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

Abstract

Objective To explore global miRNA and transcriptomic profiling of monocytes from RA patients compared with healthy controls in order to predict which aberrantly expressed miRNA can negatively modulate inflammatory molecules. Methods Using next-generation sequencing, we have performed simultaneous global analysis of miRNA (miRNA-seq) and transcriptome (RNA-seq) of monocytes from RA patients and healthy controls. Global analysis of miRNA of 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, false discovery rate = 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 next-generation sequencing, 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 DAS28 for RA with CRP (DAS28-CRP) and ESR (DAS28-ESR), whereas overexpression of miRNA-146b was able to functionally reduce RARA expression in the human monocytic cell line THP-1. Finally, circulating miRNA-146b expression in sera and SFs was significantly elevated in RA patients. Conclusions Overall, in this study we have identified a new miRNA-146b candidate that is predicted to negatively regulate the anti-inflammatory RARA transcript, whereas circulating miRNA-146b level can be used as a biomarker predicting pro-inflammatory RA progression and disease activity.

Tuning Monocytes and Macrophages for Personalized Therapy and Diagnostic Challenge in Rheumatoid Arthritis

“…Using a high throughput approach, our previous results revealed a global miRNA dysregulation and monocyte transcriptome in patients with autoimmune rheumatic diseases. Indeed, based on next generation sequencing (NGS) analysis, we identified miRNA-RNA pairs in monocytes which are important in RA pathogenesis [53]. Further validation predicted that miRNA-146b negatively regulated anti-inflammatory RARA in RA monocytes and correlated with clinical parameters including DAS28.…”

Effectiveness of Soluble CTLA-4-Fc in the Inhibition of Bone Marrow T-Cell Activation in Context of Indoleamine 2.3-Dioxygenase (IDO) and CD4+Foxp3+ Treg Induction

“…Monocytes for RNA-seq analysis were isolated from PBMC of 4 RA patients and 4 HC according to the manufacturer’s protocol with the CD14 + MACS bead isolation kit (Miltenyi-Biotec, the Netherlands) as previously described. 23 RNA from CD14 + monocytes was isolated using miRNeasy kit according to the manufacturer’s protocol (Qiagen, Manchester, UK). Following isolation, the quality and integrity of the total RNA of all samples (4 RA and 4 HC) were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).…”

“…No RS-122-2201; Illumina, USA) for 8 profiles (4 HC and 4 RA) of total RNA, according to the manufacturer protocol. 23 Differentially expressed genes (DEGs) involved in IDO and AHR-mediated pathways were mapped onto the STRING database to estimate protein–protein interactions (PPI). 32 …”

“…Monocytes, which are BM-derived leukocytes, are involved in RA progression, however under special conditions may contribute to tolerance induction due to production of IDO. 17,23,24 As monocytes and macrophages were proofed to originate from a common BM-derived precursor, we decided to analyze the genes involved in IDO and AHR-mediated pathways in peripheral monocytes to estimate their tolerogenic potential. 25,26 In this study, we investigated the influence of CTLA-4-Fc on BM cells in the context of induction of tolerogenic conditions created by IDO and CD4 + Foxp3 + regulatory T cells (Treg).…”

MicroRNA-Mediated Epigenetic Regulation of Rheumatoid Arthritis Susceptibility and Pathogenesis

“…Furthermore, miR-122-3p , miR-3925-3p , miR-342-3p , and miR-4764-5p show differential expression not only between healthy individuals and RA patients, but also between patients with RA and patients with osteoarthritis, systemic lupus erythematosus, or Graves, which show great potential as biomarkers to distinguish RA patients from HC or other diseases ( 98 ). The serum levels of miR-146a ( 99 , 100 ), miR-22-3p ( 101 ), miR-5571-3p ( 102 ), and miR-135b-5p ( 102 ) are significantly higher in RA patients than in healthy controls and osteoarthritis patients. Other differentially expressed miRNAs in patients with RA serum include miR-4634 , miR-181d , miR-3926 , miR-9-5p , miR-219-2-3p6 , miR-221 , miR-222 , miR-532 , miR-106a , and miR-98 highlighting their potential as RA-specific diagnostic markers ( 98 , 103 ).…”