Plasma AR and abiraterone-resistant prostate cancer

Abstract

Androgen receptor (AR) gene aberrations are rare in prostate cancer before primary hormone treatment but emerge with castration resistance. To determine AR gene status using a minimally invasive assay that could have broad clinical utility, we developed a targeted next-generation sequencing approach amenable to plasma DNA, covering all AR coding bases and genomic regions that are highly informative in prostate cancer. We sequenced 274 plasma samples from 97 castration-resistant prostate cancer patients treated with abiraterone at two institutions. We controlled for normal DNA in patients' circulation and detected a sufficiently high tumor DNA fraction to quantify AR copy number state in 217 samples (80 patients). Detection of AR copy number gain and point mutations in plasma were inversely correlated, supported further by the enrichment of nonsynonymous versus synonymous mutations in AR copy number normal as opposed to AR gain samples. Whereas AR copy number was unchanged from before treatment to progression and no mutant AR alleles showed signal for acquired gain, we observed emergence of T878A or L702H AR amino acid changes in 13% of tumors at progression on abiraterone. Patients with AR gain or T878A or L702H before abiraterone (45%) were 4.9 and 7.8 times less likely to have a ≥50 or ≥90% decline in prostate-specific antigen (PSA), respectively, and had a significantly worse overall [hazard ratio (HR), 7.33; 95% confidence interval (CI), 3.51 to 15.34; P = 1.3 × 10(-9)) and progression-free (HR, 3.73; 95% CI, 2.17 to 6.41; P = 5.6 × 10(-7)) survival. Evaluation of plasma AR by next-generation sequencing could identify cancers with primary resistance to abiraterone.

Figure 1. Detection of circulating tumor DNA in CRPC patients.

(A) Study profile showing the number of patients and samples with next-generation sequencing data and with a circulating tumor DNA fraction ≥0.075. *26 and †1 patient(s) had a pre-abiraterone sample(s) only. RM, Royal Marsden. IRST, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori. (B) Correlation of circulating tumor DNA fraction with serum lactate dehydrogense (LDH), serum alkaline phosphatase (ALP) and AR copy number.

Figure 2. AR gain usually occurs in a non-mutant AR allele.

(A) Distribution of AR point mutations in all samples and stratified by AR copy number (CN) status. (B) The prevalence of non-synonymous (Ka) and synonymous (Ks) substitutions rates in AR gain and AR CN neutral samples. Fisher's exact test was applied to test differences between the number of mutated versus wild-type samples across AR gain and AR CN neutral (A) and non-synonymous versus synonymous rates in AR gain versus AR CN neutral samples (B). (C) Presence of AR point mutations in serial plasma samples of study patients. For every patient, the temporal pattern of mutations detection is shown, distinguishing baseline (green), on treatment (yellow), and progression (red) samples and fractions of circulating tumor DNA (TC) level. Mutations are marked with different color and symbol and corresponding allelic fractions corrected for tumor DNA fraction are reported. Temporal patterns observed for each specific patient/mutation combination are annotated as emergence (E), persistence (P) or loss of detection (L and marked with a red box). Stars are used to mark AR point mutations that are consistently detected with disease progression.

Figure 3. AR copy number is unchanged on abiraterone.

An illustration showing the changes in AR gene status for patients where both baseline and progression samples had detectable tumor DNA fraction. Samples that are AR copy number (CN) neutral (upper row) or AR CN gain (lower row) pre-abiraterone are split into AR CN neutral or AR CN gain at progression. The area of the circles is sized to represent the magnitude of the fractions. Orange represents AR CN neutral and blue, AR CN gain. The split of patients with a decline in PSA ≥50% (light) or not (dark) is shown for every group.

Figure 4. AR gene status prior to start of abiraterone associates with treatment outcome.

(A) Water-fall plot showing the magnitude of PSA declines in patients with AR gain or an L702H or T878A point mutation or copy number (CN) neutral AR. The odds ratios for AR copy number neutral having a decline in PSA ≥50% or ≥90% were calculated using Fisher’s exact test. Clinical site and prior treatment with the novel potent AR-targeting agents enzalutamide or orteronel are identified in the matrix. Overall survival (B) and progression-free survival (C) for AR CN neutral versus AR aberrant are shown with results of univariate analysis in the inset.