Investigating drug response and resistance to IDH1R132H inhibition and hypomethylating agents in AML

Abstract

Mutations in epigenetic regulators frequently occur in AML. Furthermore, the epigenetic landscape is typically dysregulated in AML. Targeted epigenetic therapeutics that directly inhibit mutant epigenetic oncogenic drivers, such as AG120 inhibition of IDH1R132H, have shown clinical success for the treatment of IDH1-mutant AML. Other epigenetic therapies target wildtype epigenetic regulators, such as DNMT1 inhibition by hypomethylating agents, with the aim of reprogramming the transcriptional networks driving malignant progression. Despite some patients achieving clinical remission, many AML patients do not respond to epigenetic therapies or relapse post-treatment. Furthermore, the contribution of mutant epigenetic regulators to leukaemogenesis is relatively poorly understood.

A clinically and pathophysiologically relevant murine model of IDH1R132H driven AML co-expressing oncogenic DNMT3A and Nras was utilised to investigate the cellular and molecular consequences of IDH1R132H expression in leukaemia initiation and progression. Results from this thesis suggest that IDH1R132H governs distinct leukaemic properties within the different AML cell-types; IDH1R132H drove the expression of genes that underpin HSC-like self-renewal and proliferation in leukaemic progenitor-like cells, whilst IDH1R132H most profoundly impaired the differentiation capacity of leukaemic immature neutrophils. Furthermore, this thesis demonstrated that AG120 was a highly effective and on-target IDH1R132H inhibitor for the treatment of IDH1R132H driven in vivo AML, and induced neutrophil-skewed differentiation with distinct kinetics throughout the hierarchy of leukaemic cells.

Mechanisms of resistance to the hypomethylating agents AZA and GDAC were investigated utilising a genome-wide CRISPR/Cas9 screen in vitro. Members of the pyrimidine salvage pathway were implicated in the resistance to hypomethylating agents. Loss of DCK and UCK2 conferred resistance to GDAC and AZA, respectively, whilst SLC29A1 loss mediated resistance to both hypomethylating agents in both in vitro and in vivo models of haematological malignancies. This thesis demonstrated that DCK and UCK2 loss remained sensitive to AZA and GDAC, whilst cells with SLC29A1 loss were sensitive to inhibition of DHODH.

This research provided comprehensive insight of the impact of IDH1R132H on distinct leukaemic cell subsets, transcriptional mechanisms underlying leukaemogenesis, and the transcriptional perturbations that may contribute to AG120 resistance. Furthermore, the results of this thesis suggest that AZA and GDAC treatment are potential therapeutic avenues for AML resistance driven by DCK or UCK2 depletion or loss, respectively. Moreover, the results described herein suggest that targeting the de novo pyrimidine synthesis pathway, through DHODH inhibition, is a therapeutic strategy to overcome resistance to hypomethylating agents mediated by the depletion of pyrimidine salvage pathway enzymes.