Systematic Analysis of Differential Expression Profile in Rheumatoid Arthritis Chondrocytes Using Next-Generation Sequencing and Bioinformatics Approaches

Abstract

Cartilage destruction in rheumatoid arthritis (RA) occurs primarily in the pannus-cartilage interface. The close contact of the synovium-cartilage interface implicates crosstalk between synovial fibroblasts and chondrocytes. The aim of this study is to explore the differentially expressed genes and novel microRNA regulations potentially implicated in the dysregulated cartilage homeostasis in joint destruction of RA. Total RNAs were extracted from human primary cultured normal and RA chondrocytes for RNA and small RNA expression profiling using next-generation sequencing. Using systematic bioinformatics analyses, we identified 463 differentially expressed genes in RA chondrocytes were enriched in biological functions related to altered cell cycle process, inflammatory response and hypoxic stimulation. Moreover, fibroblast growth factor 9 (FGF9), kynureninase (KYNU), and regulator of cell cycle (RGCC) were among the top dysregulated genes identified to be potentially affected in the RA joint microenvironment, having similar expression patterns observed in arrays of clinical RA synovial tissues from the Gene Expression Omnibus database. Additionally, among the 31 differentially expressed microRNAs and 10 candidate genes with potential microRNA-mRNA interactions in RA chondrocytes, the novel miR-140-3p-FGF9 interaction was validated in different microRNA prediction databases, and proposed to participate in the pathogenesis of joint destruction through dysregulated cell growth in RA. The findings provide new perspectives for target genes in the management of cartilage destruction in RA.

The Interaction of miR-378i-Skp2 Regulates Cell Senescence in Diabetic Nephropathy

“…The updated DAVID Bioinformatics Resources () is a public resource that merges numerous public bioinformatics resources and it provides many tools to analyze large gene lists from genomic studies. After a gene list is uploaded, researchers can gain gene-term enrichment analysis and an overall notion of the biological functions associated with the gene list of interest [20,21].…”

“…The STRING database (version 10.5) () includes over 9.6 million proteins, 2000 organisms, and 1380 million interactions that offer the analysis and integration of direct and indirect protein-protein interactions (PPI) and their functional associations [20]. Differentially expressed genes are uploaded, and those interactions with at least medium confidence (interaction score >0.4) were selected [22].…”

“…Network analysis and canonical pathways that were obtained from Core Analysis results offer the interaction of genes/proteins. Network graphics with further overlay analysis can be generated by the software [20,23]. The IPA software also offers miRNA-mRNA filter analysis to match miRNAs and their potential targets of mRNAs according to the repression strength.…”

“…The TargetScan version 7.2 () and miRmap () software rank potential targets of a specific miRNA based on Context++ score percentiles and miRmap scores, which indicates the repression strength of a miRNA target [20,24]. The TargetScan and miRmap web also can provide miRNA target predictions for different organisms.…”

Promising targets and drugs in rheumatoid arthritis

“…An increasing number of studies have screened the potential targets of RA based on the high-throughput methods, such as microarray profiling 7 and next-generation sequencing. 8 Differentially expressed genes (DEGs) defined by specific thresholds, such as the fold change of gene expression and p-value (e.g. fold change = 2 and p = 0.05), are widely employed in the target screening of RA.…”