Abstract IA05: Biology and therapeutic targeting of NUP98 fusion oncoprotein condensates

Abstract

NUP98 fusion oncoproteins (FOs) define a high-risk subset of pediatric acute myeloid leukemia, for which more effective therapies are urgently needed. NUP98 FOs involve the intrinsically disordered, N-terminal region of NUP98 and the C-terminal region of one of over 30 identified partner genes. These partner genes commonly harbor DNA-binding or chromatin-modifying domains. In complex with other machinery needed for gene regulation, NUP98 FOs bind to the promoters of many developmental genes, including HOX clusters and MEIS1. This leads to changes in chromatin state, increased expression of target genes, and aberrant hematopoietic self-renewal. We and others showed that NUP98 FOs form biomolecular condensates via liquid-liquid phase separation, which are necessary for leukemic transformation and deregulated gene expression. Nevertheless, which proteins interact with NUP98 FOs in condensates, the role of FO-interacting proteins, and the importance of condensate formation for effective therapeutic targeting of NUP98-rearranged cells is poorly understood. Using proteomic and imaging-based approaches, we previously showed that NUP98 FOs interact with MYST family histone acetyltransferase (HAT) complex members, including KAT6A and KAT7, on chromatin and in condensates. In parallel, an in vivo CRISPR/Cas9 screen identified that MYST family HAT complex member and epigenetic reader BRPF1 is a molecular dependency in NUP98::KDM5A-driven leukemia. This result was validated and extended using a Nup98::Kdm5a;Vav-Cre;Cas9 mouse model. Hematopoietic stem and progenitor cells (HSPCs) from this model were transduced with gRNAs targeting Brpf1 or other HAT complex members and placed in competition with unedited control cells. Results showed that genetic knockout of Brpf1 as well as Kat6a, Kat7, and a subset of other HAT complex members led to decreased cell fitness. Importantly, pharmacologic inhibition of KAT6A/7 using small molecule inhibitor PF9363 was effective in multiple preclinical models of NUP98-rearranged leukemia. PF9363 treatment induced myeloid differentiation, reduced histone H3 acetylation, and decreased leukemia burden. Moreover, in a refractory NUP98::NSD1 PDX model, KAT6A/7 inhibition was synergistic in combination with Menin inhibitor SNDX-5613, a recently FDA-approved therapy for some AML subtypes. These findings demonstrate that NUP98 FO interactors may serve as therapeutic targets in NUP98-rearranged leukemia. Further studies demonstrate that other HATs play key roles in NUP98 FO-driven leukemia and may represent additional promising drug targets. Histone acetyltransferases and transcriptional coactivators CREBBP (CBP) and EP300 (p300) are known NUP98 FO interactors, and inhibition of the CBP/p300 bromodomain using CCS1477 has potent efficacy in both mouse and human models of NUP98-rearranged leukemia, while sparing wildtype HSPCs. Our ongoing work seeks to define the transcriptional and epigenetic changes underlying response to CBP/p300 inhibition and identify additional promising approaches to inhibit NUP98 FO condensates.