Screening and analysis of differentially expressed genes in synovial tissue of rheumatoid arthritis

doi:10.12307/2023.406

Abstract

Abstract: BACKGROUND: Rheumatoid arthritis is an autoimmune disease. Research on rheumatoid arthritis mainly focuses on its pathogenesis and target therapy.
OBJECTIVE: To search for differential genes by bioinformatics analysis of rheumatoid arthritis synovitis gene chip datasets, and to establish and improve the gene regulation network of rheumatoid arthritis.
METHODS: GEO2R was used to analyze the differential expression of rheumatoid arthritis chips screened from the database. R language and DAVID were used for gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes. String database was used for protein-protein interaction network analysis. Cystoscape software was used to obtain key genes. qPCR and western blot were used for experimental verification of some key target genes.
RESULTS AND CONCLUSION: There were 2 064 differentially expressed genes in the synovial tissue of patients with rheumatoid arthritis, including 625 up-regulated genes and 1 439 down-regulated genes. Differentially expressed genes are mainly involved in immune response-activated cell surface receptor signaling pathway, antigen receptor mediated signaling pathway and other biological responses. Ten key target genes, including epidermal growth factor receptor (EGFR), MYC, RELA, ITGB2, LCK, EPHB2, IRF4, NRAS, FN1, and MAPK1, were identified by the protein-protein interaction network analysis. The number of protein interaction lines based on the protein-protein interaction network and Cystoscape algorithm score were used to obtain five genes with high significance, including EGFR, MYC, RELA, ITGB2, and LCK, and the experimental verification of these genes was carried out by qPCR and western blot experiments. The mRNA and protein expression levels of EGFR, MYC, RELA, ITGB2, and LCK genes in the synovial tissue of patients with rheumatoid arthritis were significantly higher than those of the control group, and the expression of EGFR changed most significantly. To conclude, there are distinct gene expression characteristics in the synovial tissue of knee joint after rheumatoid arthritis, and EGFR is the most valuable differentially expressed gene in the synovium of rheumatoid arthritis.

Key words: rheumatoid arthritis, synovial tissue, differentially expressed gene, bioinformatics, gene regulatory network

CLC Number:

Wang Chenyu, Yao Jiawei, Xu Xiongfeng, Qiu Bo. Screening and analysis of differentially expressed genes in synovial tissue of rheumatoid arthritis[J]. Chinese Journal of Tissue Engineering Research, 2023, 27(20): 3224-3229.

Figures/Tables 6

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