Project 1: Genomic Predictors of Clinical Outcomes and Response to Targeted Therapy in Advanced Prostate Cancer

SUMMARY/ABSTRACT Clinical sequencing has only recently begun to inform the selection of FDA-approved therapies for individual patients with prostate cancer. The recent FDA approvals of rucaparib and olaparib for men with metastatic castration-resistant prostate cancers harboring alterations in DNA damage repair (DDR) genes and of pembrolizumab for microsatellite instability–high (MSI-H) or mismatch repair deficient solid tumors dictate that somatic and germline DNA profiling are now required for the optimal standard care of men with advanced prostate cancer. However, among patients with BRCA and other DNA repair pathway gene mutations, only a subset—half at best—respond to approved targeted therapies. Similarly, only a subset of patients with MSI-H prostate cancers will responds to pembrolizumab. In this project, we will leverage an institutional-scale prospective tumor and germline sequencing initiative to expand our understanding of the impact of genomic alterations on clinical outcomes and response to targeted and immune-based therapies in men with prostate cancer. Our overarching aims are to identify genomic alterations associated with progression to the lethal metastatic phenotype and to refine molecularly targeted approaches to the treatment of locally advanced and metastatic prostate cancer. We will accomplish these translational objectives through three broad approaches: 1) We will develop the largest clinical genomic data set of men with high-risk, localized prostate cancer and test the association of genomic alterations with clinical outcomes in this disease state. With a recurrence rate of at least 40%, high-risk, clinically localized prostate cancer represents an area of significant unmet need for novel treatment approaches, including the introduction of targeted therapies and molecularly guided treatment intensification to reduce the risk of recurrence. 2) We will identify molecular features of tumors with DDR alterations that are more predictive of sensitivity or resistance to PARP inhibitors than DDR mutational status alone. More specifically, we will use targeted and whole-genome sequencing analyses to explore the associations between mutational zygosity, clonality, and the presence of structural variant signatures and response to PARP inhibitor therapy. 3) We will determine the timing at which actionable DNA repair alterations arise during prostate cancer disease progression and the impact of preexisting, intrapatient heterogeneity on response to approved targeted and immunotherapies using sequential tumor and plasma sequencing. In sum, on the basis of our institutional expertise in clinical molecular profiling, our ability to generate a prospective data set of thousands of patients with prostate cancer treated with standard and investigational therapies, and our experience in advancing the clinical development of targeted therapies in prostate cancer and other malignancies, including leadership of the study that resulted in the first FDA approval of a PARP inhibitor for prostate cancer, we are in an excellent position to develop and refine targeted treatment approaches that will benefit men with locally advanced and metastatic prostate cancer.