Integrated analysis of dysregulated microRNA and mRNA expression in intestinal epithelial cells following ethanol intoxication and burn injury

Abstract

Gut barrier dysfunction is often implicated in pathology following alcohol intoxication and burn injury. MicroRNAs (miRNAs) are negative regulators of gene expression that play a central role in gut homeostasis, although their role after alcohol and burn injury is poorly understood. We performed an integrated analysis of miRNA and RNA sequencing data to identify a network of interactions within small intestinal epithelial cells (IECs) which could promote gut barrier disruption. Mice were gavaged with ~ 2.9 g/kg ethanol and four hours later given a ~ 12.5% TBSA full thickness scald injury. One day later, IECs were harvested and total RNA extracted for RNA-seq and miRNA-seq. RNA sequencing showed 712 differentially expressed genes (DEGs) (padj < 0.05) in IECs following alcohol and burn injury. Furthermore, miRNA sequencing revealed 17 differentially expressed miRNAs (DEMs) (padj < 0.1). Utilizing the miRNet, miRDB and TargetScan databases, we identified both validated and predicted miRNA gene targets. Integration of small RNA sequencing data with mRNA sequencing results identified correlated changes in miRNA and target expression. Upregulated miRNAs were associated with decreased proliferation (miR-98-3p and miR-381-3p) and cellular adhesion (miR-29a-3p, miR-429-3p and miR3535), while downregulated miRNAs were connected to upregulation of apoptosis (Let-7d-5p and miR-130b-5p) and metabolism (miR-674-3p and miR-185-5p). Overall, these findings suggest that alcohol and burn injury significantly alters the mRNA and miRNA expression profile of IECs and reveals numerous miRNA–mRNA interactions that regulate critical pathways for gut barrier function after alcohol and burn injury.

MicroRNA‐29a Compromises Hepatic Adiposis and Gut Dysbiosis in High Fat Diet‐Fed Mice via Downregulating Inflammation

“…An unambiguous relationship exists between miR-29a and the gut, a key aspect of miR-29a that is involved in intestinal permeability, improved colorectal cancer incidence, and irritable bowel syndrome with predominant diarrhea. [57][58][59] However, research has also consistently shown that miR-29a serves as a tumor suppressor or inhibits fibrogenesis under certain circumstances. [60] Based on these findings, further studies on the multifaceted physiological functions of miR-29a are warranted.…”

A comparative analysis of small extracellular vesicle (sEV) micro-RNA (miRNA) isolation and sequencing procedures in blood plasma samples

“…Further, more than 50 miRNAs were identified in each sEV miRNA isolation methodology which has sEV origin and specifically targets genes related to endosome (GO:0005768) cell compartment enrichment [ Supplementary File 1]. This analysis revealed that the majority of miRNA IDs were shared [33] between all four methodologies; however, SEC+UC method resulted in the highest yield [56] and unique [5] miRNA IDs with sEV origin relative to the rest of the three methods.…”

“…mirnet.ca/) [31] , TargetScanHuman 8.0 (http://www.targetscan.org/vert_80/) [32] and miRWalk (http://mirwalk. umm.uni-heidelberg.de/) [33] . For miRNet, bos taurus was the selected organism, miRbase ID was chosen as the ID type and the target type was miRanda genes.…”

Expression Profiles of Circulating MicroRNAs in XELOX-Chemotherapy-Induced Peripheral Neuropathy in Patients with Advanced Gastric Cancer

“…Based on the results from the small RNA sequencing, miRNA–mRNA interactions were predicted using miRNet ( accessed on 3 May 2022), which is a miRNA target computational prediction tool. The database on miRNet is a powerful web-based tool that integrates data from two servers for experimentally verified miRNA gene targets, TarBase and miRTarBase [ 47 ].…”