Fusion oncoproteins and cooperating mutations define disease phenotypes in -rearranged leukemia.

Leukemias with rearrangements exhibit heterogeneous phenotypes correlated to fusion partners, whereas the mechanism responsible for this heterogeneity is poorly understood. Through genome-wide mutational and transcriptional analyses of 177 -rearranged leukemias, we show that cooperating alterations are associated with differentiation status even among leukemias sharing the same fusions, such as acute megakaryocytic leukemia with loss or T-cell acute lymphoblastic leukemia with mutations. CUT&RUN profiling reveals that NUP98 fusion oncoproteins directly regulate differentiation-related genes, with binding patterns also influenced by differentiation stage. Using models, we show loss cooperates with NUP98::KDM5A by blocking terminal differentiation toward platelets and expanding megakaryocyte-like cells, whereas frameshifts skew differentiation toward dormant lympho-myeloid primed progenitor cells and cycling granulocyte-monocyte progenitor cells. NUP98::KDM5A models with or alterations have different sensitivities to menin inhibition, suggesting cellular differentiation stage-specific resistant mechanism against menin inhibitors with clinical implications for -rearranged leukemia.