Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis

Abstract

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease. It is well known that the formation of positive feedback between synovial hyperplasia and inflammatory infiltration is intimately associated with the occurrence and development of RA. However, the exact mechanisms still remain unknown, making the early diagnosis and therapy of RA difficult. This study was designed to identify prospective diagnostic and therapeutic biomarkers, as well as their-mediated biological mechanisms in RA. Three microarray datasets (GSE36700, GSE77298 and GSE153015) and two RNA-sequencing datasets (GSE89408 and GSE112656) of synovial tissues, as well as three other microarray datasets (GSE101193, GSE134087 and GSE94519) of peripheral blood were downloaded for integrated analysis. The differently expressed genes (DEGs) were identified by "limma" package of R software. Then, weight gene co-expression analysis and gene set enrichment analysis were performed to investigate synovial tissue-specific genes and their-mediated biological mechanisms in RA. The expression of candidate genes and their diagnostic value for RA were verified by quantitative real-time PCR and receiver operating characteristic (ROC) curve, respectively. Relevant biological mechanisms were explored through cell proliferation and colony formation assay. The suggestive anti-RA compounds were discovered by CMap analysis. We identified a total of 266 DEGs, which were mainly enriched in cellular proliferation and migration, infection and inflammatory immune signaling pathways. Bioinformatics analysis and molecular validation revealed 5 synovial tissue-specific genes, which exhibited excellent diagnostic value for RA. The infiltration level of immune cells in RA synovial tissue was significantly higher than that in control individuals. Moreover, preliminary molecular experiments suggested that these characteristic genes may be responsible for the high proliferation potential of RA fibroblast-like synoviocytes (FLSs). Finally, 8 small molecular compounds with anti-RA potential were obtained. We have proposed 5 potential diagnostic and therapeutic biomarkers (CDK1, TTK, HMMR, DLGAP5, and SKA3) in synovial tissues that may contribute to the pathogenesis of RA. These findings may shed light on the early diagnosis and therapy of RA.