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

Abstract

Importance The molecular landscape underpinning response to the androgen receptor (AR) antagonist enzalutamide in metastatic castration-resistant prostate cancer (mCRPC) patients is undefined. Consequently, there is an urgent need for practical biomarkers to guide therapy selection and understand resistance. 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. Objective To reveal genomic characteristics from cfDNA associated with clinical outcomes on enzalutamide. Design We collected temporal plasma samples (baseline, 12-week, 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. Setting Plasma samples were obtained from August 2013 to July 2015 at a single academic institution (British Columbia Cancer Agency). Participants 65 mCRPC patients. Exposure for Observational Studies Enzalutamide, 160 mg daily orally. Main Outcome Measures PSA 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 anti-cancer therapy and/or deterioration in ECOG performance status ≥ 2 levels). Results cfDNA was isolated from 122/125 plasma samples, and targeted sequencing was successful in 119/122. 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.

Genomic alterations in plasma DNA from patients with metastasized prostate cancer receiving abiraterone or enzalutamide

“…Table 3). Patient #33572 had a “heavily mutated” AR gene 16 with two mutations detected, i.e. L702H and T878A, which are both known to confer broadened ligand specificity 31 .…”

“…Additionally, gain of CYP17A1 has been associated with reduced progression-free survival (PFS) in men receiving abiraterone treatment 14 and loss of RB1 has predicted worse PFS in men treated with enzalutamide 16 . Only a few studies have employed genome-wide approaches of plasma DNA analyses in prostate cancer 11, 13, 18, 19 .…”

Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer

“…The majority of mCRPC patients studied to date have plasma ctDNA fractions (ctDNA%, the proportion of tumor-derived cfDNA) above 2% (3,5,6,10,11). cfDNA sequencing involves a tradeoff between cost, genome coverage, and sensitivity to low ctDNA%.…”

Circulating Tumor DNA Reveals Clinically Actionable Somatic Genome of Metastatic Bladder Cancer

“…However, while the proportion of cfDNA that is tumor-derived (the ctDNA fraction) is largely unknown in metastatic bladder cancer, it is often greater than 1% in advanced solid malignancies studied to date (24,37,38). In data from The Cancer Genome Atlas (TCGA), 98% of primary muscle-invasive bladder cancer had a nonsynonymous somatic mutation in at least one of 50 bladder cancer genes in our panel (13).…”

“…Prognostic and predictive ctDNA-based biomarkers are beginning to emerge in prostate, colon, and pancreatic cancer (24)(25)(26). In NSCLC, a "companion diagnostic" ctDNA test for the EGFR T790M mutation recently received FDA approval.…”