Circulating Cell-Free DNA to Guide Prostate Cancer Treatment with PARP Inhibition

Abstract

Biomarkers for more precise patient care are needed in metastatic prostate cancer. We have reported a phase II trial (TOPARP-A) of the PARP inhibitor olaparib in metastatic prostate cancer, demonstrating antitumor activity associating with homologous recombination DNA repair defects. We now report targeted and whole-exome sequencing of serial circulating cell-free DNA (cfDNA) samples collected during this trial. Decreases in cfDNA concentration independently associated with outcome in multivariable analyses (HR for overall survival at week 8: 0.19; 95% CI, 0.06-0.56; P = 0.003). All tumor tissue somatic DNA repair mutations were detectable in cfDNA; allele frequency of somatic mutations decreased selectively in responding patients (χ²P < 0.001). At disease progression, following response to olaparib, multiple subclonal aberrations reverting germline and somatic DNA repair mutations (BRCA2, PALB2) back in frame emerged as mechanisms of resistance. These data support the role of liquid biopsies as a predictive, prognostic, response, and resistance biomarker in metastatic prostate cancer.Significance: We report prospectively planned, serial, cfDNA analyses from patients with metastatic prostate cancer treated on an investigator-initiated phase II trial of olaparib. These analyses provide predictive, prognostic, response, and resistance data with "second hit" mutations first detectable at disease progression, suggesting clonal evolution from treatment-selective pressure and platinum resistance. Cancer Discov; 7(9); 1006-17. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Quigley et al., p. 999This article is highlighted in the In This Issue feature, p. 920.

Figure 1

Kaplan-Meier plots showing differences in radiological progression-free survival (rPFS) and overall survival (OS) based on the presence or absence of a ≥50% fall in total cfDNA concentration after 4- and after 8-weeks of therapy with olaparib.

Figure 2

A) Waterfall plot summarizing change in allele frequency (AF) (defined as allele frequency on treatment subtracted by the allele frequency at baseline) after 4- and 8-weeks of therapy. Stars indicate patients considered responders to olaparib in the TOPARP-A trial in the predefined primary endpoint. An absolute decrease of ≥10% in allele frequency was observed in 18/27 somatic mutations detected in responding patients as compared with 3/29 somatic events monitored in non-responding patients (Chi-squared p<0.001). None of the three allele frequency falls in non-responding patients were maintained after 8-weeks of therapy. B) Four examples of how AF of somatic HRD-associated mutations decrease in response to therapy, in parallel with decreases in total cfDNA concentrations. A patient with an ATM p.-2288fs mutation had intermittent increases and decreases in AF in parallel to drug interruptions due to haematological toxicity. C) Changes in cfDNA mutation allele frequency over time in germline deleterious mutation carriers (BRCA2 and ATM) in five patients from the TOPARP-A trial. Those patients with LOH at baseline have the cfDNA mutation allele frequency trending towards 50% in response to therapy, probably due to elimination of the tumor clone. This is not seen in the serial cfDNA samples from the patient whose tumor did not have LOH.

Figure 3

Visual representation of emerging de-novo mutations at progression that likely result in acquired drug resistance in two patients with germline BRCA2 mutations. In the top panel, a patient with a germline deleterious BRCA2 frameshift insertion that was present in both tumour and cfDNA at baseline presents at disease progression with a new frameshift deletion that restores the BRCA2 reading frame. In the lower panel, a second patient with a germline deleterious BRCA2 mutation is depicted; at progression cfDNA whole-exome sequencing identified multiple clones with different previously undetected mutations all resulting in reversion of the BRCA2 reading frame to normal.

Figure 4

Single site disease progression after 9-months of response to therapy in the right hemipelvis visualized by diffusion-weighted whole body MRI. The upper panels show fusion of the T1-weighted imaging and diffusion-weighted imaging. The bottom panels show apparent diffusion coefficient (ADC) maps. Areas of high signal on diffusion-weighted imaging and low ADC values indicate tumour bone marrow infiltration. The left panels depict the baseline MRI scan, showing diffuse tumour infiltration in the pelvic bone. The first trial biopsy was taken from the left iliac bone (red circle), and identified a deleterious BRCA2 mutation with LOH. After 12 weeks of therapy (middle panels) there was a major response to therapy reported. After 9-months (right panels) the MRI identified a focal area of tumour relapse in the right iliac bone, which was biopsied (red arrow). NGS of this biopsy confirmed a de-novo mutation in BRCA2 restoring the open reading frame.

Figure 5

Visual representation of emerging de-novo mutations at progression that likely result in acquired drug resistance in two patients originally presenting somatic frameshift mutations in BRCA2 (upper panel) and PALB2 (bottom panel) respectively in the pre-treatment samples. In both cases, the sample at treatment progression showed 2 different new deletions resulting in in-frame deletions and restoring the reading frame for BRCA2 and PALB2 respectively. In both cases, these clones were coexisting with the original clone that was present prior to treatment.