Abstract DL-1: Essential Genes and Cistromes in Breast Cancer

Steroid hormones mediate critical lineage-specific developmental and physiologic responses. While estrogen is required for normal breast development, the genes regulated by estrogen and the genomic targets of the estrogen receptor (ER) are altered in ER+ breast cancers. The requirement of most breast cancers for estrogen has led to the development of endocrine therapies that block ER action. While initial endocrine interventions are successful, in the advanced disease setting resistance to ER-targeted therapy almost invariably arises. As with other targeted therapies, gain of function mutations play a significant role in the development of therapeutic resistance to ER directed treatments in breast cancer. In addition, pathways downstream of ER are activated in cases in which ER itself is not genetically altered suggesting that these pathways remain essential. Activation of these pathways may depend on mutations in other transcription factors involved in steroid receptor networks or chromatin modifying enzymes involved in transcriptional regulation mediated by ER. These mutations may be present in the protein coding regions of the genes or in the cis-regulatory elements regulating expression of key genes in the pathways. Renewed success in targeting ER and promising advances in inhibiting the activity of the chromatin modifying enzymes provides new opportunities for the treatment of patients with breast cancer. Using genome-wide CRISPR-Cas9 knockout screens we have identified the genes essential for hormone-dependent breast cancer growth including key genes in the receptor-centered transcriptional networks. Although large sets transcription factor binding sites or cistromes have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR-Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of more than 10,000 FOXA1 and CTCF binding sites in breast cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed two classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at TAD boundaries and display distinct characteristics. Using regression methods trained on the screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts non-coding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given transcription factor and can inform the development of predictive models of cistrome function. In addition, defining the essential cistrome may shed light on the noncoding regions of the genome most likely to harbor oncogenic driver mutations. Citation Format: M Brown. Essential Genes and Cistromes in Breast Cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr DL-1.