Genomic alterations in cell-free DNA and enzalutamide resistance in castration-resistant prostate cancer

Background: The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in metastatic castration-resistant prostate cancer (mCRPC) patients is undefined. Although tissue biopsies are impractical to perform routinely in the majority of mCRPC patients, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasive method to explore tumor characteristics. Our aim was to reveal genomic characteristics from cfDNA associated with clinical outcomes on enzalutamide. Methods: Sixty-five mCRPC patients commencing enzalutamide were recruited at British Columbia Cancer Agency. We obtained temporal plasma samples (baseline, 12-week and end-of-treatment) for circulating cfDNA and performed aCGH copy number profiling and deep AR gene sequencing. Samples collected at end-of-treatment were also subjected to targeted sequencing of 19 prostate cancer-associated genes. Genomic alterations in cfDNA were linked to PSA response rate and radiographic and/or clinical progression. Results: cfDNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122 plasma samples. AR mutations and/or copy number alterations were robustly detected in 46% and 66% of baseline and progression samples, respectively. Detection of AR amplification was associated with primary resistance, as was heavily mutated AR (≥2 mutations), and RB1 loss. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR-L702H and promiscuous AR-T878A in patients with prior exposure to abiraterone. At the time of progression, cfDNA sequencing revealed mutations or copy number changes in all patients tested, including clinically actionable alterations in DNA damage repair genes and PI3K pathway genes, and a high frequency of activating CTNNB1 mutations. Conclusions and Relevance: These data demonstrate that clinically informative genomic profiling of cfDNA is feasible in nearly all mCRPC patients and provides important insights into enzalutamide response and resistance.