P004 Exon-level microarrays identify alternative splicing for ICAM3 in Crohn’s disease
S. Verstockt*1, M. Vancamelbeke2, B. Verstockt2, F. Schuit3, M. Ferrante2, S. Vermeire2, I. Cleynen1, I. Arijs2
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
Crohn’s disease (CD) is reflected by differential mucosal expression of genes involved in immune response, antimicrobial response, tissue remodelling, and cell adhesion. The majority of protein-encoding genes, including those underlying susceptibility to CD, undergo alternative splicing, thereby influencing human physiology, development, and disease. As differential splicing patterns on a genome-wide scale have not yet been studied in CD, we wanted to search for CD-associated alternative splicing events.
Total RNA was extracted from mucosal biopsies from inflamed colon of 19 CD patients, and from normal colon of 6 controls. Genome-wide alternative splicing was studied with Affymetrix Human Exon 1.0 ST Arrays. Data were analysed with R/Bioconductor (aroma.affymetrix and limma packages), and with the Exon Array Analyser (EAA). Significant (false discovery rate < 5% and > 2-fold change) alternative splicing events from both programmes were compared. Bio-functional analysis was performed with Ingenuity Pathway analysis (IPA).
We identified 350 differential splicing events, representing 243 different genes, in both R and EAA. IPA analysis highlighted cellular movement, cell death and survival, and immune cell trafficking amongst the most enriched biological functions. When comparing only the top-50 most-significant splicing events from both analysis programmes, 20 were overlapping. Of these, 5 are known alternative splicing events, located in ICAM3, AKAP9, AKAP13, SDR16C5, and IGSF9. Cluster analysis based on the expression of the corresponding probe sets distinguished CD patients from controls.
We found alternative splicing of many transcripts in colonic biopsies of CD patients, many of which are involved in biological functions related to the pathogenesis of CD. ICAM3 encodes an adhesion molecule regulating leukocyte trafficking. It represents a very promising alternative splice event in CD, as it is located in a known susceptibility region for CD. Future work should examine the role of the identified ICAM3 genetic variants on alternative splicing.