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. 2015 Sep 11;10(9):e0137551.
doi: 10.1371/journal.pone.0137551. eCollection 2015.

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

Yi-Jiang Song  1 , Guiling Li  2 , Jian-Hua He  1 , Yao Guo  1 , Li Yang  1
Affiliations

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

Yi-Jiang Song et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Flow chart depicting the study selection protocol for rheumatoid arthritis (RA) gene expression.
Fig 2
Fig 2. Genetic interaction networks for mRNA/microRNA (miRNA) pair candidates.
The dysregulated RA-associated miRNAs are indicated in blue, and miRNAs targeting up and downregulated genes are represented by red and green, respectively. A) miRNA-mRNA interaction network from microarray data; B) miRNA-mRNA interaction network from RNA-seq data.
See this image and copyright information in PMC

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Grants and funding

This work was supported by National Innovation and Attracting Talents Project (“111” Project) (B06023), National Natural Science Foundation of China (grant no. 11032012, 10902130, 30870608, 31200976).