Molecular Characterization of Prostate Cancer Specimens by Bulk and Single Cell Analysis

Version 1: We performed single-cell RNA-sequencing (scRNA-seq) of fresh biopsies from metastatic castration resistant prostate cancer. Additionally, where available, we performed matched bulk whole exome sequencing (WXS; tumor and normal paired) and whole transcriptome sequencing for the same individuals. We also performed bulk whole exome (WXS) and RNA-sequencing (RNA-Seq) from FFPE pre-treatment biopsies from patients with clinically localized high-risk prostate cancer.Version 2: We added data from a randomized phase 2 trial of radium-223 with or without pembrolizumab in patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) to bone. After enrollment, study participants underwent bone biopsy and were randomized 2:1 to receive radium-223 at 55 kBq/kg every 4 weeks + pembrolizumab at 200 mg every 3 weeks (Arm A, R223+P) or radium-223 at 55 kBq/kg every 4 weeks alone (Arm B, R223). Stratification factors were alkaline phosphatase ≥220 vs. <220 U/L and high vs. low volume bony metastases by CHAARTED criteria. Participants then underwent repeat biopsy after 8 weeks of therapy (+ 3-week window) or after 2 doses of radium-223 if delays occurred. The primary endpoint was differences in CD4+ and CD8+ T-cell infiltrate after 8 weeks of treatment vs. baseline biopsy. Key secondary endpoints were safety/tolerability, radiographic progression-free survival (rPFS), and overall survival (OS). Exploratory endpoints included rate of symptomatic skeletal events (SSEs) and PSA response.Data generated includes bulk whole exome sequencing (WXS), ultra-low pass whole genome sequencing (WGS) at 0.1X coverage, and targeted-capture sequencing. The ultra-low pass sequencing was used as part of the selection criteria for the target capture sequencing. Note: Two subjects in this study are linked to phs001577 and phs000915 respectively. ]]>
Inclusion Criteria: 18 years of age or olderHad histologically confirmed prostate adenocarcinomaEastern Cooperative Oncology Group (ECOG) performance status ≤ 1Radiographic evidence of metastatic disease to bone by conventional imagingSerum testosterone levels < 50 ng/dLEvidence of disease progression based on rising PSA or bone scan progression per Prostate Cancer Working Group 2 (PCWG2) criteria.Exclusion Criteria: Patients who previously received radium-223 or PD-1, PD-L1, or PD-L2 blocking therapySmall cell histologyPatients with visceral metastasesLocal recurrence in the prostate bedNon-nodal soft tissue lesions (including soft tissue lesions in the bone) ≥ 1 cmPatients with immunodeficiency, receiving systemic steroid therapy prednisone > 10 mg daily or equivalent, active autoimmune disease that has required systemic treatment in the past 2 years, or any history of noninfectious pneumonitis were excluded.]]>