2025, Vol. 29 ›› Issue (36): 7783-7789

Screening and cytological validation of cartilage degeneration-related genes in exosomes from osteoarthritis synovial fluid

Ma Weibang1, Xu Zhe1, 2, Yu Qiao2, 3, Ouyang Dong1, Zhang Ruguo1, Luo Wei1, Xie Yangjiang1, Liu Chen1   

Abstract: BACKGROUND: Exosomes have been confirmed to be closely related to cartilage degeneration in osteoarthritis. However, the role and mechanism of exosome-derived genes in cartilage degeneration of osteoarthritis have not been fully elucidated.
OBJECTIVE: Bioinformatics analyses were used to screen the genes related to cartilage degeneration in the synovial exosomes of patients with osteoarthritis, and to determine their biological functions and signaling pathways in order to provide new therapeutic targets for delaying cartilage degeneration in osteoarthritis.
METHODS: Firstly, osteoarthritis-related exosome dataset GSE185059 and cartilage degeneration dataset GSE114007 were downloaded from Gene Expression Omnibus (GEO) database to screen exosome-derived cartilage degeneration related genes. GO functional and KEGG pathway enrichment analyses were performed based on the screened exosome-derived cartilage degeneration related genes. Protein-protein interaction network was drawn and Ingenuity Pathway Analysis (IPA) was conducted to screen and obtain key exosome-derived cartilage degeneration-related genes. Finally, qRT-PCR was used to verify the expression of key genes in osteoarthritis cartilage tissue and interleukin-1β stimulated chondrocyte models.
RESULTS AND CONCLUSION: (1) There were 831 differentially expressed genes in the GSE185059 dataset and 5 323 differentially expressed genes in the GSE114007 dataset. A total of 94 exosome-derived cartilage degeneration related genes were screened after the intersection of these differentially expressed genes, of which 51 genes were down-regulated and 43 genes were up-regulated. (2) GO functional enrichment analysis showed that the up-regulated genes were mainly involved in the positive regulation of cell-cell adhesion, the positive regulation of T cell activation, and chronic inflammatory response, while the down-regulated genes were mainly involved in biological processes such as cell aggregation, cartilage differentiation and development, and skeletal system morphogenesis. (3) KEGG pathway enrichment analysis showed that exosome-derived cartilage degeneration-related genes were mainly involved in tryptophan enrichment metabolism, vitamin B6 metabolism, and leukocyte transendothelial migration. (4) The constructed protein-protein interaction network confirmed the existence of multiple interaction relationships among exosome-derived cartilage degeneration-related genes. Combined with five algorithms in CytoHubba software, four key exosome-derived cartilage degeneration-related genes were further screened, namely THY1, CYP1A1, NFKB2, and COL6A3. (5) The results of qRT-PCR showed that compared with normal cartilage, the expressions of THY1 and COL6A3 in osteoarthritic cartilage were increased, while the expression of CYP1A1 and NFKB2 was decreased. Similarly, compared with the unstimulated group, the expression of THY1 and COL6A3 in the interleukin-1β induced chondrocytes was upregulated, while the expression of CYP1A1 and NFKB2 was downregulated. (6) These results indicate that THY1, CYP1A1, NFKB2, and COL6A3 are genes related to cartilage degeneration in the exosomes of synovial fluid of patients with osteoarthritis, and may participate in the pathogenesis of osteoarthritis by regulating biological processes such as protein tyrosine kinase activity and lipid metabolism, as well as nuclear factor-κB signaling pathway and focal adhesion signaling pathway. However, the specific regulatory roles and molecular mechanisms of these key genes in cartilage degeneration need to be further verified by experiments.

Key words: osteoarthritis, synovial fluid, exosome, cartilage degeneration, bioinformatics analysis, cytological verification, chondrocyte, gene expression, engineered exosomes