Evaluation of the Aggressive-Variant Prostate Cancer Molecular Signature in Clinical Laboratory Improvement Amendments (CLIA) Environments

Simple Summary Alterations in two or more of the tumor suppressors TP53, RB1, and PTEN enrich for prostate cancers with an aggressive disease course which benefits from combination chemotherapies, but with poor survival. This signature could aid in patient selection for clinical trials that study novel therapies aimed towards these aggressive tumors. We assess the operational characteristics of staining tumor tissues, studying DNA obtained from the tumor directly, or studying DNA from tumor cells circulating in the blood to detect this signature. We encountered various challenges that limited the number of evaluable samples for all three assays in each patient. Overall, tissue staining had a higher detection rate and the shortest turnaround times, making it an attractive choice for use in clinical trials. There were operational barriers to accurately detecting the signature in tumor DNA as well as difficulty detecting sufficient tumor content in circulating tumor DNA.Abstract Aggressive-variant prostate cancers (AVPCs) are a subset of metastatic castrate-resistant prostate cancers (mCRPCs) characterized by defects in >= two of three of TP53, RB1, and PTEN (AVPCm), a profile linked to lineage plasticity, androgen indifference, and platinum sensitivity. Men with mCRPC undergoing biopsies for progression were assessed for AVPCm using immunohistochemistry (IHC), next-generation sequencing (NGS) of solid tumor DNA (stDNA), and NGS of circulating tumor DNA (ctDNA) assays in CLIA-certified labs. Biopsy characteristics, turnaround times, inter-reader concordance, and inter-assay concordance were assessed. AVPCm was detected in 13 (27%) patients via IHC, two (6%) based on stDNA, and seven (39%) based on ctDNA. The concordance of the IHC reads between pathologists was variable. IHC had a higher detection rate of AVPCm+ tumors with the shortest turnaround times. stDNA had challenges with copy number loss detection, limiting its detection rate. ctDNA detected the greatest proportion of AVPCm+ tumors but had a low tumor content in two thirds of patients. These data show the operational characteristics of AVPCm detection using various assays, and inform trial design using AVPCm as a criterion for patient selection or stratification.