FLT3 ITD and NUP98 Translocations Cooperate to Induce Type I Interferon Signaling That Impedes Hematopoietic Progenitor Differentiation

FLT3-Internal Tandem Duplication (FLT3 ITD) mutations occur at similar frequencies in both childhood and adult acute myeloid leukemia (AML) patients, but they cooperate with different initiating mutations at different ages. In childhood AML, FLT3 ITD often cooperates with translocations that generate fusion proteins, such as NUP98 translocations (NUP98-t). In adult AML, FLT3 ITD often cooperates with mutations that inactivate RUNX1, DNMT3A, TET2 and other genes that regulate self-renewal and myeloid differentiation. This raises the question of whether FLT3 ITD induces similar, or distinct, changes in gene expression and cell fate when it arises in the setting of pediatric and adult driver mutations. To answer this question, we evaluated pre-leukemic changes in hematopoiesis and gene expression in neonatal and juvenile mice that carried pediatric-like FLT3 ITD/NUP98-HOXD13 and adult-like FLT3 ITD/Runx1 DEL/+ mutation profiles. Both NUP98-HOXD13 (NHD13) and Runx1 DEL/+ severely depleted phenotypic hematopoietic stem cells (HSCs) when coupled with FLT3 ITD. However, FLT3 ITD/NHD13 cooperated to enhancer ectopic self-renewal capacity in lineage committed hematopoietic progenitor cells (HPCs) whereas FLT3 ITD/Runx1 DEL/+ did not. FLT3 ITD/NHD13 and FLT3 ITD/Runx1 DEL/+ both induced changes in gene expression and enhancer activation that were not seen with either mutation alone. These cooperative changes were almost entirely non-overlapping. The most notable cooperative change in FLT3 ITD/NHD13 HPCs was activation of a type I Interferon target gene signature. By contrast, this signature was actively repressed in FLT3 ITD/Runx1 DEL/+ HPCs due to mir155 activation. Thus, FLT3 ITD/NHD13 and FLT3 ITD/Runx1 DEL/+ mutations have largely non-overlapping, cooperative effects on hematopoietic cell fate and gene expression.