Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data

Abstract

Patients with inflammatory bowel disease (IBD) are known to have perturbations in microRNA (miRNA) levels as well as altered miRNA regulation. Although experimental methods have provided initial insights into the functional consequences that may arise due to these changes, researchers are increasingly utilising novel bioinformatics approaches to further dissect the role of miRNAs in IBD. The recent exponential increase in transcriptomics datasets provides an excellent opportunity to further explore the role of miRNAs in IBD pathogenesis. To effectively understand miRNA-target gene interactions from gene expression data, multiple database resources are required, which have become available in recent years. In this technical note, we provide a step-by-step protocol for utilising these state-of-the-art resources, as well as systems biology approaches to understand the role of miRNAs in complex disease pathogenesis. We demonstrate through a case study example how to combine the resulting miRNA-target gene networks with transcriptomics data to find potential disease-specific miRNA regulators and miRNA-target genes in Crohn’s disease. This approach could help to identify miRNAs that may have important disease-modifying effects in IBD and other complex disorders, and facilitate the discovery of novel therapeutic targets.

Detection and Quantification of Immunoregulatory miRNAs in Human Milk and Infant Milk Formula

“…miRNAs play an important role in the regulation of gene expression and contribute to the pathogenesis of complex diseases, such as IBD [28]. Several studies have revealed that levels of certain miRNAs are altered in IBD patients in comparison to healthy individuals, such as miR-124, miR-320, miR-21, miR-31, and miR-141 [29].…”

Exploring the theranostic potentials of miRNA and epigenetic networks in autoimmune diseases: A comprehensive review

“…[ [116][117][118][119][120] miRNA-24, miRNA-107, miRNA-10a, miRNA-223, miRNA-9, miRNA-21, miRNA-874, miRNA-150, miRNA-125b, miRNA-17-92,…”

Where Do We Stand in the Behavioral Pathogenesis of Inflammatory Bowel Disease? The Western Dietary Pattern and Microbiota—A Narrative Review

“…Such epigenetic research opens up a broad field of research that generates exciting insights into IBD pathophysiology. The patterns of DNA methylation and histone modification as well as microRNA (miRNA) molecules post-transcriptional regulation may in the future serve not only as biomarkers of disease predisposition, disease activity, or disease course, but also as new targets in therapeutic interventions in IBD patients [34,35]. According to data from the Online Mendelian Inheritance in Man (OMIM) database, to date 28 regions (IBD1-28) have been defined in the human genome containing specific genes and changes that are associated with an increase in IBD incidence (Table 1).…”