P698 Methylomic profiling in Inflammatory Bowel Disease: New insights into disease pathogenesis and activity
E. McDermott*1, E. Ryan1, M. Tosetto1, J. Burrage2, J. Mill2, G. Doherty1, G. Cullen1, H. Mulcahy1, T. Murphy2
1St. Vincent's University Hospital, Centre for Colorectal Disease, Dublin, Ireland, 2University of Exeter , Medical School, Exeter, United Kingdom
The precise aetiology of IBD is not known. However, both environmental and genetic factors contribute and epigenetic regulation e.g. DNA methylation may integrate these factors. The goal of this study is to identify site-specific DNA methylation changes associated with IBD and disease activity.
One hundred and fifty patients (88 Crohn's disease, 83 male, median age 34 years, disease duration 6.7 years) with histologically confirmed IBD attending a university teaching hospital donated a blood sample from which peripheral blood mononuclear cells were isolated. Genomic DNA (500ng) was bisulfite converted using the EZ-96 DNA Methylation Kit. DNA methylation was quantified using the Illumina Infinium HumanMethylation450 BeadChip array with data normalisation and pre-processing performed using WateRmelon. The final analyses included 430821 probes and 188 (149 IBD cases, 39 controls) samples passed our stringent quality control filter. Statistical analysis was performed using R 3.1.1. Linear regression was used to examine differences in DNA methylation scores and p values were adjusted for multiple testing according to the false discovery rate procedure. Pathway analysis of genes associated with the 100 top-ranked DMPs identified in the IBD cases versus control analysis and the 100 top-ranked DMPs identified in the active versus inactive disease analysis was performed using Ingenuity Pathway Analysis. Gene expression was quantified using Real time quantitative PCR.
A total of 22,556 probes were significantly differentially methylated between IBD cases and controls, after adjustment for multiple testing. Network analysis of genes associated with the 100 top-ranked DMPs highlighted significant enrichment for pathways associated with immunological disease, including notch signalling and histidine degradation. DMPs associated with disease activity were significantly enriched for pathways associated with inflammatory and antimicrobial response, including IL-6 and TGF-beta signalling. Traf-6 and Peli-1, both hypermethylated in IBD versus controls, were identified as targets for validation. Gene expression (n=50) was significantly reduced in IBD for both Traf-6 (p=0.008) and Peli-1 (p=0.006).
DNA methylation profiles of differed significantly between IBD patients and controls and with disease activity. Moreover, Traf-6 and Peli1 mRNA was significantly reduced in IBD cases compared to controls. Our data provide new insights into potential pathways and molecules which are targets of aberrant DNA methylation and may contribute to the pathogenesis and activity of IBD.