Identification and Verification of Hub Mitochondrial Dysfunction Genes in Osteoarthritis Based on Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38292759", "kind": "science-record", "revision": 3, "content_hash": "sha256:6b7551926965bb6ab565fbd6aefd30cc252eb763727d000f65b6f7fda7b24a81", "created_at": "2026-11-01T19:20:13Z", "updated_at": "2026-11-01T22:11:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Verification of Hub Mitochondrial Dysfunction Genes in Osteoarthritis Based on Bioinformatics Analysis.", "doi": "10.1155/2024/6822664", "pmid": "38292759", "authors": ["Hui Niu", "Xingxing Deng", "Qian Zhang", "Yijun Zhao", "Jinfeng Wen", "Wenyu Li", "Huan Liu", "Xiong Guo", "Cuiyan Wu"], "journal": "Journal of immunology research", "year": 2024, "abstract": "Objective: Age-related mitochondrial dysfunction and associated oxidative stress may contribute to the development of osteoarthritis. The aim of this study was to identify hub genes associated with mitochondrial dysfunction in osteoarthritis (OA) patients, helping predict the risk of OA, and revealing the mechanism of OA progression.\nMethods: OA expression data and mitochondrial dysfunction genes were downloaded from GEO (GSE55235, GSE82107, and GSE114007) and GeneCard databases. The differentially expressed mitochondrial dysfunction genes (DEMDFGs) between OA and control samples were screened. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes pathways were analyzed for DEMDFGs. The hub genes were determined by WGCNA and LASSO regression analysis. ROC curves manifested the diagnostic efficacy of each hub gene. A nomogram model was constructed and validated to predict OA risk. The expression of hub genes in OA and normal chondrocytes was verified by external datasets, qRT-PCR and western blotting.\nResults: A total of 31 DEMDFGs were identified, with 15 genes upregulated and 16 genes downregulated. GO functional enrichment analysis revealed that DEMDFGs were enriched in biological processes related to energy metabolism and cellular respiration. By employing weighted gene coexpression network analysis, we identified four distinct coexpression modules, among which the blue module exhibited the strongest correlation with OA. The intersection between DEMDFGs and this module yielded eight candidate genes. After LASSO analysis of the data, four hub genes (ACADL, CYBA, SLC19A2, and UCP2) were identified as potential biomarkers for OA. The expression levels of these four genes were externally validated in the GSE114007 dataset. And the biologically differential expression of these four genes has been verified in OA and normal chondrocytes. Moreover, the four hub genes had good sensitivity and specificity by ROC curve analysis, and the risk model constructed with these four genes showed promising performance. In conclusion, our study may provide novel mitochondrial dysfunction hub genes with potential clinical applications for understanding the pathology, diagnosis, and treatment of OA.", "claims": [{"id": "claim-method", "statement": "Further, to identify the hub MDFGs for OA, least absolute shrinkage and selection operator (LASSO) regression analysis was conducted by using the “glmnet” package for CGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38292759", "locator": "sections[5] \"2.3. Weighted Gene Coexpression Network Analysis (WGCNA) and Hub MDFGs Identification\" paragraph 2", "quote": "Further, to identify the hub MDFGs for OA, least absolute shrinkage and selection operator (LASSO) regression analysis was conducted by using the “glmnet” package for CGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38292759", "locator": "sections[23] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A nomogram model based on the four hub genes ACADL, CYBA, SLC19A2, and UCP2 achieved an ROC AUC of 0.938 for predicting OA risk.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38292759", "locator": "sections[15] \"3.3. Diagnostic Value of Hub MDFGs and Risk Model\" paragraph 3", "quote": "The ROC analysis of the model was further performed (Figure 5(c)), and the AUC for this model was 0.938."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A nomogram model based on the four hub genes ACADL, CYBA, SLC19A2, and UCP2 achieved an ROC AUC of 0.938 for predicting OA risk.", "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:38292759"], "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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