Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes

• Published in: PloS one Vol. 10; no. 9; p. e0137551
• Main Authors: Song, Yi-Jiang, Li, Guiling, He, Jian-Hua, Guo, Yao, Yang, Li
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 11.09.2015; Public Library of Science (PLoS)
• Subjects: Analysis; Annotations; Arthritis; Arthritis, Rheumatoid - genetics; Autoimmune diseases; Bioengineering; Bioinformatics; Biomarkers; Calcium; Calcium-Binding Proteins - genetics; Calcium-Binding Proteins - metabolism; Cancer; Care and treatment; Carrier Proteins - genetics; Carrier Proteins - metabolism; Case-Control Studies; Chronic illnesses; Complications and side effects; Cytokines; Disease; DNA methylation; DNA microarrays; Education; Epigenetics; Gene expression; Gene Regulatory Networks; Gene sequencing; Genes; Genetic markers; Genomes; Genomics; Humans; Kinases; Laboratories; Lymphocytes; Markers; MicroRNA; MicroRNAs; MicroRNAs - genetics; miRNA; Multiple myeloma; Oncology; Pathogenesis; Proteins; Receptor Tyrosine Kinase-like Orphan Receptors - genetics; Receptor Tyrosine Kinase-like Orphan Receptors - metabolism; Regulators; Rheumatism; Rheumatoid arthritis; Ribonucleic acid; Risk factors; RNA; RNA sequencing; RNA, Messenger - genetics; RNA, Messenger - metabolism; Science; Studies; Synovitis; Target recognition; TNF inhibitors; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0137551

MicroRNAs (miRNAs) act as epigenetic markers and regulate the expression of their target genes, including those characterized as regulators in autoimmune diseases. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases. The potential roles of miRNA-regulated genes in RA pathogenesis have greatly aroused the interest of clinicians and researchers in recent years. In the current study, RA-related miRNAs records were obtained from PubMed through conditional literature retrieval. After analyzing the selected records, miRNA targeted genes were predicted. We identified 14 RA-associated miRNAs, and their sub-analysis in 5 microarray or RNA sequencing (RNA-seq) datasets was performed. The microarray and RNA-seq data of RA were also downloaded from NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), analyzed, and annotated. Using a bioinformatics approach, we identified a series of differentially expressed genes (DEGs) by comparing studies on RA and the controls. The RA-related gene expression profile was thus obtained and the expression of miRNA-regulated genes was analyzed. After functional annotation analysis, we found GO molecular function (MF) terms significantly enriched in calcium ion binding (GO: 0005509). Moreover, some novel dysregulated target genes were identified in RA through integrated analysis of miRNA/mRNA expression. The result revealed that the expression of a number of genes, including ROR2, ABI3BP, SMOC2, etc., was not only affected by dysregulated miRNAs, but also altered in RA. Our findings indicate that there is a close association between negatively correlated mRNA/miRNA pairs and RA. These findings may be applied to identify genetic markers for RA diagnosis and treatment in the future.