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.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Unknown (R35)
Project #
1R35CA197561-01
Application #
8956066
Study Section
Special Emphasis Panel (ZCA1-GRB-S (M1))
Program Officer
Mufson, R Allan
Project Start
2015-08-13
Project End
2022-07-31
Budget Start
2015-08-13
Budget End
2016-07-31
Support Year
1
Fiscal Year
2015
Total Cost
$915,000
Indirect Cost
$315,000
Name
Washington University
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
068552207
City
Saint Louis
State
MO
Country
United States
Zip Code
63130
Christopher, Matthew J; Petti, Allegra A; Rettig, Michael P et al. (2018) Immune Escape of Relapsed AML Cells after Allogeneic Transplantation. N Engl J Med 379:2330-2341
Chen, David; Christopher, Matthew; Helton, Nichole M et al. (2018) DNMT3AR882-associated hypomethylation patterns are maintained in primary AML xenografts, but not in the DNMT3AR882C OCI-AML3 leukemia cell line. Blood Cancer J 8:38
Uy, G L; Duncavage, E J; Chang, G S et al. (2017) Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy. Leukemia 31:872-881
Cole, Christopher B; Russler-Germain, David A; Ketkar, Shamika et al. (2017) Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies. J Clin Invest 127:3657-3674
Spencer, David H; Russler-Germain, David A; Ketkar, Shamika et al. (2017) CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression. Cell 168:801-816.e13
Duncavage, Eric J; Uy, Geoffrey L; Petti, Allegra A et al. (2017) Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy. Blood 129:1397-1401
Wong, Terrence N; Miller, Christopher A; Klco, Jeffery M et al. (2016) Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML. Blood 127:893-7
Welch, John S; Petti, Allegra A; Miller, Christopher A et al. (2016) TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes. N Engl J Med 375:2023-2036
Duncavage, E J; O'Brien, J; Vij, K et al. (2016) Targeted sequencing informs the evaluation of normal karyotype cytopenic patients for low-grade myelodysplastic syndrome. Leukemia 30:2422-2426
Miller, Christopher A; McMichael, Joshua; Dang, Ha X et al. (2016) Visualizing tumor evolution with the fishplot package for R. BMC Genomics 17:880

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