Genome wide peripheral blood leukocyte DNA methylation microarrays failed to identify associations with Inflammatory Bowel Diseases

Abstract

Background: Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel diseases (IBD). Monozygotic (MZ) twin discordance rates and other epidemiologic data implicate that environmental and potential epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. Methylation changes in peripheral blood leukocyte (PBL) DNA have been shown to associate with autoimmune diseases, such as systemic lupus erythematosus. We investigated whether similar epigenetic modification might be connected with IBD. Methods: Two different microarray based methods for genome wide DNA methylation analysis were employed. First, DNA isolated from MZ twins concordant (CD: 4; UC: 3) and discordant (CD: 4; UC: 7) for IBD was interrogated by a custom made methylation specific amplification microarray (MSAM). Second, Illumina Infinium HumanMethylation450 BeadChip arrays were used on 48 samples of PBL DNA from discordant MZ twins (CD:3; UC:3) and untreated pediatric cases of IBD (CD:14; UC:8), as well as controls (n=14). The microarrays were validated with bisulfite pyrosequencing. Results: Neither the MSAM nor the Methylation BeadChip approach demonstrated significant associations between DNA methylation and IBD. ConclusionS: Microarray interrogation of IBD dependent DNA methylation from PBLs is less likely to yield significant results. More detailed and/or intestinal tissue specific approaches may be useful for the elucidation of connections between the DNA methylome and IBD.