ArticleFrontiers in bioinformatics2025
Identification and functional analysis of hub genes in knee osteoarthritis via bioinformatics and experimental validation.
Article in Frontiers in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Objective: Knee osteoarthritis (KOA) is a prevalent chronic degenerative joint disease that causes chronic pain and mobility restrictions in the elderly, significantly impacting quality of life. Current treatments focus on symptom relief, lacking effective interventions targeting the underlying mechanisms. Understanding KOA's molecular mechanisms and identifying key pathogenic genes are essential for developing targeted therapies. Methods: Gene expression data from KOA patients and healthy controls were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to reveal the associated biological processes and signaling pathways. Protein-protein interaction (PPI) network analysis and Gene Ontology-based semantic similarity calculations were used to identify hub genes. Gene Set Variation Analysis (GSVA) assessed enrichment in KOA-related pathways. Immune infiltration analysis (CIBERSORT) assessed the immune cell distribution in KOA tissues. Finally, hub gene expression changes were validated using the IL-1β-treated CHON-001 cell model and real-time quantitative PCR (RT-qPCR). Results: A total of 3,290 upregulated and 2,536 downregulated DEGs were identified. GO and KEGG enrichment analyses revealed these genes were primarily involved in extracellular matrix remodeling, transmembrane transport, and inflammation-related pathways. Key hub genes, including HSPA5, FOXO1, and YWHAE, were identified. GSVA showed that these genes were significantly enriched in multiple KOA-associated signaling pathways. Immune infiltration analysis revealed significant differences in the levels of six immune cell types in KOA tissues, which were associated with the hub genes expression. In CHON-001 cell, the expression levels of GRB2, IKBKG, and HSPA12A were upregulated, whereas YWHAE, HSPB1, and DCAF8 were downregulated, consistent with the tissue samples. Conclusion: This study identified key pathogenic genes and their regulatory pathways in KOA, highlighting their potential role in disease progression via inflammation and immune modulation. These findings provide insights for developing targeted therapeutic strategies for KOA.
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