PLoS ONE (Jan 2018)

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease.

  • Hirofumi Chiba,
  • Yoichi Kakuta,
  • Yoshitaka Kinouchi,
  • Yosuke Kawai,
  • Kazuhiro Watanabe,
  • Munenori Nagao,
  • Takeo Naito,
  • Motoyuki Onodera,
  • Rintaro Moroi,
  • Masatake Kuroha,
  • Yoshitake Kanazawa,
  • Tomoya Kimura,
  • Hisashi Shiga,
  • Katsuya Endo,
  • Kenichi Negoro,
  • Masao Nagasaki,
  • Michiaki Unno,
  • Tooru Shimosegawa

DOI
https://doi.org/10.1371/journal.pone.0194036
Journal volume & issue
Vol. 13, no. 3
p. e0194036

Abstract

Read online

BACKGROUND:Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. METHODS:CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. RESULTS:We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). CONCLUSIONS:We confirmed the existence of cis-regulated ASM around IBD susceptibility genes and the association between ASM SNP (rs36221701) genotype and SMAD3 expression, a susceptibility gene for IBD. These results give us supporting evidence that DNA methylation mediates genetic effects on disease susceptibility.