DNMT3A and stem cell function: new insights into old pathways

DNA methylation represents an important epigenetic regulator of gene expression which impacts cellular developmental programs through alterations in gene expression. DNA methylation is established by highly related de novo DNA methyltransferases Dnmt3a and Dnmt3b, and maintained by Dnmt1.1 Inhibition of DNA methylation by DNA methyltransferase inhibitors represents an important therapeutic option for patients with myeloid malignancies.2 However, it can lead to de-repression of genes promoting cancer progression in certain cancer models.3,4 Consistent with these observations, recurrent somatic nonsense and missense mutations in DNMT3A have been identified in acute myeloid leukemia (AML)5,6 and myelodysplastic syndrome.7

A study by Challen and colleagues reported recently in Nature Genetics8 utilized conditional Mx-Cre-driven excision to examine the effects of Dnmt3a loss on hematopoietic stem cell (HSC) function. Dnmt3a-deleted HSCs contributed normally to hematopoiesis in primary recipients. By contrast, in secondary transplants the authors observed a dramatic expansion of the stem cell compartment, which may have not been investigated in previous studies.9 Moreover, despite a marked expansion of stem/progenitor cells, Dnmt3a-deficient cells did not show a parallel increase in contribution to differentiated hematopoietic lineages, suggesting a differentiation defect. Indeed, the differentiation quotient of Dnmt3a-deleted HSCs declined in tertiary and quaternary transplantation recipients despite preserved self-renewal potential. DNA methylation analysis using reduced representation bisulfite sequencing (RRBS) allowed the authors to identify epigenetic alterations at specific loci, which in some cases were hypomethylated and, in others, were paradoxically hypermethylated. Gene expression analysis showed that Dnmt3a loss leads to up-regulated expression of “HSC fingerprint” genes and lower expression of genes with a known role in HSC differentiation.

These studies provide several novel insights, and raise a number of important questions regarding the functional role of Dnmt3a in hematopoiesis and leukemogenesis. The lack of correlation between DNA methylation and gene expression changes in Dnmt3a-null cells suggests either indirect repression through methylation and diminished expression of transcription factors, or the inability of the methylation studies used in this paper to fully characterize the effects of Dnmt3a ablation on genome-wide methylation. Moreover, since the heterozygous missense DNMT3A mutations detected in AML have been shown to exhibit diminished enzymatic activity, these mutations may, at least in part, contribute to leukemogenesis through a reduction in wild-type DNMT3A enzymatic function.6 However, the lack of an overt leukemic phenotype in these studies suggests that Dnmt3a loss by itself is insufficient to induce malignant disease,8 making identification of cooperating lesions critical for the understanding of the pathogenesis of DNMT3A mutant leukemias. Curiously, Dnmt3a deletion in a lung cancer model promoted tumor progression but not initiation,3 and resulted in anchorage-independent growth and expression of metastasis-associated genes in breast cancer cell lines.4 In the light of these data, it would be valuable to investigate whether Dnmt3a-null HSCs are dependent on the bone marrow microenvironment or can support hematopoiesis outside this niche.

In summary, this study represents a step forward in our understanding of the relationship between Dnmt3a, epigenetic regulation and hematopoietic stem cell renewal and differentiation, and provides valuable insight into the biology of DNMT3A mutant hematopoietic malignancies.