Colonic Epithelial miR-31 Associates with the Development of Crohn’s Phenotypes

Abstract

Crohn’s disease (CD) is highly heterogeneous, due in large part to variability in cellular processes that underlie the natural history of CD, thereby confounding effective therapy. There is a critical need to advance understanding of the cellular mechanisms that drive CD heterogeneity. In this study, small RNA-sequencing and microRNA profiling in the colon revealed two distinct molecular subtypes, each with different clinical associations, in both adult and treatment-naïve pediatric CD patients. Notably, we found that microRNA-31 (miR-31) expression by itself can stratify patients into these two subtypes. Through detailed analysis of several colonic mucosa cell types from adult patients, we found that differential levels of miR-31 are particularly pronounced in epithelial cells. We generated patient crypt-derived epithelial colonoids and showed that miR-31 expression differences preserved in this ex-vivo system. In adult patients, low colonic miR-31 expression levels at the time of surgery are associated with post-operative recurrence of ileal disease. In pediatric patients, lower miR-31 expression at the time of diagnosis is associated with the future development of fibrostenotic ileal CD requiring surgery. These findings represent an important step forward in designing more effective clinical trials and developing personalized therapies for CD.

Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn’s Disease

“…In this study, we identified ALK1 as a target of miR-31-5p. 4,5 We showed a dramatic reduction of ALK1 in the colonic IECs of CD patients and showed that ALK1 controls colonocyte differentiation and intestinal epithelial barrier capacity.…”

“…However, increased miR-31-5p also was found in CD14-negative resident macrophages and B lymphocytes in the colon of CD patients. 4 Future investigation will be required to understand the potential impact of decreased E2F2 expression in these nonepithelial cells. We did not examine the impact of ALK1 signaling on IECs from the small intestine.…”

“…We previously reported an up-regulation of miR-31-5p in the ileal tissue of CD patients compared with NIBD controls. 4 Given that ALK1 is expressed in the IECs of the small intestine as well as the colon, 27 investigation of the role of ALK1 signaling in small intestinal IECs will be informative. We also did not investigate the impact of decreased ALK1 on vascular development in the intestine.…”

“…We previously generated and studied expression profiles of messenger RNAs (mRNAs) 6 and miRNAs 4 in the uninflamed colonic mucosa of 21 adult CD patients and 11 NIBD controls. We found a unique subset of CD patients with especially high miR-31-5p expression (high-miR-31-5p patients), which we determined was driven primarily by miR-31-5p expression in isolated IECs compared with other intestinal immune cell populations.…”

“…Colonic epithelial cells were isolated as previously described. 4 In brief, dissected colonic mucosa was cut into small pieces and incubated in magnesium-free Hank's balanced salt solution (HBSS) containing 2 mmol/L EDTA and 2.5% heat-inactivated fetal bovine serum for 30 minutes with shaking at 37 C. To remove mucus, 1 mmol/L dithiothreitol was added and incubated for an additional 10 minutes with shaking. Collected supernatants were centrifuged, resuspended in HBSS containing 1 mg/mL collagenase type 4 (17104019; Thermo Fisher Scientific), and incubated for 10 minutes at 37 C to further remove the mucus.…”