Screening and identification of Hub genes in osteoarthritis based on bioinformatics

doi:10.12307/2023.567

Abstract

Abstract: BACKGROUND: Osteoarthritis is a degenerative disease characterized by joint pain, stiffness and swelling. At present, the pathogenesis of osteoarthritis is not clear.
OBJECTIVE: To screen out Hub genes in osteoarthritis-related data sets based on bioinformatics and then identify them using cell experiments to screen the key biomarkers of osteoarthritis.
METHODS: Osteoarthritis-related data sets were searched from GEO database and differentially expressed genes were identified by GEO2R analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed for differentially expressed genes. Meanwhile, a gene set enrichment analysis was performed for all genes in the data set. Protein-protein network was constructed by inputting differentially expressed genes on String website. The functional modules of the protein-protein network were analyzed by MCODE plug-in in Cytoscape software and the top 10 Hub genes were identified by CytoHubba plug-in. The knee meniscus cells of Sprague-Dawley rats were extracted. In the experimental group, interleukin-1β (10 ng/mL) was used to intervene the cells for 24 hours. Cells with no intervention were used as controls. The expression of Hub genes was detected by RT-qPCR.
RESULTS AND CONCLUSION: A total of 147 differentially expressed genes were up-regulated and 212 down-regulated. Gene ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and gene set enrichment analyses showed that the enriched pathways and biological processes mainly involved collagen fiber organization, extracellular matrix interaction, Th17 cell differentiation and interleukin-17. CytoHubba, a plug-in in Cytoscape software, was used to identify the top 10 Hub genes in MCC algorithm, including COL1A1, COL3A1, COL5A1, COL5A2, COL6A3, LOX, LOXL1, LOXL2, POSTN, and PLOD1. RT-qPCR results showed that compared with the control group, the mRNA expression of COL1A1, COL3A1, COL5A1, COL5A2, COL6A3, LOXL1, and LOXL2 decreased (P < 0.000 1), while the mRNA expression of LOX and POSTN increased (P < 0.000 1). However, there was no significant difference in the PLOD1 expression between the two groups (P > 0.05). To conclude, differentially expressed Hub genes in osteoarthritis may provide new insights into the development of osteoarthritis in the future.

Key words: osteoarthritis, meniscal cell, bioinformatics, Hub gene, meniscus

CLC Number:

Wu Suwen, Chen Zheng, Jiang Yuankang, Chen Leilei. Screening and identification of Hub genes in osteoarthritis based on bioinformatics[J]. Chinese Journal of Tissue Engineering Research, 2023, 27(28): 4525-4532.

Figures/Tables 7

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