Abstract A19: Targeting epigenetic regulators to override cellular identity programs and induce therapeutic differentiation in MLL-rearranged acute myeloid leukemia

Abstract

Acute myeloid leukemia (AML) is a poor-prognosis disease that is universally characterized by a prominent differentiation block. Chemotherapeutic regimens and disease outcomes have not changed in decades, and there is great need for novel therapeutic treatments and approaches. Differentiation therapy is a fundamentally different therapy that aims to reactivate latent maturation programs to induce proliferation arrest and apoptosis. This approach is curative in the promyelocytic AML subtype but not others. It is therefore critical to identify the enforcers of differentiation arrest in non-APL AML. Here, we performed a cell-fate selection CRISPR screen for chromatin factors whose inhibition promotes AML cell differentiation. We found that both genetic and chemical inhibition of the histone acetyltransferase KAT6A induces myeloid maturation, most prominently in MLL-rearranged AML. KAT6A loss markedly reduces self-renewal and extinguishes the proliferative capacity of AML cells. Through ChIP-seq, RNA-seq, and clinical dataset analyses, we found that KAT6A is the likely initiator of a newly-described "writer-reader" module that drives oncogene expression in AML. KAT6A catalyzes promoter H3K9 acetylation, which is bound by the H3K9ac reader ENL, leading to Super-elongation complex recruitment and release of paused RNA PolII at oncogenic loci such as MYC. KAT6A is elevated in human AMLs compared to matched normal tissue, and its downregulation correlates with monocytic differentiation in clinical AML datasets. These findings suggest the potential of targeting KAT6A and/or ENL to disrupt this writer-reader module and ablate downstream MYC transcriptional programs in MLL-rearranged AML. This strategy may be viable in the near future, as a recently developed KAT6A/B inhibitor has already entered clinical trials for breast cancer. In follow-up work, we performed differentiation-specific "synergy screens," in which we delivered sgRNA libraries to U937 cells and ER-Hoxb8 cells treated with or without an LSD1 inhibitor (LSD1i). We identified multiple genes whose knockout synergized with LSD1i treatment to induce complete, terminal differentiation with low toxicity. Genetic results were confirmed with small molecule inhibitors of selected hits, and the most synergistic drug combination was pursued further. We found that AML cells dependent on hyperactivity of both Hoxa9 and Meis1 are most sensitive to this drug combination. Preliminary data suggest that LSD1i treatment alone fails to downregulate Meis1 expression, and that the ability of the second drug to fully ablate Meis1 is the likely mechanism underlying the observed synergy. Importantly, the second drug is also in clinical trials and will be discussed in the abstract presentation. Altogether, this work advances our understanding of the AML differentiation block and nominates a specific drug combination for AML differentiation therapy. Citation Format: Andres Blanco. Targeting epigenetic regulators to override cellular identity programs and induce therapeutic differentiation in MLL-rearranged acute myeloid leukemia [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A19.