RNA-seq analysis of synovial fibroblasts in human rheumatoid arthritis

Abstract

The aim of the present study was to identify differentially expressed genes (DEGs) between individuals with rheumatoid arthritis (RA) and healthy controls, in order to provide a theoretical foundation for RA diagnosis and targeted gene therapy. Illumina mRNA sequence data (RNA-Seq) corresponding to RA and control samples were downloaded from the Sequence Read Archive (SRA) database. Gene Ontology (GO) enrichment analysis was performed with the GOstat tool in order to identify over-represented biological functions among DEGs, and the related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified using the KEGG Automatic Annotation Server (KAAS). A total of 293 DEGs were identified, among which 16 DEGs have been previously shown to associate with RA, such as those encoding matrix metalloproteinase-1 (MMP-1), interleukin-1 receptor type 1 (IL1R1), and chemokine (C-X3-C motif) ligand 1 (CX3CL1). GO functional annotation and enrichment analysis showed that the DEGs are enriched for 309 GO terms, mainly protein-protein interactions, membrane formation and stability. KEGG pathway analysis demonstrated that these DEGs are involved in 131 pathways, including Wnt and calcium signaling, and cell adhesion molecule (CAM)-related pathways. In conclusion, the results provide both expansive and detailed insights into the molecular pathogenesis of RA, particularly with regards to the development of therapeutic targets, and may inspire further experimentation aiming to identify new strategies for RA treatment.