Misregulation of the epigenome is a fundamental mechanism in cancer, which results in corruption of the highly specific transcriptional programs, leading to abnormal cell proliferation and expansion. Recent advances in genome analysis reveal that genetic aberrations in human cancer are extremely complex. While most driver mutations remain undruggable, the dependency on resulting aberrant chromatin states holds great promise for the development of targeted therapies.
The causal relationships between histone and DNA modifications, their influence on transcription and functional DNA element integrity are complex and incompletely understood. A primary challenge in the study of aberrant gene regulation in cancer has been to elucidate how chromatin networks influence the millions of putative regulatory elements throughout the genome, which orchestrate the control of tens of thousands of genes in a highly coordinated and context-specific manner.
To gain a better understanding of these regulatory epigenetic networks, and ultimately to identify innovative therapeutic strategies and novel biomarkers, we apply a variety of genetic tools, ranging from advanced RNAi to CRISPR/Cas9 technologies combined with tractable fluorescent reporter systems, which are stably integrated into the genome of mouse and human cancer cell lines.
The transcriptional output of effector proteins (e.g. epigenetic effectors, transcription factors or nuclear receptors) is determined by a highly complex network of coregulators. Our limited mechanistic understanding of most of these coregulators complicate the understanding of their function in different cancer contexts. Concurrently, the dependence of effector proteins on accessory proteins gives various opportunities for therapeutic intervention. Traditional biochemical approaches like immunoprecipitation (IP) and chromatin IP (ChIP) have mostly provided a static picture of regulatory chromatin complexes. These approaches have been insufficient to generate a comprehensive understanding of regulatory chromatin networks controlling the expression of essential gene regulatory circuits. We combine fluorescent reporter systems with multiplexed RNAi and CRISPR screening approaches to functionally characterize these diverse complexes. Our initial efforts focus on selected key drug targets and cancer types.
Cancer-specific dependencies on functional DNA elements cannot be predicted from conventional epigenome analyses, but can only be revealed through hypothesis-driven or systematic functional genetic studies. Using multiplexed RNAi screening technologies combined with extensive functional characterization, we have shown in a recent publication (Rathert et. al., 2015) that epigenetic events are crucial for acquired and primary resistance to BET inhibitors (BETis) in leukemia. We are currently expanding this view to other drugs and cancer contexts.