A distinct DNA methylation signature defines pediatric pre-B cell acute lymphoblastic leukemia

Abstract

Pre-B cell acute lymphoblastic leukemia (ALL) is the most prevalent childhood malignancy and remains one of the highest causes of childhood mortality. Despite this, the mechanisms leading to disease remain poorly understood. We asked if recurrent aberrant DNA methylation plays a role in childhood ALL and have defined a genome-scale DNA methylation profile associated with the ETV6-RUNX1 subtype of pediatric ALL. Archival bone marrow smears from 19 children collected at diagnosis and remission were used to derive a disease specific DNA methylation profile. The gene signature was confirmed in an independent cohort of 86 patients. A further 163 patients were analyzed for DNA methylation of a three gene signature. We found that the DNA methylation signature at diagnosis was unique from remission. Fifteen loci were sufficient to discriminate leukemia from disease-free samples and purified CD34+ cells. DNA methylation of these loci was recurrent irrespective of cytogenetic subtype of pre-B cell ALL. We show that recurrent aberrant genomic methylation is a common feature of pre-B ALL, suggesting a shared pathway for disease development. By revealing new DNA methylation markers associated with disease, this study has identified putative targets for development of novel epigenetic-based therapies.

Hypermethylation and down-regulation of DLEU2 in paediatric acute myeloid leukaemia independent of embedded tumour suppressor miR-15a/16-1

“…The utility of these samples for DNA methylation and miRNA expression analysis has been outlined previously [34,50]. Cryogenically frozen patient bone marrows were also used where available.…”

A decade of DNA methylation profiling in cancer: What have we learned?

“…DNA methylation is the most robust epigenetic mark and will survive typical sample processing procedures and storage conditions. DNA methylation can be determined in histological specimens such as formalin-fixed, paraffin-embedded (FFPE) samples (Thirlwell et al 2012) and microscopic preparations (Wong et al 2012). Finally, it may reasonably be anticipated that sensitive techniques for methylation detection and quantification amenable to biomarker identification will become progressively easier and more economical to perform in the clinical setting.…”

Validation of DNA Methylation Biomarkers for Diagnosis of Acute Lymphoblastic Leukemia

“…As a biomarker in clinical oncology, DNA methylation analysis eliminates the need for expensive patient-specific genetic testing yet can robustly define disease state and direct-targeted therapeutics (5)(6)(7)(8)(9)(10). Recently, Wong et al (8 ) discovered a panel of 15 hypermethylated gene promoters associated with childhood acute lymphoblastic leukemia (ALL) 9 regardless of disease subtype and suggested that these markers may serve as molecular biomarkers for disease diagnosis and tracking.…”

“…MALDI-TOF mass spectrometry technology is a useful and commonly used tool for measuring DNA methylation in research (8,12,13 ). Here we used synthetic DNA methylation reference materials that enabled us to determine the diagnostic thresholds and LOD of novel and established MALDI-TOF MS techniques.…”

“…Here we used synthetic DNA methylation reference materials that enabled us to determine the diagnostic thresholds and LOD of novel and established MALDI-TOF MS techniques. As a logical step toward developing this methodology, we targeted 2 gene promoters, TLX3 (T-cell leukemia homeobox 3) 10 and FOXE3 (forkhead box E3), which displayed the largest differential methylation between pediatric ALL patients and nonleukemic controls in validation experiments (8 ). Two complementary techniques were used to interrogate TLX3 and FOXE3 promoter methylation within pediatric ALL patient samples (8 ).…”