Transcriptional overload: unlocking a new anti-cancer paradigm by targeting DDX19A

About This Grant

PROJECT SUMMARY/ABSTRACT: A key problem in the treatment of cancer is targeting master transcription factors (TFs) that drive oncogenesis. Many malignancies are characterized by TFs that regulate aberrant epigenetic and gene expression programs. A phenomenon that has been observed in the regulation of malignant TFs is the necessity to restrain oncogenic TF activity in order to preserve cancer cell wellbeing. We have identified DDX19A as a top genomic dependency in Ewing sarcoma (ES), an aggressive bone malignancy driven by the fusion oncoprotein and potent TF EWSR1:FLI1 (EWS/FLI). Intriguingly, we have observed that loss of DDX19A leads to marked global upregulation of transcription, chromatin opening, and increase in enhancer binding by H3K27Ac in ES cells, suggesting that this RNA helicase is a crucial negative regulator of transcription in ES tumors. We have gone on, through chemical screening efforts, to develop seed compounds that selectively target DDX19A. The objective of this proposal is to examine the mechanism of action of DDX19A in ES, and to use medicinal chemistry optimization to develop small molecule probes with which to target this protein. Our central hypothesis is that DDX19A constrains transcription and epigenetic programs directed by EWS/FLI, and that the loss of DDX19A leads to toxicity from transcriptional overload subsequent cell death. Thus, we believe that DDX19A is a promising new target for therapeutic development. We will test this hypothesis in two parallel specific aims: 1) Interrogate how DDX19A regulates gene expression programs controlled by EWS/FLI, and 2) Develop potent and selective allosteric inhibitors of DDX19A. First, we will use state-of-the-art functional genomic, epigenomic, and proteomic approaches to examine how DDX19A activity is critical specifically in EWS/FLI-driven tumors. Next, we will rigorously interrogate how DDX19A regulates nascent transcription specific to ES. Next, we will use chemical biology methods to validate specific DDX19A engagement and functional modulation in ES cells. Through a hit-to-lead strategy, we will obtain inhibitors with optimized pharmacokinetic properties, which will serve as lead compounds for therapeutic discovery. We will test optimized compounds for efficacy using in vitro ES cell lines as well as in vivo in ES PDX models. Importantly, animal subjects are indispensable for establishing pre-clinical rationale for development of new targeted therapeutics. Specifically, animal subjects are the only available means to study in vivo pharmacokinetics, test dosing schedules/routes, examine pharmacodynamics (in tumor-bearing animals), and measure toxicities that may impact human patients. These studies are innovative as they combine extensive molecular biologic investigation with sophisticated chemistry approaches to target ES, an aggressive, difficult-to-treat malignancy. Our proposal is significant because it will expand our understanding of how cancer cells control oncogenic transcription in order to promote cell survival. Successful completion of these aims will provide proof-of-concept that de-repressing TF activity and initiating transcriptional overload is a viable strategy for treating TF-driven malignancies.