HBO1 is required for the maintenance of leukaemia stem cells [ChIP-seq]

Acute myeloid leukaemia (AML) is a heterogeneous disease characterised by transcriptional dysregulation resulting in a block in differentiation and increased malignant self-renewal. Various epigenetic therapies aimed at reversing these hallmarks of AML have progressed into clinical trials, with most showing modest efficacy due to an inability to effectively eradicate leukaemia stem cells (LSC). To specifically identify novel dependencies in LSC we screened a bespoke library of small hairpin RNAs (shRNAs) targeting chromatin regulators in a unique ex vivo model of LSC. We identified the MYST acetyltransferases HBO1 (KAT7) and several known members of the HBO1 protein complex as critical regulators of LSC maintenance ex vivo and conditional ablation of HBO1 confirmed its requirement for LSC maintenance in vivo. CRISPR domain screening identified the histone acetyltransferases (HAT) domain of HBO1 as being essential to acetylate histone H3K14, which is required for the expression of the key genes including HOXA9 and HOXA10 that maintain the immature phenotype and self-renewal properties of LSC. To leverage this dependency therapeutically we developed highly potent small molecule inhibitors of HBO1 and provide structural data to demonstrate their mode of activity as competitive analogues of acetyl-CoA. These inhibitors phenocopy our genetic data and show efficacy in a broad range of human cell lines and primary patient samples encompassing the most common genetic subtypes of AML. ChIP-seq of BET inhibitor resistant leukaemic cells transduced with HBO1 sgRNA.