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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 Methylation™ 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