Vamp8 modulates cerebral ischemia-reperfusion injury via the autophagy-lysosome pathway.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41047376", "kind": "science-record", "revision": 3, "content_hash": "sha256:3f13c5577df19973dda64803340611ca86da433131d4ed4a795c331fc7ae1a49", "created_at": "2026-11-01T20:31:06Z", "updated_at": "2026-11-01T22:14:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Vamp8 modulates cerebral ischemia-reperfusion injury via the autophagy-lysosome pathway.", "doi": "10.1038/s41598-025-20879-w", "pmid": "41047376", "authors": ["Yu-Xin Fu", "Jie Cao", "Xiang Yin", "Yue Lang", "Tengfei Su", "Li Cui"], "journal": "Scientific reports", "year": 2025, "abstract": "Lysosomal autophagy plays a critical role in ensuring the continuity of autophagic flux, however bioinformatics studies investigating biomarkers associated with lysosomal autophagy in cerebral ischemia-reperfusion injury(CIRI) remain scarce. Three datasets (GSE61616, GSE97537, and GSE82146) were retrieved from the GEO database. After batch correction, GSE61616 and GSE97537 were integrated into a combined dataset, while GSE82146 served as the validation set. Lysosomal autophagy-related genes (LRGs) obtained from the GeneCards database were intersected with differentially expressed genes (DEGs) identified between the CIRI group and the control group, resulting in the identification of 36 lysosomal autophagy-related differentially expressed genes (LRDEGs). Functional enrichment analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) revealed that LRDEGs are primarily involved in biological processes such as membrane fusion and SNARE binding and are significantly enriched in inflammation-related pathways. We built a diagnostic model for CIRI and identified the biomarkers Vamp8. The results were further validated by quantitative real-time PCR (qPCR) and Western blotting. Simultaneously, immune infiltration analysis was performed. Finally, the mRNA-miRNA and mRNA-RBP interaction regulatory networks of the key genes revealed that Vamp8 is regulated by miR-325-3p, Elavl1, Zfp36, and Pabpc1.", "claims": [{"id": "claim-method", "statement": "Thereafter, Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was conducted on the screened LRDEGs using the glmnet R package20, with parameters set.seed(500) and family=\"binomial”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41047376", "locator": "sections[6] \"Construction of a diagnostic model for MCAO/R\" paragraph 2", "quote": "Thereafter, Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was conducted on the screened LRDEGs using the glmnet R package20, with parameters set.seed(500) and family=\"binomial”."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available in a public, open access repository. All data relevant to the study are included in the article or uploaded as supplemental information.GEO database (https://www.ncbi.nlm.nih.gov/geo/); Genecards database(https://www.ncbi.nlm.nih.gov/gds); MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/index.jsp).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41047376", "locator": "sections[34] \"Data availability\" paragraph 2", "quote": "Data are available in a public, open access repository. All data relevant to the study are included in the article or uploaded as supplemental information.GEO database (https://www.ncbi.nlm.nih.gov/geo/); Genecards database(https://www.ncbi.nlm.nih.gov/gds); MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/index.jsp)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We built a diagnostic model for CIRI and identified the biomarkers Vamp8.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41047376", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We built a diagnostic model for CIRI and identified the biomarkers Vamp8."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We built a diagnostic model for CIRI and identified the biomarkers Vamp8.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41047376"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE61616"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE61616"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41047376", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-20879-w", "sha256": "sha256:fa6405cd2e887ebc52b0f086fb2b2543dea365ecc4910ce40a71f85ce2c53c64", "bytes": 51235, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-20879-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12497871", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE61616", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61616", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61616", "version": null, "note": "Data are available in a public, open access repository. 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Simultaneously, immun", "sults were further validated by quantitative real-time PCR (qPCR) and Western blotting. Simultaneously,"], "order_basis": "paper_text_order:1253", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ted by quantitative real-time PCR (qPCR) and Western blotting. Simultaneously, immune infiltration analysi"], "order_basis": "paper_text_order:1278", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rimental Animal Co. Ltd(Beijing, China). The rats were raised at the Institute of Translational Med", "ording to the experimental requirements, the rats were randomly divided into 5 groups, with 6 rats", "oup, MCAO/ R 24 h, 48 h, 72 h, 7 days group. Rats were subjected to transient MCAO as previously de", "t 24 h, 48 h, 72 h, and 7 days after MCAO/R. Rats were euthanized via intraperitoneal injection of"], "order_basis": "paper_text_order:1580", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Mann-Whitney"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}