Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia
Umeda, M.; Hiltenbrand, R.; Michmerhuizen, N. L.; Barajas, J. M.; Thomas, M. E.; Arthur, B.; Walsh, M. P.; Song, G.; Ma, J.; Westover, T.; Kumar, A.; Pölönen, P.; Mecucci, C.; Di Giacomo, D.; Locatelli, F.; Masetti, R.; Bertuccio, S. N.; Pigazzi, M.; Pruett-Miller, S. M.; Pounds, S.; Rubnitz, J.; Inaba, H.; Papadopoulos, K. P.; Wick, M. J.; Iacobucci, I.; Mullighan, C. G.; Klco, J. M.
Show abstract
Leukemias with NUP98 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 NUP98-rearranged leukemias, we show that cooperating alterations are associated with differentiation status even among leukemias sharing the same NUP98 fusions, such as NUP98::KDM5A acute megakaryocytic leukemia with RB1 loss or T-cell acute lymphoblastic leukemia with NOTCH1 mutations. CUT&RUN profiling reveals that NUP98 fusion oncoproteins directly regulate differentiation-related genes, with binding patterns also influenced by differentiation stage. Using in vitro models, we show RB1 loss cooperates with NUP98::KDM5A by blocking terminal differentiation toward platelets and expanding megakaryocyte-like cells, whereas WT1 frameshifts skew differentiation toward dormant lympho-myeloid primed progenitor cells and cycling granulocyte-monocyte progenitor cells. NUP98::KDM5A models with RB1 or WT1 alterations have different sensitivities to menin inhibition, suggesting cellular differentiation stage-specific resistant mechanism against menin inhibitors with clinical implications for NUP98-rearranged leukemia.
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