From: The role of epigenetic modifications for the pathogenesis of Crohn's disease
Matrix | Techniques | Results | Limitations | Source |
---|---|---|---|---|
Whole blood cells | Â | |||
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 | Â | [55] |
PBC | MassARRAY EpiTYPER platform | DEFA5 and TNF as a speculative biomarker for CD | Only 12 genes investigated | [56] |
Leukocytes and PBMCs | ||||
PBL | Illumina 450Â 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 | Â | [64] |
CD14+ monocytes | EZ DNA Methylationâ„¢ kit (Zymo); Illumina HumanMethylation 450Â 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] |