Whole-genome DNA methylation characteristics in pediatric precursor B cell acute lymphoblastic leukemia (BCP ALL)

Abstract

In addition to genetic alterations, epigenetic abnormalities have been shown to underlie the pathogenesis of acute lymphoblastic leukemia (ALL)—the most common pediatric cancer. The purpose of this study was to characterize the whole genome DNA methylation profile in children with precursor B-cell ALL (BCP ALL) and to compare this profile with methylation observed in normal bone marrow samples. Additional efforts were made to correlate the observed methylation patterns with selected clinical features. We assessed DNA methylation from bone marrow samples obtained from 38 children with BCP ALL at the time of diagnosis along with 4 samples of normal bone marrow cells as controls using Infinium MethylationEPIC BeadChip Array. Patients were diagnosed and stratified into prognosis groups according to the BFM ALL IC 2009 protocol. The analysis of differentially methylated sites across the genome as well as promoter methylation profiles allowed clear separation of the leukemic and control samples into two clusters. 86.6% of the promoter-associated differentially methylated sites were hypermethylated in BCP ALL. Seven sites were found to correlate with the BFM ALL IC 2009 high risk group. Amongst these, one was located within the gene body of the MBP gene and another was within the promoter region- PSMF1 gene. Differentially methylated sites that were significantly related with subsets of patients with ETV6-RUNX1 fusion and hyperdiploidy. The analyzed translocations and change of genes’ sequence context does not affect methylation and methylation seems not to be a mechanism for the regulation of expression of the resulting fusion genes.

The distinguishable DNA whole genome methylation profile of 2 cases of pediatric precursor B acute lymphoblastic leukaemia (BCP ALL) with prodromal, preleukemic phase

“…In our previous study [ 5 ] material comprised 38 samples of BM obtained from patients with pediatric precursor-B acute lymphoblastic leukaemia, at the time of the final ALL diagnosis, and 4 control non-leukemic samples. The analysis of cytogenetic ALL subtypes revealed that among BCP ALL SC patients there were 2 cases of triploidy and 12 cases of hyperploidy which might serve as a control for the analyzed BCP ALL PP patients.…”

“…The previous results also showed, that factors such as gender and age are not important confounders for the global methylation profile differentiation of pediatric leukaemia. [ 5 ] DNA was purified using QIAamp DNA Blood Mini Kit (QIAGEN), assessed for fragmentation by agarose gel electrophoresis and quantified using Qubit 2.0 fluorimeter (Thermo Fisher Scientific). CpG methylation analysis was performed using Illumina (San Diego, CA) MethylationEPIC BeadChip, allowing analysis of 850K sites per sample.…”

“… Principal component analysis based on probes differing in methylation level between B-cell precursor acute lymphoblastic leukaemia with incomplete feature prodromal phase (BCP ALL PP) and both BCP ALL with the standard course (BCP ALL SC) and control samples. [ 5 ] BCP ALL PP = B-cell precursor acute lymphoblastic leukaemia with incomplete feature prodromal phase, SC = standard course. …”

“…In our previous work, hierarchical clustering of whole-genome DNA methylation profiles obtained from BM cells aspirated at diagnosis of a group of 38 patients with pediatric B-cell precursor (BCP) ALL revealed 2 cases with noticeably different methylation profiles. [ 5 ] Detailed clinical analysis of these patients showed that both had preceding clinical symptoms of leukaemia many weeks before ALL diagnosis was established. This pre-leukemic phase with incomplete features was misleading and delayed treatment.…”

Epigenetic Priming in Childhood Acute Lymphoblastic Leukemia

“…Besides aberrant genetic modifications, epigenetic irregularities have been shown to trigger the pathogenesis of childhood ALL (Taylor et al, 2007; Chaber et al, 2017). It has been described that aberrant methylation is associated with prognosis (Wong et al, 2000), cytogenetic subtype (Zheng et al, 2004), prediction of treatment outcome (Milani et al, 2010) and relapse (Matsushita et al, 2004; Hogan et al, 2011) in childhood acute leukemias.…”