Discovery of inflammatory bowel disease-associated miRNAs using a novel bipartite clustering approach

Abstract

Background: Multidimensional data mining from an integrated environment of different data sources is frequently performed in computational system biology. The molecular mechanism from the analysis of a complex network of gene-miRNA can aid to diagnosis and treatment of associated diseases. Methods: In this work, we mainly focus on finding inflammatory bowel disease (IBD) associated microRNAs (miRNAs) by biclustering the miRNA-target interactions aided by known IBD risk genes and their associated miRNAs collected from several sources. We rank different miRNAs by attributing to the dataset size and connectivity of IBD associated genes in the miRNA regulatory modules from biclusters. We search the association of some top-ranking miRNAs to IBD related diseases. We also search the network of discovered miRNAs to different diseases and evaluate the similarity of those diseases to IBD. Results: According to different literature, our results show the significance of top-ranking miRNA to IBD or related diseases. The ratio analysis supports our ranking method where the top 20 miRNA has approximately tenfold attachment to IBD genes. From disease-associated miRNA network analysis we found that 71% of different diseases attached to those miRNAs show more than 0.75 similarity scores to IBD. Conclusion: We successfully identify some miRNAs related to IBD where the scoring formula and disease-associated network analysis show the significance of our method. This method can be a promising approach for isolating miRNAs for similar types of diseases.

Serum miRNAs Are Pharmacodynamic Biomarkers Associated With Therapeutic Response in Pediatric Inflammatory Bowel Disease

“…Specifically, they found that let-7c may be highly related to IBD due to number of relevant miRNA-target interactions. 30 The miRNA let-7c also promotes M2 macrophage polarization (anti-inflammatory) and suppresses M1 (pro-inflammatory) polarization. 31 …”

MicroRNA and Gut Microbiota: Tiny but Mighty—Novel Insights into Their Cross-talk in Inflammatory Bowel Disease Pathogenesis and Therapeutics

“…As previously mentioned, the research field of miRNAs in IBD has grown rapidly after their discovery. Several studies have found significantly different profiles of hundreds of miRNAs 20 , 38 between IBD and healthy individuals, 39 paediatric and adult patients, 40 inflamed and non-inflamed mucosa, and in relation to disease activity. 15 , 35 , 37 , 40 To date, there are enough collected data to say that miRNAs are important regulatory factors that play a relevant role in the pathogenesis of IBD.…”

“…Additionally, a recent meta-analysis used a novel bipartite approach to find miRNA associated with IBD. 38 Among the most relevant was the Let-7 family. This is a multifaceted family of miRNA highly conserved across diverse animal species and related with cell proliferation, cell cycle, metabolism, and cell migration.…”

“…This is a multifaceted family of miRNA highly conserved across diverse animal species and related with cell proliferation, cell cycle, metabolism, and cell migration. 38 In more detail, the expression of multiple members of this family appears to be altered during inflammation. Regulated by NF-kB 46 and in direct relation with IL-6 expression, the Let-7 family is part of positive feedback loops that induce enhanced inflammatory responses and cell transformation.…”

MiRNA-374b-5p and miRNA-106a-5p are related to inflammatory bowel disease via regulating IL-10 and STAT3 signaling pathways

“…Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is a frequent gastrointestinal disease worldwide, which can affect any part of the digestive tract [ 1 ]. Epidemiological evidence indicates that the rate of IBD is increased every year, and there is currently no specific treatment for this disease [ 2 ]. IBD pathogenesis is a result of the interplay between environmental, genetic and immune response factors.…”