Project 3: Towards Understanding Prostate Cancer Heterogeneity

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PROJECT 3: SUMMARY Although high risk localized prostate cancer (PCa) is often cured by multimodal therapy including radical prostatectomy, radiation therapy [RT] and androgen deprivation therapy [ADT], the development of castration resistant prostate cancer (CRPC) after metastatic progression is lethal. Studies from several groups have profiled untreated localized PCa and CRPC, however these studies represent static snapshots from convenient samples or rapid autopsies from earlier treatment eras. Lacking are molecular studies addressing PCa progression during current treatments or clinical trials. Recently, a multi-institutional “Dream Team” was formed to perform whole exome (WES) and RNA sequencing on metastatic tumor biopsies (and germline DNA) from 500 CRPC patients (the “CRPC500” study) prior to enrollment on trials involving enzalutamide, abiraterone, and a PARP inhibitor (olaparib). We recently published the first 150 cases (Robinson et al., Cell 2015) and over 500 men have been enrolled with clinical follow-up expected through the next 3 years. We now have the extraordinary opportunity to examine the original untreated diagnostic material from the prostates of the CRPC500 patients and compare it to the metastatic samples to explore key critical questions relevant to progression to CRPC and treatment response. Our team developed next generation sequencing (NGS) assays enabling interrogation of formalin-fixed paraffin embedded (FFPE) samples. EXaCT-1 is a CLEP (CLIA) approved WES assay with an associated analysis pipeline used on over 700 metastatic and primary sample/normal pairs (Weill Cornell Medicine). Complementing this assay is a PCa-specific version of the Oncomine Cancer Panel optimized for 10-20ng FFPE DNA and RNA (Univ. Michigan). These approaches allow analysis of untreated primary tumors from CRPC500 patients. Our overarching goal is to determine the extent to which early mutations/other molecular alterations inform on disease progression and response to AR or PARP directed therapy.!