Genetic aberrations in lymphoid malignancies, including acute lymphoblastic leukemias (ALLs), often include chromosomal rearrangements that result in the dramatic upregulation or dysregulation of transcription factors and other chromatin-associating proteins. This results in altered chromatin states and transcriptional outputs that lead to increased cellular proliferation and other malignant phenotypes. While the activity of transcription factors is very difficult to inhibit directly with small molecule drugs, chromatin-associating transcription co- factors that bind to histones have recently been shown to be amenable to small molecule inhibition. We have discovered and developed chemical probes for a class of protein modules called bromodomains, which are principally involved in the recognition of acetylated lysines on histones. Using these chemical probes, we have established a rationale for targeting this class of proteins in ALL. Treatment of ALL cells with bromodomain inhibitors leads to a dramatic reduction in expression of specific ALL oncogenes, including the notoriously 'undruggable' oncogenic transcription factor MYC. Selective disruption of oncogene expression leads to a decrease in ALL cell proliferation both in vitro and in murine xenograft models. The studies proposed here aim to characterize the mechanism by which bromodomain inhibition selectively effects specific oncogene expression in ALL cells, and to use these insights to further exploit putative ALL cell dependencies on chromatin-associating factors. Ours studies show that loss of MYC expression is a direct result of inhibiting the bromodomain-containing protein BRD4 from the MYC gene locus, leading to the hypothesis that BRD4 is an ALL-dependency gene. However, as BRD4 is widely expressed in many cell types, it remains to be seen how its inhibition leads to potent anti-ALL effects.
In Aim 1, we will perfor genome-wide studies of bromodomain protein displacement with chemical probes using ChIP-seq, particularly focusing on effects within promoter distal cis-regulatory control elements of the genome, or enhancers.
In Aim 2 we will study bromodomain inhibition in combination with other chromatin-targeting small molecules in ALL cells, primarily focusing on compounds that target histone acetylation including histone deacetylase and acetyltransferase probes. We will model these potential therapeutic combinations in murine models of disseminated ALL.
Aim 3 of this proposal seeks to expand the chemical toolbox of chromatin-targeting small molecules, specifically focusing on the bromodomain of the ATAD2 protein, a MYC co-activator that is highly expressed in ALL. We will use high- throughput compound screening and iterative medicinal chemistry employing a suite of optimized bromodomain-binding assay systems. To achieve these aims, I have assembled an excellent and seasoned advisory team, including Dr. James Bradner [Mentor, DFCI], an expert in chemical biology and hematologic malignancies; Dr. Thomas Look [Co-mentor, DFCI] an expert in leukemogenesis and animal models of ALL; and Dr. Richard Young [Co-mentor, MIT], an expert in chromatin biology and transcriptional networks.
Chromatin-targeting drugs are a focus of intense study in many cancers. This project aims to build on expertise using bromodomain-targeting small molecule probes to study mechanisms of dependency in models of acute lymphoblastic leukemia. These studies will greatly inform the development of this class of compounds as potential therapeutics in cancer.
|Ott, Christopher J; Federation, Alexander J; Schwartz, Logan S et al. (2018) Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. Cancer Cell 34:982-995.e7|