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P087. Differentially expressed microRNAs regulate expression of genes with clinical interest in inflamed colon of patients with ulcerative colitis

J. Van der Goten1, L. Van Lommel2, W. Vanhove1, V. De Preter1, M. Ferrante1, F. Schuit2, P. Rutgeerts1, S. Vermeire1, I. Arijs1, 1KU Leuven, Translational Research in GastroIntestinal Disorders (TARGID), Leuven, Belgium, 2KU Leuven, Gene Expression Unit, Department of Molecular Cell Biology, Leuven, Belgium

Background

Ulcerative colitis (UC) is associated with colonic differential expression of genes involved in immune response, barrier integrity and tissue remodeling. MicroRNAs (miRNAs) control gene expression post-transcriptionally by repressing translation. Recently, miRNAs have emerged as key regulators of various immune-related diseases. We investigated if miRNA expression in UC mucosa is altered and correlated our findings with mucosal gene expression.

Methods

Colonic mucosal biopsies were obtained from 17 UC (10 active and 7 inactive) patients, and 10 controls. Total RNA, incl. small RNA, was extracted and used to analyze the miRNA expression via Affymetrix miRNA 2.0 arrays. To assess gene expression, total RNA isolated from biopsies was analyzed via Affymetrix Human Gene 1.0ST arrays. Data was analyzed with Bioconductor software. Predicted target genes were identified using the miRWalk software tool. Microarray data were validated by qRT-PCR analysis.

Results

We identified 51 (24 ↑ and 27 ↓) miRNAs and 1543 (976 ↑ and 567 ↓) gene probe sets that were significantly different (false discovery rate (FDR) <5% and >2-fold change) in active UC vs. controls. These genes were mainly involved in immune-related functions. In contrast, in inactive UC vs. controls, no significant miRNA expression differences were found while 155 gene probe sets (73 ↑ and 82 ↓) were significantly different. Next, we identified potential target genes using in silico analysis of the significantly dysregulated miRNAs and genes in active UC vs. controls. Out of 333 pairs of miRNAs and target genes of clinical interest in UC, a highly significant inverse correlation was observed between the expression of hsa-miR-200c-3p and IL8, a UC susceptibility gene (Spearman ρ = −0.92; FDR <0.001), and between hsa-miR-200c-3p and CDH11, a gene related to intestinal epithelial barrier function (Spearman ρ = −0.88; FDR <0.001). Colonic expression of hsa-miR-200c-3p was 2.4-fold lower in active UC vs. controls (FDR = 0.001), while expression of its target genes CDH11 and IL8 was respectively 3.2-fold (FDR = 1.9E-06) and 7.8-fold (FDR = 8.7E-06) increased in active UC vs. controls. qRT-PCR confirmed array data of hsa-miR-200c-3p, IL8 and CDH11.

Conclusion

Altered expression of miRNAs plays an important role in the expression of immune- and barrier-related genes in inflamed UC mucosa. Integrated analysis of miRNA and gene expression profiles revealed potential targets, such as hsa-miR-200c-3p, for use of miRNA mimics as therapeutics.