Integrative Analysis Identified rs907091 at the miRNA Binding Region of the IKZF3 Gene as a Potential Functional Variant for Rheumatoid Arthritis

Abstract

Objective: Previous studies have identified a large number of associations between genetic variants and rheumatoid arthritis (RA), but the functional mechanisms underlying the associations are largely unknown. Methods: Based on publicly available datasets and results, we explored the functional mechanisms underlying the associations between regulatory polymorphisms in miRNA target sites (poly-miRTSs) and RA by combining integrative analyses (expression quantitative trait locus analysis, eQTL, and gene enrichment analysis) with in-house molecular experiments (allelic expression imbalance experiment, AEI, and dual-luciferase reporter gene assay). Results: By integrating the results from the MirSNP and eQTL databases, a total of 114 pairs between poly-miRTSs and target genes were identified, which correspond to 70 unique poly-miRTSs and 28 genes. Most of the 28 genes were located in the HLA region, and they tended to be enriched in multiple immune-related GO terms or pathways, e.g., “antigen processing and presentation” and “immune response”. Among these poly-miRTSs, rs907091 in the 3’UTR of IKZF3 (non-HLA region) was highlighted. Further AEI experiments showed that the C allele had a higher expression of ~18% than the T allele, suggesting an obvious allelic expression imbalance. Dual-luciferase reporter gene assays showed that miR-326 and miR-330-5p could regulate IKZF3 expression (P<0.05) mediated by rs907091 in the 3’UTR binding site. Conclusion: Our study explored some functional mechanisms underlying the associations between poly-miRTSs and target genes and highlighted rs907091 at the miRNA binding region of the IKZF3 gene as a potential functional variant for rheumatoid arthritis.