51
|
Tan W, Zheng T, Wang A, Roacho J, Thao S, Du P, Jia S, Yu J, King BL, Kohli M. Dynamic changes in gene alterations during chemotherapy in metastatic castrate resistant prostate cancer. Sci Rep 2022; 12:4672. [PMID: 35304525 PMCID: PMC8933498 DOI: 10.1038/s41598-022-08520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
Docetaxel chemotherapy is a standard treatment option for metastatic castrate resistant prostate cancer (mCRPC) patients. To date, the genomic perturbations underlying the emergence of resistance in mCRPC patients during chemotherapy treatment have not been fully characterized. Previous studies have established that AR, TP53, RB1 and PTEN gene alterations are frequent at this stage of progression and that TP53, RB1 and PTEN, but not AR alterations are associated with poor outcome. However, the clonal dynamics of these key driver cancer genes during chemotherapy in mCRPC patients have not been described. Toward this goal, we performed a retrospective analysis of serially profiled cell-free DNA (cfDNA) alterations in blood samples collected from mCRPC patients before and after starting chemotherapy who were followed for response and clinical outcomes. While AR alterations and measures of mutational load were significantly reduced in patients with stable or decreased PSA levels after 3 cycles of chemotherapy, reductions in RB1, TP53 and PTEN alterations were relatively modest, which may represent the persistence of a clonal signature associated with the emergence of treatment-induced lineage plasticity (TILP) underlying resistance. The ability to monitor these driver gene clonal dynamics during chemotherapy may have utility in the clinical setting.
Collapse
Affiliation(s)
- Winston Tan
- Department of Medicine, Mayo Clinic, Jacksonville, USA
| | - Tiantian Zheng
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Amy Wang
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Joanna Roacho
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Seng Thao
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Pan Du
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Shidong Jia
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Jianjun Yu
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA
| | - Bonnie L King
- Predicine, Inc., 3555 Arden Road, Hayward, CA, 94545, USA.
| | - Manish Kohli
- Division of Oncology, Department of Medicine, Jack R. and Hazel M. Robertson Presidential Endowed Chair, Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr. Rm. 4263, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
52
|
Van der Eecken K, Vanwelkenhuyzen J, Deek MP, Tran PT, Warner E, Wyatt AW, Kwan EM, Verbeke S, Van Dorpe J, Fonteyne V, Lumen N, De Laere B, Ost P. Tissue- and Blood-derived Genomic Biomarkers for Metastatic Hormone-sensitive Prostate Cancer: A Systematic Review. Eur Urol Oncol 2021; 4:914-923. [PMID: 34801437 DOI: 10.1016/j.euo.2021.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022]
Abstract
CONTEXT Multiple studies have reported on the genomic characteristics of metastatic hormone-sensitive prostate cancer (mHSPC). The impact of these findings on prognostication, treatment selection, and clinical trial design remains unclear. OBJECTIVE To summarise genomic alteration prevalences in liquid and/or tissue biopsies, infer their clinical implications, and compare genomic alteration frequencies across different disease states and clinical phenotypes. EVIDENCE ACQUISITION The PubMed and Web of Knowledge databases were systematically searched up to January 2021. Quality assessment was performed using the Joanna Briggs Institute Critical Appraisal tools. EVIDENCE SYNTHESIS In total, 11 studies encompassing 1682 mHSPC patients were included. High-volume disease was associated with more frequent alterations in TP53, DNA damage repair, and Wnt pathways. Tumours from patients with de novo mHSPC were enriched for alterations in TP53 and CDK12 compared with recurrent disease. Alterations in AR, TP53, cell cycle signalling, and MYC were associated with a poorer clinical outcome. A comparative analysis of gene alteration frequencies across disease states revealed a relative increase from localised to castration-resistant tumours, with noteworthy enrichment of CTNNB1 alterations in mHSPC (5%), which warrants further investigation. This study was limited by variability in methodology and definitions used among the eligible studies, including differences in sequencing methods, analytes (being either tissue or liquid), alteration calling thresholds, and target patient populations with a relative under-representation of recurrent metastatic disease. CONCLUSIONS Several genomic alterations are associated with differential prognosis and clinical phenotypes in mHSPC. We urge that emerging data on these potential predictive biomarkers must be validated in biomarker-driven randomised controlled trials before any clinical implementation. Alignment of the assay methodology and reporting will be critical for ensuring rapid scalability. PATIENT SUMMARY We reviewed current data on genomic alterations of metastatic hormone-sensitive prostate cancer, and summarised key genomic subtypes that associate with specific clinical phenotypes and treatment outcomes.
Collapse
Affiliation(s)
- Kim Van der Eecken
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium.
| | - Jan Vanwelkenhuyzen
- Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium; Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Matthew P Deek
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Phuoc T Tran
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia; Department of Medical Oncology, Monash Health, Melbourne, Australia
| | - Sofie Verbeke
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute (CRIG), Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute (CRIG), Ghent, Belgium
| | - Valérie Fonteyne
- Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium; Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium; Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Bram De Laere
- Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium; Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Piet Ost
- Cancer Research Institute (CRIG), Ghent, Belgium; Department of Human Structure and Repair, Ghent University, Belgium; Department of Radiation Oncology, Iridiumnetwerk, Antwerp, Belgium
| |
Collapse
|
53
|
Lieb V, Abdulrahman A, Weigelt K, Hauch S, Gombert M, Guzman J, Bellut L, Goebell PJ, Stöhr R, Hartmann A, Wullich B, Taubert H, Wach S. Cell-Free DNA Variant Sequencing Using Plasma and AR-V7 Testing of Circulating Tumor Cells in Prostate Cancer Patients. Cells 2021; 10:cells10113223. [PMID: 34831445 PMCID: PMC8620951 DOI: 10.3390/cells10113223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Prostate cancer (PCa) is the second most common malignant cancer and is a major cause of morbidity and mortality among men worldwide. There is still an urgent need for biomarkers applicable for diagnosis, prognosis, therapy prediction, or therapy monitoring in PCa. Liquid biopsies, including cell-free DNA (cfDNA) and circulating tumor cells (CTCs), are a valuable source for studying such biomarkers and are minimally invasive. In our study, we investigated the cfDNA of 34 progressive PCa patients, via targeted sequencing, for sequence variants and for the occurrence of CTCs, with a focus on androgen receptor splice variant 7 (AR-V7)-positive CTCs. The cfDNA content was associated with overall survival (OS; p = 0.014), disease-specific survival (DSS; p = 0.004), and time to treatment change (TTC; p = 0.001). Moreover, when considering all sequence variants grouped by their functional impact and allele frequency, a significant association with TTC (p = 0.017) was observed. When investigating only pathogenic or likely pathogenic gene variants, variants of the BRCA1 gene (p = 0.029) and the AR ligand-binding domain (p = 0.050) were associated with a shorter TTC. Likewise, the presence of CTCs was associated with a shorter TTC (p = 0.031). The presence of AR-V7-positive CTCs was associated with TTC (p < 0.001) in Kaplan–Meier analysis. Interestingly, all patients with AR-V7-positive CTCs also carried TP53 point mutations. Altogether, analysis of cfDNA and CTCs can provide complementary information that may support temporal and targeted treatment decisions and may elucidate the optimal choice within the variety of therapy options for advanced PCa patients.
Collapse
Affiliation(s)
- Verena Lieb
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Amer Abdulrahman
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Katrin Weigelt
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | | | | | - Juan Guzman
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Laura Bellut
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Peter J. Goebell
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Robert Stöhr
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Institute of Pathology, University Hospital Erlangen, FAU Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Bernd Wullich
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| | - Helge Taubert
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
- Correspondence: ; Tel.: +49-93138523373
| | - Sven Wach
- Department of Urology and Pediatric Urology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (V.L.); (A.A.); (K.W.); (J.G.); (L.B.); (P.J.G.); (B.W.); (S.W.)
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), 91054 Erlangen, Germany; (R.S.); (A.H.)
| |
Collapse
|
54
|
Dong X, Zheng T, Zhang M, Dai C, Wang L, Wang L, Zhang R, Long Y, Wen D, Xie F, Zhang Y, Huang Y, Dong J, Liu H, Du P, King BL, Tan W, Jia S, Lu CX, Kohli M, Wang H, Yu J. Circulating Cell-Free DNA-Based Detection of Tumor Suppressor Gene Copy Number Loss and Its Clinical Implication in Metastatic Prostate Cancer. Front Oncol 2021; 11:720727. [PMID: 34504797 PMCID: PMC8422845 DOI: 10.3389/fonc.2021.720727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Current liquid biopsy assays lack sufficient sensitivity to detect copy number loss, which limits the interrogation of critical tumor suppressor gene deletions during cancer progression and treatment. Here we describe a liquid biopsy assay with improved sensitivity for detection of copy number loss in blood samples with low levels of circulating tumor DNA, and demonstrate its utility by profiling PTEN, RB1, and TP53 genetic loss in metastatic prostate cancer patients.
Collapse
Affiliation(s)
| | | | - Minhua Zhang
- Department of Translational Medicine, Laekna Therapeutics Shanghai Co., Ltd., Shanghai, China
| | - Chao Dai
- Predicine Inc., Hayward, CA, United States
| | - Lili Wang
- Department of Oncology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Lei Wang
- Department of Oncology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Ruipeng Zhang
- Department of Translational Medicine, Laekna Therapeutics Shanghai Co., Ltd., Shanghai, China
| | - Yuan Long
- Department of New Assay Development, Shanghai Lide Biotech Co., Ltd., Shanghai, China
| | - Danyi Wen
- Shanghai Lide Biotech Co., Ltd., Shanghai, China
| | - Feng Xie
- Huidu Shanghai Medical Sciences Ltd., Shanghai, China
| | - Yue Zhang
- Huidu Shanghai Medical Sciences Ltd., Shanghai, China
| | - Yong Huang
- Huidu Shanghai Medical Sciences Ltd., Shanghai, China
| | - Jianguo Dong
- Huidu Shanghai Medical Sciences Ltd., Shanghai, China
| | - Huan Liu
- Department of Biology, Shanghai Lide Biotech Co., Ltd., Shanghai, China
| | - Pan Du
- Predicine Inc., Hayward, CA, United States
| | | | - Winston Tan
- Division of Medical Oncology, Department of Medicine, Mayo Clinic, Jacksonville, FL, United States
| | | | - Chris X Lu
- Laekna Therapeutics Shanghai Co., Ltd., Shanghai, China
| | - Manish Kohli
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Haitao Wang
- Department of Oncology, Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jianjun Yu
- Predicine Inc., Hayward, CA, United States
| |
Collapse
|
55
|
Kim CJ, Dong L, Amend SR, Cho YK, Pienta KJ. The role of liquid biopsies in prostate cancer management. LAB ON A CHIP 2021; 21:3263-3288. [PMID: 34346466 DOI: 10.1039/d1lc00485a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Liquid biopsy has emerged as a complement to invasive tissue biopsy to guide cancer diagnosis and treatment. The common liquid biopsy biomarkers are circulating tumor cells (CTCs), extracellular vesicles (EVs), and circulating tumor DNA (ctDNA). Each biomarker provides specific information based on its intrinsic characteristics. Prostate cancer is the second most common cancer in males worldwide. In men with low-grade localized prostate cancer, the disease can often be managed by active surveillance. For men who require treatment, the 5-year survival rate of localized prostate cancer is the highest among all cancer types, but the metastatic disease remains incurable. Metastatic prostate cancer invariably progresses to involve multiple bone sites and develops into a castration-resistant disease that leads to cancer death. The need to appropriately diagnose and guide the serial treatment of men with prostate cancer has led to the implementation of many studies to apply liquid biopsies to prostate cancer management. This review describes recent advancements in isolation and detection technology and the strength and weaknesses of the three circulating biomarkers. The clinical studies based on liquid biopsy results are summarized to depict the future perspective in the role of liquid biopsy on prostate cancer management.
Collapse
Affiliation(s)
- Chi-Ju Kim
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | | | | | | | | |
Collapse
|
56
|
Avelumab Combined with Stereotactic Ablative Body Radiotherapy in Metastatic Castration-resistant Prostate Cancer: The Phase 2 ICE-PAC Clinical Trial. Eur Urol 2021; 81:253-262. [PMID: 34493414 DOI: 10.1016/j.eururo.2021.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Immune checkpoint inhibitor monotherapy in metastatic castration-resistant prostate cancer (mCRPC) has produced modest results. High-dose radiotherapy may be synergistic with checkpoint inhibitors. OBJECTIVE To evaluate the efficacy and safety of the PD-L1 inhibitor avelumab with stereotactic ablative body radiotherapy (SABR) in mCRPC. DESIGN, SETTING, AND PARTICIPANTS From November 2017 to July 2019, this prospective phase 2 study enrolled 31 men with progressive mCRPC after at least one prior androgen receptor-directed therapy. Median follow-up was 18.0 mo. INTERVENTION Avelumab 10 mg/kg intravenously every 2 wk for 24 wk (12 cycles). A single fraction of SABR (20 Gy) was administered to one or two disease sites within 5 d before the first and second avelumab treatments. OUTCOMES MEASUREMENTS AND STATISTICAL ANALYSIS The primary endpoint was the disease control rate (DCR), defined as a confirmed complete or partial response of any duration, or stable disease/non-complete response/non-progressive disease for ≥6 mo (Prostate Cancer Clinical Trials Working Group 3-modified Response Evaluation Criteria in Solid Tumours version 1.1). Secondary endpoints were the objective response rate (ORR), radiographic progression-free survival (rPFS), overall survival (OS), and safety. DCR and ORR were calculated using the Clopper-Pearson exact binomial method. RESULTS AND LIMITATIONS Thirty-one evaluable men were enrolled (median age 71 yr, 71% with ≥2 prior mCRPC therapy lines, 81% with >5 total metastases). The DCR was 48% (15/31; 95% confidence interval [CI] 30-67%) and ORR was 31% (five of 16; 95% CI 11-59%). The ORR in nonirradiated lesions was 33% (four of 12; 95% CI 10-65%). Median rPFS was 8.4 mo (95% CI 4.5-not reached [NR]) and median OS was 14.1 mo (95% CI 8.9-NR). Grade 3-4 treatment-related adverse events occurred in six patients (16%), with three (10%) requiring high-dose corticosteroid therapy. Plasma androgen receptor alterations were associated with lower DCR (22% vs 71%, p = 0.13; Fisher's exact test). Limitations include the small sample size and the absence of a control arm. CONCLUSIONS Avelumab with SABR demonstrated encouraging activity and acceptable toxicity in treatment-refractory mCRPC. This combination warrants further investigation. PATIENT SUMMARY In this study of men with advanced and heavily pretreated prostate cancer, combining stereotactic radiotherapy with avelumab immunotherapy was safe and resulted in nearly half of patients experiencing cancer control for 6 months or longer. Stereotactic radiotherapy may potentially improve the effectiveness of immunotherapy in prostate cancer.
Collapse
|
57
|
Lin HM, Huynh K, Kohli M, Tan W, Azad AA, Yeung N, Mahon KL, Mak B, Sutherland PD, Shepherd A, Mellett N, Docanto M, Giles C, Centenera MM, Butler LM, Meikle PJ, Horvath LG. Aberrations in circulating ceramide levels are associated with poor clinical outcomes across localised and metastatic prostate cancer. Prostate Cancer Prostatic Dis 2021; 24:860-870. [PMID: 33746214 PMCID: PMC8387438 DOI: 10.1038/s41391-021-00338-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/10/2021] [Accepted: 01/28/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Dysregulated lipid metabolism is associated with more aggressive pathology and poorer prognosis in prostate cancer (PC). The primary aim of the study is to assess the relationship between the plasma lipidome and clinical outcomes in localised and metastatic PC. The secondary aim is to validate a prognostic circulating 3-lipid signature specific to metastatic castration-resistant PC (mCRPC). PATIENTS AND METHODS Comprehensive lipidomic analysis was performed on pre-treatment plasma samples from men with localised PC (N = 389), metastatic hormone-sensitive PC (mHSPC)(N = 44), or mCRPC (validation cohort, N = 137). Clinical outcomes from our previously published mCRPC cohort (N = 159) that was used to derive the prognostic circulating 3-lipid signature, were updated. Associations between circulating lipids and clinical outcomes were examined by Cox regression and latent class analysis. RESULTS Circulating lipid profiles featuring elevated levels of ceramide species were associated with metastatic relapse in localised PC (HR 5.80, 95% CI 3.04-11.1, P = 1 × 10-6), earlier testosterone suppression failure in mHSPC (HR 3.70, 95% CI 1.37-10.0, P = 0.01), and shorter overall survival in mCRPC (HR 2.54, 95% CI 1.73-3.72, P = 1 × 10-6). The prognostic significance of circulating lipid profiles in localised PC was independent of standard clinicopathological and metabolic factors (P < 0.0002). The 3-lipid signature was verified in the mCRPC validation cohort (HR 2.39, 95% CI 1.63-3.51, P = 1 × 10-5). CONCLUSIONS Elevated circulating ceramide species are associated with poorer clinical outcomes across the natural history of PC. These clinically actionable lipid profiles could be therapeutically targeted in prospective clinical trials to potentially improve PC outcomes.
Collapse
Affiliation(s)
- Hui-Ming Lin
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia,St Vincent’s Clinical School, UNSW Sydney, New South Wales, Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Manish Kohli
- Huntsman Cancer Institute, Division of Oncology, Department of Medicine, 2000 Circle of Hope Drive, Salt Lake City, UT 84012, United States of America
| | - Winston Tan
- Mayo Clinic Florida, Jacksonville, Florida, United States of America
| | - Arun A. Azad
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia,Monash University, Victoria, Australia
| | - Nicole Yeung
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia
| | - Kate L. Mahon
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia,Monash University, Victoria, Australia,Chris O’ Brien Lifehouse, Camperdown, New South Wales , Australia,University of Sydney, Sydney, New South Wales, Australia
| | - Blossom Mak
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia,Chris O’ Brien Lifehouse, Camperdown, New South Wales , Australia,University of Sydney, Sydney, New South Wales, Australia
| | | | - Andrew Shepherd
- Royal Adelaide Hospital, Adelaide, South Australia, Australia,Adelaide Medical School and Freemason’s Foundation Centre for Men’s Health, University of Adelaide, Adelaide, South Australia, Australia
| | - Natalie Mellett
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Margaret M. Centenera
- Adelaide Medical School and Freemason’s Foundation Centre for Men’s Health, University of Adelaide, Adelaide, South Australia, Australia,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Lisa M. Butler
- Adelaide Medical School and Freemason’s Foundation Centre for Men’s Health, University of Adelaide, Adelaide, South Australia, Australia,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Peter J. Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Lisa G. Horvath
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia,St Vincent’s Clinical School, UNSW Sydney, New South Wales, Australia,Chris O’ Brien Lifehouse, Camperdown, New South Wales , Australia,University of Sydney, Sydney, New South Wales, Australia,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| |
Collapse
|
58
|
Fettke H, Kwan EM, Bukczynska P, Steen JA, Docanto M, Ng N, Parente P, Mant A, Foroughi S, Pezaro C, Hauser C, Nguyen-Dumont T, Southey MC, Azad AA. Independent prognostic impact of plasma NCOA2 alterations in metastatic castration-resistant prostate cancer. Prostate 2021; 81:992-1001. [PMID: 34254334 DOI: 10.1002/pros.24194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/21/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND The androgen receptor (AR) pathway-associated gene nuclear receptor coactivator 2 (NCOA2) has an established oncogenic role in early prostate cancer and likewise is a driver of metastatic disease and castration-resistant prostate cancer. However, its significance as a biomarker in metastatic castration-resistant prostate cancer (mCRPC), both alone and in conjunction with co-occurring AR alterations using a liquid biopsy approach has not been investigated. METHODS Ninety-one patients were included in this study, (n = 68 receiving an androgen receptor pathway inhibitor and n = 23 receiving taxane chemotherapy). Up to 30 ml of peripheral blood was collected before commencing treatment from each patient. Plasma cell-free DNA, along with a matched germline sample, underwent targeted next-generation sequencing using a validated, highly sensitive in-house prostate cancer panel. Variants in AR and NCOA2 were identified and correlated with clinical outcomes. RESULTS Plasma AR and NCOA2 aberrations were identified in 35% and 13% of the cohort, respectively, whilst 8% had concurrent AR and NCOA2 alterations. NCOA2 copy number gain and any NCOA2 aberration predicted for lower prostate-specific antigen (PSA) response rates. Likewise, median overall survival was shorter for NCOA2 gain (10.1 vs. 18.3 months; p = .004), remaining significant after adjusting for covariates including circulating tumor DNA fraction and tumor suppressor gene alterations. Importantly, dual AR and NCOA2 aberrations were also associated with inferior outcomes, including no PSA responses in patients treated with AR pathway inhibitors (0% vs. 64%; p = .02). CONCLUSIONS These data highlight the importance of identifying multiple markers of AR pathway modulation in mCRPC and represent the first instance of the assessment of plasma NCOA2 status as a prognostic biomarker for standard-of-care therapies. Further assessment is warranted to determine if NCOA2 aberrations are a marker of primary resistance to AR pathway inhibitors.
Collapse
Affiliation(s)
- Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Edmond M Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Monash Health, Melbourne, Australia
| | | | - Jason A Steen
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
| | - Maria Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | - Nicole Ng
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Phillip Parente
- Medical Oncology Unit, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Andrew Mant
- Medical Oncology Unit, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Siavash Foroughi
- Personalised Oncology Division, The Water and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Carmel Pezaro
- Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, England
| | - Christine Hauser
- Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Melissa C Southey
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences, Monash Health, Melbourne, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
| | - Arun A Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| |
Collapse
|
59
|
Shaya J, Nonato T, Cabal A, Randall JM, Millard F, Stewart T, McKay RR. Analysis of the Prognostic Significance of Circulating Tumor DNA in Metastatic Castrate Resistant Prostate Cancer. Clin Genitourin Cancer 2021; 19:564.e1-564.e10. [PMID: 34452870 DOI: 10.1016/j.clgc.2021.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 07/18/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND There has been considerable interest in ctDNA next generation sequencing platforms to assess genomic alterations in mCRPC given its accessibility and identification of temporal genomic data. PATIENTSAND METHODS In this retrospective analysis, we analyzed 63 patients who underwent ctDNA genomic profiling during their mCRPC disease course using a CLIA-certified commercial assay. The primary objective was to assess the feasibility of commercial ctDNA analysis in a real world mCRPC cohort. Key secondary objectives included assessment of the landscape of pathogenic ctDNA alterations and the prognostic significance of ctDNA detection on overall survival (OS). RESULTS Among the cohort, at the time of ctDNA collection, median age was 70 years, and 47.6% (N = 30/63) had bone-only metastases. ctDNA was detected in the majority of patients with at least 1 pathogenic alteration detected in 90.5% (N = 57/63) of individuals. The most common alterations detected were in AR, TP53, and PIK3CA. Actionable alterations with FDA-approved therapies were found in 15.8% (N = 10) of the cohort. The presence of ≤ 1 versus > 1 alteration on ctDNA analysis was strongly associated with inferior OS with a median OS of 26.1 versus 8.8 months, respectively (HR = 7.0, 95% CI, 2.2-23.1, P < .001). In multivariate analysis, the number of detected alterations remained a significant predictor for OS. Lastly, there was weak correlation between Prostate-Specific Antigen (PSA), and ctDNA characteristics. CONCLUSION ctDNA is a viable next generation sequencing (NGS) platform in mCRPC and can be utilized to identify actionable alterations. The presence and extent of ctDNA alterations appear to be prognostic of OS in mCRPC.
Collapse
Affiliation(s)
- Justin Shaya
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - Taylor Nonato
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - Angelo Cabal
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - James Michael Randall
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - Frederick Millard
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - Tyler Stewart
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA
| | - Rana R McKay
- Division of Hematology-Oncology, Department of Medicine, University of California San Diego, San Diego, CA.
| |
Collapse
|
60
|
Smith MR, Thomas S, Gormley M, Chowdhury S, Olmos D, Oudard S, Feng FY, Rajpurohit Y, Urtishak K, Ricci DS, Rooney B, Lopez-Gitlitz A, Yu M, Wyatt AW, Li M, Attard G, Small EJ. Blood Biomarker Landscape in Patients with High-risk Nonmetastatic Castration-Resistant Prostate Cancer Treated with Apalutamide and Androgen-Deprivation Therapy as They Progress to Metastatic Disease. Clin Cancer Res 2021; 27:4539-4548. [PMID: 34112710 DOI: 10.1158/1078-0432.ccr-21-0358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE In the placebo-controlled SPARTAN study, apalutamide added to androgen-deprivation therapy (ADT) improved metastasis-free survival, second progression-free survival (PFS2), and overall survival (OS) in patients with nonmetastatic castration-resistant prostate cancer (nmCRPC). Mechanisms of resistance to apalutamide in nmCRPC require evaluation. PATIENTS AND METHODS In a subset of patients from SPARTAN, aberrations were assessed at baseline and end of study treatment (EOST) using targeted next-generation sequencing or qRT-PCR. Circulating-tumor DNA (ctDNA) levels were assessed qualitatively. Select aberrations in androgen receptor (AR) and other common PC-driving genes were detected and summarized by the treatment group; genomic aberrations were summarized in ctDNA-positive samples. Association between detection of aberrations in all patients and outcomes was assessed using Cox proportional-hazards models and multivariate analysis. RESULTS In 247 patients, the overall prevalence of ctDNA, AR aberrations, and TP53 inactivation increased from baseline (40.6%, 13.6%, and 22.2%) to EOST (57.1%, 25.4%, and 35.0%) and was comparable between treatment groups at EOST. In patients who received subsequent androgen signaling inhibition after study treatment, detectable biomarkers at EOST were significantly associated with poor outcomes: ctDNA with PFS2 or OS (HR, 2.01 or 2.17, respectively; P < 0.0001 for both), any AR aberration with PFS2 (1.74; P = 0.024), and TP53 or BRCA2 inactivation with OS (2.06; P = 0.003; or 3.1; P < 0.0001). CONCLUSIONS Apalutamide plus ADT did not increase detectable AR/non-AR aberrations over ADT alone. Detectable ctDNA, AR aberrations, and TP53/BRCA2 inactivation at EOST were associated with poor outcomes in patients treated with first subsequent androgen signaling inhibitor.
Collapse
Affiliation(s)
- Matthew R Smith
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
| | - Shibu Thomas
- Janssen Research & Development, Spring House, Pennsylvania
| | | | - Simon Chowdhury
- Guy's, King's and St. Thomas' Hospitals, Great Maze Pond, London, United Kingdom
| | - David Olmos
- Spanish National Cancer Research Center (CNIO), and Hospital Universitario Virgen de la Victoria y Regional de Málaga, Madrid, Spain
| | - Stéphane Oudard
- Oncology Department, Georges Pompidou Hospital, University of Paris, Paris, France
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | | | - Karen Urtishak
- Janssen Research & Development, Spring House, Pennsylvania
| | | | - Brendan Rooney
- Janssen Research & Development, High Wycombe, United Kingdom
| | | | - Margaret Yu
- Janssen Research & Development, Los Angeles, California
| | - Alexander W Wyatt
- The University of British Columbia, Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | - Mark Li
- Resolution Bioscience, Kirkland, Washington
| | - Gerhardt Attard
- University College London Cancer Institute, London, United Kingdom
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| |
Collapse
|
61
|
Ladurner M, Wieser M, Eigentler A, Seewald M, Dobler G, Neuwirt H, Kafka M, Heidegger I, Horninger W, Bektic J, Klocker H, Obrist P, Eder IE. Validation of Cell-Free RNA and Circulating Tumor Cells for Molecular Marker Analysis in Metastatic Prostate Cancer. Biomedicines 2021; 9:biomedicines9081004. [PMID: 34440208 PMCID: PMC8391593 DOI: 10.3390/biomedicines9081004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Since tissue material is often lacking in metastatic prostate cancer (mPCa), there is increasing interest in using liquid biopsies for treatment decision and monitoring therapy responses. The purpose of this study was to validate the usefulness of circulating tumor cells (CTCs) and plasma-derived cell-free (cf) RNA as starting material for gene expression analysis through qPCR. CTCs were identified upon prostate-specific membrane antigen and/or cytokeratin positivity after enrichment with ScreenCell (Westford, Massachusetts, USA) filters or the microfluidic ParsortixTM (Guildford, Surrey, United Kingdom) system. Overall, 50% (28/56) of the patients had ≥5 CTCs/7.5 mL of blood. However, CTC count did not correlate with Gleason score, serum PSA, or gene expression. Notably, we observed high expression of CD45 in CTC samples after enrichment, which could be successfully eliminated through picking of single cells. Gene expression in picked CTCs was, however, rather low. In cfRNA from plasma, on the other hand, gene expression levels were higher compared to those found in CTCs. Moreover, we found that PSA was significantly increased in plasma-derived cfRNA of mPCa patients compared to healthy controls. High PSA expression was also associated with poor overall survival, indicating that using cfRNA from plasma could be used as a valuable tool for molecular expression analysis.
Collapse
Affiliation(s)
- Michael Ladurner
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Manuel Wieser
- Tyrolpath Obrist Brunhuber GmbH, 6511 Zams, Austria; (M.W.); (M.S.); (P.O.)
| | - Andrea Eigentler
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Martin Seewald
- Tyrolpath Obrist Brunhuber GmbH, 6511 Zams, Austria; (M.W.); (M.S.); (P.O.)
| | - Gabriele Dobler
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Hannes Neuwirt
- Department of Internal Medicine IV-Nephrology and Hypertension, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Mona Kafka
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Isabel Heidegger
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Wolfgang Horninger
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Jasmin Bektic
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Helmut Klocker
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
| | - Peter Obrist
- Tyrolpath Obrist Brunhuber GmbH, 6511 Zams, Austria; (M.W.); (M.S.); (P.O.)
| | - Iris E. Eder
- Department of Urology, Medical University Innsbruck, 6020 Innsbruck, Austria; (M.L.); (A.E.); (G.D.); (M.K.); (I.H.); (W.H.); (J.B.); (H.K.)
- Correspondence: ; Tel.: +43-512-504-24819; Fax: +43-512-504-24817
| |
Collapse
|
62
|
Brady-Nicholls R, Zhang J, Zhang T, Wang AZ, Butler R, Gatenby RA, Enderling H. Predicting patient-specific response to adaptive therapy in metastatic castration-resistant prostate cancer using prostate-specific antigen dynamics. Neoplasia 2021; 23:851-858. [PMID: 34298234 PMCID: PMC8322456 DOI: 10.1016/j.neo.2021.06.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/27/2022] Open
Abstract
Abiraterone acetate (AA) has been proven effective for metastatic castration-resistant prostate cancer (mCRPC), and it has been proposed that adaptive AA may reduce toxicity and prolong time to progression, when compared to continuous AA. We developed a simple quantitative model of prostate-specific antigen (PSA) dynamics to evaluate prostate cancer (PCa) stem cell enrichment as a plausible driver of AA treatment resistance. The model incorporated PCa stem cells, non-stem PCa cells and PSA dynamics during adaptive therapy. A leave-one-out analysis was used to calibrate and validate the model against longitudinal PSA data from 16 mCRPC patients receiving adaptive AA in a pilot clinical study. Early PSA treatment response dynamics were used to predict patient response to subsequent treatment. We extended the model to incorporate metastatic burden and also investigated the survival benefit of adding concurrent chemotherapy for patients predicted to become resistant. Model simulations demonstrated PCa stem cell self-renewal as a plausible driver of resistance to adaptive therapy. Evolutionary dynamics from individual treatment cycles combined with metastatic burden measurements predicted patient response with 81% accuracy (specificity=92%, sensitivity=50%). In those patients predicted to progress, simulations of the addition of concurrent chemotherapy suggest a benefit between 1% and 11% reduction in probability of progression when compared to adaptive AA alone. This study developed the first mCRPC patient-specific mathematical model to use early PSA treatment response dynamics to predict subsequent responses to adaptive AA, demonstrating the putative value of integrating mathematical modeling into clinical decision making.
Collapse
Affiliation(s)
- Renee Brady-Nicholls
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
| | - Jingsong Zhang
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Tian Zhang
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, 20 Duke Medicine Cir, Durham, NC, USA
| | - Andrew Z Wang
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert Butler
- Physical Sciences Oncology Center, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, , USA
| | - Robert A Gatenby
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Heiko Enderling
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA; Department of Radiation Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| |
Collapse
|
63
|
Tukachinsky H, Madison RW, Chung JH, Gjoerup OV, Severson EA, Dennis L, Fendler BJ, Morley S, Zhong L, Graf RP, Ross JS, Alexander BM, Abida W, Chowdhury S, Ryan CJ, Fizazi K, Golsorkhi T, Watkins SP, Simmons A, Loehr A, Venstrom JM, Oxnard GR. Genomic Analysis of Circulating Tumor DNA in 3,334 Patients with Advanced Prostate Cancer Identifies Targetable BRCA Alterations and AR Resistance Mechanisms. Clin Cancer Res 2021; 27:3094-3105. [PMID: 33558422 PMCID: PMC9295199 DOI: 10.1158/1078-0432.ccr-20-4805] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Comprehensive genomic profiling (CGP) is of increasing value for patients with metastatic castration-resistant prostate cancer (mCRPC). mCRPC tends to metastasize to bone, making tissue biopsies challenging to obtain. We hypothesized CGP of cell-free circulating tumor DNA (ctDNA) could offer a minimally invasive alternative to detect targetable genomic alterations (GA) that inform clinical care. EXPERIMENTAL DESIGN Using plasma from 3,334 patients with mCRPC (including 1,674 screening samples from TRITON2/3), we evaluated the landscape of GAs detected in ctDNA and assessed concordance with tissue-based CGP. RESULTS A total of 3,129 patients (94%) had detectable ctDNA with a median ctDNA fraction of 7.5%; BRCA1/2 was mutated in 295 (8.8%). In concordance analysis, 72 of 837 patients had BRCA1/2 mutations detected in tissue, 67 (93%) of which were also identified using ctDNA, including 100% of predicted germline variants. ctDNA harbored some BRCA1/2 alterations not identified by tissue testing, and ctDNA was enriched in therapy resistance alterations, as well as possible clonal hematopoiesis mutations (e.g., in ATM and CHEK2). Potential androgen receptor resistance alterations were detected in 940 of 2,213 patients (42%), including amplifications, polyclonal and compound mutations, rearrangements, and novel deletions in exon 8. CONCLUSIONS Genomic analysis of ctDNA from patients with mCRPC recapitulates the genomic landscape detected in tissue biopsies, with a high level of agreement in detection of BRCA1/2 mutations, but more acquired resistance alterations detected in ctDNA. CGP of ctDNA is a compelling clinical complement to tissue CGP, with reflex to tissue CGP if negative for actionable variants.See related commentary by Hawkey and Armstrong, p. 2961.
Collapse
Affiliation(s)
| | | | - Jon H Chung
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Lucas Dennis
- Foundation Medicine Inc., Cambridge, Massachusetts
| | | | | | - Lei Zhong
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Ryon P Graf
- Foundation Medicine Inc., Cambridge, Massachusetts
| | - Jeffrey S Ross
- Foundation Medicine Inc., Cambridge, Massachusetts
- Upstate Medical University, Syracuse, New York
| | | | - Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Simon Chowdhury
- Guy's, King's, and St. Thomas' Hospital, London, England, United Kingdom
| | - Charles J Ryan
- University of Minnesota Medical School, Minneapolis, Minnesota
| | | | | | | | | | | | | | | |
Collapse
|
64
|
Underhill HR. Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology? Mol Diagn Ther 2021; 25:389-408. [PMID: 34018157 PMCID: PMC8249304 DOI: 10.1007/s40291-021-00534-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy’s molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.
Collapse
Affiliation(s)
- Hunter R Underhill
- Division of Medical Genetics, Department of Pediatrics, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA. .,Department of Radiology, University of Utah, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
65
|
Kessel A, Kohli M, Swami U. Current management of metastatic castration-sensitive prostate cancer. Cancer Treat Res Commun 2021; 28:100384. [PMID: 33951556 DOI: 10.1016/j.ctarc.2021.100384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/12/2021] [Accepted: 04/17/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer affects one in nine men and once metastatic is incurable. The treatment for metastatic castration-sensitive prostate cancer (mCSPC) has evolved rapidly over the last decade with the addition of upfront intensification with novel hormonal therapies (abiraterone, enzalutamide, apalutamide) or docetaxel in addition to androgen deprivation therapy. In this review, we discuss the phase III studies that lead to the approval of these upfront intensification therapies. We also review the recent approval of relugolix, the first oral, gonadotropin-releasing hormone antagonist for patients with advanced prostate cancer. A comparison of various agents is made and variables that can help in treatment selection are reviewed. We also summarize our current understanding of the role of germline and somatic alterations in the mCSPC setting. Finally, we review the ongoing clinical trials which can change the current treatment paradigm.
Collapse
Affiliation(s)
- Adam Kessel
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Manish Kohli
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Umang Swami
- Division of Medical Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, United States.
| |
Collapse
|
66
|
Kwan EM, Dai C, Fettke H, Hauser C, Docanto MM, Bukczynska P, Ng N, Foroughi S, Graham LJK, Mahon K, Tan W, Wang X, Zhao Z, Zheng T, Zhou K, Yu J, Du P, Horvath LG, Jia S, Kohli M, Azad AA. Plasma Cell-Free DNA Profiling of PTEN-PI3K-AKT Pathway Aberrations in Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol 2021; 5:PO.20.00424. [PMID: 34250422 PMCID: PMC8232889 DOI: 10.1200/po.20.00424] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/10/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor tissue from metastatic castration-resistant prostate cancer (mCRPC) harbors frequent copy number variations (CNVs) in the PTEN-PI3K-AKT pathway. However, identifying CNVs in plasma cell-free DNA (cfDNA) has proven to be challenging. With emerging data supporting Akt inhibition in PTEN-deficient mCRPC, we profiled PTEN-PI3K-AKT pathway aberrations in patients with mCRPC using a novel cfDNA assay optimized for CNV detection. METHODS A next-generation sequencing-based cfDNA assay was used to profile 231 patients with mCRPC from two independent cohorts (Australian, n = 78; United States, n = 153). PTEN-PI3K-AKT pathway genomic aberrations were correlated with clinical outcomes, including progression-free survival and overall survival (OS). RESULTS PTEN loss and PIK3CA gain were detected in 37% (85 of 231) and 17% (39 of 231) of patients, respectively. Poorer outcomes were observed in patients with PTEN-PI3K-AKT pathway aberrations, including those with dual PTEN loss and PIK3CA gain (hazard ratio 2.3, 95% CI 1.2 to 4.4). Cumulative CNV burden in the PTEN-PI3K-AKT and androgen receptor (AR) pathways was associated with significantly worse clinical outcomes (0 v 1 v ≥ 2 CNVs in Australian cohort: median OS 33.5 v 17.2 v 9.7 months, P < .001; 0 v 1 v ≥ 2 CNVs in US cohort: median OS 35.5 v 14.3 v 9.2 months, P < .001). Notably, 21% (31 of 146) of PTEN-neutral patients harbored alternative PTEN-PI3K-AKT pathway aberrations. CONCLUSION PTEN-PI3K-AKT pathway CNVs were readily detected using our cfDNA assay, with the prevalence of PTEN loss comparable with tissue-based studies. Additional PTEN-PI3K-AKT pathway aberrations were found in one fifth of PTEN-neutral cases. Concurrent CNVs in the PTEN-PI3K-AKT and AR pathways portended poor survival, and identifying this high-risk patient subset for dual AR/Akt inhibition may optimize precision treatment with Akt inhibitors in mCRPC.
Collapse
Affiliation(s)
- Edmond M. Kwan
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Monash Health, Melbourne, Australia
| | | | - Heidi Fettke
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | | | - Maria M. Docanto
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
| | | | - Nicole Ng
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Siavash Foroughi
- Personalized Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | | | - Kate Mahon
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, Australia
- University of Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Winston Tan
- Division of Medical Oncology, Department of Medicine, Mayo Clinic, Jacksonville, FL
| | | | | | | | | | | | - Pan Du
- Predicine Inc, Hayward, CA
| | - Lisa G. Horvath
- Medical Oncology, Chris O'Brien Lifehouse, Sydney, Australia
- University of Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Manish Kohli
- Division of Medical Oncology, Department of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Arun A. Azad
- Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| |
Collapse
|
67
|
Annala M, Fu S, Bacon JVW, Sipola J, Iqbal N, Ferrario C, Ong M, Wadhwa D, Hotte SJ, Lo G, Tran B, Wood LA, Gingerich JR, North SA, Pezaro CJ, Ruether JD, Sridhar SS, Kallio HML, Khalaf DJ, Wong A, Beja K, Schönlau E, Taavitsainen S, Nykter M, Vandekerkhove G, Azad AA, Wyatt AW, Chi KN. Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial. Ann Oncol 2021; 32:896-905. [PMID: 33836265 DOI: 10.1016/j.annonc.2021.03.205] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Treatment of poor prognosis metastatic castration-resistant prostate cancer (mCRPC) includes taxane chemotherapy and androgen receptor pathway inhibitors (ARPI). We sought to determine optimal treatment in this setting. PATIENTS AND METHODS This multicentre, randomised, open-label, phase II trial recruited patients with ARPI-naive mCRPC and poor prognosis features (presence of liver metastases, progression to mCRPC after <12 months of androgen deprivation therapy, or ≥4 of 6 clinical criteria). Patients were randomly assigned 1 : 1 to receive cabazitaxel plus prednisone (group A) or physician's choice of enzalutamide or abiraterone plus prednisone (group B) at standard doses. Patients could cross over at progression. The primary endpoint was clinical benefit rate for first-line treatment (defined as prostate-specific antigen response ≥50%, radiographic response, or stable disease ≥12 weeks). RESULTS Ninety-five patients were accrued (median follow-up 21.9 months). First-line clinical benefit rate was greater in group A versus group B (80% versus 62%, P = 0.039). Overall survival was not different between groups A and B (median 37.0 versus 15.5 months, hazard ratio (HR) = 0.58, P = 0.073) nor was time to progression (median 5.3 versus 2.8 months, HR = 0.87, P = 0.52). The most common first-line treatment-related grade ≥3 adverse events were neutropenia (cabazitaxel 32% versus ARPI 0%), diarrhoea (9% versus 0%), infection (9% versus 0%), and fatigue (7% versus 5%). Baseline circulating tumour DNA (ctDNA) fraction above the cohort median and on-treatment ctDNA increase were associated with shorter time to progression (HR = 2.38, P < 0.001; HR = 4.03, P < 0.001). Patients with >30% ctDNA fraction at baseline had markedly shorter overall survival than those with undetectable ctDNA (HR = 38.22, P < 0.001). CONCLUSIONS Cabazitaxel was associated with a higher clinical benefit rate in patients with ARPI-naive poor prognosis mCRPC. ctDNA abundance was prognostic independent of clinical features, and holds promise as a stratification biomarker.
Collapse
Affiliation(s)
- M Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - S Fu
- Department of Medical Oncology, BC Cancer, Vancouver, Canada; Oncology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - J V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - J Sipola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - N Iqbal
- Medical Oncology, Saskatoon Cancer Centre, University of Saskatchewan, Saskatoon, Canada
| | - C Ferrario
- Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - M Ong
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital and the University of Ottawa, Ottawa, Canada
| | - D Wadhwa
- BC Cancer - Kelowna Centre, Kelowna, Canada
| | - S J Hotte
- Oncology, Juravinski Cancer Centre, Hamilton, Canada
| | - G Lo
- Department of Medical Oncology, R. S. McLaughlin Durham Regional Cancer Centre, Lakeridge Health, Oshawa, Canada
| | - B Tran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - L A Wood
- QEII Health Sciences Centre, Halifax, Canada
| | - J R Gingerich
- Department of Medical Oncology and Hematology, Cancer Care Manitoba, Winnipeg, Canada
| | - S A North
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - C J Pezaro
- Eastern Health Clinical School, Monash University, Australia; Department of Oncology, Eastern Health, Australia
| | | | - S S Sridhar
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada
| | - H M L Kallio
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - D J Khalaf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - A Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - K Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - E Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - S Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - M Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - G Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - A A Azad
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - A W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
| | - K N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Department of Medical Oncology, BC Cancer, Vancouver, Canada.
| |
Collapse
|
68
|
Dror CM, Wyatt AW, Chi KN. Olaparib for the treatment of metastatic prostate cancer. Future Oncol 2021; 17:2413-2429. [PMID: 33769071 DOI: 10.2217/fon-2020-1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent innovations in the treatment of metastatic prostate cancer have improved patient outcomes. Nonetheless, this disease remains fatal and additional treatment approaches are needed. Greater understanding of the molecular landscape of metastatic prostate cancer has revealed recurrent alterations in key pathways amenable to therapeutic targeting. One such pathway is DNA repair, particularly alterations in genes directly or indirectly associated with homologous recombination repair found in up to one-quarter of patients with metastatic castrate-resistant prostate cancer (mCRPC). Olaparib, an inhibitor of poly-ADP-ribose polymerase, has recently gained approval for the treatment of mCRPC harboring alterations in homologous recombination repair genes. This review will provide a summary of evidence regarding PARP inhibition in the treatment of mCRPC, with a specific focus on olaparib.
Collapse
Affiliation(s)
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada.,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Kim N Chi
- BC Cancer, Vancouver, Vancouver, BC, V5Z 4S6, Canada.,Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, V5Z 4S6, Canada
| |
Collapse
|
69
|
Sheng IY, Barata P, Alameddine R, Garcia JA. Volume matters and intensification is needed: emerging trends in the management of advanced prostate cancer. Drugs Context 2021; 10:2020-10-2. [PMID: 33796138 PMCID: PMC7968923 DOI: 10.7573/dic.2020-10-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/07/2020] [Indexed: 11/21/2022] Open
Abstract
Significant changes in the management of patients with de novo metastatic prostate cancer have led to the use of novel oral agents and docetaxel-based chemotherapy earlier in the natural history of their disease. Our main challenge is the lack of prospective randomized data comparing these regimens. It is clear that treatment intensification is needed. Yet, the heterogeneity of this patient population coupled with the lack of understanding of the specific biology for a given individual makes treatment selection challenging. The aim of this narrative review is to discuss the importance of defining advanced disease by volume, the necessity for treatment intensification, and the current and future landscape of metastatic hormone-sensitive prostate cancer management.
Collapse
Affiliation(s)
- Iris Y Sheng
- Department of Hematology and Medical Oncology, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH, USA
| | - Pedro Barata
- Department of Internal Medicine, Section of Hematology Oncology, Tulane University Medical School, New Orleans, LA, USA
| | - Raafat Alameddine
- Department of Hematology Oncology, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| | - Jorge A Garcia
- Department of Hematology Oncology, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| |
Collapse
|
70
|
Warner E, Herberts C, Fu S, Yip S, Wong A, Wang G, Ritch E, Murtha AJ, Vandekerkhove G, Fonseca NM, Angeles A, Beigi A, Schönlau E, Beja K, Annala M, Khalaf D, Chi KN, Wyatt AW. BRCA2, ATM, and CDK12 Defects Differentially Shape Prostate Tumor Driver Genomics and Clinical Aggression. Clin Cancer Res 2021; 27:1650-1662. [PMID: 33414135 DOI: 10.1158/1078-0432.ccr-20-3708] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/22/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE DNA damage repair (DDR) defects are common across cancer types and can indicate therapeutic vulnerability. Optimal exploitation of DDR defects in prostate cancer requires new diagnostic strategies and a better understanding of associated clinical genomic features. EXPERIMENTAL DESIGN We performed targeted sequencing of 1,615 plasma cell-free DNA samples from 879 patients with metastatic prostate cancer. Depth-based copy-number calls and heterozygous SNP imbalance were leveraged to expose DDR-mutant allelic configuration and categorize mechanisms of biallelic loss. We used split-read structural variation analysis to characterize tumor suppressor rearrangements. Patient-matched archival primary tissue was analyzed identically. RESULTS BRCA2, ATM, and CDK12 were the most frequently disrupted DDR genes in circulating tumor DNA (ctDNA), collectively mutated in 15% of evaluable cases. Biallelic gene disruption via second somatic alteration or mutant allele-specific imbalance was identified in 79% of patients. A further 2% exhibited homozygous BRCA2 deletions. Tumor suppressors TP53, RB1, and PTEN were controlled via disruptive chromosomal rearrangements in BRCA2-defective samples, but via oncogene amplification in context of CDK12 defects. TP53 mutations were rare in cases with ATM defects. DDR mutations were re-detected across 94% of serial ctDNA samples and in all available archival primary tissues, indicating they arose prior to metastatic progression. Loss of BRCA2 and CDK12, but not ATM, was associated with poor clinical outcomes. CONCLUSIONS BRCA2, ATM, and CDK12 defects are each linked to distinct prostate cancer driver genomics and aggression. The consistency of DDR status in longitudinal samples and resolution of allelic status underscores the potential for ctDNA as a diagnostic tool.
Collapse
Affiliation(s)
- Evan Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Fu
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada.,Auckland City Hospital, Auckland, New Zealand
| | - Steven Yip
- Tom Baker Cancer Centre, University of Calgary, Calgary, Alberta, Canada
| | - Amanda Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gang Wang
- Department of Pathology, BC Cancer, Vancouver, British Columbia, Canada
| | - Elie Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew J Murtha
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Arshia Beigi
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Finland
| | - Daniel Khalaf
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| |
Collapse
|
71
|
Carson JJK, Di Lena MA, Berman DM, Siemens DR, Mueller CR. Development and initial clinical correlation of a DNA methylation-based blood test for prostate cancer. Prostate 2020; 80:1038-1042. [PMID: 32506642 DOI: 10.1002/pros.24025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND One of the principle limitations for more precise management of advanced prostate cancer is the lack of accurate biomarkers allowing estimation of tumor burden, ongoing assessment of progression, and response to treatment. Although prostate-specific antigen (PSA) performs modestly, nonsecreting cancers including those with early castrate-resistance warrant investigation of other predictive biomarkers. The objectives of these studies were to develop and perform initial validation of a circulating tumor DNA (ctDNA) methylation assay. METHODS Methylation DETection of Circulating Tumor DNA (mDETECT) is a highly multiplexed targeted sequencing DNA methylation-based ctDNA blood test that captures the vast majority of prostate cancer phenotypes due to a careful development process that ensures that each probe region is methylated in at least 50% of all methylation-based subtypes and is not methylated in normal tissues. Next-generation sequencing of targeted polymerase chain reaction (PCR) products whose amplification is biased towards methylated DNA ensures the specificity of the assay by identifying multiple tumor-specific methylated CpG residues in each read. RESULTS The final test is comprised of 46 PCR probes to 40 regions. It is relatively resistant to contaminating normal DNA and as a result functions in both serum and plasma samples. The assay was initially validated in a variety of prostate cancer cell lines to ensure specificity. Using a small number of longitudinal samples from prostate cancer patients initiating androgen deprivation therapy, the ability of mDETECT to track tumor burden was assessed compared with PSA. The mDETECT test signal generally paralleled that of PSA increasing and decreasing commensurate with tumor evolution in these patients. In two cases it appeared to anticipate clinical progression by a number of months compared to PSA and in a PSA nonproducing case, it was able to track tumor progression. CONCLUSIONS mDETECT offers a promising tool for the assessment of prostate cancer burden based on the sensitive detection of prostate-specific ctDNA and requires further validation.
Collapse
Affiliation(s)
- Jacob J K Carson
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael A Di Lena
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - D Robert Siemens
- Department of Urology, Queen's University, Kingston, Ontario, Canada
| | - Christopher R Mueller
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Division of Cancer Biology and Genetics, Queen's Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
- Department of Biological and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
72
|
Ponti G, Maccaferri M, Percesepe A, Tomasi A, Ozben T. Liquid biopsy with cell free DNA: new horizons for prostate cancer. Crit Rev Clin Lab Sci 2020; 58:60-76. [PMID: 32805148 DOI: 10.1080/10408363.2020.1803789] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although prostate cancer (PCa) is one of the most common tumors in European males, the only minimally invasive diagnostic tool in PCa setup is the determination of PSA in serum. Cell-free DNA (cfDNA) has been demonstrated to be helpful for PCa diagnosis but has not yet been integrated into the clinical setting. This review aims to provide a systematic update of cfDNA and its fragmentation patterns in PCa reported in literature published over the last twenty years. Due to the high variability of the scientific methods adopted and a lack of standardized median cfDNA levels, results fluctuate across different studies. These differences may be due to the cfDNA source, the quantification method, or the fragmentation pattern. Blood plasma is the most frequently analyzed biological fluid, but seminal plasma has been reported to contain higher cfDNA concentration due to its vicinity to the tumor origin. CfDNA has been shown to be composed of single-stranded (ssDNA) and double-stranded DNA (dsDNA), so the total cfDNA concentration should be preferred as it corresponds best to the tumor mass. Fluorometry and capillary electrophoresis (CE) may be quick and cost-effective tools for cfDNA assessment in a clinical setting. The greatest future challenge is the elaboration of common guidelines and standardized procedures for diagnostic laboratories performing cfDNA analysis. A multiparametric approach combining the analysis of total cfDNA (both ssDNA and dsDNA), cfDNA fragment length, and specific genetic mutations (ctDNA assessment) is required for optimal future applications of liquid biopsy.
Collapse
Affiliation(s)
- Giovanni Ponti
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Monia Maccaferri
- Dermatology Unit, Azienda Ospedaliero-Universitaria of Modena, Modena, Italy
| | - Antonio Percesepe
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria of Parma, Parma, Italy
| | - Aldo Tomasi
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Tomris Ozben
- Faculty of Medicine, Department of Clinical Biochemistry, Akdeniz University, Antalya, Turkey
| |
Collapse
|
73
|
Du M, Huang CC, Tan W, Kohli M, Wang L. Multiplex Digital PCR to Detect Amplifications of Specific Androgen Receptor Loci in Cell-Free DNA for Prognosis of Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel) 2020; 12:E2139. [PMID: 32752286 PMCID: PMC7465398 DOI: 10.3390/cancers12082139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
Amplification of androgen receptor (AR) is a common genomic event in metastatic castration-resistant prostate cancer (mCRPC). To evaluate the prognostic value of the amplifications of specific loci in the AR gene in cell-free DNA, we developed a multiplex digital PCR (dPCR) assay that targeted AR enhancer (AR-En), AR exon 1 (AR-E1), AR exon 8 (AR-E8) and OPHN1 (downstream of AR). We selected three relatively stable genes, C2orf16, FAM111B, and GRIA3, as reference controls for copy number normalization. One hundred and eight mCRPC patients were recruited to test the association of specific AR loci amplification with clinical outcome. Using a normalized ratio ≥ 1.92 as cutoff, amplification of AR-En, AR-E1, AR-E8 and OPHN1 was observed in 28, 25, 24 and 19 of 108 mCRPC patients, respectively. Among the 41 patients with AR region amplification, 9 (21.9%) showed amplification at all four selected regions and 15 (36.6%) showed amplification at AR-En, AR-E1, and AR-E8. Six (14.6%) patients showed independent AR-En amplification, while the remaining 3 (7.3%) demonstrated AR-E8 amplification only. Kaplan-Meier analysis showed overall survival's association with the amplification of AR-En (p = 0.02, HR = 1.68 (1.07-2.65)), AR-E8 (p = 0.02, HR = 1.78 (1.08-2.92)) and AR-En-E8 (the combination of AR-En and AR-E8 (p = 0.009, HR = 1.77 (1.15-2.73)). Multivariate models that included AR-En-E8 amplification and clinical factors significantly improved prognostic performance (p = 0.0001). With further validation, the multiplex dPCR assay may assist in prognostication of mCRPC patients.
Collapse
Affiliation(s)
- Meijun Du
- Department of the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA;
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chiang-Ching Huang
- Department of Biostatistics, Zilber School of Public Health, University of Wisconsin, Milwaukee, WI 53205, USA;
| | - Winston Tan
- Department of Medicine, Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Manish Kohli
- Division of Oncology, Department of Medicine, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Liang Wang
- Department of Pathology, MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| |
Collapse
|