Differential miRNA expression in ileal and colonic tissues reveals an altered immunoregulatory molecular profile in individuals with Crohn's disease versus healthy subjects.

MicroRNAs (miRNAs) are key modulators of gene expression in Crohn's disease (CD) and may drive tissue-specific molecular alterations underlying CD susceptibility. In this study we analysed differential miRNA expression between CD and healthy subjects across ileal and colonic tissues. A cohort of CD and healthy control (HC) subjects was recruited and clinical data collected. Endoscopically quiescent CD (CDq) was defined as inactive or mild by the Simple Endoscopic Score for CD. Total RNA was extracted from endoscopic biopsies taken from the terminal ileum and sigmoid colon. miRNA expression was quantified using NanoString Technologies. Statistical significance was assessed across biopsy site and diagnosis per miRNA and corrected for multiple testing. In total, 23 CDq and 38 HC subjects were enrolled. 112 samples were included in the analysis, 51 from the ileum and 61 from the colon. We found 47 miRNAs differentially expressed by biopsy site in healthy tissue. Nine miRNAs were differentially expressed across HC and CDq accounting for biopsy location. One of these, miR-223-3p, showed age and sex effects. We identified miRNA expression driven by diagnosis targeting genes involved in chemokine and cytokine signalling. miR-31-5p expression was driven by location and may be a biomarker for location subtypes in CD. We identified differentially expressed miRNAs in healthy ileal and colonic tissues. We discovered spatial miRNA expression patterns in CD and HC suggesting site-specific regulation in subjects with no or minimal intestinal inflammation. These miRNAs target genes involved in immunoregulatory processes, suggesting a functional, tissue-specific role in CD.

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