Two-stage Genome-wide Methylation Profiling in Childhood-onset Crohn's Disease Implicates Epigenetic Alterations at the VMP1/MIR21 and HLA Loci

The last decade has seen tremendous success in identifying genetic loci associated with inherited susceptibility to Crohn's diesease (CD), with 140 loci identified in the most recent GWAS meta-analysis.1 However, these determinants collectively explain only an estimated 13.6%1 of disease variability, and the biological variation each confers is unclear. The importance of noninherited factors in pathogenesis has been highlighted by studies on the increasing incidence of CD, especially in children,2,3 and in the developing world,4,5 and by a greater understanding of the effects of gut microbiota and diet on risk.6,7 A critical objective for CD research is to characterize the interaction between genetic and environmental factors. Epigenetic alteration has emerged as a potential mechanism through which these interactions may occur.8 Developments allowing rapid assaying of cytosine methylation at nearly 5 × 105 positions, and insights into confounding effects in study design9 have provided the impetus to build on promising pilot data from previous generation technology to allow epigenome-wide association studies (EWAS) to become a valuable complement to the more mature GWAS.10 Epigenome mapping has been used to identify DNA regulatory elements, explore cancer biology, and provide a growing body of findings in complex diseases, such as rheumatoid arthritis,11 multiple sclerosis,12 type 2 diabetes, and obesity.13,14 Although the relationship between methylation and gene expression and function is incompletely understood, relevant modifying influences include age, ethnicity, smoking, gut microbiota, and diet.15–18 DNA-binding factors can directly influence methylation, and in turn, altering methylation can directly influence expression.19,20 We hypothesized that identification of altered levels of methylation, which are significantly associated with disease state, whether predating or following disease, offers the potential for discovering new pathways integral to the disease process and for predicting disease status.