Analysis of BRCA2 Copy Number Loss and Genomic Instability in Circulating Tumor Cells from Patients with Metastatic Castration-resistant Prostate Cancer

• Published in: European urology 2023-02, Vol.83 (2), p.112-120
• Main Authors: Barnett, Ethan S., Schultz, Nikolaus, Stopsack, Konrad H., Lam, Ernest T., Arfe, Andrea, Lee, Jerry, Zhao, Jimmy L., Schonhoft, Joseph D., Carbone, Emily A., Keegan, Niamh M., Wibmer, Andreas, Wang, Yipeng, Solit, David B., Abida, Wassim, Wenstrup, Richard, Scher, Howard I.
• Format: Article
• Language: English
• Subjects: Biomarkers, Tumor - genetics; BRCA2; BRCA2 Protein - genetics; Circulating tumor cells; Copy number loss; DNA Copy Number Variations; Genomic Instability; Homologous recombination deficiency; Humans; Male; Neoplastic Cells, Circulating - pathology; Prostatic Neoplasms, Castration-Resistant - drug therapy; Single-cell sequencing
• ISSN: 0302-2838; 1873-7560
• DOI: 10.1016/j.eururo.2022.08.010

Whole-genome sequencing of circulating tumor cells (CTCs) can detect BRCA2 loss in a majority of tissue-confirmed cases and in additional patients without tissue-confirmed loss. CTCs with BRCA2 loss have increased chromosomal instability, supporting the accuracy of the calls. CTCs can potentially address shortcomings of tissue/cell-free DNA for BRCA2 loss detection. BRCA2 alterations predict for a response to poly-ADP-ribose polymerase inhibition in metastatic castration-resistant prostate cancer (mCRPC). However, detection is hindered by insufficient tumor tissue and low sensitivity of cell-free DNA for detecting copy number loss. To evaluate the BRCA2 loss detection using single-cell, shallow whole-genome sequencing (sWGS) of circulating tumor cells (CTCs) in patients with mCRPC. We analyzed CTC samples collected concurrently with tumor biopsies intended for clinical sequencing in patients with progressing mCRPC. Differences in proportions were evaluated using the chi-square test. Correlations between assays were analyzed in linear regression models. Associations between alterations and genomic instability were assessed on the single-cell level using mixed-effect negative binomial models. We identified 138 patients with concurrent CTC and biopsy samples. CTC sWGS generated copy number profiles in a similar proportion of patients to biopsy samples (83% vs 78%, p = 0.23), but was more effective than bone biopsies (79% vs 50%; p = 0.009). CTC sWGS detected BRCA2 loss in more patients than tissue at the ≥1 (42% vs 16%; p < 0.001) and ≥2 (27% vs 16%; p = 0.028) CTC thresholds. The overall prevalence of BRCA2 loss was not increased in CTCs using sample-level composite z scores (p = 0.4), but was significantly increased compared with a lower-than-expected prevalence in bone samples (21% vs 3%, p = 0.014). Positive/negative predictive values for CTC BRCA2 loss were 89%/96% using the ≥1 CTC threshold and 67%/92% using the composite z score. CTC BRCA2 loss was associated with higher genomic instability in univariate (1.4-fold large-scale transition difference, 95% confidence interval [CI]: 1.2–1.6; p < 0.001) and multivariable analysis (1.4-fold difference, 95% CI: 1.2–1.6; p < 0.001). Copy number profiles can reliably be generated using CTC sWGS, which detected a majority of tissue-confirmed BRCA2 loss and “CTC-only” losses. BRCA2 losses were supported by increases in genomic instability. Current testing strategies have limitations in their ability to detect BRCA