Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

Abstract

Genetic heterogeneity contributes to clinical outcome and progression of most tumors. Yet, little is known regarding allelic diversity for epigenetic compartments and almost no data exists for acute myeloid leukemia (AML). Here we examined epigenetic heterogeneity as assessed by cytosine methylation within defined genomic loci with four CpGs (epigenetic alleles), somatic mutations and transcriptomes of AML patient samples at serial time points. We observe that epigenetic allele burden is linked to inferior outcome and varies considerably during disease progression. Epigenetic and genetic allelic burden and patterning follow different patterns and kinetics during disease progression. We observed a subset of AMLs with high epiallele and low somatic mutation burden at diagnosis, a subset with high somatic mutation and lower epiallele burdens at diagnosis, and a subset with a mixed profile, suggesting distinct modes of tumor heterogeneity. Genes linked to promoter-associated epiallele shifts during tumor progression display increased single-cell transcriptional variance and differential expression, suggesting functional impact on gene regulation. Thus, genetic and epigenetic heterogeneity can occur with distinct kinetics, each likely able to impact biological and clinical features of tumors.

Leukemic stem cells: identification and clinical application

“…Recently it was shown that the constitution of AML at relapse may differ from diagnosis due to clonal changes including clonal evolution, clonal regression and clonal selection, with possible changes on immunophenotypic [32,33], cytogenetic [34], genetic [34,35] and epigenetic [35] level. Detailed whole genome sequencing studies, analyzing paired diagnosis-relapse samples, showed that at time of diagnosis, patients could present with a wide array of small subclones of which some remained in relapse [36]: indicative for clonal selection under therapy pressure.…”

When clinical heterogeneity exceeds genetic heterogeneity: thinking outside the genomic box in chronic myelomonocytic leukemia

“…Epi-alleles also contain information relevant to clinical prognosis that are independent of mutation status. 53 Although what drives the underlying epigenetic heterogeneity is unclear, it appears to be contributory to the molecular heterogeneity in AML and should be explored in CMML.…”

Germline loss of MBD4 predisposes to leukaemia due to a mutagenic cascade driven by 5mC

“…Whole exome sequencing and whole genome sequencing Whole exome sequencing on EMC-AML-1 was performed as previously described 3 . For WEHI-AML-1 and WEHI-AML-2, DNA was extracted using either the MagAttract DNA Blood M48 Kit or QIAsymphony DSP DNA Mini Kit (Qiagen, Venlo, the Netherlands).…”

“…Aligned sequencing data (BAM files aligned to hg38) was downloaded from GDC, together with variant calls. Preliminary variant detection of WEHI-AML-1, WEHI-AML-2, EMC-AML-1, the EMC cohort [phs001027] 3 and all TCGA-AML [phs000178] 6 samples was performed with samtools version 0.1.19-44428cd, followed by Varscan v2.3.6 7 . These preliminary calls were refined with superFreq 0.9.15 with default settings, which also provided clonality estimates for copy number and somatic SNV calls 8 .…”

“…Cells endure hundreds of 5mC deamination events each day and an intricate repair network is engaged to restrict this damage. Central to this network are the DNA glycosylases MBD4 2 and TDG 3,4 , which recognise T:G mispairing and initiate base excision repair (BER). Here we describe a novel cancer predisposition syndrome resulting from germline biallelic inactivation of MBD4 that leads to the development of acute myeloid leukaemia (AML).…”