Epigenetic Control and Genome Organization

OVERALL PROGRAM SUMMARY Gary Stein and Janet Stein, Program Directors Our Program Project is a thematically, experimentally and operationally integrated multidisciplinary team approach to address key components of genome organization that are functionally linked to modified epigenetic control of gene expression in breast cancer. The thematic focus and working hypothesis of our Program is that genomic organization and epigenetic control of gene expression coordinately facilitate physiological regulation, including hormone responsiveness, of normal and cancer cell growth, proliferation and cell identity. Our highly collaborative research team established paradigm-shifting insights into parameters of nuclear organization that include: 1. Mitotic gene bookmarking by phenotypic transcription factors to control fidelity of gene expression as cells divide; 2. Relationships between fidelity of nuclear organization, transcription factor localization and metastasis of breast cancer to bone; 3. Dynamic modifications of higher-order inter- and intra-chromosomal interactions in breast cancer cells; 4. Coordinate control of cell growth and phenotype by tissue-specific transcription factors; 5. Epitranscriptomic profiling of endocrine therapy resistant and advanced breast cancer cells in response to selective estrogen receptor modulators; and 6. Noncoding RNA-mediated regulation of the aggressive breast cancer phenotype. This application captures the scientific progress, synergy and momentum of our research team and leverages powerful new technologies for editing the genome, visualizing cells at super resolution and in real time, and decoding higher-order genome organization. We will use normal mammary epithelial, subtype-specific and endocrine resistant breast cancer cell models for discovery, then validate key findings and examine potential clinical relevance using animal models, public databases and patient tumor specimens and organoids. Emphasis will be on exploring molecular mechanisms that integrate multiple dimensions of epigenetic control with modified genome organization in breast cancer. Each of the three projects focuses on a unique aspect of epigenetic control that is required for fidelity of gene expression and is compromised in breast cancer, including: the pivotal role of mitotic gene bookmarking in stabilizing the normal mammary epithelial phenotype (Project 1); novel functions of bromodomain chromatin readers in endocrine therapy resistance (Project 2); and contributions of the novel long noncoding RNA MANCR to deregulated genome organization in aggressive breast cancer (Project 3). A shared resource core will support integrated bioinformatics and biostatistics analyses; standardized experimental design; cell, organoid and in vivo models; and resource authentication to ensure scientific rigor and reproducibility. An administrative core will maximize scientific and programmatic integration, prioritization and oversight. The impact of this program will be the integration of multiple levels of genome organization and of epigenetic control to understand how gene regulation is disrupted in breast cancer.