Identification of aberrant DNA methylation in pediatric acute myeloid leukaemia by multiplex methylation sensitive PCR

Background

The aim of this study is to develop a system of DNA methylation markers of acute myeloid leukaemia (AML) in children. Aberrant methylation diagnostic potential can be used for determining minimal residual disease (MRD), as well as to identify AML subtypes having different sensitivity to therapeutic regimens in particular with the use of epigenetic modifiers.

Methods

Our study involves 53 bone marrow samples from pediatric AML patients before treatment and after the first course of chemotherapy. Primary identification of aberrant DNA methylation is carried out by an unbiased DNA differential methylation screening method developed within this study. We propose a system of 13 DNA methylation markers (belonging to the promoter regions of ABCG4, AIFM3, CLDN7, CXCL14, DLK2, EGFLAM, GSG1L, KHSRP, MAFA, RXRA, SOX8, TMEM200B, TMEM176A /TMEM176B genes) for the assessment of aberrant DNA methylation. The DNA methylation frequency is estimated using the system of 4 multiplex methylation sensitive PCR reactions with the internal controls. Methylation is determined at the BstHHI restriction enzyme site; it was used because having many restriction sites within the loci studied, to determine the homogeneity of the CpG methylation across the region.

Results

Methylation frequencies for 6 genes are as follows (before treatment/after the first course of chemotherapy): TMEM176A/TMEM176B (0,642/0,472), SOX8(0,434/0), CLDN7(0,283/0,66), DLK2(0,113/0), EGFLAM (0,113/0,226), GSG1L(0,094/0,038). The promoter regions of ABCG4, AIFM3, CXCL14, KHSRP, MAFA, RXRA, TMEM200B demonstrated high heterogeneity of methylation of CpG pairs and were not included in the analysis. Significant association was shown for TMEM176A /TMEM176B methylation status with the acute myeloid leukemia without maturation (p = 0,0481, 19/34). Differential methylation of these 6 genes in the samples before and after treatment may be indicative of clonal evolution of malignant transformation.

Conclusions

Our study provides technical opportunities for determine the minimal residual disease in AML. And also for profiling the epigenetic abnormalities for a given individual, promising the development of individualized approaches in the therapy of AML.

Clinical trial identification

Legal entity responsible for the study

Research Centre of Medical Genetics

Funding

Research Centre of Medical Genetics

Disclosure

All authors have declared no conflicts of interest.