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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







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


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


Rectum biopsies

EZ DNA Methylation Gold Kit; HumanMethylation27 BeadChip array

Methylation differences reversible after medicinal treatment in CD patients

A limited number of subjects


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


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


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


Intestinal epithelial cells

Illumina HumanMethylation450; Illumina EPIC bead chips

Gut-segment specific DNA methylation differences in CD patients

Limited sample size


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


  1. TSGs tumor suppressor genes