Table 1 Studies subjected to DNA methylation validation
Publication | Studied region/gene | Sample type | Methylation detection method | Clinical significance | Notes | Test cohort (n) | Validation cohort (n) |
|---|---|---|---|---|---|---|---|
Lin et al. [13] | CEBPA distal promoter | BM | Bisulfite sequencing, quantitative MassArray | Higher methylation was associated with longer OS in AML with normal karyotype without CEBPAmut and NPM1mut, and in AML excluding favorable karyotype, CEBPAmut and NPM1mut | Methylation of the CEBPA distal promoter inversely correlated with CEBPA expression | 193 de novo AML, prognostic significance in CN-AML without CEBPAmut and NPM1mut (n = 25) and in AML excluding favorable karyotype, CEBPAmut and NPM1mut (n = 59) | None |
Hájková et al. [8] | Promoters of tumor suppressor genes (CDKN2B, ESR1, MYOD1, CALCA, SOCS1, CDH1) | PB or BM MNC | MethyLight PCR | Hypermethylation of SOCS1 promoter associated with better outcome. Patients with smaller number of hypermethylated genes (p = 0.012) or with lower levels of cumulative DNA methylation value computed from methylation levels of all studied regions have worse OS. and EFS | Studied negative impact of HOX genes and tumor suppressors promoters hypomethylation caused by DNMT3A mutations | 79 diagnostic AML excluding favorable karyotype | None |
Treppendahl et al. [18] | VTRNA2-1 promoter | BM | pyrosequencing | Patients with hypermethylation (≥ 10% or > 38%) had poorer survival | Methylation was inversely correlated with expression | 101 diagnostic AML | None |
Hájková et al. [10] | PBX3 (TAF1 binding site) | PB or BM MNC | NGS, pyrosequencing | Lower methylation correlated with higher expression of PBX3 that was associated with higher incidence of relapse | Newly discovered hypomethylation pattern specific to CBFB-MYH11 fusion with corresponding gene overexpression | 123 diagnostic AML, prognostic significance in 40 AML that underwent standard curative therapy and did not die during the first induction | None |
Jost et al. [11] | Promoter region of DNMT3A | PB | TCGA data, pyrosequencing (validation) | Hypermethylation (> 10%) associated with shorter EFS and OS in TCGA data, but not validated on authors' cohort of patients | Higher methylation in the region was mostly observed in patients without DNMT3Amut and was associated with moderate downregulation of DNMT3A transcription | 194 diagnostic AML of TCGA study, prognostic significance after excluding DNMT3mut AML | 88 diagnostic AML, prognostic significance not validated |
Marcucci et al. [15] | DMRs in promoters of seven genes (CD34, RHOC, SCRN1, F2RL1, FAM92A1, MIR155HG, and VWA8) | BM | NGS: MethylCap enriched by MBD2, RRBS (validation), MassArray (validation) | High DMRs methylation associated with lower expression linked to higher CR rate and longer survival in CN-AML. Patients with lower weighted summary score of expression levels had higher disease-free survival and OS | FLT3-ITD and DNMT3A mutations associated with low methylation at DMRs, NPM1 and IDH mutations associated with higher methylation at DMRs | 134 CN-AML | four independent CN-AML patient sets ( n = 355) |
Božić et al. [21] | One CpG in C1R gene | PB | TCGA data, pyrosequencing (validation) | Higher methylation (> 27%) associated with longer OS | Only moderate association of DNA methylation and expression of C1R | 194 diagnostic AML of TCGA study | two independent datatasets—62 CN-AML and 84 AML |
Zhou et al. [19] | GPX3 promoter | BM MNC | qMSP | non-M3 AML patients with GPX3 methylation showed shorter OS | GPX3 methylation does not correlate with expression | 181 de novo AML, clinical significance in 104 non-M3 AML | none |
Zhou et al. [20] | DLX4 | BM MNC | qMSP | Patients with methylated DLX4 presented lower CR rate and shorter OS | DLX4 methylation was negatively associated with the expression of shorter DLX4 isoform | 133 de novo AML | None |
Guo et al. [9] | SFRP1 and SFRP2 promoter regions | BM | qMSP | Higher methylation associated with shorter OS | Higher SFRP1 methylation associated with N/K-RAS mutations. Higher SFRPs methylation in older patients (≥ 50 years) | 139 de novo non-M3 AML | None |
Li et al. [12] | NKD2 promoter | BM MNC | qMSP | Higher methylation correlated with lower expression of NKD2 which was associated with shorter OS in CN-AML | The role of DNA methylation in silencing of NKD2 expression was confirmed in THP1 leukemic cell line | 101 diagnostic AML, clinical significance proved in 42 CN-AML | Two independent datatasets—162 CN-AML and 78 CN-AML |
Liu et al. [14] | RASSF1A promoter | BM | qMSP | Hypermethylation connected with decreased OS and EFS | Hypermethylation of RASSF1A associated with ASXL1 mutations and decreased mRNA levels | 226 diagnostic non-M3 AML | None |
Qu et al. [16] | CGI shores of LZTS2 and NR6A1 | PB or BM | CHARMcox, pyrosequencing (validation), TCGA data (validation) | Hypomethylation in either of the two regions associated with worse OS | Studied on CN - AML patients | 72 CN-AML in discovery cohort + 65 CN-AML in model-building cohort | 65 CN-AML + 93 CN-AML from TCGA study |
Šestáková et al. [17] | GZMB enhancer | PB | pyrosequencing | Hypermethylation associated with inferior OS between high and low methylation groups) | Concurrent presence of both DNMT3Amut and IDH1/2mut partially cancel out the opposite influence of these aberrations on DNA methylation resulting in a mixed methylation and hydroxymethylation profiles | 104 diagnostic AML | None |