MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq]

NUP98 fusion oncoproteins (FOs) are a hallmark of childhood acute myeloid leukemia (AML) and drive leukemogenesis through liquid-liquid phase separation-mediated nuclear condensate formation. However, the composition and consequences of NUP98 FO-associated condensates are incompletely understood. Here we show that MYST family histone acetyltransferase (HAT) complex proteins including MOZ/KAT6A, HBO1/KAT7, and the common MOZ/HBO1 complex subunit BRPF1 associate with NUP98 FOs on chromatin and within condensates. MYST HATs are molecular dependencies in NUP98-rearranged (NUP98-r) leukemia, and genetic inactivation or pharmacologic inhibition of Moz and Hbo1 impairs NUP98-r cell fitness. MOZ/HBO1 inhibition decreased global H3K23ac levels, displaced NUP98::HOXA9 from chromatin at the Meis1 locus, and led to myeloid cell differentiation. Additionally, MOZ/HBO1 inhibition decreased leukemic burden in multiple NUP98-r leukemia xenograft mouse models, synergized with Menin inhibitor treatment, and was efficacious in Menin inhibitor-resistant cells. In summary, we show that MYST family HATs are therapeutically actionable dependencies in NUP98-r AML. For RNA-seq experiments in Figure 6, murine NUP98-HOXA9 leukemia cells were treated with DMSO, 500 nM PF9363, 2 uM SNDX-5613, or a combination of both (500 nM PF9363 + 2 uM SNDX-5613) for 72 hours. For RNA-seq experiments in Figure 7, human CD45+ cells were isolated from animals who were treated with vehicle or PF9363 for 30 days. Mice were sacrificed and bone marrow was harvested at the end of the treatment period on Day 54, and mouse cell depletion was performed to enrich for human CD45+ cells. For RNA-seq experiments from CRISPR-edited cell lines, murine NUP98-HOXA9 leukemia cells constitutively expressing the CRISPR-Cas9 enzyme were transduced with lentivirus containing sgRNA targeting various components of the Kat6a/6b/7 complex. The plasmid encoding each sgRNA also contains an IRES-RFP. On day 4 following transduction, RFP+ cells were sorted and RNA and DNA were isolated. CRISPR editing efficiency was confirmed using PCR primers to amplify the sgRNA cut site, followed by Sanger sequencing and analysis using the Synthego ICE algorithm. RNA was used to generate RNA-seq libraries for analysis of differential gene expression upon genetic inactivation of each Kat6a/6b/7 component. A non-targeting sgRNA (NTC) was used as a control.