Epigenetic mechanisms of therapeutic resistance

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Project Summary/Abstract Cellular phenotypic heterogeneity is a key mechanism underlying neoplastic disease progression and therapeutic resistance, yet its regulation is poorly understood at the molecular level. We have found that elevated therapeutic resistance is associated with higher levels of cell-to-cell transcriptomic heterogeneity and that decreasing such heterogeneity by modulating the activity of epigenetic histone-modifying enzymes such as KDM5B improves responses to treatment. We also determined that acquired resistance to epigenetic drug agents, including KDM5 and BET bromodomain inhibitors, is due to epigenetic mechanisms, whereas acquired endocrine resistance reflects a selection for a pre-existing, genetically distinct sub-populations of cells. The goal of this Project is to investigate the population dynamics of cellular phenotypic heterogeneity in response to and resistance to cancer therapies in luminal estrogen receptor positive (ER+) and triple-negative breast cancer (TNBC). Our hypothesis is that cellular states governed by epigenetic regulators are highly variable and dynamic and that this underlies acquired therapeutic resistance. We also hypothesize that by modulating the activity of epigenetic regulators and by identifying mechanisms of synthetic lethality and the acquired resistance to epigenetic agents, we can decrease transcriptomic heterogeneity and improve therapeutic response. To test our hypotheses, we will characterize the impact of genetic and epigenetic heterogeneity on acquired resistance to endocrine, chemo-, and epigenetic therapies (Aim 1). We will use barcoded cells to follow population dynamics during the development of acquired resistance, characterize the epigenetic landscape and transcriptomic heterogeneity of drug-tolerant and -resistant populations, and build mathematical models based on experimental data to predict the evolution of therapeutic resistance to different agents. Additionally, to define synthetic-lethal interactions and mechanism of acquired resistance to epigenetic therapies we will perform CRISPR/Cas9 screens (Aim 2) in ER+ and TNBC cell lines that are sensitive versus resistant to epigenetic agents. Overall, the project will significantly advance our knowledge of the regulation of phenotypic heterogeneity and the role this plays in therapeutic responses and resistance.