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Table 1 DNA methylation studies on blood samples in Crohn's disease patients

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

Matrix

Techniques

Results

Limitations

Source

Whole blood cells

 

WBC

Illumina Human Methylation27 BeadChip system

Methylated loci predominantly involved in immune-related pathways in CD

No differentiation between blood cell subtypes

[54]

PBC

Illumina HumanMethylation450 platform; Illumina TrueSeq

Sample Preparation Kit; EpiTexy Bisulfite Kit; EZ-96 DNA Methylation Kit (Zymo)

Samples clustered by disease status and blood cell subtype

 

[55]

PBC

MassARRAY EpiTYPER platform

DEFA5 and TNF as a speculative biomarker for CD

Only 12 genes investigated

[56]

Leukocytes and PBMCs

PBL

Illumina 450 k DNA methylation analysis

Duplicated results of further GWAS and EWAS in CD for two genes

No differentiation between blood cell subtypes

[57]

PBL

EZ DNA Methylationâ„¢ Kit (Zymo); Illumina HumanMethylation450k Bead-Chip Array

Duplicated results of further GWAS and EWAS in CD for 33 genes

Limited sample size, minor effect sizes; systematic meta-analysis necessary

[58]

PBL

Methylation-Specific Amplification

Microarray (MSAM); Illumina Infinium HumanMethylation450 BeadChip Kit; EZ DNA Methylation-Gold Kit (Zymo)

No significant differences in DNA methylation between CD and control

Limited sample size; limited coverage/resolution of microarrays employed; clinical heterogeneity of the control and IBD group; no specific cell type investigated

[59]

PBMCs

EZ 96 DNA Methylation Kit; Illumina HumanMethylation450 BeadChip Array

No significant differences in DNA methylation between CD and control

Limited sample size, no comparison between different cell types

[60]

PBMCs

EZ DNA Methylation-Gold kit (Zymo); MethylationEPIC BeadChip (Illumina)

No significant differences in DNA methylation between CD and control

Differentiation between blood cell subtypes

[61]

Defined cell types

B cells

Methylation-Gold Kit (Zymo); GoldenGate Bead Array (Illumina); Bisulfite PCR-based RFLP analysis

Different DNA methylation of immune regulatory genes in CD patients

SNPs or repetitive elements in the probes influenced methylation analysis

[63]

CD8+ T cells

Illumina EPIC array

DNA methylation correlated not with disease outcome in CD patients

 

[64]

CD14+ monocytes

EZ DNA Methylation™ kit (Zymo); Illumina HumanMethylation 450 k BeadChip array

Different methylation profiles in monocytes subclasses of CD patients

Limited sample size

[65]

Serum

Human serum

EZ DNA Methylation Kit (Zymo)

57% of the CD patients displayed DNA methylation in TCERG1L

Limited clinical information of CD patients; no correlation to healthy controls; only one gene investigated

[62]

  1. WBCs whole blood cells, PBCs peripheral blood cells, PBLs peripheral blood leukocytes, PBMCs peripheral blood mononuclear cells, CD14 cluster of differentiation 14, CD8 cluster of differentiation 8, DEFA5 Defensin alpha 5, TNF tumor necrosis factor, TCERG1L transcription elongation regulator 1-like protein