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Table 2 DNA methylation studies on tissue samples in Crohn's disease patients

From: The role of epigenetic modifications for the pathogenesis of Crohn's disease

Tissue Techniques Results Limitations Source
Ascending colon biopsies EZ DNA Methylation Kit; Methylation-specific PCR (MSP) Identification of hypermethylated promoters of TSGs in CD Lack of control samples; no clinical information of included patients; limited sample size, unbalanced ratio (2:1) between male and female patients [73]
Descending colon biopsies Illumina Infinium HumanMethylation450 BeadChip Kit; EZ DNA Methylation-Gold Kit (Zymo) Epigenetically associated gene expression linked to colonic mucosal immune and defense responses in CD No sufficient statistical power; limited sample size [67]
Rectum biopsies EZ DNA Methylation Gold Kit; HumanMethylation27 BeadChip array Methylation differences reversible after medicinal treatment in CD patients A limited number of subjects [74]
Separated cells from biopsies
Human adipose stem cells Illumina EPIC/850 k array; Gene expression analysis Different DNA methylation related to the immune system and cell differentiations processes in active and inactive CD; changes in DNA methylation-related gene expression partially restored in quiescent CD Observational study; limited sample size [68]
Human intestinal fibroblasts from colon biopsies MethylMiner Methylated DNA Enrichment Kit; Illumina's ChIP-Seq DNA Sample Prep Kit The majority of different DNA methylation was within introns and intergenic regions and not associated with CpG islands in CD patients Tiny patient numbers; little diversity [75]
Human intestinal fibroblasts of terminal ileal Methylation analysis Illumina EPIC BeadChip array Methylation changes depend on inflammation status in the tissue of CD patients Limited sample size [78]
Intestinal epithelial cells Illumina HumanMethylation450; Illumina EPIC bead chips Gut-segment specific DNA methylation differences in CD patients Limited sample size [76]
Intestinal epithelial cells Illumina Infinium HumanMethylation450 BeadChip Methylation changes between fetal and pediatric samples indicate importance in embryonal development; IBD-specific intestinal epithelial DNA methylation signature in CD and UC patients Limited sample size [79]
  1. TSGs tumor suppressor genes