Remethylation of <i>Dnmt3a</i> ^−/− hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing

Abstract

Mutations in the DNA methyltransferase 3A (<i>DNMT3A</i>) gene are the most common cause of age-related clonal hematopoiesis (ARCH) in older individuals, and are among the most common initiating events for acute myeloid leukemia (AML). The most frequent <i>DNMT3A</i> mutation in AML patients (R882H) encodes a dominant-negative protein that reduces methyltransferase activity by ∼80% in cells with heterozygous mutations, causing a focal, canonical DNA hypomethylation phenotype; this phenotype is partially recapitulated in murine <i>Dnmt3a</i>^<i>-/-</i> bone marrow cells. To determine whether the hypomethylation phenotype of <i>Dnmt3a</i>^-/- hematopoietic cells is reversible, we developed an inducible transgene to restore expression of <i>DNMT3A</i> in transplanted bone marrow cells from <i>Dnmt3a</i>^-/- mice. Partial remethylation was detected within 1 wk, but near-complete remethylation required 6 mo. Remethylation was accurate, dynamic, and highly ordered, suggesting that differentially methylated regions have unique properties that may be relevant for their functions. Importantly, 22 wk of <i>DNMT3A</i> addback partially corrected dysregulated gene expression, and mitigated the expansion of myeloid cells. These data show that restoring <i>DNMT3A</i> expression can alter the epigenetic "state" created by loss of Dnmt3a activity; this genetic proof-of-concept experiment suggests that this approach could be relevant for patients with ARCH or AML caused by loss-of-function <i>DNMT3A</i> mutations.