Genome-wide DNA methylation analysis in pediatric acute myeloid leukemia

Abstract

We investigated genome-wide DNAmethylation patterns in 64 pediatric patientswith acute myeloid leukemia (AML). Based on unsupervised clusteringwith the 567most variably methylated cytosine guanine dinucleotide (CpG) sites, patientswere categorized into 4 clusters associatedwith genetic alterations. Clusters 1 and 3were characterized by the presence of known favorable prognostic factors, such as RUNX1-RUNX1T1 fusion andKMT2A rearrangementwith lowMECOMexpression, and biallelic CEBPAmutations (all 8 patients), respectively. Clusters 2 and 4 comprised patients exhibitingmolecular features associatedwith adverse outcomes, namely internal tandemduplication of FLT3 (FLT3-ITD), partial tandem duplication ofKMT2A, andhighPRDM16 expression.Depending on themethylation values of the 1243 CpG sites thatwere significantly different between FLT3-ITD1 and FLT3-ITD2 AML, patientswere categorized into 3 clusters: A, B, and C. The STAT5-bindingmotifwasmost frequently found close to the 1243 CpG sites. All 8 patientswith FLT3-ITDinclusterAharbored high PRDM16 expression and experienced adverse events,whereas only 1 of 7 patientswith FLT3-ITD in the other clusters experienced adverse events. PRDM16 expression levelswere also related toDNAmethylation patterns,whichwere drastically changed at the cutoff value of PRDM16/ABL150.10. The assay for transposase-accessible chromatin sequencing of AMLs supported enhanced chromatin accessibility around genomic regions, such asHOXB cluster genes, SCHIP1, andPRDM16,whichwere associatedwithDNAmethylation changes in AMLs with FLT3-ITD and high PRDM16 expression.Our results suggest that DNAmethylation levels at specific CpG sites are useful to support genetic alterations and gene expression patterns of patientswith pediatric AML.