Investigating the role of KAT6A in MLL-rearranged acute myeloid leukemia

Acute myeloid leukemia (AML) is a disease of blocked differentiation in which blasts fail to mature
and proliferate continuously. Differentiation therapy, which aims to reactivate latent maturation
programs and induce cell cycle exit, is curative in the promyelocytic (APL) AML subtype, but not in
other AML subtypes. Epigenetic factors help sustain the differentiation block, and inhibitors of
regulators such as the LSD1, BRD4, and DOT1L has recently been shown to re-activate myeloid
differentiation programs in selected AML models. However, these inhibitors generally do not achieve
terminal differentiation and disease remission. Accordingly, there is significant need to identify more
regulators of the AML differentiation block and to test whether their inhibitors can induce terminal
differentiation when used individually or in combination regiments. To identify novel regulators of AML
differentiation, we recently performed a chromatin-focused CRISPR sgRNA screen using gain-of-
differentiation as a readout. This screen identified the H3K9 histone acetyltransferase KAT6A as a
key driver of AML differentiation arrest, and mechanistic work showed that KAT6A and the H3K9ac
histone binding protein ENL closely cooperate to active promoters of AML oncogenes. We confirmed
that both genetic (CRISPR) and small molecule inhibition of KAT6A markedly induces differentiation
and reduces proliferation most commonly in MLL-rearranged (MLL-r) AMLs, and also in selected
MLL-wild type (MLL-WT) AMLs. Further, KAT6A inhibitors synergize with inhibitors of either LSD1 or
DOT1L to induce near-terminal differentiation and fully halt proliferation in vitro. This proposal has
three goals: First, we will determine the mechanisms by which KAT6A and ENL are recruited to
chromatin and activate transcription. We will identify the protein domains in KAT6A and the MOZ
complex it resides in that are responsible for its binding to chromatin at MLL-AF9 targets and non-
MLL-AF9 targets. We will also identify any transcription factors interacting with KAT6A and ENL and
test their effect on recruitment of the KAT6A-ENL module to chromatin. Our second goal is to test the
therapeutic potential of targeting KAT6A, individually or in combination with LSD1 or DOT1L
inhibitors, in genetically-defined AML mouse models. We will employ an Mll-Af9 model and a
Dnm3a/Flt3-ITD model and test the effect of inhibitor treatment schemes on disease progression and
overall survival. We will also test the effect of inhibitor treatments on normal hematopoiesis. Our third
goal will be to test the response of clinical AML patient samples to inhibition of KAT6A, individually or
in combination with LSD1 or DOT1L inhibitors. We will perform drug response assays in MLL-r and
MLL-WT samples in vitro using OP9 feeder layer culturing methodology, and will also perform PDX
transplant models and test the response to KAT6A and LSD1 or DOT1L inhibitors in vivo.

Grant Number: 3R01CA266641-04S1
NIH Institute/Center: NIH
Principal Investigator: Mario Blanco