly interact with the lysosomal membrane, nor do they distort local membrane curvature. Lysosomes in PFF-treated cells were structurally intact. Extensive protein aggregates of similar character were seen in both the lysosomal lumen and in the cytosol proximal to lysosomes. The observations are consistent with the PFF-induced co-aggregation of tau with other cellular materials within lysosomes, with leakage to the cytosol attributed to reversible holes in the lysosome membrane.",
"42327061": "ID: 42327061\nTitle: Lipid transfer protein ORP3 mediates lysosomal repair via LC3B and ubiquitin-TAK1-p38 signaling.\nAbstract: Lysosomal membrane damage triggers a multi-stage repair response essential for cellular homeostasis. Here we identify the oxysterol-binding protein-related protein ORP3 as a critical mediator of late-stage lysosomal membrane repair. Following lysosomal damage induced by L-leucine-leucine methyl ester (LLOME) or cationic amphiphilic drugs (CADs), ORP3 is phosphorylated and recruited to ER-lysophagosome contact sites via a signaling cascade initiated by lysosomal membrane ubiquitination, TAK1, p38 MAPK, and, to a lesser extent, IKK. p38-dependent phosphorylation promotes direct interaction between ORP3 and LC3B, which together with PI(4,5)P\u2082 binding, is required for autophagic lysosome recruitment. ORP3 depletion impairs late-stage lysosomal recovery, elevates lysosomal lipid peroxidation, and reduces cell survival. A lipid transfer-deficient ORP3 mutant fails to restore lysosome function despite normal recruitment, indicating that ER-to-lysophagosome transfer of phosphatidylcholine by ORP3 is functionally required. ORP3 activity is subsequently terminated by VCP/p97-mediated deubiquitination of lysosomes. These findings define ORP3 as a MAPK regulated lipid transfer protein during the late autophagic phase of the endolysosomal damage response. Lysosomal membrane damage triggers ubiquitination that activates a TAK1-p38 signaling cascade, phosphorylating the lipid transfer protein ORP3 and recruiting it to damaged lysosomes via LC3B interaction. ORP3-mediated phosphatidylcholine transfer from the ER is essential for late-stage lysosomal repair and cell survival.",
"42332197": "ID: 42332197\nTitle: mRAVE governs lysosomal catabolism through basal and mTORC1-regulated V-ATPase assembly.\nAbstract: Acidification of lysosomes, endosomes and the Golgi underpins organelle-specific functions within the endomembrane system. This process is driven by vacuolar-type H\u2009+\u2009-ATPases (V-ATPases), proton pumps that reversibly assemble from peripheral V1 and membrane-integral Vo domains to regulate organelle pH. In yeast, V1-Vo assembly at the vacuole is mediated by the RAVE complex, but V-ATPase assembly in mammalian cells remains less well understood. Here, we systematically characterize physiological roles of the mammalian RAVE complex, composed of the subunits Dmxl1 or Dmxl2, Wdr7 and Rogdi. Under basal conditions, mRAVE broadly promotes V-ATPase assembly and luminal acidification of endomembrane organelles. Upon mTORC1 inactivation, mRAVE is recruited to lysosomes and required for the resulting increase in V-ATPase assembly and catabolic activity. Loss of mRAVE disrupts organelle acidification, leading to suppression of lysosomal catabolism, accumulation of dysfunctional lysosomes and lysosomal exocytosis. Restoring lysosomal pH rescues basal function in mRAVE-deficient cells but not the mTORC1-regulated increase in catabolic activity. Thus, mRAVE is an essential V-ATPase assembly factor that couples acidification to organelle function and nutrient signaling.",
"42338213": "ID: 42338213\nTitle: [Progress on mechanism of mitochondrial autophagy in pathogenesis of intervertebral disc degeneration based on PINK1/Parkin signaling pathway].\nAbstract: Intervertebral disc degeneration (IVDD) is one of the main causes of lower back pain. The chronic accumulation of aging and apoptosis of nucleus pulposus cells (NPCs) is believed to be related to IVDD. In recent years, mitochondrial autophagy which as an important clearance mechanism within cells, has gradually attracted attention. The PINK1/Parkin signaling pathway is regarded as the key pathway regulating mitochondrial autophagy, and it plays a significant role in physiological and pathological processes of NPCs. The mechanism by which PINK1/Parkin signaling pathway mediates mitochondrial autophagy could be understood as follows, PINK1, as the sensor for mitochondrial quality regulation, is activated. It recruits and activates Parkin to the mitochondrial membrane through phosphorylation of ubiquitin, and then undergoes Parkin-dependent substrate ubiquitination, recruitment of autophagy receptors, formation of autophagosomes, and fusion with lysosomes, ultimately completing the extremely important autophagy process. Current research indicates that abnormality of PINK1/Parkin signaling pathway may be closely related to IVDD, but the specific mechanism still requires further exploration. The paper explores research progress of mechanism by which mitochondrial autophagy affects IVDD based on PINK1/Parkin signaling pathway, with the aim of providing new strategies and targets for the treatment of IVDD.",
"42344932": "ID: 42344932\nTitle: AKT-mediated phosphorylation of ZDHHC5 promotes NOD1 palmitoylation and innate immune signaling.\nAbstract: Nucleotide-binding oligomerization domain 1 (NOD1) is an intracellular pattern recognition receptor that detects bacterial peptidoglycan and initiates innate immune responses through membrane-associated signaling complexes. NOD1 activation depends on ZDHHC5-mediated palmitoylation, which promotes its membrane recruitment. However, whether growth factors and insulin modulate this NOD1 activation remains poorly defined. We investigated the effects of growth factors and insulin on NOD1 signaling using biochemical and cell-based approaches. Protein phosphorylation and interactions were analyzed by immunoblotting, co-immunoprecipitation, and mutagenesis assays. NOD1 palmitoylation, membrane localization, and downstream signaling activities were evaluated following modulation of AKT signaling and ZDHHC5 phosphorylation. We found that growth factors and insulin positively regulate NOD1 activation through an AKT-ZDHHC5-NOD1 signaling axis. Mechanistically, AKT directly phosphorylated the palmitoyltransferase ZDHHC5 at Ser345 and Ser380, promoting its retention at the plasma membrane and enhancing its enzymatic activity toward NOD1. AKT-dependent phosphorylation increased NOD1 palmitoylation and membrane recruitment, thereby facilitating activation of downstream innate immune signaling pathways. These findings identify a previously unrecognized mechanism linking growth factor- and insulin-mediated AKT activation to innate immune signaling. AKT-dependent phosphorylation of ZDHHC5 promotes NOD1 palmitoylation and activation, revealing a positive regulatory axis that integrates metabolic cues with innate immune responses. The AKT-ZDHHC5 pathway may therefore represent a potential target for modulating NOD1- driven inflammatory diseases.",
"42353031": "ID: 42353031\nTitle: PKC\u03b2II Activation Promotes Membrane-Proximal Enrichment of Ribosome-Bound RACK1.\nAbstract: The scaffold protein RACK1 (Receptor for Activated C Kinase 1) integrates signaling and translation, acting as a core component of the 40S ribosomal subunit. It binds activated Protein Kinase C (PKC) isoforms and membrane receptors. We used an auxin-inducible degron (AID2) system in human HAP1 cells to selectively deplete the free (cytoplasmic) pool of RACK1. The engineered RACK1-mAID-mClover3 fusion was rapidly degraded in the cytoplasm upon addition of 5-phenyl-indole-3-acetic acid (5-Ph-IAA), while the ribosome-bound pool remained detectable in ribosomal fractions, indicating that ribosome association makes RACK1 relatively less accessible to AID2-mediated proteolysis. Upon activation of PKC\u03b2II with phorbol-12-myristate-13-acetate (PMA), imaging at defined time points revealed closely matched kinetics of PKC\u03b2II membrane recruitment and membrane-proximal enrichment of ribosome-bound RACK1, peaking at ~10 min. Our data support a model in which activated PKC\u03b2II engages ribosome-bound RACK1 at membrane-proximal sites, consistent with a diffusion-capture mechanism in which PKC\u03b2II first accumulates at the membrane and then captures ribosome-bound RACK1, thereby recruiting the translational machinery to sites of signal input for membrane-proximal translation. These findings provide new insights into the spatial organization of translation.",
"42365211": "ID: 42365211\nTitle: A new paradigm in Parkinson's disease: kidney-origin \u03b1-synuclein pathology driven by PKC signaling and aurothioglucose.\nAbstract: Protein Kinase C (PKC), a zinc-dependent signaling enzyme essential for cellular homeostasis, has recently emerged as a critical regulator of \u03b1-synuclein (\u03b1-Syn) dynamics beyond the central nervous system. Growing evidence suggests that PKC may contribute to \u03b1-Syn accumulation in kidney cells through multiple converging mechanisms, including direct phosphorylation of \u03b1-Syn, which promotes its aggregation, disruption of the autophagy-lysosome pathway leading to impaired protein clearance, and amplification of oxidative stress and inflammatory responses that enhance \u03b1-Syn toxicity. In a paradigm-shifting discovery, recent findings from Wuhan University indicate that Parkinson's disease (PD) pathology may originate in peripheral organs such as the kidneys rather than the brain. Abnormal \u03b1-Syn aggregates have been identified in renal tissues of affected individuals, and experimental models demonstrate that compromised kidney function facilitates the systemic spread of these toxic proteins to the brain, potentially initiating neurodegeneration. Notably, \u03b1-Syn accumulation has also been observed in patients with chronic kidney disease in the absence of neurological symptoms, suggesting a potential early reservoir function of the kidneys. In this context, aurothioglucose (ATG), a gold-based anti-inflammatory agent, emerges as a promising therapeutic candidate due to its ability to modulate PKC signaling, attenuate inflammation, and restore proteostatic balance. This review highlights a novel kidney-brain axis in PD pathogenesis and proposes PKC-targeted interventions, including ATG, as potential strategies for early disease modification.",
"42366573": "ID: 42366573\nTitle: Radial outer retina reflectivity (RORR) sign in LAMP2-associated retinopathy.\nAbstract: To describe the radial outer retina reflectivity (RORR) sign in patients carrying pathogenic variants in the X-linked lysosome-associated membrane protein-2 (LAMP2) gene and to review the histologic characteristics of LAMP2 expression in the human retina. International multicentre observational case series and experimental laboratory study of patients with LAMP2 deficiency. Baseline demographics and multimodal retinal imaging including colour and fundus autofluorescence (FAF), optical coherence tomography (OCT) with en face reconstruction and fluorescein angiography were obtained. Sections through the retina of a human donor eye were processed for immunofluorescence combining antibodies against LAMP2 with markers for M\u00fcller glia, rod and cone photoreceptors. Sections were imaged using high-resolution multichannel confocal microscopy. Assessment of en face OCT reflectivity profiles at 5-50\u2009\u03bcm internal to the plane of external limiting membrane (ELM) was performed as well as histologic localisation of LAMP2. We recruited 11 cases with pathogenic variants in LAMP2 across five countries. Six cases demonstrated peripheral radial streaks of hyper- and hypopigmentation with UWF imaging. The RORR sign was best visualised 10-25\u2009\u03bcm internal to ELM in 9 cases. We hypothesise the radial pattern to be secondary to X-chromosome inactivation. LAMP2 immunoreactivity was observed internal and external to the ELM. Our findings expand the phenotypic spectrum of LAMP2-associated retinopathy by demonstrating the RORR sign using en face OCT. Histologic sections revealed LAMP2 expression in the neuroretina.",
"42372161": "ID: 42372161\nTitle: Two-step mechanism of Bruton's tyrosine kinase membrane recruitment and activation.\nAbstract: Peripheral membrane proteins (PMPs) are critical mediators of signaling cascades initiated at the cell surface. Their functions depend on their innate ability to interact dynamically with membranes in response to changing cellular conditions. This membrane recruitment may occur via high-affinity interactions with specific lipids/proteins or via transient, low-affinity interactions with the membrane. These weak and dynamic interactions, which are critical regulators of PMP function, are challenging to capture. Taking Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase essential for B cell activation, we demonstrate a native mass spectrometry platform to understand lipid-mediated recruitment of PMPs by directly studying it from lipid bilayers customized to target membranes. Our data demonstrate that BTK recognizes phosphatidylserine (PS) independently of phosphatidylinositol (3, 4, 5) phosphate (PIP3) binding. We show that PS-bound BTK retains PIP3 binding via high-affinity sites, while exhibiting PIP3-independent basal membrane recruitment. Biochemical assays show that this PS-mediated recruitment sensitizes BTK to PIP3-mediated activation at near-physiological PIP3 concentrations. Thus, we propose a two-step model for BTK membrane recruitment and activation. A low-affinity interaction with high-copy number PS enables plasma membrane recruitment of BTK and increases its membrane-bound concentration. Upon B cell activation, this prerecruited, membrane-bound BTK population localizes to PIP3-rich domains via electrostatic gliding along the membrane, driven by low-affinity PS and high-affinity PIP3 binding. This indicates a cooperative mechanism in which PS can amplify B cell signaling by increasing membrane-bound BTK levels. Our work demonstrates a general model of regulation of PH domain-containing proteins by weak protein-lipid interactions, which can be extended to other PMPs.",
"42400323": "ID: 42400323\nTitle: A PARK9 iPSC-Derived Dopaminergic Neuron Model Enables Drug Screening Targeting Autophagy-Lysosome Pathway Dysfunction in Parkinson's Disease.\nAbstract: Parkinson's disease (PD) is a neurodegenerative disease characterized by dopaminergic neuronal degeneration in the substantia nigra, in which lysosomal dysfunction and impaired autophagy-lysosome pathway activity are increasingly recognized as important pathogenic mechanisms. However, disease-modifying therapies targeting this pathway remain unavailable. Here, we generated induced pluripotent stem cells (iPSCs) from a PARK9 patient carrying an ATP13A2 mutation and established mutation-corrected isogenic control iPSCs. PARK9 iPSC-derived neurons recapitulated lysosomal dysfunction-associated cellular phenotypes, including impaired lysosomal acidification, reduced mature cathepsin D levels, CD63-positive vesicle accumulation, LC3B-positive autophagosome accumulation, cytoplasmic pSer129 \u03b1-synuclein accumulation, and increased cleaved caspase-3 signals. These phenotypes were ameliorated in mutation-corrected neurons, supporting the contribution of ATP13A2 dysfunction to these abnormalities. We then performed high-content imaging-based compound screening targeting LC3B-positive autophagosome accumulation in PARK9 neurons. A three-step workflow identified 19 candidate compounds that reduced autophagosome accumulation consistent with partial improvement of lysosome-dependent downstream autophagosome processing rather than simple suppression of autophagosome formation. Among these, paroxetine, Ro 25-6981, amisulpride, and PK11195 showed additional, compound-dependent effects on PARK9-associated phenotypes, including lysosomal acidification, CD63-positive vesicle accumulation, cytoplasmic pSer129 \u03b1-synuclein signals, and cleaved caspase-3 signals. These findings establish PARK9 iPSC-derived neurons as a useful model of lysosomal dysfunction-associated PD pathology and provide a practical screening platform for identifying candidate compounds that modulate autophagy-lysosome pathway-related cellular phenotypes.",
"42443527": "ID: 42443527\nTitle: DCAF13: a positive regulator of colon cancer cell proliferation via the AMER2/ Wnt/\u03b2-catenin pathway.\nAbstract: The Wnt/\u03b2-catenin pathway plays a critical role in colorectal cancer (CRC) development. The significance of Wnt/\u03b2-catenin in maintaining the stability of adult tissues and challenges in identifying suitable molecular targets have limited the application of targeting the Wnt/\u03b2-catenin pathway. As one of the Cullin RING Ligase 4 adapters, DNA damage-binding protein 1 (DDB1) - and CUL4 correlation factor 13 (DCAF13) appears strongly expressed in different tumors. Our findings confirm enhanced expression of DCAF13 in tissues of CRC origin and related cell. In colon cancer cells, DCAF13 regulated adenomatous polyposis coli membrane recruitment 2 (AMER2) through ubiquitination, DCAF13 deletion increased AMER2 expression, which inhibited Wnt/\u03b2-catenin activity, suppressing cell proliferation. This effect was further validated in mice with gut-specific DCAF13 knockout. The ubiquitin-proteasome system is a potential target for drug development and cancer treatment. Beta-propeller proteins, such as CRL4 adapter DCAFs, are easily targeted by drugs. DCAF-proteolysis-targeting chimeras (PROTACs) can overcome drug resistance and selectively target tumor drivers by leveraging the unique substrate specificity of the DCAF subunits. DCAF13 emerges as a promising target for CRC, acting via the DCAF13-AMER2-Wnt /\u03b2-catenin axis.",
"42455619": "ID: 42455619\nTitle: Clearance and secretion of \u03b1-synuclein by RTN3L-mediated endoplasmic reticulum autophagy.\nAbstract: The misfolding and aggregation of \u03b1-synuclein (\u03b1-syn), an abundant synaptic protein, leads to the pathogenesis of Parkinson's disease and related synucleinopathies. The cell-to-cell propagation of seeding-competent \u03b1-syn is initiated by unconventional protein secretion, yet the physiological pathway(s) underlying this process remain poorly defined. Here we show that \u03b1-syn secretion in human cells is mediated by Reticulon-3L (RTN3L)-dependent endoplasmic reticulum autophagy (ER-phagy), a conserved protein quality-control pathway that safeguards ER protein homeostasis. We also demonstrate that RTN3L cooperates with several autophagy regulators, including the ULK1 cofactor FIP200, to drive the delivery of \u03b1-syn into an acidic endolysosomal compartment. Increasing concentrations of \u03b1-syn disrupt ER-lysosome traffic and \u03b1-syn-containing vesicles appear to be rerouted to the cell surface. Consistent with this proposal, knockdown of vesicle associated SNAREs, that mediate fusion at the cell surface, disrupt \u03b1-syn secretion. These findings suggest that pathogenic \u03b1-syn secretion arises as a by-product of a physiological clearance mechanism, driven by the fusion of autophagosome-derived vesicles with the plasma membrane. Our results provide a conceptual framework for understanding how an intracellular proteostasis pathway, when mis-regulated, could contribute to the spread of neurodegenerative pathology.",
"42463431": "ID: 42463431\nTitle: VPS35 Regulates Microglial Lipid Droplet Accumulation in Parkinson's Disease via Rab7.\nAbstract: Microglial dysfunction and aberrant lipid metabolism are emerging as key contributors to Parkinson's disease (PD) pathogenesis. However, the specific role and regulation of lipid droplets (LDs) within microglia remain poorly defined. In this study, we employed MPTP- and LPS-induced PD mouse models and an in\u00a0vitro system utilizing astrocyte-conditioned medium to model disease-relevant lipid stress and found enhanced LD accumulation in microglia. VPS35 expression was decreased in microglia, correlating with elevated microglial LD levels in PD mouse models. We then performed genetic manipulations (knockdown and overexpression) of VPS35, including the PD-associated D620N mutant, in primary microglia and assessed LD accumulation, phagocytic function, inflammatory responses, and integrated stress pathways. We showed that VPS35 knockdown exacerbated the accumulation of LDs in microglia. Conversely, VPS35 overexpression ameliorated LD formation, improved phagocytic function, and reduced inflammatory and integrated stress responses in microglia. The PD-related VPS35[D620N] mutation abolished these protective effects. We further found that VPS35 interacts with Rab7 to maintain lysosomal function, and the D620N mutation disrupts this interaction, leading to defective LD clearance. Our findings reveal VPS35 dysfunction as a key pathogenic mechanism in PD, where the D620N mutation disrupts microglial lipid handling to promote disease progression, thereby nominating VPS35 restoration as a promising therapeutic strategy.",
"42463668": "ID: 42463668\nTitle: Reconstitution of Ras-PI3K\u03b3 membrane communication and feedback using light-induced signaling inputs.\nAbstract: Reactions involving small GTPases and phosphatidylinositol phosphate (PIP) lipids serve essential roles in signal transduction at the plasma membrane. In cells, these distinct classes of molecules are linked through positive and negative feedback loops that give rise to emergent properties such as excitability and polarization. Here, we reconstitute communication and feedback between Ras GTPase and phosphatidylinositol 3-kinase gamma (PI3K\u03b3)-mediated PIP3 production on supported membranes using purified proteins. We employ light-induced membrane recruitment to rapidly shift steady-state conditions and observe the spatiotemporal response of the signaling module. Alone, the Ras-PI3K\u03b3 module exhibits transient and reversible activation due to global inhibition. The introduction of GEF-mediated positive feedback enables sustained threshold crossing and local amplification of Ras(GTP) and PIP3, resulting in a traveling, bistable wave of activity with characteristics of an excitable network. Spatial coupling between Ras(GTP) and PIP3 lipids depends on lateral diffusion and feedback circuit architecture. This work illuminates the roles activation thresholds, membrane diffusion, and positive feedback play in regulating the dynamics of Ras-PI3K\u03b3 membrane signaling reactions in the presence of global inhibition.",
"42477140": "ID: 42477140\nTitle: Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.\nAbstract: Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), which restores lysosomal function during hypoxia-reoxygenation stress. During B-fission, damaged lysosomes generate membrane buds that undergo scission to form small, fully functional lysosomes, independently of autophagic lysosome reformation. Mechanistically, mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission. MIRO2 promotes the formation of MFF+ MDVs through direct interaction with MFF, while the lysosomal membrane protein ITM2C binds MIRO2 to tether and guide MFF+ MDVs to lysosomes, enabling efficient MFF delivery and subsequent B-fission. Notably, AMPK activation by 991 or metformin promotes MFF-dependent lysosomal B-fission under normoxic conditions, whereas AMPK inhibition by dorsomorphin suppresses B-fission during hypoxia-reoxygenation. This stress-responsive ITM2C-MIRO2-MFF-DRP1 axis co-opts the mitochondrial division machinery to drive lysosomal fission from damaged lysosomes, thereby enabling the undamaged components to reorganize into daughter lysosomes and promote lysosomal renewal. Thus, our findings uncover a fundamental mode of lysosomal renewal and reveal an unexpected role for MDV-mediated mitochondria-lysosome communication in mediating lysosomal quality control during ischaemia-reperfusion and related stresses."
},
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"mice, inbred c57bl": 8,
"parkinson disease": 17,
"cells, cultured": 3,
"male": 9,
"humans": 47,
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"polyethylene": 1,
"water pollutants, chemical": 1,
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"comet assay": 1,
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"marine pollution": 1,
"polyethylene microplastics (pe-mps)": 1,
"clearance": 2,
"integrin \u03b1v/\u03b25": 1,
"irisin": 1,
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"neurons": 4,
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"cell line": 1,
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"cyclic guanosine monophosphate-adenosine monophosphate synthase": 2,
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"map3k12": 1,
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"lysosomal homeostasis": 1,
"astrocytes": 3,
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"glucose": 2,
"endoplasmic reticulum": 4,
"reactive oxygen species": 4,
"glucose transporter type 1": 1,
"er\u2013mitochondria\u2013lysosome dysfunction": 1,
"lrrk2 gtpase domain mutation": 1,
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"nanoparticles": 5,
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"1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine": 2,
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"liver": 3,
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"tripeptidyl peptidase ii": 1,
"parkinson\u00b4 disease - alpha-synuclein - genetics - environment - risk factors": 1,
"endosomal sorting complexes required for transport": 2,
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"ea": 1,
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"brain": 2,
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"pregnancy": 1,
"lactation": 2,
"maternal exposure": 1,
"prenatal exposure delayed effects": 1,
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"drosophila proteins": 1,
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"cell membrane": 9,
"protein binding": 4,
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"enzyme activation": 2,
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"kinase regulation": 1,
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"protein\u2013lipid interaction": 2,
"receptors for activated c kinase": 1,
"ribosomes": 1,
"protein kinase c beta": 1,
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"tetradecanoylphorbol acetate": 1,
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"rack1": 1,
"local translation": 1,
"ribosome": 1,
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"phosphorylation": 4,
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"insulin": 2,
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"exons": 1,
"peptides": 1,
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"huntington's disease": 1,
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"lysine": 1,
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"protein kinase inhibitors": 1,
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"models, molecular": 2,
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"chemotaxis": 2,
"dictyostelium": 1,
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"heterotrimeric gtp-binding proteins": 1,
"adaptation, physiological": 1,
"g protein-coupled receptor (gpcr)": 1,
"ras gtpase activating protein (rasgap)": 1,
"adaptation": 1,
"heterotrimeric g protein": 1,
"phospholipase c gamma": 1,
"cell movement": 1,
"optogenetics": 1,
"stat3 transcription factor": 2,
"ovarian neoplasms": 1,
"oxidoreductases acting on ch-ch group donors": 1,
"drug resistance, neoplasm": 1,
"membrane microdomains": 1,
"nerve tissue proteins": 1,
"atp binding cassette transporter, subfamily b, member 1": 1,
"cholesterol": 2,
"dhcr24": 1,
"p-gp": 1,
"stat3": 3,
"chemotherapy resistance": 1,
"ovarian cancer": 1,
"enteric nervous system": 1,
"food contamination": 1,
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"lipids": 1,
"lysophagy": 2,
"membrane damage": 2,
"cp: cancer": 1,
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"ufl1": 1,
"ufmylation": 1,
"lung adenocarcinoma": 1,
"macrophages": 3,
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"needles": 1,
"receptors, igg": 1,
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"engulfment capacity": 1,
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"zipper mechanism": 1,
"prkcg mutation": 1,
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"cell differentiation": 1,
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"temperature": 1,
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"protein domains": 2,
"plant proteins": 1,
"fibrosis": 1,
"rats": 1,
"wnt proteins": 1,
"myocytes, smooth muscle": 1,
"urinary bladder": 1,
"rats, sprague-dawley": 1,
"biochemistry": 1,
"biological sciences": 1,
"gpcr signaling": 1,
"g\u03b2\u03b3": 1,
"pip2": 1,
"plc\u03b23": 1,
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"plakophilins": 1,
"cadherins": 1,
"animals, newborn": 1,
"desmosomes": 1,
"cell adhesion": 1,
"gamma catenin": 1,
"cardiomyocyte": 1,
"cell\u2013cell adhesion": 1,
"desmosome interactome": 1,
"intercalated disc": 1,
"plakophilin 2": 1,
"muscle, skeletal": 1,
"insulin resistance": 2,
"mice, knockout": 2,
"obesity": 1,
"glucose transporter type 4": 1,
"scaffold protein ilk": 1,
"ecm": 1,
"integrin": 1,
"metabolism": 1,
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"adp-ribosylation factor 1": 2,
"cryoelectron microscopy": 2,
"adaptor protein complex 4": 1,
"protein transport": 3,
"occludin": 1,
"tight junctions": 1,
"caco-2 cells": 1,
"toll-like receptor 2": 1,
"intestinal mucosa": 1,
"up-regulation": 1,
"bifidobacterium bifidum": 1,
"intestinal barrier function": 1,
"probiotics": 1,
"epithelial cells": 1,
"interleukin-1 receptor-associated kinases": 1,
"sorting nexins": 1,
"pulmonary fibrosis": 1,
"wnt signaling pathway": 1,
"beta catenin": 1,
"bleomycin": 1,
"lung": 1,
"endosomes": 4,
"crispr/cas9": 1,
"live cell imaging": 1,
"saiyan system": 1,
"small gtpase": 1,
"split fluorescent protein": 1,
"brucella abortus": 1,
"brucellosis": 1,
"brucella": 1,
"zdhhc": 1,
"cryo-em": 1,
"fam126a": 1,
"hdx-ms": 1,
"pi4ka": 1,
"pi4p": 1,
"ttc7a": 1,
"ttc7b": 1,
"nanobody": 1,
"autophagy\u2013lysosome pathway": 1,
"microbiome\u2013gut\u2013brain axis": 1,
"mitochondrial": 1,
"neuroinflammation": 1,
"precision medicine": 1,
"proto-oncogene proteins b-raf": 1,
"14-3-3 proteins": 1,
"protein multimerization": 1,
"cysteine": 1,
"braf\u2010specific region": 1,
"raf kinases": 1,
"autoinhibition": 1,
"fluorescence correlation spectroscopy (fcs)": 1,
"supported lipid bilayers": 1,
"total internal reflection fluorescence (tirf) microscopy": 1,
"prpsc proteins": 1,
"tau proteins": 1,
"prion diseases": 1,
"ftld": 1,
"msa": 1,
"prp": 1,
"prion protein": 1,
"tau": 1,
"therapeutics": 1,
"a-syn": 1,
"prion": 1,
"danon disease": 1,
"lamp2": 1,
"m\u00fcller glia cells": 1,
"x\u2010linked carrier": 1,
"dilated cardiomyopathy": 1,
"external limiting membrane": 1,
"hypertrophic cardiomyopathy": 1,
"inherited retinal disease": 1,
"optical coherence tomography": 1,
"retina": 1,
"pten-induced putative kinase": 2,
"protein kinases": 1,
"intervertebral disc degeneration": 2,
"ubiquitin-protein ligases": 1,
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