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OP007 Comprehensive epigenome-wide DNA methylation profiling in inflammatory bowel disease

N. Ventham*1, N. Kennedy1, A. Adams1, R. Kalla1, S. Heath2, K. O’Leary1, H. Drummond1, D. Wilson3, T. IBD-BIOM Consortium1, T. IBD-CHARACTER Consortium1, I. Gut2, E. R. Nimmo1, J. Satsangi1

1University of Edinburgh, CGEM, Edinburgh, United Kingdom, 2Centro Nacional de Análisis Genómico, Barcelona, Spain, 3University Of Edinburgh, Department of Child Life and Health, Edinburgh, United Kingdom

Background

Epigenetic alterations including DNA methylation may provide important insights into gene-environment interaction in complex immune diseases such as inflammatory bowel disease (IBD). While whole tissue methylation changes may provide clinically useful biomarkers, epigenetic changes are cell-type specific. This study aimed to characterise the circulating methylome in IBD, and relate changes seen in whole blood to the methylation profile in separated leucocytes and to genetic and gene expression data.

Methods

Genome-wide DNA methylation was assessed at over 485,000 CpG sites across the genome in 240 patients (121 Crohn’s disease [CD], 119 ulcerative colitis [UC]) and 191 controls (HC) using the Illumina 450k array. Technical validation and independent replication was performed using whole-genome bisulphite sequencing (WGBS, 9 patients) and pyrosequencing respectively (CD, n = 121, UC = 119, HC = 98). Differentially methylated sites discovered in whole blood were also investigated in immunomagnetically separated leucocytes (CD4+ and CD8+ lymphocytes, CD14+ monocytes). DNA methylation data were correlated with genetic and gene expression data.

Results

There were 439 differentially methylated positions (DMPs) meeting epigenome-wide significance as defined as a Holm corrected p-value of < 0.05 (uncorrected p ≤ 1.1 × 10–7) in IBD cases vs control (Figure 1a and 1b).




Manhattan plot demonstrating differentially methylated positions (DMPs) in patients with IBD vs controls.




Circular representation of DNA methylation. A: IBD vs HC DMPs. B: Paediatric CD vs HC DMPs from Adams et al.1 WGBS data averaged into 1-Mbp bins for UC (C, n = 3), CD (D, n = 3), and HC (E, n = 3); heat maps indicate DNA methylation change vs HC.

There were 5 differentially methylated regions (DMRs) with unidirectional methylation change in ≥ 3 adjacent markers which have been mapped in detail using WGBS. Both established and novel pathways pertinent to disease pathogenesis are strongly implicated. The most significantly DMP in whole blood (RPS6KA2 [discovery corrected p = 1.1 × 10–16, independent replication uncorrected p = 7 × 10–11] was also hypo methylated in monocytes in UC (uncorrected p = 3.5 × 10–6). The most significant DMR, VMP1/miR21 (p = 4.9 × 10–14) strongly replicates our previously published finding.1 Linear discriminant analysis using 2 CpG sites discriminated IBD cases and controls with high accuracy (area under curve 0.87)

Conclusion

This is the most detailed characterisation of the epigenome carried out in IBD to date. The findings strongly validate this approach in complex disease. Further, the findings are replicable, and they provide clear translational opportunities.

References

[1] Adams AT, Kennedy NA, Hansen R, et al. Two-stage genome-wide methylation profiling in childhood-onset Crohn’s disease implicates epigenetic alterations at the VMP1/MIR21 and HLA loci. Inflammatory bowel diseases, Inflamm Bowel Dis 2014; 20(10):1784–93.