Comprehensive microRNA and transcriptomic profiling of rheumatoid arthritis monocytes: role of microRNA-146b in proinflammatory progression

Objective: To explore global miRNA and transcriptomic profiling of monocytes from rheumatoid arthritis (RA) patients compared with healthy controls (HC) to predict which aberrantly expressed microRNA (miRNA) can negatively modulate inflammatory molecules.

Methods: Using next generation sequencing (NGS), we have performed simultaneous global analysis of miRNA (miRNA-seq) and transcriptome (RNA-seq) of monocytes from RA patients, HC. Global analysis of miRNA of systemic sclerosis (SSc) monocytes was also performed. Following differential analysis and negative correlation, miRNA-RNA pairs were selected.

Results: We found that 20 specific miRNA candidates are predicted to silence inflammatory mediators, out of 191 significantly changed miRNAs in RA monocytes. Based on the highest scoring in terms of negative correlation (r=-0.97, p= 1.75e-07, FDR = 0.04) and the number of seeds in miRNA responsible for negative regulation, we selected miRNA-146b and its target gene anti-inflammatory retinoic acid receptor alpha (RARA). Similarly, to NGS, qPCR analysis also confirmed negative correlation between miRNA-146b and RARA expression (r= -0.45, p= 0.04,). Additionally, miRNA-146b expression in RA monocytes significantly correlated with clinical parameters including disease activity score-28 for RA with c-reactive protein (DAS28-CRP) and erythrocyte sedimentation rate (DAS28-ESR). Whereas overexpression of miRNA-146b was able to functionally reduce RARA expression in THP-1 monocytic cell line. Finally, circulating miRNA-146b expression in sera and synovial fluids was significantly elevated in RA patients.

Conclusions: Overall, in this study we have identified a new miRNA-146b candidate which is predicted to negatively regulate anti-inflammatory RARA transcript, whereas circulating miRNA-146b level can be used as a biomarker predicting proinflammatory RA progression and disease activity.

Keywords: biomarkers; microRNA; monocytes; retinoic acid receptor alpha; rheumatoid arthritis; sequencing; transcriptomic.