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P065 Molecular landscape of early Crohn’s disease using an integrated approach of mRNA/miRNA profiling and genomics

S. Verstockt*1, J. Van der Goten2, M. Vancamelbeke2, B. Verstockt2, F. Schuit3, P. Rutgeerts2, M. Ferrante2, S. Vermeire2, I. Arijs2, I. Cleynen1

1KU Leuven, Department of Human Genetics, Leuven, Belgium, 2KU Leuven, Department of Clinical and Experimental Medicine, Translational Research Centre for Gastrointestinal Disorders, Leuven, Belgium, 3KU Leuven, Department of Cellular and Molecular Medicine, Gene Expression Unit, Leuven, Belgium

Background

Crohn’s disease (CD) is a chronic inflammatory condition of the gut, characterised by a progression to stricturing and/or penetrating complications in most patients. Effective intervention before the onset of bowel damage, and thus in the early phase of the disease, will be required to optimise patient outcomes. We aimed to define the molecular landscape of early CD, looking at microRNA (miRNA)- and SNP-mediated gene regulation. An eminent model to study this early phase is that of early postoperative recurrence (POR) in CD.

Methods

Ileal biopsies were obtained from inflamed mucosa of 25 CD patients with POR (< 1 year after ileo-colonic resection, Rutgeerts’ score i2, i3, or i4), and from normal mucosa of 12 controls. Total RNA was used to study mRNA and miRNA expression via Affymetrix Human Gene 1.0 ST and Affymetrix miRNA 2.0 arrays, respectively. Data were analysed with R/Bioconductor. A false discovery rate (FDR) < 5% and >2-fold change (mRNA) or >1.5-fold change (miRNA) were considered biologically significant. Gene and miRNA expression profiles were integrated using the Ingenuity microRNA Target Filter, and experimentally validated interactions were annotated using TarBase. To identify expression quantitative trait loci (eQTL) for mRNAs, Matrix eQTL (FDR < 5%) was applied to a subset of 18 POR CD patients and on a different set of 15 CD patients in different stages of disease.

Results

When comparing POR patients with controls, 333 (222 up and 111 down) gene probe sets and 24 miRNAs (7 up and 17 down) gave significantly different signals. We identified 92 miRNA-mRNA pairs with negative correlation in expression profiles (17 different miRNAs and 72 different mRNAs). Of these, there were 54 pairs where the miRNA is predicted to repress the expression of its target mRNA to 40% of its normal level. Four pairs are experimentally supported: let-7a-5p is known to target PRDM1 and PTGS2, and miR-30c-5p targets SLC7A11 and WNT5A. There were no cis-eQTLs (within 1 Mb of their target gene) and 114 trans-eQTL signals. In contrast, in another dataset with CD patients in different stages of their disease, we found 66 cis-eQTL and 1367 trans-eQTL signals.

Conclusion

Integrated analysis of gene and miRNA expression profiles in POR in CD patients revealed potential miRNA targets that alter the expression of many genes related to CD pathogenesis. Let-7a-5p is a promising target, as it regulates the expression of PRDM1, which is a susceptibility gene for CD and encodes a β-IFN repressor. The lack of cis- and trans-eQTL signals within the POR patient group could reflect the homogeneity in gene expression in POR CD patients, and it highlights its usefulness as a model to study early disease.