In this proposal, we will attempt to determine the precise molecular mechanisms by which acute myeloid leukemia (AML)-initiating mutations act, and to exploit these mechanisms therapeutically. The vast majority of patients who develop AML still die from their disease. New therapies that are more efficacious and less toxic are urgently needed. Recent AML genome sequencing studies have taught us that virtually all AML tumors are clonally heterogeneous. Each tumor originates from a founding clone that was created by an initiating mutation that allowed a single hematopoietic stem/progenitor cell (HSPC) to achieve a clonal advantage. This `preleukemic' clone acquires additional, cooperating mutations that lead to the development of a founding clone, and clinically apparent AML. Subclones arise from the founding clone, or can evolve from other subclones. Regardless, all subclones contain the founding clone mutations. Although cooperating mutations are often attractive for targeted therapies (e.g. FLT3 and/or IDH1/2 inhibitors), they are sometimes found in subclones (i.e. they are only in a fraction of the total leukemic cell population); therapeutic targeting of subclones cannot be expected to be curative. The central hypothesis of this work is that a complete understanding of the consequences of initiating mutations is required to fully understand AML pathogenesis. We also hypothesize that therapeutic approaches directed against initiating mutations are the most likely to provide long-term benefit for AML patients. We will fully characterize two common, well-validated AML-initiating mutations (PML-RARA and DNMT3A R882H) that are both associated with profound epigenetic alterations in hematopoietic cells. We will utilize state-of-the-art techniques (including comprehensive, strand-specific RNA-seq of large and small RNAs, whole genome bisulfite sequencing, chromatin accessibility studies, and ChIP-seq studies for oncogene binding and histone modifications) to pinpoint the key genomic targets of these initiating mutations, and unbiased proteomic techniques to comprehensively identify proteins that interact specifically with the mutant proteins. We will integrate these data to identify genes, RNAs, loci, and pathways that are altered by the initiating mutations, and develop new hypotheses regarding mechanisms that may be relevant for AML pathogenesis. We will model AML-initiating mutations and downstream pathways both in human embryonic stem cells, and in transgenic mice expressing PML-RARA or DNMT3A R882H, to fully explore the contributions of pathways (e.g. DNA methylation and/or histone modifiers) and/or cooperating mutations that may be critical for their actions. As a translational goal of thi work, we will attempt to develop a novel drug that will inhibit the action of the mutant DNMT3A R882H protein, which acts as a dominant negative inhibitor of WT DNMT3A, thereby suppressing de novo DNA methylation in HSPCs. This mutation causes in focal, canonical, DNA hypomethylation, an event that may be reversed by an effective inhibitor, which may restore normal HSPC function.
Acute myeloid leukemia (AML) is a devastating malignancy of hematopoietic stem and progenitor cells (HSPCs), and it is fatal for most of the patients who develop it. In this proposal, we will use state-of-the-art genomic, proteomic, and disease modeling approaches to fully understand how AML-initiating mutations alter HSPCs to give them a clonal advantage. We will use this information to develop novel approaches to target AML-initiating mutations, and eliminate AML founding clones.
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