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Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies
Christopher B. Cole, … , Christopher A. Miller, Timothy J. Ley
Christopher B. Cole, … , Christopher A. Miller, Timothy J. Ley
Published September 5, 2017
Citation Information: J Clin Invest. 2017;127(10):3657-3674. https://doi.org/10.1172/JCI93041.
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Research Article Hematology Oncology

Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies

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Abstract

The gene that encodes de novo DNA methyltransferase 3A (DNMT3A) is frequently mutated in acute myeloid leukemia genomes. Point mutations at position R882 have been shown to cause a dominant negative loss of DNMT3A methylation activity, but 15% of DNMT3A mutations are predicted to produce truncated proteins that could either have dominant negative activities or cause loss of function and haploinsufficiency. Here, we demonstrate that 3 of these mutants produce truncated, inactive proteins that do not dimerize with WT DNMT3A, strongly supporting the haploinsufficiency hypothesis. We therefore evaluated hematopoiesis in mice heterozygous for a constitutive null Dnmt3a mutation. With no other manipulations, Dnmt3a+/– mice developed myeloid skewing over time, and their hematopoietic stem/progenitor cells exhibited a long-term competitive transplantation advantage. Dnmt3a+/– mice also spontaneously developed transplantable myeloid malignancies after a long latent period, and 3 of 12 tumors tested had cooperating mutations in the Ras/MAPK pathway. The residual Dnmt3a allele was neither mutated nor downregulated in these tumors. The bone marrow cells of Dnmt3a+/– mice had a subtle but statistically significant DNA hypomethylation phenotype that was not associated with gene dysregulation. These data demonstrate that haploinsufficiency for Dnmt3a alters hematopoiesis and predisposes mice (and probably humans) to myeloid malignancies by a mechanism that is not yet clear.

Authors

Christopher B. Cole, David A. Russler-Germain, Shamika Ketkar, Angela M. Verdoni, Amanda M. Smith, Celia V. Bangert, Nichole M. Helton, Mindy Guo, Jeffery M. Klco, Shelly O’Laughlin, Catrina Fronick, Robert Fulton, Gue Su Chang, Allegra A. Petti, Christopher A. Miller, Timothy J. Ley

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Figure 7

DNA methylation phenotypes of Dnmt3a+/+, Dnmt3a+/–, and Dnmt3a–/– mice.

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DNA methylation phenotypes of Dnmt3a+/+, Dnmt3a+/–, and Dnmt3a–/– mice.
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(A) Mean CpG methylation levels from whole-genome bisulfite sequencing of bone marrow cells from Dnmt3a+/+ (n = 4), Dnmt3a–/– (n = 4), and Dnmt3a+/– mice (n = 7). Values for specific annotated regions of the genome are shown. Hypothesis testing was performed via 2-tailed, pairwise t tests, with Bonferroni’s correction for multiple testing within genome regions; **P < 0.01; ***P < 0.001. (B) Density plot of methylation values from all CpGs for each bone marrow sample shown in A. (C) Density plot of methylation values from 7,029 DMRs defined by comparing the 4 Dnmt3a+/+ and 4 Dnmt3a–/– samples, all obtained from bone marrow of 2-week-old mice. Values for the same DMRs were plotted passively for Dnmt3a+/– samples. (D) Heatmap showing mean methylation values for the 7,029 DMRs as defined above. Note that the Dnmt3a+/– samples are plotted as a function of the age of the mice at harvest. (E) Heatmap showing mean methylation values for the 1,665 DMRs (from the set of 7,029) significantly different between Dnmt3a+/+ and Dnmt3a+/– samples. (F) Mean methylation values for all 7,029 DMRs from all samples, plotted by genotype from the center of the DMRs. (G) Fraction of 7,029 DMRs associated with annotated regions of the genome (Dnmt3a–/– DMRs are shown in red, and DMRs also significant in Dnmt3a+/– mice are shown in blue). (H) Primary methylation values for each CpG (shown as a bar from 0%–100% methylated for each sample) in a Dnmt3a–/– hypomethylated DMR inside the Casz1 gene body (not significantly hypomethylated in the Dnmt3a+/– samples, P = 0.19 by Mann-Whitney U test with Bonferroni’s correction).

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ISSN: 0021-9738 (print), 1558-8238 (online)

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