Crypt-top and crypt-bottom colonic epithelial cell microRNA profiling reveals cell type-specific response in active and quiescent ulcerative colitis

BackgroundColonic epithelial cells form a frontline intestinal barrier and maintain its function which deteriorates early in ulcerative colitis (UC). MicroRNAs (miRNAs) participate in regulation of intestinal epithelial integrity and barrier permeability. However, there is a lack of understanding about cell type-specific expression of miRNAs in UC.MethodsTwo independent cohorts composed of active and quiescent UC patients (n=74), and healthy controls (HC; n=50) were studied. Crypt-bottom (CD44+) and crypt-top (CD66a+) colonic epithelial cell populations were enriched using FACS. Small RNA-sequencing was performed on colon biopsy and colonic epithelial cell population samples. Data processing encompassed differential expression, gene-set enrichment analysis (GSEA) and clinical correlation analysis.ResultsWe describe differentially expressed miRNAs among active and quiescent UC compared to HC colon tissue and propose their involvement in intestinal barrier integrity regulation. We further focus on crypt-bottom and crypt-top colonic epithelial cells and characterise common and cell population-specific miRNA expression in response to UC-caused inflammation. We suggest that differentially expressed miRNAs are commonly involved in inflammation- and intestinal barrier integrity-related processes (such as signalling of interleukin-4 and interleukin-13), while differences between cell populations might reflect their function, i.e., crypt-bottom cell miRNA target genes are enriched in regulation of cell differentiation. Moreover, we show cell population-specific miRNA expression correlations with endoscopic disease activity, i.e., let-7b-5p and let-7e-5p negatively correlates with activity score only in the crypt-bottom cells, while miR-24-3p and miR-27a-3p positively correlates only in the crypt-top cells.ConclusionsChanges in miRNA expression during UC are epithelial cell type- and UC activity-specific (including correlations with endoscopic Mayo score). Further, irrespective of the UC stage and colonic cell population, deregulated miRNAs are potentially involved in signalling pathways responsible for regulation of intestinal barrier integrity and permeability.Key MessagesWhat is already known?Colonic epithelium plays an important role in pathogenesis of ulcerative colitis (UC), while microRNAs (miRNA) have been implicated in modulation of intestinal homeostasis.What is new here?Cell type-specific miRNA expression of colonic epithelial cells during UC was unknown. Here, we show cell population-specific miRNA expression in response to UC-caused inflammation in crypt-top and crypt-bottom colonic cells.How can this study help patient care?The identified cell type-specific correlations of miRNA expression and endoscopic Mayo score might be further evaluated in UC monitoring and diagnostics as well as selected as targets for further therapeutics development.Graphical abstractSummaryWe present microRNA transcriptome analysis on different levels - colon tissue and epithelial cell population - in ulcerative colitis. Results indicate cell type- and disease stage-dependent microRNA deregulation, unveil associations with disease activity, and putative biological role of deregulated microRNAs.