Identification of related-genes of T cells in lung tissue of chronic obstructive pulmonary disease based on bioinformatics and experimental validation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38802460", "kind": "science-record", "revision": 4, "content_hash": "sha256:78d2ae452b3996d2622e11a38f4709444c46f32a4cb365399412efe34a2e902e", "created_at": "2026-11-01T19:20:45Z", "updated_at": "2026-11-01T22:11:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of related-genes of T cells in lung tissue of chronic obstructive pulmonary disease based on bioinformatics and experimental validation.", "doi": "10.1038/s41598-024-62758-w", "pmid": "38802460", "authors": ["Ting Xue", "Fei Dong", "Jinglin Gao", "Xiaoning Zhong"], "journal": "Scientific reports", "year": 2024, "abstract": "T cells are one of the main cell types shaping the immune microenvironment in chronic obstructive pulmonary disease (COPD). They persist andplay cytotoxic roles. The purpose of this study aimed to explore the potential related-genes of T cells in lung tissue of COPD. Chip data GSE38974 and single_celldata GSE196638 were downloaded from the GEO database. Difference analyses and WGCNA of GSE38974 were performed to identify DEGs and the modules most associated with the COPD phenotype. Various cell subsets were obtained by GSE196638, and DEGs of T cells were further identified. GO, GSEA and KEGG enrichment analyses were conducted to explore the biological functions and regulatory signaling pathways of the DEGs and DEGs of T cells. The intersection of the DEGs, module genes and DEGs of T cells was assessed to acquire related-genes of T cells. The mRNA and protein expression levels of related-genes ofT cells were verified in lung tissue of mouse with emphysema model. Based on GSE38974 difference analysis, 3811 DEGs were obtained. The results of WGCNA showed that the red module had the highest correlation coefficient with the COPD phenotype. GSE196638 analysis identified 124 DEGs of T cells. The GO, GSEAand KEGG enrichment analyses mainly identified genes involved in I-kappaB kinase/NF-kappaB signaling, receptor signaling pathway via STAT, regulationof CD4-positive cells, regulation of T-helper cell differentiation, chemokine signaling pathway, Toll-likereceptor signaling pathway, CD8-positive cells, alpha-beta T cell differentiation, MAPK signaling pathway and Th17 cell differentiation. The DEGs, genes of the red module and DEGs of T cells were overlapped to acquire FOXO1 and DDX17. The results of RT-qPCR and Western Blot indicate that the mRNA and protein expression levels of FOXO1 and DDX17 in lung tissue of emphysema mice were significantly higher compared with those in air-exposed mice. FOXO1 as well as DDX17 may be related-genesof T cells in lung tissue of patient with COPD, and their participation in the biological processes of different signaling pathways may inspire further COPD research.", "claims": [{"id": "claim-data-access", "statement": "The datasets are available from the GEO database. GSE38974 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi), GSE196638 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38802460", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The datasets are available from the GEO database. GSE38974 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi), GSE196638 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "FOXO1 and DDX17 may be related-genesof T cells in lung tissue of patient with COPD, and their participation in the biological processes of different signaling pathways may inspire further COPD research.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38802460", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "FOXO1 as well as DDX17 may be related-genesof T cells in lung tissue of patient with COPD, and their participation in the biological processes of different signaling pathways may inspire further COPD research."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "FOXO1 and DDX17 may be related-genesof T cells in lung tissue of patient with COPD, and their participation in the biological processes of different signaling pathways may inspire further COPD research.", "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:38802460"], "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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Based on GSE38974 diff", "es of T cells. (b–c) H&E-stained sections of mouse lung tissue of AIR and CS group. (d) The mea"], "order_basis": "paper_text_order:1055", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d to acquire FOXO1 and DDX17. The results of RT-qPCR and Western Blot indicate that the mRNA and", "o acquire FOXO1 and DDX17. The results of RT-qPCR and Western Blot indicate that the mRNA and", "ed to identify genes related to T cells. The RT-qPCR experimental verification Total RNA was extr", "ficantly increased (Fig. 8d). 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