Deduction of Novel Genes Potentially Involved in Osteoblasts of Rheumatoid Arthritis Using Next-Generation Sequencing and Bioinformatic Approaches.

Yi-Jen Chen,Chia-Hsin Chen,Po-Lin Kuo,Ya-Ling Hsu,Wei-An Chang

doi:10.3390/ijms18112396

Abstract

The role of osteoblasts in peri-articular bone loss and bone erosion in rheumatoid arthritis (RA) has gained much attention, and microRNAs are hypothesized to play critical roles in the regulation of osteoblast function in RA. The aim of this study is to explore novel microRNAs differentially expressed in RA osteoblasts and to identify genes potentially involved in the dysregulated bone homeostasis in RA. RNAs were extracted from cultured normal and RA osteoblasts for sequencing. Using the next generation sequencing and bioinformatics approaches, we identified 35 differentially expressed microRNAs and 13 differentially expressed genes with potential microRNA–mRNA interactions in RA osteoblasts. The 13 candidate genes were involved mainly in cell–matrix adhesion, as classified by the Gene Ontology. Two genes of interest identified from RA osteoblasts, A-kinase anchoring protein 12 (AKAP12) and leucin rich repeat containing 15 (LRRC15), were found to express more consistently in the related RA synovial tissue arrays in the Gene Expression Omnibus database, with the predicted interactions with miR-183-5p and miR-146a-5p, respectively. The Ingenuity Pathway Analysis identified AKAP12 as one of the genes involved in protein kinase A signaling and the function of chemotaxis, interconnecting with molecules related to neovascularization. The findings indicate new candidate genes as the potential indicators in evaluating therapies targeting chemotaxis and neovascularization to control joint destruction in RA.

Highlights

Rheumatoid arthritis (RA) is an autoimmune disease characterized by systemic inflammation, presence of autoantibodies, and targeted synovitis, affecting approximately 0.5–1% of population [1]
To identify differentially expressed miRNAs and mRNAs between osteoblasts of normal and rheumatoid arthritis (RA) bones, and potential miRNA–mRNA interactions involved in the inflammatory process and bone homeostasis, we simultaneously performed RNA-seq and small RNA-seq by next generation sequencing (NGS) of normal osteoblasts and RA osteoblasts
We found 434 protein-coding genes with >2.0-fold change and >0.3 fragments per kilobase of transcript per million (FPKM), where 199 genes were up-regulated and 235 genes were down-regulated in RA osteoblasts, compared to normal osteoblasts

Summary

Introduction

Rheumatoid arthritis (RA) is an autoimmune disease characterized by systemic inflammation, presence of autoantibodies, and targeted synovitis, affecting approximately 0.5–1% of population [1]. Synoviocytes and chondrocytes are cell types within the joint dominantly affected by RA. Activated synovial fibroblasts within the inflamed synovium have altered morphology and behavior, and attach directly to cartilage and release matrix degradation enzymes, leading to the destruction of cartilage tissue [1,5,6]. They interact indirectly with adjacent macrophages through the release of receptor activator of nuclear factor κB ligand (RANKL) and mediate the differentiation of macrophage precursors into osteoclasts [6,7]

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