Identification and experimental validation of ulcerative colitis-associated hub genes through integrated WGCNA and lysosomal autophagy analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40597456", "kind": "science-record", "revision": 3, "content_hash": "sha256:614e185fd0bba0f5d1bea583c8ccf04e3418fa3727047537c4be73e64cc92f82", "created_at": "2026-11-01T20:30:41Z", "updated_at": "2026-11-01T22:14:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and experimental validation of ulcerative colitis-associated hub genes through integrated WGCNA and lysosomal autophagy analysis.", "doi": "10.1186/s40246-025-00783-0", "pmid": "40597456", "authors": ["Yuanpei Zhao", "Yijun Li", "Qingwen Xu", "Lili Ding", "Weiming Li", "Qinghua Zou", "Yichen Hu", "Kaiwen Shi", "Hongyuan Liu"], "journal": "Human genomics", "year": 2025, "abstract": "OBJECTIVE: This study aims to systematically identify differentially expressed genes associated with lysosomal autophagy in ulcerative colitis (UC) and validate key candidate genes in an animal model, thereby providing novel insights driving UC pathogenesis.\nMETHODS: The GSE47908 dataset from the Gene Expression Omnibus (GEO) was subjected to principal component analysis (PCA), followed by stratified identification of differentially expressed genes (DEGs) across UC subtypes. Immune cell infiltration of these gene sets was evaluated using the CIBERSORT algorithm. Lysophagy-related genes set were retrieved from the GeneCards database. Bioinformatics methods were employed to stratify UC DEGs, weighted gene co-expression network analysis (WGCNA) module genes, and lysophagy-associated DEGs, which were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A protein-protein interaction (PPI) network was constructed via the STRING database, and Cytoscape was used to identify core genes highly associated with lysophagy. Core genes were validated using external datasets, and experimental UC mouse model was established to confirm their expression levels by real-time quantitative reverse transcription PCR (RT-qPCR).\nRESULTS: PCA of the GSE47908 dataset across UC subtypes revealed distinct spatial separation, integrated and subgroup analyses identified lysophagy-related key genes, and enrichment analyses demonstrated differences in core genes and pathways between overall UC and its subtypes. A PPI network highlighted five hub genes in UC (CASP1, CXCL1, LCN2, PSMB9, AGT). Upregulation of these genes was confirmed via external datasets and animal experiments. Moreover, immune infiltration analysis of UC samples demonstrated immune dysregulation during disease progression, underscoring the interplay between lysophagy and inflammation in UC.\nCONCLUSION: The five genes identified-CASP1, CXCL1, LCN2, PSMB9, and AGT-exhibit strong associations with lysosomal autophagy. Our findings suggest that these genes may function as critical regulators of lysosomal autophagy in UC.", "claims": [{"id": "claim-method", "statement": "The GSE47908 dataset was employed in weighted gene co-expression network analysis to identify modules associated with UC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40597456", "locator": "sections[5] \"Construction of co-expression network and module identification\" paragraph 2", "quote": "The GSE47908 dataset was employed in weighted gene co-expression network analysis to identify modules associated with UC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No datasets were generated or analysed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40597456", "locator": "sections[27] \"notes\" paragraph 1", "quote": "No datasets were generated or analysed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A PPI network highlighted five hub genes in UC (CASP1, CXCL1, LCN2, PSMB9, AGT).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40597456", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A PPI network highlighted five hub genes in UC (CASP1, CXCL1, LCN2, PSMB9, AGT)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "A PPI network highlighted five hub genes in UC (CASP1, CXCL1, LCN2, PSMB9, AGT).", "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:40597456"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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