Identifying the Key Mitochondria-Related Genes in COPD by Integrating Machine Learning and Bioinformatics Analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41127826", "kind": "science-record", "revision": 4, "content_hash": "sha256:5d29c209dee3949fadb744172ac90e420d7cd9195e6815867be8603c22a673de", "created_at": "2026-11-01T20:31:10Z", "updated_at": "2026-11-01T22:57:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying the Key Mitochondria-Related Genes in COPD by Integrating Machine Learning and Bioinformatics Analyses.", "doi": "10.1155/ijog/7060748", "pmid": "41127826", "authors": ["Jiajia Qu", "Mengyu Zhang", "Yajie Hu", "Guang Yang", "Xiaoning Zhang", "Wenqing Zhang", "Yiqing Qu"], "journal": "International journal of genomics", "year": 2025, "abstract": "Background: Chronic obstructive pulmonary disease (COPD), a prevalent chronic respiratory disorder with high morbidity and mortality, is closely associated with mitochondrial dysfunction and immune dysregulation; however, the underlying mechanisms remain unclear.\nAims: The aim of this study is to identify mitochondrial hub genes and evaluate their diagnostic potential in COPD.\nMethods: This study combined bioinformatics and experimental methods to investigate mitochondria-related differentially expressed genes (MitoDEGs) in COPD pathogenesis. Two GEO datasets (GSE38974/GSE8545) were analyzed to identify MitoDEGs, which were functionally characterized and refined via machine learning (LASSO/SVM-RFE). Key genes were further validated using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot in bronchial epithelial cells and COPD mouse model lung tissues. Immune infiltration analysis revealed connections between MitoDEGs and immune dysregulation in COPD that were experimentally confirmed using immunohistochemistry (IHC) and immunofluorescence (IF).\nResults: Among 28 identified MitoDEGs, five feature genes (BAX, DLST, FKBP10, FUNDC2, and RMDN1) were selected. Subsequent validation through qRT-PCR, Western blot, and ROC curve further confirmed BAX and DLST as core hub genes. Immune profiling revealed significantly increased M0 macrophage infiltration and reduced activated NK cells in COPD. BAX and DLST expression was positively correlated with M0 macrophages but negatively with activated NK cells, a finding corroborated by IHC and IF assays.\nConclusions: These findings highlight BAX and DLST as potential mitochondrial dysfunction biomarkers in COPD, linking their roles to immune cell infiltration. This study provides novel insights into cigarette smoke-induced COPD pathogenesis and underscores the diagnostic utility of targeting mitochondrial-immune interactions.", "claims": [{"id": "claim-method", "statement": "Normalized GSE38974 data were analyzed using limma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41127826", "locator": "sections[4] \"2.2. Identification of Differentially Expressed Genes (DEGs) and Mitochondria‐Related Differentially Expressed Genes (MitoDEGs)\" paragraph 2", "quote": "Normalized GSE38974 data were analyzed using limma."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are publicly available from the Gene Expression Omnibus database: GSE38974 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38974) and GSE8545 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8545).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41127826", "locator": "sections[31] \"Data Availability Statement\" paragraph 2", "quote": "The datasets analyzed during the current study are publicly available from the Gene Expression Omnibus database: GSE38974 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38974) and GSE8545 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8545)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "These findings highlight BAX and DLST as potential mitochondrial dysfunction biomarkers in COPD, linking their roles to immune cell infiltration.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41127826", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "These findings highlight BAX and DLST as potential mitochondrial dysfunction biomarkers in COPD, linking their roles to immune cell infiltration."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "These findings highlight BAX and DLST as potential mitochondrial dysfunction biomarkers in COPD, linking their roles to immune cell infiltration.", "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:41127826"], "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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