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

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.

Systematic Analysis of Transcriptomic Profile of the Effects of Low Dose Atropine Treatment on Scleral Fibroblasts using Next-Generation Sequencing and Bioinformatics

“…The NGS technique was used for examining the expression profiles of miRNAs and mRNAs as described in our previous studies 34-36. Total RNA from the atropine-treated and normal scleral fibroblasts were extracted with TRIzol ® Reagent (Invitrogen, USA.)…”

High-Throughput MicroRNA Profiling of Vitreoretinal Lymphoma: Vitreous and Serum MicroRNA Profiles Distinct from Uveitis

“…miR-146a-5p is a tumor suppressor in malignancies, regulating proliferation and apoptosis. Its role in inflammation is less well studied but has been suggested to be a potential biomarker for rheumatoid arthritis [53][54][55]. Furthermore, similar to rheumatoid arthritis patients, miR-146a-5p expression levels are reduced in hepatocellular cell carcinoma [56].…”

Membrane proteome characterization of periodontal ligament cell sets from deciduous and permanent teeth

“…LRRC15, also named LIB, is a member of the leucine‐rich repeat superfamily, members of which have been found to be involved in cell‒cell and cell‒extracellular matrix interactions, including adhesion, target recognition or receptor‒ligand binding, has been reported to be induced and highly expressed in various cancer types, and has been recently identified as one of the two critical factors potentially involved with osteoblasts in rheumatoid arthritis . Other molecules containing leucine‐rich repeat motifs include members of the small leucine‐rich proteoglycan (SLRP), the Toll‐like receptor (TLR) gene family, and proteins involved in neurological development .…”