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Original Investigation
December 2016

Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer

Author Affiliations
  • 1Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
  • 2Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
  • 3School of Clinical Sciences, Monash University, Melbourne, Australia
  • 4Institute of Biosciences and Medical Technology, Tampere, Finland
JAMA Oncol. 2016;2(12):1598-1606. doi:10.1001/jamaoncol.2016.0494
Key Points

Question  What are the genomic mechanisms underpinning resistance to the androgen receptor (AR) antagonist enzalutamide in metastatic castration-resistant prostate cancer (mCRPC)?

Findings  In this study, genomic profiling was performed on serially collected cell-free DNA (cfDNA) from 65 patients with mCRPC treated with enzalutamide and performed integrated genomic profiling. Aberrations associated with both primary resistance (AR amplification, multiple AR mutations, RB1 loss) and acquired resistance (AR-L702H and AR-T878A mutations, PI3K pathway alterations, CTNNB1 mutations) were identified.

Meaning  Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and provided important insights into enzalutamide resistance.


Importance  The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in patients with metastatic castration-resistant prostate cancer (mCRPC) is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and elucidate resistance. Although tissue biopsies are impractical to perform routinely in the majority of patients with mCRPC, the analysis of plasma cell-free DNA (cfDNA) has recently emerged as a minimally invasive method to explore tumor characteristics.

Objective  To reveal genomic characteristics from cfDNA associated with clinical outcomes during enzalutamide treatment.

Design, Setting, and Participants  Plasma samples were obtained from August 4, 2013, to July 31, 2015, at a single academic institution (British Columbia Cancer Agency) from 65 patients with mCRPC. We collected temporal plasma samples (at baseline, 12 weeks, end of treatment) for circulating cfDNA and performed array comparative genomic hybridization 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.

Exposure  Enzalutamide, 160 mg, daily orally.

Main Outcomes and Measures  Prostate-specific antigen response rate (decline ≥50% from baseline confirmed ≥3 weeks later). Radiographic (as per Prostate Cancer Working Group 2 Criteria) and/or clinical progression (defined as worsening disease-related symptoms necessitating a change in anticancer therapy and/or deterioration in Eastern Cooperative Group performance status ≥2 levels).

Results  The 65 patients had a median (interquartile range) age of 74 (68-79) years. Prostate-specific antigen response rate to enzalutamide treatment was 38% (25 of 65), while median clinical/radiographic progression-free survival was 3.5 (95% CI, 2.1-5.0) months. Cell-free DNA was isolated from 122 of 125 plasma samples, and targeted sequencing was successful in 119 of 122. AR mutations and/or copy number alterations were robustly detected in 48% (31 of 65) and 60% (18 of 30) of baseline and progression samples, respectively. Detection of AR amplification, heavily mutated AR (≥2 mutations), and RB1 loss were associated with worse progression-free survival, with hazard ratios of 2.92 (95% CI, 1.59-5.37), 3.94 (95% CI, 1.46-10.64), and 4.46 (95% CI, 2.28-8.74), respectively. AR mutations exhibited clonal selection during treatment, including an increase in glucocorticoid-sensitive AR L702H and promiscuous AR T878A in patients with prior abiraterone treatment. 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 (4 of 14) of activating CTNNB1 mutations.

Conclusions and Relevance  Clinically informative genomic profiling of cfDNA was feasible in nearly all patients with mCRPC and can provide important insights into enzalutamide response and resistance.