Beyond gene discovery in inflammatory bowel disease: the emerging role of epigenetics

Abstract

In the past decade, there have been fundamental advances in our understanding of genetic factors that contribute to the inflammatory bowel diseases (IBDs) Crohn's disease and ulcerative colitis. The latest international collaborative studies have brought the number of IBD susceptibility gene loci to 163. However, genetic factors account for only a portion of overall disease variance, indicating a need to better explore gene-environment interactions in the development of IBD. Epigenetic factors can mediate interactions between the environment and the genome; their study could provide new insight into the pathogenesis of IBD. We review recent progress in identification of genetic factors associated with IBD and discuss epigenetic mechanisms that could affect development and progression of IBD.

Keywords: CD; CpG; Crohn’s Disease; Crohn’s disease; DNA Methylation; DNA methyltransferase; DNMT; EWAS; Epigenetics; GWAS; HAT; HDAC; HDACi; IBD; IL; NF-κB; PBMC; SNP; T-helper; TNF; Th; UC; Ulcerative Colitis; cytosine-guanine dinucleotides; epigenome-wide methylation association studies; genome-wide association studies; histone acetyl transferase; histone deacetylase; histone deacetylatase inhibitors; inflammatory bowel disease; interleukin; mRNA; messenger RNA; miR; microRNA; nuclear factor κB; peripheral blood mononuclear cell; single nucleotide polymorphism; tumor necrosis factor; ulcerative colitis.

Figure 1

Roles for epigenetics in pathogenesis. Epigenetics could mediate between the genetic environment and environmental factors to help determine the phenotype of IBD. The classic paradigm of genotype leading to phenotype and disease (A) has been expanded to embrace key etiologic factors in IBD (B). Epigenetics (purple) may interact with both genetic factors (blue) and environmental factors (green) in affecting the immune system (orange). The subsequent immune response has consequences on whether insults are tolerated or chronic inflammation is initiated and propagated (red).

Figure 2

The structure and function of chromatin. The structure of chromatin helps determine whether genes are transcribed or not. Chromatin comprises DNA strands that entwine an octamer of histone proteins, comprising histone subtypes H2a, H2b (2× dimer), H3, and H4 (1× tetramer). In a simple model, chromatin exists as heterochromatin or euchromatin. (A) Heterochromatin is a condensed form of chromatin that does not allow access of transcription factors such as RNA polymerase and therefore prevents gene transcription. In its condensed form, heterochromatin is linked with various corepressors, methylated DNA, low levels of histone acetylation, and methylation of key lysine residues (H3 lysine 9 [H3K9Me] and 27 [H3K27Me]). (B) Euchromatin is a relaxed form of chromatin that allows access to DNA and RNA polymerases and transcription to occur. Euchromatin is associated with coactivators and specific histone acetylation (acetylation on lysine 16 of histone 4 [H4K16Ac]) that together form a large protein complex called an enhanceosome. This enhanceosome then recruits RNA polymerase to perform transcription.

Figure 3

The relationship between genetic polymorphisms and epigenetic factors. Epigenetic features of T cells in patients with IBD affect Th1 and Th17 cell differentiation. (A) STAT4 is associated with several immune diseases, acting as a transcription factor for IL-12 and IL-23 that leads to Th1 and Th17 cell differentiation. An SNP in STAT4, rs7574865, is associated with several immune disorders, including IBD, rheumatoid arthritis, type 1 diabetes, and lupus. The rs7574865 risk variants (T/T + G/T) are associated with promoter region hypomethylation in colon tissues and PBMCs of patients with IBD. STAT4 promoter hypomethylation was associated with increases in STAT4 mRNA and could promote the Th1 phenotype and interferon γ production. In T cells from patients with asthma, STAT4 expression is also regulated by DNA methylation at promoter regions. Interestingly, STAT4 expression was markedly increased after treatment with a DNMT inhibitor. (B) An IBD-associated SNP in IL23-R, rs10889677, is associated with increased levels of IL-23R mRNA and protein. This could result from reduced binding of microRNAs Let-7e and Let-7f at the regulatory 3′ untranslated region of the rs10889677 risk variant (A) compared with cells from patients without IBD (C). Reduced binding of Let-7e and Let-7f to rs10889677 is associated with increased levels of IL23R mRNA and protein, potentially leading to sustained activation of Th17 cells and the chronic inflammation associated with IBD.

Figure 4

Loci identified in GWAS indicating roles for the innate immune response to the microbiota and autophagy in the pathogenesis of CD. Several CD risk alleles were identified in GWAS in genes that control autophagy, including TLR4, ATG16L1, IRGM, and ULK1. (A) The ULK1 locus has been associated with susceptibility to CD; it encodes a serine-threonine kinase involved in the autophagy response to starvation. ULK1 is hypermethylated in cells from patients with CD compared with controls. (B) IRGM encodes a gene that regulates the innate response to intracellular organisms, including Mycobacterium tuberculosis. The CD risk allele rs10065172 is associated with a deletion upstream of IRGM. This SNP had been termed noncausative due to an absence in alteration of protein sequence or splice sites. However, the risk variant has an altered binding site for microRNA-196. Individuals with this SNP down-regulate IGRM. The consequence is a functional reduction of autophagy and processing of the adhesive invasive Escherichia coli, which has been associated with CD.