The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region

Abstract

The Human Leucocyte Antigen (HLA) locus and other DNA sequence variants identified in Genome-Wide Association (GWA) studies explain around 50% of the heritability of celiac disease (CD). However, the pathogenesis of CD could be driven by other layers of genomic information independent from sequence variation, such as DNA methylation, and it is possible that allele-specific methylation explains part of the SNP associations. Since the DNA methylation landscape is expected to be different among cell types, we analyzed the methylome of the epithelial and immune cell populations of duodenal biopsies in CD patients and controls separately. We found a cell type-specific methylation signature that includes genes mapping to the HLA region, namely TAP1 and HLA-B. We also performed Immunochip SNP genotyping of the same samples and interrogated the expression of some of the affected genes. Our analysis revealed that the epithelial methylome is characterized by the loss of CpG island (CGI) boundaries, often associated to altered gene expression, and by the increased variability of the methylation across the samples. The overlap between differentially methylated positions (DMPs) and CD-associated SNPs or variants contributing to methylation quantitative trait loci (mQTLs) is minimal. In contrast, there is a notable enrichment of mQTLs among the most significant CD-associated SNPs. Our results support the notion that DNA methylation alterations constitute a genotype-independent event and confirm its role in the HLA region (apart from the well-known, DQ allele-specific effect). Finally, we find that a fraction of the CD-associated variants could exert its phenotypic effect through DNA methylation.

The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells

“…This locus presents strong linkage disequilibrium and encodes a number of genes related to immune response and immune regulation through self-recognition [49,51], and strongly predisposes to autoimmune diseases such as CeD. In our previous work [34], we claimed to have found a genotype-independent methylation signature in coeliac duodenal epithelia. The finding of a signature in the HLA region common to IBD and CeD reinforces this idea, given that the HLA association with IBD is much weaker (variance explained <5%) than with CeD, and moreover, different HLA haplotypes drive these associations [45].…”

“…We therefore chose coeliac disease (CeD), a chronic inflammatory condition of the GI tract with a well-characterized genetic component, to get further insight into methylome specificity. In addition, DNA methylation data for epithelial and immune components of CeD were analysed separately [34]. When we crossed IBD-DMPs with epithelial CeD-DMPs we found that, out of 4205 IBD-DMPs and 43 CeD epithelial-DMPs, 8 were common (representation factor = 17.7, p < 1.5e-08) ( Table 6).…”

The DNA Methylome of Inflammatory Bowel Disease (IBD) reflects intrinsic and extrinsic factors in intestinal epithelial cells

“…This locus presents strong linkage disequilibrium and encodes a number of genes related to immune response and immune regulation through self-recognition 37,39 , and strongly predisposes to autoimmune diseases such as CeD. In our previous work 29 , we claimed to have found a genotype-independent methylation signature in celiac duodenal epithelia. The finding of a signature in the HLA region common to IBD and CeD reinforces this idea, given that the HLA association with IBD is much weaker (variance explained <5%) than with CeD, and moreover, different HLA haplotypes drive these associations 33 .…”

“…We therefore chose celiac disease (CeD), a chronic inflammatory condition of the GI tract with a well characterized genetic component, to get further insight into methylome specificity. In addition, DNA methylation data for epithelial and immune components of CeD were analyzed separately 29 . When we crossed IBD-DMPs with epithelial CeD-DMPs we found that, out of 4280 IBD-DMPs and 43 CeD epithelial-DMPs, 7 were common (representation factor=17.1, p < 1e-05) ( Table 5).…”

“…In addition, we searched for those CpGs that apart from being differentially methylated in IBD according to our metanalysis, were previously reported to be differentially methylated in a previous work performed by our group in CeD 29 . CeD is a genetic, inflammatory condition of the duodenum in which the Human Leucocyte Antigen (HLA) region explains around 40% of the heritability, and HLA-DQ2/-DQ8 molecules are necessary for gliadin presentation and activation of the autoimmune response.…”