Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing.

Chia-Chun Tseng,Jeng-Hsien Yen,Tsan-Teng Ou,Wan-Yu Sung,Ling-Yu Wu,Po-Lin Kuo,Wen-Chan Tsai,Cheng-Chin Wu

doi:10.3390/diagnostics9030098

Abstract

Using next-generation sequencing to decipher the molecular mechanisms underlying aberrant rheumatoid arthritis synovial fibroblasts (RASF) activation, we performed transcriptome-wide RNA-seq and small RNA-seq on synovial fibroblasts from rheumatoid arthritis (RA) subject and normal donor. Differential expression of mRNA and miRNA was integrated with interaction analysis, functional annotation, regulatory network mapping and experimentally verified miRNA–target interaction data, further validated with microarray expression profiles. In this study, 3049 upregulated mRNA and 3552 downregulated mRNA, together with 50 upregulated miRNA and 35 downregulated miRNA in RASF were identified. Interaction analysis highlighted contribution of miRNA to altered transcriptome. Functional annotation revealed metabolic deregulation and oncogenic signatures of RASF. Regulatory network mapping identified downregulated FOXO1 as master transcription factor resulting in altered transcriptome of RASF. Differential expression in three miRNA and corresponding targets (hsa-miR-31-5p:WASF3, hsa-miR-132-3p:RB1, hsa-miR-29c-3p:COL1A1) were also validated. The interactions of these three miRNA–target genes were experimentally validated with past literature. Our transcriptomic and miRNA interactomic investigation identified gene signatures associated with RASF and revealed the involvement of transcription factors and miRNA in an altered transcriptome. These findings help facilitate our understanding of RA with the hope of serving as a springboard for further discoveries relating to the disease.

Highlights

Rheumatoid arthritis (RA) is an autoimmune disease characterized by sustained chronic inflammation resulting in joint damage and severe disability
With rheumatoid arthritis (RA)-specific network were noted (p = 8.48 × 10−17 ) (Figure 2). This observation indicated a contribution of dysregulated miRNA/mRNA to RA development
These results highlight the particular roles played by these transcription factors and miRNA in RA synovial fibroblasts

Summary

Introduction

Rheumatoid arthritis (RA) is an autoimmune disease characterized by sustained chronic inflammation resulting in joint damage and severe disability. New and more effective therapies developed over the past two decades targeting the inflammatory mediators and immune cells [1,2]. Therapies targeting different aspects of the immune response render patients more. Diagnostics 2019, 9, 98 susceptible to infection [5]. In light of these challenges, approaches that focus on other components of joint inflammation have been proposed as potential solutions [4]. In RA, inflammatory cytokines, such as interleukin (IL)-6 and tumor necrosis factor-alpha (TNF-α), cause dysregulated proliferation and drive a migratory and invasive phenotype of synovial fibroblast [6,7] ( known as fibroblast-like synoviocytes (FLS)) [8], resulting in pannus formation

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Discussion

Conclusion