KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [CUT&Run]

KAT6A-CBP (K/C) and KAT6A-P300 (K/P) fusions are recurrent genetic alterations in acute myeloid leukemia(AML) that are associated with poor prognosis. The large size of these fusion proteins has posed challenges in developing preclinical models, limiting mechanistic studies. To address this, we employed a domain-focused truncation strategy to generate de novo murine models of K/C and K/P fusions, which faithfully recapitulate the morphological, immunophenotypic, and transcriptomic features of KAT6A-rearranged AML. Genomic profiling revealed that KAT6A fusions preferentially localize to H3K4me2/3-marked regions and interact with the Nucleosome Remodeling Factor (NURF), a critical H3K4me2/3 reader. Disrupting NURF-chromatin interactions impaired K/C recruitment to target loci and disrupted MLL/COMPASS-mediated H3K4me2 deposition, thereby establishing an epigenetic regulatory module involving KAT6A chimeras, NURF, and MLL/COMPASS. Concurrently, CBP/P300 inhibition reduced histone acetylation, chromatin accessibility, and genomic targeting of the module. Therapeutically, NURF inhibition induced cell cycle arrest and suppressed leukemia proliferation, while CBP/P300 inhibition promoted leukemia differentiation. Both strategies demonstrated promising efficacy in K/C murine models, with superior effects observed with combined NURF and CBP/P300 inhibition. These findings uncover a self-reinforcing epigenetic module centered on histone reader proteins and modifying enzymes, providing mechanistic insights into KAT6A-rearranged AML and identifying promising combinatorial therapeutic vulnerabilities. RNA-seq profiling of MPs and c-Kit-enriched HSPCs, K/C-III leukemia cells, and K/P-III leukemia cells. RNA-seq profiling of K/C-III leukemia cells treated with 2 μM A485 or BZ1 for 6 or 12 hours. RNA-seq profiling of K/C-III leukemia cells treated with 0.5 μM A485 and 1 μM BZ1 combination for 6 hours. CUT&RUN analysis of KAT6A variants (NT1, NT2, fusions), Pol II, and histone modifications in HEK293T cells. CUT&RUN analysis of KAT6A mutants (NT1, ΔWH1, ΔMYST, G657E) in HEK293T cells. CUT&RUN analysis of KAT6A and BPTF in HEK293T cells expressing KAT6A-NT1 with either BPTF knockdown or GFP knockdown. CUT&RUN profiling of K/C-III, BPTF, SMARCA1, and histone modifications (H3K4me2/3, H3K27ac) in murine K/C-III leukemia cells. CUT&RUN profiling of K/C-III, BPTF, and MLL in murine K/C-III leukemia cells following 6-hour treatment with 2 μM BZ1. CUT&RUN profiling of K/C-III and H3K27ac in murine K/C-III leukemia cells following 6-hour treatment with 2 μM A485. ChIP-seq analysis of Pol II, WDR5, H3K4me1, and H3K4me2 in murine K/C-III leukemia cells treated with 2 μM BZ1 for 6 hours. ChIP-seq analysis of BPTF, MLL, and Pol II in murine K/C-III leukemia cells treated with 2 μM A485 for 6 hours. ATAC-seq analysis of murine K/C-III leukemia cells treated with 2 μM A485 or BZ1 for 6 hours. ChIP-MNase analysis of H3K4me2 in HEK293T cells expressing K/C-III, treated with 2 μM BZ1 for 6 or 12 hours.