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

Biopsies

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]