Computational Approaches towards Micro-RNA Expression Analysis for Identification of Biomarkers in Inflammatory Bowel Disease Subtypes

Abstract

Background and Aim: The potential biomarkers of inflammatory bowel diseases (IBDs) were analyzed from GSE53867 dataset. The current study aimed to identify miRNAs as potential diagnostic and prognostic biomarkers to delineate the IBD subtypes. Methods: Differentially expressed microRNAs (DEMs)-genes and protein-protein interaction networks were constructed and hub genes were selected using Cytoscape. Differentially expressed genes were analyzed for GO (Gene Ontology) and Reactome-pathway. Results: Seven DEMs were upregulated in Crohn’s disease (CD), 4 downregulated in ulcerative colitis (UC), 8 upregulated and 2 downregulated in IBD. A 620, 2377 and 1821 target-genes were in CD, UC and IBD, respectively. SOCS3, upregulated by miR-650, was hub gene in CD, induced by cytokines, through NFKB-signalling pathway to mediate ubiquitin-proteasomal degradation. CIRH1A, downregulated by miR-16, was hub gene of UC, acted by impairing ribosomebiogenesis. SKP2 and ASB1, up- and downregulated, by miR-142 and miR-665, respectively, were hub genes of IBD, induced cytokines through activation of TLR- and TNF-signalling pathways to mediate ubiquitin-proteasomal degradation. Conclusion: The SOCS3, CIRH1A, SKP2 and ASB1 genes might serve as valuable biomarkers to differentiate CD, UC and IBD.