Two-stage Genome-wide Methylation Profiling in Childhood-onset
Crohn’s Disease Implicates Epigenetic Alterations at the
VMP1/MIR21 and HLA Loci
Background: As a result of technological and analytical advances, genome-wide characterization of key epigenetic alterations is now feasible in complex diseases. We hypothesized that this may provide important insights into gene-environmental interactions in Crohn’s disease (CD) and is especially pertinent to early onset disease.
Methods: The Illumina 450K platform was applied to assess epigenome-wide methylation profiles in circulating leukocyte DNA in discovery and replication pediatric CD cohorts and controls. Data were corrected for differential leukocyte proportions. Targeted replication was performed in adults using pyrosequencing. Methylation changes were correlated with gene expression in blood and intestinal mucosa.
Results: We identified 65 individual CpG sites with methylation alterations achieving epigenome-wide significance after Bonferroni correction (P , 1.1 · 1027), and 19 differently methylated regions displaying unidirectional methylation change. There was a highly significant enrichment of methylation changes around GWAS single nucleotide polymorphisms (P ¼ 3.7 · 1027), notably the HLA region and MIR21.
Two-locus discriminant analysis in the discovery cohort predicted disease in the pediatric replication cohort with high accuracy (area under the curve, 0.98). The findings strongly implicate the transcriptional start site of MIR21 as a region of extended epigenetic alteration, containing the most significant individual probes (P ¼ 1.97 · 10215) within a GWAS risk locus. In extension studies, we confirmed hypomethylation of MIR21 in adults (P ¼ 6.6 · 1025, n ¼ 172) and show increased mRNA expression in leukocytes (P , 0.005, n ¼ 66) and in the inflamed intestine (P ¼ 1.4 · 1026, n ¼ 99).
Conclusions: We demonstrate highly significant and replicable differences in DNA methylation in CD, defining the disease-associated epigenome. The data strongly implicate known GWAS loci, with compelling evidence implicating MIR21 and the HLA region.
Further Readings of Interest
Human leukocyte antigen
The human leukocyte antigen (HLA) system is the locus of genes that encode for proteins on the surface of cells that are responsible for regulation of the immune system in humans.
The HLA genes are the human versions of the major histocompatibility complex (MHC) genes that are found in most vertebrates (and thus are the most studied of the MHC genes).
HLA and Autism
MHC and Autism
Inflammatory Bowel Disease and Autism