Molecular Cooperativity of Dnmt3a and Npm1 Mutations in Transformation from Clonal Hematopoiesis to Myeloid Malignancy

Driver somatic mutations in adult acute myeloid leukemia (AML) may be preceded by a benign state termed clonal hematopoiesis (CH). To develop therapeutic strategies to prevent leukemia development from CH, it is important to understand the mechanisms by which CH-driving and AML-driving mutations cooperate. Here, we utilize mice with inducible mutant alleles common in CH (DNMT3AR882; mouse Dnmt3aR878H/+) and AML (NPM1c; mouse Npm1cA/+). We find that Dnmt3aR878H/+ hematopoietic stem cells (HSCs), but not multipotent progenitor cell (MPP) subsets, have reduced expression of cytokine and pro-inflammatory transcriptional signatures and a functional competitive advantage over their wild-type counterparts. These Dnmt3aR878H/+ HSCs are transformed by activation of Npm1cA/+, generating myeloid malignancies in which few additional cooperating somatic mutation events were detected. At a molecular level, Npm1cA/+ acutely increased accessibility of a distinct set of promoters in cooperation with Dnmt3aR878H/+ than it did as a single mutation. These promoters were enriched for pro-inflammatory response signatures, p53 pathway, DNA repair and targets of transcription factors implicated in AML, including Hmgb1 and Pax4. These results suggest cooperativity between pre-existing Dnmt3a mutation and Npm1 mutation at the chromatin level, where specific loci altered in accessibility by the Npm1 mutation are dependent on Dnmt3a mutation status. These findings have implications for biological understanding and therapeutic intervention of the transformation from CH to AML. Overall design: 1 x 10^6 whole bone marrow cells from young WT (Mx-Cre), Dnmt3a-flR878H/+, Npm1-frt/+, or Dnmt3a-flR878H/+;Npm1-frt/+ were transplanted into young, lethally irradiated CD45.1 recipients. 4 wks post-transplant, all recipient mice received poly(I:C), and 4 wks post-poly(I:C), all mice recieved tamoxifen. 4 wks post-tamoxifen, the bone marrow was harvested and LT-HSCs and MPP3s were sorted via FACS and used for ATAC-library prep.