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Fettke H, Dai C, Kwan EM, Zheng T, Du P, Ng N, Bukczynska P, Docanto M, Kostos L, Foroughi S, Brown S, Graham LJK, Mahon K, Horvath LG, Jia S, Kohli M, Azad AA. BRCA-deficient metastatic prostate cancer has an adverse prognosis and distinct genomic phenotype. EBioMedicine 2023; 95:104738. [PMID: 37549632 PMCID: PMC10412463 DOI: 10.1016/j.ebiom.2023.104738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Genomic alterations in DNA damage response (DDR) genes are common in metastatic castration-resistant prostate cancer (mCRPC). Understanding how these genomic events impact prognosis and/or treatment response is vital for optimising clinical outcomes. METHODS Targeted sequencing was performed on 407 plasma samples from 375 men with mCRPC. Using the CLIA-certified PredicineCARE™ cell-free DNA (cfDNA) assay, pathogenic alterations in 152 key genes (including 27 DDR-related genes) were assessed, as was the presence and mechanisms of biallelic loss in BRCA2. FINDINGS At least one DDR alteration was present in 34.5% (129/375) of patients (including monoallelic alterations). The most frequently altered DDR genes were BRCA2 (19%), ATM (13%), FANCA (5%), CHEK2 (5%) and BRCA1 (3%). Patients with BRCA alterations, especially BRCA2, had significantly worse progression-free survival (PFS) (Hazard ratio (HR) 3.3 [95% CI 1.9-6.0]; Cox regression p < 0.001), overall survival (HR 2.2 [95% CI 1.1-4.5]; Cox regression p = 0.02) and PSA response rates to androgen receptor (AR) pathway inhibitors (32% vs 60%, chi-square p = 0.02). BRCA-deficient tumours were also enriched for alterations within multiple genes including in the AR and PI3K pathways. Zygosity of BRCA2 alterations had no discernible impact on clinical outcomes, with similarly poor PFS for monoallelic vs biallelic loss (median 3.9 months vs 3.4 months vs copy neutral 9.8 months). INTERPRETATION These data emphasise that the BRCA genes, in particular BRCA2, are key prognostic biomarkers in mCRPC. The clinical utility of BRCA2 as a marker of poor outcomes may, at least in cfDNA assays, be independent of the zygosity state detected. Enrichment of actionable genomic alterations in cfDNA from BRCA-deficient mCRPC may support rational co-targeting strategies in future clinical trials. FUNDING Several funding sources have supported this study. A full list is provided in the Acknowledgments. No funding was received from Predicine, Inc. during the conduct of the study.
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Affiliation(s)
- Heidi Fettke
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia.
| | - Chao Dai
- Predicine Inc., Hayward, CA, USA
| | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | | | - Pan Du
- Predicine Inc., Hayward, CA, USA
| | - Nicole Ng
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Maria Docanto
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Louise Kostos
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Siavash Foroughi
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Australia; Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Stephen Brown
- Medical Oncology, Ballarat Base Hospital, Ballarat, Australia
| | | | - Kate Mahon
- Medical Oncology, Chris O'Brien Lifehouse, Camperdown, Australia; University of Sydney, Sydney, Australia; Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Lisa G Horvath
- Medical Oncology, Chris O'Brien Lifehouse, Camperdown, Australia; University of Sydney, Sydney, Australia; Garvan Institute of Medical Research, Darlinghurst, Australia; Royal Prince Alfred Hospital, Camperdown, Australia
| | | | - Manish Kohli
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Arun A Azad
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia; Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
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Mizuno K, Sumiyoshi T, Okegawa T, Terada N, Ishitoya S, Miyazaki Y, Kojima T, Katayama H, Fujimoto N, Hatakeyama S, Shiota M, Yoshimura K, Matsui Y, Narita S, Matsumoto H, Kurahashi R, Kanno H, Ito K, Kimura H, Kamiyama Y, Sunada T, Goto T, Kobayashi T, Yamada H, Tsuchiya N, Kamba T, Matsuyama H, Habuchi T, Eto M, Ohyama C, Ito A, Nishiyama H, Okuno H, Kamoto T, Fujimoto A, Ogawa O, Akamatsu S. Clinical Impact of Detecting Low-Frequency Variants in Cell-Free DNA on Treatment of Castration-Resistant Prostate Cancer. Clin Cancer Res 2021; 27:6164-6173. [PMID: 34526361 DOI: 10.1158/1078-0432.ccr-21-2328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/09/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Although cell-free DNA (cfDNA) testing is expected to drive cancer precision medicine, little is known about the significance of detecting low-frequency variants in circulating cell-free tumor DNA (ctDNA) in castration-resistant prostate cancer (CRPC). We aimed to identify genomic profile including low-frequency variants in ctDNA from patients with CRPC and investigate the clinical utility of detecting variants with variant allele frequency (VAF) below 1%. EXPERIMENTAL DESIGN This prospective, multicenter cohort study enrolled patients with CRPC eligible for treatment with abiraterone or enzalutamide. We performed targeted sequencing of pretreatment cfDNA and paired leukocyte DNA with molecular barcodes, and ctDNA variants with a VAF ≥0.1% were detected using an in-house pipeline. We investigated progression-free survival (PFS) and overall survival (OS) after different ctDNA fraction cutoffs were applied. RESULTS One hundred patients were analyzed (median follow-up 10.7 months). We detected deleterious ATM, BRCA2, and TP53 variants even in samples with ctDNA fraction below 2%. When the ctDNA fraction cutoff value of 0.4% was applied, significant differences in PFS and OS were found between patients with and without defects in ATM or BRCA2 [HR, 2.52; 95% confidence interval (CI), 1.24-5.11; P = 0.0091] and TP53 (HR, 3.74; 95% CI, 1.60-8.71; P = 0.0014). However, these differences were no longer observed when the ctDNA fraction cutoff value of 2% was applied, and approximately 50% of the samples were classified as ctDNA unquantifiable. CONCLUSIONS Detecting low-frequency ctDNA variants with a VAF <1% is important to identify clinically informative genomic alterations in CRPC.
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Affiliation(s)
- Kei Mizuno
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Sumiyoshi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takatsugu Okegawa
- Department of Urology, Kyorin University School of Medicine, Mitaka, Japan
| | - Naoki Terada
- Department of Urology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Satoshi Ishitoya
- Department of Urology, Japanese Red Cross Otsu Hospital, Otsu, Japan
| | - Yu Miyazaki
- Department of Urology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Takahiro Kojima
- Department of Urology, Faculty of Medicine and Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Hiromichi Katayama
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naohiro Fujimoto
- Department of Urology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Shingo Hatakeyama
- Department of Advanced Blood Purification Therapy, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Masaki Shiota
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Yoshimura
- Department of Urology, Shizuoka General Hospital, Sizuoka, Japan
| | - Yoshiyuki Matsui
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Shintaro Narita
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroaki Matsumoto
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Ryoma Kurahashi
- Department of Urology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hidenori Kanno
- Department of Urology, Yamagata University School of Medicine, Yamagata, Japan
| | - Katsuhiro Ito
- Department of Urology, Ijinkai Takeda General Hospital, Kyoto, Japan
| | - Hiroko Kimura
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yuki Kamiyama
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takuro Sunada
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Goto
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Kobayashi
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hitoshi Yamada
- Department of Urology, Ijinkai Takeda General Hospital, Kyoto, Japan
| | - Norihiko Tsuchiya
- Department of Urology, Yamagata University School of Medicine, Yamagata, Japan
| | - Tomomi Kamba
- Department of Urology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideyasu Matsuyama
- Department of Urology, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Tomonori Habuchi
- Department of Urology, Akita University Graduate School of Medicine, Akita, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Ohyama
- Department of Urology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Akihiro Ito
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroyuki Nishiyama
- Department of Urology, Faculty of Medicine and Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Okuno
- Department of Urology, National Hospital Organization Kyoto Medical Center, Kyoto, Japan
| | - Toshiyuki Kamoto
- Department of Urology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Osamu Ogawa
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shusuke Akamatsu
- Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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