Bioinformatic Analysis of Genes Associated with Autophagy in Vitiligo.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38841253", "kind": "science-record", "revision": 3, "content_hash": "sha256:937e180da6591ef95655cfc33b4ba11114092c3b5e41fd677d8933bea5e48fb9", "created_at": "2026-11-01T19:20:47Z", "updated_at": "2026-11-01T22:11:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic Analysis of Genes Associated with Autophagy in Vitiligo.", "doi": "10.4103/ijd.ijd_655_23", "pmid": "38841253", "authors": ["Yilu Zhao", "Kang Ge", "Yan Cheng", "Ru-Zhi Zhang"], "journal": "Indian journal of dermatology", "year": 2024, "abstract": "Background: As vitiligo progresses, autophagy becomes more and more important.\nObjectives: To validate potential genes associated with autophagy in vitiligo through bioinformatics analysis and experimental testing.\nMaterials and Methods: Dataset GSE75819 of mRNA expression profiles was obtained from GEO. After data normalisation, gene set enrichment analyse enrichment analysis and abundance analysis of infiltrating immune cells were performed. A list of autophagy-related differentially expressed genes (ARDEGs) associated with vitiligo was generated using R software. Protein-protein interaction (PPI) analysis, correlation analysis, and enrichment analysis on gene ontology (GO) and Kyoto encyclopaedia of genes and genome (KEGG) pathways were conducted on the ARDEG data. The microRNAs associated with hub genes were predicted using the TargetScan database. Finally, RNA expression of 10 hub genes and Western blotting (WB) of autophagy pathway factors were further verified.\nResults: From the lesions of 15 vitiligo patients, 44 ARDEGs were identified. PPI analysis demonstrated that these ARDEGs interacted with each other. GO and KEGG analyses of ARDEGs revealed that several enriched terms were associated with macroautophagy (biological process), vacuolar membranes (cellular components), cysteine-type peptidase activity (molecular function), and autophagy in animals, neurodegeneration-multiple disease pathways, and apoptosis. In vitiligo lesions, qRT-PCR and sequencing validation analyses showed expression levels of CCL2, RB1CC1, TP53, and ATG9A that were consistent with bioinformatic analysis of the microarray. WB results also showed that autophagy-related proteins were differentially expressed.\nConclusions: Forty-four potential ARDEGs were identified in vitiligo by bioinformatic analysis. Vitiligo may be affected by autophagy regulation through CCL2, RB1CC1, TP53, and ATG9A.", "claims": [{"id": "claim-method", "statement": "Based on 15 individuals’ lesional vitiligo skin expression profiles, GSEA was performed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38841253", "locator": "sections[5] \"Analysis of gene set enrichment\" paragraph 2", "quote": "Based on 15 individuals’ lesional vitiligo skin expression profiles, GSEA was performed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-seq data for GSE75819 were procured from the Gene Expression Omnibus (GEO) at http://www.ncbi.nlm.nih.gov/geo/. A comprehensive set of 30 samples were collected from 15 lesional skin specimens and 15 nonlesional skin specimens with vitiligo.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38841253", "locator": "sections[3] \"Data preprocessing and acquisition\" paragraph 2", "quote": "RNA-seq data for GSE75819 were procured from the Gene Expression Omnibus (GEO) at http://www.ncbi.nlm.nih.gov/geo/. A comprehensive set of 30 samples were collected from 15 lesional skin specimens and 15 nonlesional skin specimens with vitiligo."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Forty-four potential ARDEGs were identified in vitiligo by bioinformatic analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38841253", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Forty-four potential ARDEGs were identified in vitiligo by bioinformatic analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Forty-four potential ARDEGs were identified in vitiligo by bioinformatic analysis.", "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:38841253"], "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. 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