Adam Foye

Analysis of circulating cell-free DnA identifies multiclonal heterogeneity of BRCA2 reversion mutations associated with resistance to PARP inhibitors

Approximately 20% of metastatic prostate cancers harbor mutations in genes required for DNA repair by homologous recombination repair (HRR) such as BRCA2 HRR defects confer synthetic lethality to PARP inhibitors (PARPi) such as olaparib and talazoparib. In ovarian or breast cancers, olaparib resistance has been associated with HRR restoration, including by BRCA2 mutation reversion. Whether similar mechanisms operate in prostate cancer, and could be detected in liquid biopsies, is unclear. Here, we identify BRCA2 reversion mutations associated with olaparib and talazoparib resistance in patients with prostate cancer. Analysis of circulating cell-free DNA (cfDNA) reveals reversion mutation heterogeneity not discernable from a single solid-tumor biopsy and potentially allows monitoring for the emergence of PARPi resistance.Significance: The mechanisms of clinical resistance to PARPi in DNA repair-deficient prostate cancer have not been described. Here, we show BRCA2 reversion mutations in patients with prostate cancer with metastatic disease who developed resistance to talazoparib and olaparib. Furthermore, we show that PARPi resistance is highly multiclonal and that cfDNA allows monitoring for PARPi resistance. Cancer Discov; 7(9); 999-1005. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.

Successful whole-exome sequencing from a prostate cancer bone metastasis biopsy

Background:Comprehensive molecular characterization of cancer that has metastasized to bone has proved challenging, which may limit the diagnostic and potential therapeutic opportunities for patients with bone-only metastatic disease.Methods:We describe successful tissue acquisition, DNA extraction, and whole-exome sequencing from a bone metastasis of a patient with metastatic, castration-resistant prostate cancer (PCa).Results:The resulting high-quality tumor sequencing identified plausibly actionable somatic genomic alterations that dysregulate the phosphoinostide 3-kinase pathway, as well as a theoretically actionable germline variant in the BRCA2 gene.Conclusions:We demonstrate the feasibility of diagnostic bone metastases profiling and analysis that will be required for the widespread application of prospective ‘precision medicine’ to men with advanced PCa.

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study

Purpose The prevalence and features of treatment-emergent small-cell neuroendocrine prostate cancer (t-SCNC) are not well characterized in the era of modern androgen receptor (AR)-targeting therapy. We sought to characterize the clinical and genomic features of t-SCNC in a multi-institutional prospective study. Methods Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy and were followed for survival. Metastatic biopsy specimens underwent independent, blinded pathology review along with RNA/DNA sequencing. Results A total of 202 consecutive patients were enrolled. One hundred forty-eight (73%) had prior disease progression on abiraterone and/or enzalutamide. The biopsy evaluable rate was 79%. The overall incidence of t-SCNC detection was 17%. AR amplification and protein expression were present in 67% and 75%, respectively, of t-SCNC biopsy specimens. t-SCNC was detected at similar proportions in bone, node, and visceral organ biopsy specimens. Genomic alterations in the DNA repair pathway were nearly mutually exclusive with t-SCNC differentiation ( P = .035). Detection of t-SCNC was associated with shortened overall survival among patients with prior AR-targeting therapy for mCRPC (hazard ratio, 2.02; 95% CI, 1.07 to 3.82). Unsupervised hierarchical clustering of the transcriptome identified a small-cell-like cluster that further enriched for adverse survival outcomes (hazard ratio, 3.00; 95% CI, 1.25 to 7.19). A t-SCNC transcriptional signature was developed and validated in multiple external data sets with > 90% accuracy. Multiple transcriptional regulators of t-SCNC were identified, including the pancreatic neuroendocrine marker PDX1. Conclusion t-SCNC is present in nearly one fifth of patients with mCRPC and is associated with shortened survival. The near-mutual exclusivity with DNA repair alterations suggests t-SCNC may be a distinct subset of mCRPC. Transcriptional profiling facilitates the identification of t-SCNC and novel therapeutic targets.

An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer

Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.

Abstract A12: Identification of pathways associated with abiraterone resistance in metastatic castration resistant prostate cancer: Preliminary results from the SU2C/AACR West Coast Prostate Cancer Dream Team

Background: The efficacy of androgen signaling inhibitors such as Abiraterone (Abi) or Enzalutamide (Enz) has changed the standard of care in mCRPC. However, adaptive resistance to these agents is a consistent outcome with this therapy that undermines their benefit. The mechanisms underlying acquired resistance to Abi or Enz are poorly understood. The goals of the WCDT project are to identify the molecular pathways underlying the adaptive response to these targeted therapies through expression and mutational analysis of metastatic biopsies. Methods: Following central radiologic review, eligible mCRPC pts underwent biopsy at one of 5 WCDT clinical sites, using a uniform biopsy protocol. Tissue was both frozen, and formalin fixed/paraffin embedded (FFPE). Frozen samples were subject to laser capture microdissection for isolation of RNA and DNA enriched for mCRPC. FFPE tissue underwent a CLIA-certified assessment of a mutational panel, IHC for PTEN, and fluorescence in situ hybridization (FISH) for AR+. Pathway assessment is performed using RNA-seq and mutation data from mCRPC biopsies mapped onto a comprehensive pathway database connecting a tumor sample with genetic regulatory logic. Results: 70 of 300 planned mCRPC pts have undergone a metastasis biopsy. To date, biopsies have been obtained prior to treatment and following progression from one patient receiving Abi and one receiving Enz. Data collection from biopsies has been possible in 52 of 72 samples (72% success rate), and clinically actionable results have been returned to the care providers for 50 samples. The most commonly mutated gene assessed by the mutational panel was p53. Importantly, acquired mutation did not appear to be a mechanism for drug resistance in mCRPC, as the prevalence of tumors positive for mutations in genes contained in the panel was lower in patients who had progressed on Abi or Enz (9 of 16, 56%) than it was in treatment naive patients (14 of 17, 82%). Gene expression-based signatures uncovered several pathways enriched in Abiraterone naive compared to resistant samples. Conclusions: Genomic sequencing and expression analysis can be accomplished in small bone and soft tissue mCRPC biopsies. Pathway-based gene expression analysis appears to be a promising strategy to identify adaptive processes and targeting opportunities in Abi resistant mCRPC. Citation Format: Jack F. Youngren, Adam Foye, George Thomas, Joshua M. Stuart, Ted Goldstein, Baertsch Robert, Adrian Bivol, Artem Sokolov, Charles J. Ryan, Nader Pourmand, Tomasz M. Beer, Christopher P. Evans, Christopher P. Evans, Primo Lara, Jr., Martin E. Gleave, Kim N. Chi, Robert E. Reiter, Matthew Rettig, Owen Witte, Eric J. Small. Identification of pathways associated with abiraterone resistance in metastatic castration resistant prostate cancer: Preliminary results from the SU2C/AACR West Coast Prostate Cancer Dream Team. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A12.