RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease

To understand the pathogenesis of cartilage damage in Kashin-Beck disease (KBD) and rheumatoid arthritis (RA) which similar clinical symptoms.

RNA sequencing (RAN-seq) analysis was used to reveal the different pathogeneses between KBD and RA. The messenger RNA expression profiles of articular cartilage isolated from KBD patients (n = 3) and RA patients (n = 3) were compared using RNA-seq analysis. Differentially expressed genes (DEGs) were determined using the Benjamini-Hochberg approach. The Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7) was employed to assess functional categories and Gene Ontology (GO). The Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS 2.0) was used to identify significantly enriched KEGG pathways.

In the individually sequenced dataset, we identified 1568 significant DEGs in KBD compared to RA (232 up-regulated genes and 1336 down-regulated genes). GO function analysis identified nine significant biological processes (BPs), eight molecular functions (MFs), and five cell components (CCs) in KBD, and also the top ten ranked significant BPs, MFs and CCs were found in RA. The KEGG pathway enrichment analysis identified biosynthesis of amino acids involved in KBD. The chemokine signaling pathway, nuclear factor-kappa B signaling pathway, B cell receptor signaling pathway, leukocyte transendothelial migration, and osteoclast differentiation were involved in RA.

RNA-seq revealed that proteoglycan-mediated metabolic disorders contributed to the onset of KBD, whereas immune dysregulation was apparently involved in the pathogenesis of RA.