Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia

E Jost,W Wagner,S Koschmieder,O Herrmann,Q Lin,S Wilop,M Hoffmann,T Walenda,T H Brümmendorf,C I Weidner,M Zenke,M Schemionek

doi:10.1038/leu.2013.362

Abstract

Mutations in the genetic sequence of the DNA de novo methyltransferase DNMT3A (DNA methyltransferase 3A) are found in many patients with acute myeloid leukemia (AML). They lead to dysfunction of DNMT3A protein and represent a marker for poor prognosis. Effects of genetic mutations can be mimicked by epigenetic modifications in the DNA methylation (DNAm) pattern. Using DNAm profiles of the Cancer Genome Atlas Research Network (TCGA), we identified aberrant hypermethylation at an internal promoter region of DNMT3A, which occurred in about 40% of AML patients. Bisulfite pyrosequencing assays designed for this genomic region validated hypermethylation specifically in a subset of our AML samples. High DNAm levels at this site are particularly observed in samples without genetic mutations in DNMT3A. Epimutations and mutations of DNMT3A were associated with related gene expression changes such as upregulation of the homeobox genes in HOXA and HOXB clusters. Furthermore, epimutations in DNMT3A were enriched in patients with poor or intermediate cytogenetic risk, and in patients with shorter event-free survival and overall survival (OS). Taken together, aberrant DNA hypermethylation within the DNMT3A gene, in analogy to DNMT3A mutations, is frequently observed in AML and both modifications seem to be useful for risk stratification or choice of therapeutic regimen.

Highlights

DNA methylation (DNAm) of CpG dinucleotides is a key epigenetic process
DMR2 and DMR3 comprised each a CGI (Figure 1a). They correspond to an upstream promoter region of transcript 2, which we have recently identified in hematopoietic stem and progenitor cells: DMR2 was non-methylated in CD34 þ cells from cord blood and revealed some of the most significant hypermethylation upon culture expansion in vitro (Po10 À 46).[21]
We describe that acute myeloid leukemia (AML) patients often reveal aberrant hypermethylation in DNMT3A and the same effect was observed in AML cell lines

Summary

Introduction

DNA methylation (DNAm) of CpG dinucleotides is a key epigenetic process. The DNAm pattern is maintained on the newly synthesized DNA strand, by DNA methyltransferase 1 (DNMT1), whereas DNMT3A and DNMT3B act as de novo methyltransferases.[1] In addition, a coregulatory methyltransferase-like protein, DNMT3L, modulates activity and targeting of DNMT3A and DNMT3B.2,3. All three catalytically active DNMTs are subject to extensive tissue- or developmental stage-specific alternative splicing. Different variants of DNMT3s, with different interaction and binding properties, are even coexpressed within the same cell.[4] Such alternatively spliced forms of DNMTs may process altered enzymatic activity and they may favor specific genomic regions.[5,6]

Methods

Results

Conclusion