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P055. Integrated miRNA and gene expression profiling in patients with ulcerative colitis before and after infliximab treatment

J. Van der Goten1, I. Arijs1, L. Van Lommel2, W. Vanhove1, M. Ferrante1, G. Van Assche1, P. Rutgeerts1, F. Schuit2, S. Vermeire1, 1KU Leuven, Department of Clinical and Experimental Medicine, Translational Research Center for GastroIntestinal Disorders (TARGID), Leuven, Belgium, 2KU Leuven, Department of Cellular and Molecular Medicine, Gene Expression Unit, Leuven, Belgium

Background

MicroRNAs (miRNAs) are increasingly recognized as major regulators of gene expression in many processes, including inflammation and tissue remodeling. Recently, altered expression of miRNAs has been reported in association with ulcerative colitis (UC). In this study, we investigated the effect of controlling inflammation with infliximab (IFX) on the miRNA expression in UC and we correlated our findings with mucosal gene expression.

Methods

Colonic mucosal biopsies were obtained during endoscopy from 7 UC patients before and after IFX induction therapy (infusions at weeks 0, 2 and 6) and from 10 normal controls. Endoscopic response was assessed at 14 weeks after start of IFX and was defined as a Mayo endoscopic subscore of 0 or 1. Endoscopic non-response was defined as a Mayo endoscopic subscore of 2 or 3. Total RNA, including small RNA, was extracted from the biopsies and used to analyze the miRNA expression via Affymetrix GeneChip® miRNA 2.0 arrays. To assess gene expression, total RNA was analyzed via Affymetrix Human Gene 1.0ST arrays. A false discovery rate <5% combined with >2-fold change was considered as significant. Predicted target genes were identified using the miRWalk software tool. Microarray data were validated by qRT-PCR analysis.

Results

Four out of 7 patients showed endoscopic response. In these 4 responders, expression of 893 gene probe sets (200↑ and 693↓) was significantly different after IFX therapy when compared to their baseline samples. We also identified 4 miRNAs that were significantly upregulated and 6 downregulated. By contrast, in the 3 non-responders IFX did not significantly affect gene or miRNA expression. Five miRNAs were selected for validation. In responders, we could confirm the upregulation after IFX therapy of miR-375 (p = 0.07), and the downregulation of miR-21–5p (p = 0.14), miR-31–5p (p = 0.07) and miR-155–5p (p = 0.07). Upregulation of miR-422a could not be confirmed. Next, we identified potential target genes in responders before and after IFX treatment using in silico analysis of the significantly dysregulated miRNAs and genes. The target genes encode proteins that were predominantly involved in hematological system development and function, immune cell trafficking and tissue development. Out of 39 pairs of miRNAs and target genes of clinical interest in UC, a highly significant inverse correlation was observed between the expression of miR-378a-5p and IL1R1, identified as one of the UC susceptibility genes (Spearman ρ = −0.84; FDR = 0.003).

Conclusion

IFX therapy has a profound effect on the mucosal gene and miRNA expression. Integrated analysis of miRNA and gene expression profiles revealed potential mucosal biomarkers, such as miR-378a-5p and its target IL1R1, for response to IFX therapy.