Bioinformatics analysis and identification of hub genes and their role in immune infiltration in osteoarthritis

doi:10.12307/2025.704

Abstract

Abstract:

BACKGROUND: Low-grade, chronic inflammation is thought to play a central role in the pathogenesis of osteoarthritis. However, the specific molecular mechanisms are still unclear.
OBJECTIVE: To screen and explore the potential hub genes and immune cell infiltration in osteoarthritis.
METHODS: We merged data from the GSE206848 on the GPL570 and the GSE55235 and GSE55457 on the GPL96 to form the row dataset. Outlier samples were removed using weighted gene co-expression network analysis, followed by the identification of differentially expressed genes, and subsequent functional enrichment analysis of differentially expressed genes. Further, a protein-protein interaction network of differentially expressed genes was constructed, and hub genes were identified using two different algorithms in Cytoscape. Additionally, the CIBERSORT algorithm was employed to assess differences in immune cell infiltration proportions between osteoarthritis samples and normal controls. Finally, the diagnostic efficacy of hub genes for osteoarthritis was validated using quantitative reverse transcription polymerase chain reaction experiments conducted on synovial tissue samples collected from patients with osteoarthritis, in conjunction with the GSE12021 dataset from the GPL96 sequencing platform as an independent dataset.
RESULTS AND CONCLUSION: After eliminating 5 outlier samples, we identified a total of 340 differentially expressed genes, comprising 159 up-regulated genes and 181 down-regulated genes. Six hub genes were obtained by weighted gene co-expression network analysis and Cytoscape. CIBERSORT analysis revealed a difference in the proportion of multiple types of immune cell infiltration in osteoarthritic tissues compared with normal tissues. Moreover, the expression levels of the six hub genes exhibited strong correlation with the relative proportion of multiple immune cells in osteoarthritis. The results of RT-qPCR indicated that the relative expression levels of the six genes were down-regulated relative to normal tissues. However, there was no significant difference in the expression of NFKBIA and PTGS2 (P > 0.05). Simultaneously, receiver operator characteristic curves in both the original and external datasets demonstrated that the six hub genes exhibited strong diagnostic capabilities for osteoarthritis (area under the curve > 0.8). To conclude, four hub genes, CDKN1A, MYC, C-X-C motif chemokine ligand 2, and vascular endothelial growth factor A, are finally identified and may serve as molecular targets for future treatment by mediating immune response and inflammatory processes.

中国组织工程研究杂志出版内容重点：组织构建；骨细胞；软骨细胞；细胞培养；成纤维细胞；血管内皮细胞；骨质疏松；组织工程

Key words: osteoarthritis, synovial tissue, hub gene, immune infiltration, bioinformatics, weighted gene co-expression network analysis

CLC Number:

Cai Wei, Zhu Yukun, Xu Jianzhong. Bioinformatics analysis and identification of hub genes and their role in immune infiltration in osteoarthritis [J]. Chinese Journal of Tissue Engineering Research, 2025, 29(18): 3747-3757.

Figures/Tables 9

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