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Graham LS, Henderson NC, Kellezi O, Hwang C, Barata PC, Bilen MA, Kilari D, Pierro M, Thapa B, Tripathi A, Mo G, Labriola M, Park JJ, Rothstein S, Garje R, Koshkin VS, Patel VG, Dorff T, Armstrong AJ, McKay RR, Alva A, Schweizer MT. DNA-Damaging Therapies in Patients With Prostate Cancer and Pathogenic Alterations in Homologous Recombination Repair Genes. JCO Precis Oncol 2024; 8:e2400014. [PMID: 39178368 PMCID: PMC11346579 DOI: 10.1200/po.24.00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/25/2024] [Accepted: 07/26/2024] [Indexed: 08/25/2024] Open
Abstract
PURPOSE Outcomes data for DNA-damaging therapeutics for men with prostate cancer (PC) and non-BRCA1/2 homologous recombination repair (HRR) mutations are limited. We evaluated outcomes by HRR alteration in men with PC treated with poly(ADP-ribose)polymerase inhibitors (PARPi) and/or platinum chemotherapy. METHODS Retrospective data from the PROMISE consortium were used. Clinical outcomes differences were assessed between patients with BRCA1/2 mutations (cohort A) and those with HRR mutations without direct BRCA complex interaction (cohort B: ATM, CDK12, CHEK1, CHEK2, and FANCL). Outcomes in patients with HRR mutations with direct BRCA complex interaction were also explored (cohort C: RAD51B/C/D, RAD54L2, BARD1, GEN1, PALB2, FANCA, and BRIP1). RESULTS One hundred and forty-six patients received PARPi (cohort A: 94, cohort B: 45, cohort C: 7) and 104 received platinum chemotherapy (cohort A: 48, cohort B: 44, cohort C: 10). PSA50 response rate to PARPi was higher in cohort A (61%) than cohort B (5%), P < .001. Median clinical/radiographic progression-free survival (crPFS) with PARPi in cohort A was significantly longer than in cohort B: 15.9 versus 8.7 months, P = .005. PSA50 response rate to platinum therapy was higher in cohort A (62%) than in cohort B (32%), P = .024, although crPFS was not significantly different. PSA50 response rate to PARPi and platinum was 40% and 32%, respectively, in cohort C. In multivariable analysis, cohort A had significantly improved overall survival and crPFS compared with cohort B with PARPi but not platinum chemotherapy. CONCLUSION Patients with BRCA1/2-mutated PC had significantly improved outcomes to PARPi but not platinum chemotherapy compared with those with HRR mutations without direct BRCA complex interaction.
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Affiliation(s)
| | | | | | - Clara Hwang
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Pedro C. Barata
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | - Mehmet A. Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Deepak Kilari
- Department of Medicine, Clinical Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael Pierro
- Department of Medicine, Clinical Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bicky Thapa
- Department of Medicine, Clinical Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - George Mo
- University of Washington/Fred Hutchinson Cancer Center, Seattle, Washington
| | - Matthew Labriola
- Division of Medical Oncology, Duke University Medical Center, Duke Cancer Institute Center for Prostate and Urologic Cancer, Duke University, Durham, NC, USA
| | - Joseph J. Park
- Division of Medical Oncology, Duke University Medical Center, Duke Cancer Institute Center for Prostate and Urologic Cancer, Duke University, Durham, NC, USA
| | | | - Rohan Garje
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
| | - Vadim S. Koshkin
- Division of Hematology and Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Vaibhav G. Patel
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tanya Dorff
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Andrew J. Armstrong
- Division of Medical Oncology, Duke University Medical Center, Duke Cancer Institute Center for Prostate and Urologic Cancer, Duke University, Durham, NC, USA
| | - Rana R. McKay
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ajjai Alva
- University of Michigan, Ann Arbor, MI, USA
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Broderick A, Pan E, Li J, Chu A, Hwang C, Barata PC, Cackowski FC, Labriola M, Ghose A, Bilen MA, Kilari D, Thapa B, Piero M, Graham L, Tripathi A, Garje R, Koshkin VS, Hernandez E, Dorff TB, Schweizer MT, Alva AS, McKay RR, Armstrong AJ. Clinical implications of Wnt pathway genetic alterations in men with advanced prostate cancer. Prostate Cancer Prostatic Dis 2024:10.1038/s41391-024-00869-1. [PMID: 39019980 PMCID: PMC11739431 DOI: 10.1038/s41391-024-00869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Aberrant Wnt signaling has been implicated in prostate cancer tumorigenesis and metastasis in preclinical models but the impact of genetic alterations in Wnt signaling genes in men with advanced prostate cancer is unknown. METHODS We utilized the Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort (PROMISE) clinical-genomic database for this retrospective analysis. Patients with activating mutations in CTNNB1 or RSPO2 or inactivating mutations in APC, RNF43, or ZNRF3 were defined as Wnt-altered, while those lacking such alterations were defined as Wnt non-altered. We compared patient characteristics and clinical outcomes as well as co-occurring genetic alterations according to Wnt alteration status. RESULTS Of the 1498 patients included, 193 (12.9%) were Wnt-altered. These men had a statistically significant 2-fold increased prevalence of liver and lung metastases as compared with Wnt non-altered patients at the time of initial diagnosis, (4.66% v 2.15% ; 6.22% v 3.07%), first metastatic disease diagnosis (10.88% v 5.29%; 13.99% v 6.21%), and CRPC development (11.40% v 6.36%; 12.95% v 5.29%). Wnt alterations were associated with more co-occurring alterations in RB1 (10.4% v 6.2%), AR (38.9% vs 25.7%), SPOP (13.5% vs 4.1%), FOXA1 (6.7% vs 2.8%), and PIK3CA (10.9% vs 5.1%). We found no significant differences in overall survival or other clinical outcomes from initial diagnosis, first metastatic disease, diagnosis of CRPC, or with AR inhibition for mCRPC between the Wnt groups. CONCLUSIONS Wnt-altered patients with prostate cancer have a higher prevalence of visceral metastases and are enriched in RB1, AR, SPOP, FOXA1, and PIK3CA alterations. Despite these associations, Wnt alterations were not associated with worse survival or treatment outcomes in men with advanced prostate cancer.
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Affiliation(s)
- Amanda Broderick
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
| | - Elizabeth Pan
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jinju Li
- Rogel Cancer Center, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Alec Chu
- Pathology Department, University of Michigan, Ann Arbor, MI, USA
| | - Clara Hwang
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Pedro C Barata
- Department of Internal Medicine, University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | | | - Matthew Labriola
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA
| | - Alyssa Ghose
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | - Deepak Kilari
- Department of Medicine, Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bicky Thapa
- Department of Medicine, Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael Piero
- Department of Medicine, Medical College of Wisconsin Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Laura Graham
- University of Colorado Cancer Center Anschutz Medical Campus, Aurora, CO, USA
| | - Abhishek Tripathi
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Rohan Garje
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
| | - Vadim S Koshkin
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Erik Hernandez
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Tanya B Dorff
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Ajjai Shivaram Alva
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Rana R McKay
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC, USA.
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3
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Antonarakis ES, Zhang N, Saha J, Nevalaita L, Ikonen T, Tsai LJ, Garratt C, Fizazi K. Prevalence and Spectrum of AR Ligand-Binding Domain Mutations Detected in Circulating-Tumor DNA Across Disease States in Men With Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol 2024; 8:e2300330. [PMID: 38781544 PMCID: PMC11486455 DOI: 10.1200/po.23.00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/08/2024] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
PURPOSE Metastatic castration-resistant prostate cancer (mCRPC) is typically treated with agents directly or indirectly targeting the androgen receptor (AR) pathway. However, such treatment is limited by resistance mechanisms, including the development of activating mutations in the AR ligand-binding domain (AR-LBD). METHODS This study evaluated a database of over 15,000 patients with advanced prostate cancer (PC) undergoing comprehensive circulating-tumor DNA analysis (Guardant360, Redwood City, CA) between 2014 and 2021, with associated clinical information from administrative claims (GuardantINFORM database). RESULTS Of 15,705 patients with PC included, 54% had mCRPC at the time of their blood draw. Of those, 49% had previous treatment with an AR pathway inhibitor (ARPi). AR-LBD mutation prevalence was 15% in patients with mCRPC who were untreated with a next-generation ARPi, 22% in those after one line of ARPi therapy, and 24% in those after two lines of ARPi treatment. Next-generation ARPi treatment yielded an increase in AR L702H and T878A/S mutations after abiraterone, and an increase in AR L702H and F877L mutations after enzalutamide. AR-LBD+ patients demonstrated unique biology, including increased concurrent mutations in the cell-cycle, wingless-related integration site, homologous recombination repair, and phospho-inositide 3-kinase pathways (all P < .0005), and greater low-level (copy number <10) AR amplifications (P = .0041). AR-LBD+ patients exhibited worse overall survival (OS) relative to a matched cohort of AR-LBD- patients (50.1 v 60.7 months, unadjusted log-rank P = .013). CONCLUSION This large database analysis demonstrates that AR-LBD mutation prevalence increases after next-generation ARPi use. AR-LBD+ tumors demonstrate unique biology (more oncogenic pathway mutations and low-level AR amplification) and reduced OS. These findings inform the development of novel therapies designed to circumvent AR-mediated therapeutic resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Karim Fizazi
- Institut Gustave Roussy, University of Paris-Saclay, Villejuif, France
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4
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Spratt DE, Dorff T, McKay RR, Lowentritt BH, Fallick M, Gatoulis SC, Flanders SC, Ross AE. Evaluating relugolix for the treatment of prostate cancer in real-world settings of care: the OPTYX study protocol. Future Oncol 2024; 20:727-738. [PMID: 38488039 DOI: 10.2217/fon-2023-0748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
OPTYX is a multi-center, prospective, observational study designed to further understand the actual experience of patients with advanced prostate cancer treated with relugolix (ORGOVYX®), an oral androgen deprivation therapy (ADT), by collecting clinical and patient-reported outcomes from routine care settings. The study aims to enroll 1000 consented patients with advanced prostate cancer from community, academic and government operated clinical practices across the USA. At planned timepoints, real-world data analysis on treatment patterns, adherence and safety as well as health outcomes and health-related quality-of-life (HRQOL) after treatment discontinuation will be published in scientific peer-reviewed journals and presented at relevant conferences. This study will provide real-world data for practitioners and researchers in their understanding of the safety and effectiveness of relugolix. Clinical Trial Registration: NCT05467176 (ClinicalTrials.gov).
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Affiliation(s)
- Daniel E Spratt
- Radiation Oncology, UH Seidman Cancer Center/Case Western Reserve University, Cleveland, OH 441062, USA
| | - Tanya Dorff
- Medical Oncology, City of Hope, Duarte, CA 910103, USA
| | - Rana R McKay
- Medical Oncology, UC San Diego, La Jolla, CA 920374, USA
| | | | | | | | - Scott C Flanders
- Myovant Sciences Inc., Brisbane, CA & Sumitomo Pharma America Inc., Marlborough, MA 017528, USA
| | - Ashley E Ross
- Urology, Northwestern Medicine, Chicago, IL 60611, USA
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5
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Park JJ, Chu A, Li J, Ali A, McKay RR, Hwang C, Labriola MK, Jang A, Kilari D, Mo G, Ravindranathan D, Graham LS, Sokolova A, Tripathi A, Pilling A, Jindal T, Ravindra A, Cackowski FC, Sweeney PL, Thapa B, Amery TS, Heath EI, Garje R, Zakharia Y, Koshkin VS, Bilen MA, Schweizer MT, Barata PC, Dorff TB, Cieslik M, Alva AS, Armstrong AJ. Repeat Next-Generation Sequencing Testing on Progression in Men With Metastatic Prostate Cancer Can Identify New Actionable Alterations. JCO Precis Oncol 2024; 8:e2300567. [PMID: 38579192 PMCID: PMC11018169 DOI: 10.1200/po.23.00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/03/2024] [Accepted: 02/07/2024] [Indexed: 04/07/2024] Open
Abstract
PURPOSE There are limited data available on the real-world patterns of molecular testing in men with advanced prostate cancer. We thus sought to evaluate next-generation sequencing (NGS) testing in the United States, focused on single versus serial NGS testing, the different disease states of testing (hormone-sensitive v castration-resistant, metastatic vs nonmetastatic), tissue versus plasma circulating tumor DNA (ctDNA) assays, and how often actionable data were found on each NGS test. METHODS The Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort clinical-genomic database was used for this retrospective analysis, including 1,597 patients across 15 institutions. Actionable NGS data were defined as including somatic alterations in homologous recombination repair genes, mismatch repair deficiency, microsatellite instability (MSI-high), or a high tumor mutational burden ≥10 mut/MB. RESULTS Serial NGS testing (two or more NGS tests with specimens collected more than 60 days apart) was performed in 9% (n = 144) of patients with a median of 182 days in between test results. For the second NGS test and beyond, 82.1% (225 of 274) of tests were from ctDNA assays and 76.1% (217 of 285) were collected in the metastatic castration-resistant setting. New actionable data were found on 11.1% (16 of 144) of second NGS tests, with 3.5% (5 of 144) of tests detecting a new BRCA2 alteration or MSI-high. A targeted therapy (poly (ADP-ribose) polymerase inhibitor or immunotherapy) was given after an actionable result on the second NGS test in 31.3% (5 of 16) of patients. CONCLUSION Repeat somatic NGS testing in men with prostate cancer is infrequently performed in practice and can identify new actionable alterations not present with initial testing, suggesting the utility of repeat molecular profiling with tissue or blood of men with metastatic castration-resistant prostate cancer to guide therapy choices.
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Affiliation(s)
- Joseph J. Park
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC
| | - Alec Chu
- Division of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Jinju Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI
| | - Alicia Ali
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Rana R. McKay
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Clara Hwang
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Matthew K. Labriola
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC
| | - Albert Jang
- Tulane Cancer Center, Tulane University, New Orleans, LA
| | - Deepak Kilari
- Department of Medicine, Froedtert Cancer Center, Medical College of Wisconsin, Milwaukee, WI
| | - George Mo
- University of Washington/Fred Hutchinson Cancer Center, Seattle, Washington
| | | | | | - Alexandra Sokolova
- Division of Medical Oncology, Oregon Health Science University, Portland, OR
| | - Abhishek Tripathi
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Amanda Pilling
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Tanya Jindal
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | | | | | | | - Bicky Thapa
- Department of Medicine, Froedtert Cancer Center, Medical College of Wisconsin, Milwaukee, WI
| | - Taylor S. Amery
- Division of Medical Oncology, Oregon Health Science University, Portland, OR
| | | | | | | | - Vadim S. Koshkin
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | | | | | | | - Tanya B. Dorff
- Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Marcin Cieslik
- Division of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Ajjai S. Alva
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Andrew J. Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC
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Carignan D, Morales B, Després P, Foster W, Martin AG, Vigneault E. Differential outcomes of re-stratified high-risk prostate cancer patients treated with external beam radiation therapy plus high-dose-rate brachytherapy boost. J Contemp Brachytherapy 2024; 16:103-110. [PMID: 38808208 PMCID: PMC11129645 DOI: 10.5114/jcb.2024.139277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
Purpose We report outcomes of high-risk prostate cancer (PCa) patients, initially classified according to a 3-tier NCCN classification system, treated with external beam radiation therapy (EBRT) and high-dose-rate brachytherapy boost (HDR-BT). Patients were analyzed based on a re-stratification of their risk grouping using CAPRA score and a newer 5-tier NCCN classification. Material and methods 471 high-risk PCa patients treated with EBRT, HDR-BT, and androgen deprivation therapy (ADT) between 1999 and 2018 were included. Competing risk survival analyses to compare individuals with CAPRA scores < 6 vs. ≥ 6 for biochemical relapse (BCR) and metastasis incidence were conducted. Also, overall survival (OS) for both groups using Kaplan-Meier analysis was assessed. The same analyses were repeated using a 5-tier NCCN stratification comparing those classified as high-risk vs. very high-risk patients. Results The median age was 71 years, and the median follow-up period was 72 months. The whole cohort received an EQD2 of 74 Gy or greater, with a median EQD2 of 106.89 Gy. Both a CAPRA score ≥ 6 and belonging to the NCCN very high-risk group were associated with BCR, with subdistribution hazard ratios (sHRs) of 3.04 (p = 0.015) and 2.53 (p = 0.013), respectively. For metastasis incidence, both the CAPRA and NCCN groups had similar sHRs of 2.60 (p = 0.094) and 2.71 (p = 0.037), respectively. For 10-year OS, patients with CAPRA score ≥ 6 and belonging to the NCCN very high-risk group presented similar HRs of 2.11 (p = 0.005) and 2.10 (p = 0.002). Conclusions We showed that high-risk PCa patients classified according to the 3-tier NCCN system benefit from further stratification using the CAPRA score or the 5-tier NCCN stratification method. Patients with a CAPRA score ≥ 6 or classified as very high-risk demonstrate a higher hazard of BCR, metastasis, and death. These patients might benefit from further intensification of their investigations and treatment, based on ongoing research.
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Affiliation(s)
- Damien Carignan
- Centre de Recherche du CHU de Québec-Université Laval, Axe Oncologie, Québec, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada
| | - Brandon Morales
- Centre de Recherche du CHU de Québec-Université Laval, Axe Oncologie, Québec, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada
- CHU de Québec-Université Laval, Service de Radio-Oncologie, Québec, Canada
| | - Philippe Després
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada
- Faculté des Sciences et de Génie de l’Université Laval, Département de Physique, Génie Physique et Optique, Pavillon Alexandre-Vachon, Québec, Canada
- Centre de Recherche de l’Institut Université de Cardiologie Pneumologie de Québec, Québec, Canada
| | - William Foster
- Centre de Recherche du CHU de Québec-Université Laval, Axe Oncologie, Québec, Canada
- CHU de Québec-Université Laval, Service de Radio-Oncologie, Québec, Canada
| | - André-Guy Martin
- Centre de Recherche du CHU de Québec-Université Laval, Axe Oncologie, Québec, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada
- CHU de Québec-Université Laval, Service de Radio-Oncologie, Québec, Canada
| | - Eric Vigneault
- Centre de Recherche du CHU de Québec-Université Laval, Axe Oncologie, Québec, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, Canada
- CHU de Québec-Université Laval, Service de Radio-Oncologie, Québec, Canada
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7
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Vandekerkhove G, Giri VN, Halabi S, McNair C, Hamade K, Bitting RL, Wyatt AW. Toward Informed Selection and Interpretation of Clinical Genomic Tests in Prostate Cancer. JCO Precis Oncol 2024; 8:e2300654. [PMID: 38547422 PMCID: PMC10994438 DOI: 10.1200/po.23.00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/15/2023] [Accepted: 02/07/2024] [Indexed: 04/02/2024] Open
Abstract
Clinical genomic testing of patient germline, tumor tissue, or plasma cell-free DNA can enable a personalized approach to cancer management and treatment. In prostate cancer (PCa), broad genotyping tests are now widely used to identify germline and/or somatic alterations in BRCA2 and other DNA damage repair genes. Alterations in these genes can confer cancer sensitivity to poly (ADP-ribose) polymerase inhibitors, are linked with poor prognosis, and can have potential hereditary cancer implications for family members. However, there is huge variability in genomic tests and reporting standards, meaning that for successful implementation of testing in clinical practice, end users must carefully select the most appropriate test for a given patient and critically interpret the results. In this white paper, we outline key pre- and post-test considerations for choosing a genomic test and evaluating reported variants, specifically for patients with advanced PCa. Test choice must be based on clinical context and disease state, availability and suitability of tumor tissue, and the genes and regions that are covered by the test. We describe strategies to recognize false positives or negatives in test results, including frameworks to assess low tumor fraction, subclonal alterations, clonal hematopoiesis, and pathogenic versus nonpathogenic variants. We assume that improved understanding among health care professionals and researchers of the nuances associated with genomic testing will ultimately lead to optimal patient care and clinical decision making.
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Affiliation(s)
- Gillian Vandekerkhove
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Veda N. Giri
- Yale School of Medicine and Yale Cancer Center, New Haven, CT
| | | | | | | | | | - Alexander W. Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
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8
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Zengin ZB, Henderson NC, Park JJ, Ali A, Nguyen C, Hwang C, Barata PC, Bilen MA, Graham L, Mo G, Kilari D, Tripathi A, Labriola M, Rothstein S, Garje R, Koshkin VS, Patel VG, Schweizer MT, Armstrong AJ, McKay RR, Alva A, Dorff T. Clinical implications of AR alterations in advanced prostate cancer: a multi-institutional collaboration. Prostate Cancer Prostatic Dis 2024:10.1038/s41391-024-00805-3. [PMID: 38383885 DOI: 10.1038/s41391-024-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/09/2024] [Accepted: 02/06/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND AR gene alterations can develop in response to pressure of testosterone suppression and androgen receptor targeting agents (ARTA). Despite this, the relevance of these gene alterations in the context of ARTA treatment and clinical outcomes remains unclear. METHODS Patients with castration-resistant prostate cancer (CRPC) who had undergone genomic testing and received ARTA treatment were identified in the Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort (PROMISE) database. Patients were stratified according to the timing of genomic testing relative to the first ARTA treatment (pre-/post-ARTA). Clinical outcomes such as time to progression, PSA response, and overall survival were compared based on alteration types. RESULTS In total, 540 CRPC patients who received ARTA and had tissue-based (n = 321) and/or blood-based (n = 244) genomic sequencing were identified. Median age was 62 years (range 39-90) at the time of the diagnosis. Majority were White (72.2%) and had metastatic disease (92.6%) at the time of the first ARTA treatment. Pre-ARTA genomic testing was available in 24.8% of the patients, and AR mutations and amplifications were observed in 8.2% and 13.1% of the patients, respectively. Further, time to progression was longer in patients with AR amplifications (25.7 months) compared to those without an AR alteration (9.6 months; p = 0.03). In the post-ARTA group (n = 406), AR mutations and AR amplifications were observed in 18.5% and 35.7% of the patients, respectively. The most common mutation in post-ARTA group was L702H (9.9%). CONCLUSION In this real-world clinicogenomics database-driven study we explored the development of AR alterations and their association with ARTA treatment outcomes. Our study showed that AR amplifications are associated with longer time to progression on first ARTA treatment. Further prospective studies are needed to optimize therapeutic strategies for patients with AR alterations.
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Affiliation(s)
- Zeynep B Zengin
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Joseph J Park
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alicia Ali
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Charles Nguyen
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Clara Hwang
- Division of Hematology/Oncology, Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Pedro C Barata
- Tulane Cancer Center, Tulane University, New Orleans, LA, USA
| | - Mehmet A Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Laura Graham
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George Mo
- University of Washington/Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Deepak Kilari
- Department of Medicine, Froedtert Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Matthew Labriola
- Division of Medical Oncology, Duke University Medical Center, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC, USA
| | | | - Rohan Garje
- Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | - Vadim S Koshkin
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vaibhav G Patel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Arvinas Inc, New Haven, CT, USA
| | | | - Andrew J Armstrong
- Division of Medical Oncology, Duke University Medical Center, Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University, Durham, NC, USA
| | - Rana R McKay
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Ajjai Alva
- Division of Hematology and Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Tanya Dorff
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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9
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Bakhshi P, Nourizadeh M, Sharifi L, Nowroozi MR, Mohsenzadegan M, Farajollahi MM. Impaired monocyte-derived dendritic cell phenotype in prostate cancer patients: A phenotypic comparison with healthy donors. Cancer Rep (Hoboken) 2024; 7:e1996. [PMID: 38351552 PMCID: PMC10864738 DOI: 10.1002/cnr2.1996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Dendritic cells (DCs) play a crucial role in immunity. Research on monocyte-derived DCs (Mo-DCs) cancer vaccines is in progress despite limited success in clinical trials. This study focuses on Mo-DCs generated from prostate cancer (PCA) patients, comparing them with DCs from healthy donors (HD-DCs). METHODS Mo-DCs were isolated from PCA patient samples, and their phenotype was compared to HD-DCs. Key parameters included monocyte count, CD14 expression, and the levels of maturation markers (HLA-DR, CD80, CD86) were assessed. RESULTS PCA samples exhibited a significantly lower monocyte count and reduced CD14 expression compared to healthy samples (p ⟨ 0.0001). Additionally, PCA-DCs expressed significantly lower levels of maturation markers, including HLA-DR, CD80, and CD86, when compared to HD-DCs (p = 0.123, p = 0.884, and p = 0.309, respectively). CONCLUSION The limited success of DC vaccines could be attributed to impaired phenotypic characteristics. These observations suggest that suboptimal characteristics of Mo-DCs generated from cancer patient blood samples might contribute to the limited success of DC vaccines. Consequently, this study underscores the need for alternative strategies to enhance the features of Mo-DCs for more effective cancer immunotherapies.
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Affiliation(s)
- Parisa Bakhshi
- Department of Medical Biotechnology, School of Allied Medical SciencesIran University of Medical SciencesTehranIran
| | - Maryam Nourizadeh
- Immunology, Asthma and Allergy Research InstituteTehran University of Medical SciencesTehranIran
| | - Laleh Sharifi
- Uro‐Oncology Research CenterTehran University of Medical SciencesTehranIran
| | | | - Monireh Mohsenzadegan
- Department of Medical Laboratory Sciences, School of Allied Medical SciencesIran University of Medical SciencesTehranIran
| | - Mohammad M. Farajollahi
- Department of Medical Biotechnology, School of Allied Medical SciencesIran University of Medical SciencesTehranIran
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10
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Paller CJ, Barata PC, Lorentz J, Appleman LJ, Armstrong AJ, DeMarco TA, Dreicer R, Elrod JAB, Fleming M, George C, Heath EI, Hussain MHA, Mao S, McKay RR, Morgans AK, Orton M, Pili R, Riedel E, Saraiya B, Sigmond J, Sokolova A, Stadler WM, Tran C, Macario N, Vinson J, Green R, Cheng HH. PROMISE Registry: A prostate cancer registry of outcomes and germline mutations for improved survival and treatment effectiveness. Prostate 2024; 84:292-302. [PMID: 37964482 DOI: 10.1002/pros.24650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Recently approved treatments and updates to genetic testing recommendations for prostate cancer have created a need for correlated analyses of patient outcomes data via germline genetic mutation status. Genetic registries address these gaps by identifying candidates for recently approved targeted treatments, expanding clinical trial data examining specific gene mutations, and understanding effects of targeted treatments in the real-world setting. METHODS The PROMISE Registry is a 20-year (5-year recruitment, 15-year follow-up), US-wide, prospective genetic registry for prostate cancer patients. Five thousand patients will be screened through an online at-home germline testing to identify and enroll 500 patients with germline mutations, including: pathogenic or likely pathogenic variants and variants of uncertain significance in genes of interest. Patients will be followed for 15 years and clinical data with real time patient reported outcomes will be collected. Eligible patients will enter long-term follow-up (6-month PRO surveys and medical record retrieval). As a virtual study with patient self-enrollment, the PROMISE Registry may fill gaps in genetics services in underserved areas and for patients within sufficient insurance coverage. RESULTS The PROMISE Registry opened in May 2021. 2114 patients have enrolled to date across 48 US states and 23 recruiting sites. 202 patients have met criteria for long-term follow-up. PROMISE is on target with the study's goal of 5000 patients screened and 500 patients eligible for long-term follow-up by 2026. CONCLUSIONS The PROMISE Registry is a novel, prospective, germline registry that will collect long-term patient outcomes data to address current gaps in understanding resulting from recently FDA-approved treatments and updates to genetic testing recommendations for prostate cancer. Through inclusion of a broad nationwide sample, including underserved patients and those unaffiliated with major academic centers, the PROMISE Registry aims to provide access to germline genetic testing and to collect data to understand disease characteristics and treatment responses across the disease spectrum for prostate cancer with rare germline genetic variants.
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Affiliation(s)
- Channing J Paller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pedro C Barata
- University Hospitals Seidman Cancer Center, Cleveland, Ohio, USA
| | - Justin Lorentz
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Leonard J Appleman
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Andrew J Armstrong
- Duke Cancer Institute Center for Prostate & Urologic Cancers, Durham, North Carolina, USA
| | | | - Robert Dreicer
- University of Virginia Comprehensive Cancer Center, Charlottesville, Virginia, USA
| | - Jo Ann B Elrod
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
| | - Mark Fleming
- Virginia Oncology Associates, Norfolk, Virginia, USA
| | - Christopher George
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Elisabeth I Heath
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Maha H A Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Shifeng Mao
- Allegheny Health Network Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Rana R McKay
- Department of Oncology, University of California San Diego Moores Cancer Center, La Jolla, California, USA
| | - Alicia K Morgans
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Matthew Orton
- Indiana University Health Arnett Cancer Center, Lafayette, Indiana, USA
| | - Roberto Pili
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Elyn Riedel
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Biren Saraiya
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | | | - Alexandra Sokolova
- Oregon Health & Science University Knight Cancer Institute, Portland, Oregon, USA
| | - Walter M Stadler
- Department of Medicine, The University of Chicago Comprehensive Cancer Center, The University of Chicago Medicine, Chicago, Illinois, USA
| | - Christina Tran
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Natalie Macario
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Jacob Vinson
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Rebecca Green
- Prostate Cancer Clinical Trials Consortium, New York, New York, USA
| | - Heather H Cheng
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
- University of Washington, Department of Medicine, Seattle, Washington, USA
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11
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Hwang C, Henderson NC, Chu SC, Holland B, Cackowski FC, Pilling A, Jang A, Rothstein S, Labriola M, Park JJ, Ghose A, Bilen MA, Mustafa S, Kilari D, Pierro MJ, Thapa B, Tripathi A, Garje R, Ravindra A, Koshkin VS, Hernandez E, Schweizer MT, Armstrong AJ, McKay RR, Dorff TB, Alva AS, Barata PC. Biomarker-Directed Therapy in Black and White Men With Metastatic Castration-Resistant Prostate Cancer. JAMA Netw Open 2023; 6:e2334208. [PMID: 37721753 PMCID: PMC10507489 DOI: 10.1001/jamanetworkopen.2023.34208] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/09/2023] [Indexed: 09/19/2023] Open
Abstract
Importance Black men have higher incidence and mortality from prostate cancer. Whether precision oncology disparities affect Black men with metastatic castration-resistant prostate cancer (mCRPC) is unknown. Objective To compare precision medicine data and outcomes between Black and White men with mCRPC. Design, Setting, and Participants This retrospective cohort study used data collected by the Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort (PROMISE) consortium, a multi-institutional registry with linked clinicogenomic data, from April 2020 to December 2021. Participants included Black and White patients with mCRPC with molecular data. Data were analyzed from December 2021 to May 2023. Exposures Database-reported race and ethnicity. Main Outcomes and Measures The primary outcome was the frequency of actionable molecular data, defined as the presence of mismatch repair deficiency (MMRD) or high microsatellite instability (MSI-H), homologous recombination repair deficiency, or tumor mutational burden of 10 mutations per megabase or greater. Secondary outcomes included the frequency of other alterations, the type and timing of genomic testing performed, and use of targeted therapy. Efficacy outcomes were prostate-specific antigen response rate, site-reported radiographic response, and overall survival. Results A total of 962 eligible patients with mCRPC were identified, including 204 Black patients (21.2%; median [IQR] age at diagnosis, 61 [55-67] years; 131 patients [64.2%] with Gleason scores 8-10; 92 patients [45.1%] with de novo metastatic disease) and 758 White patients (78.8%; median [IQR] age, 63 [57-69] years; 445 patients [58.7%] with Gleason scores 8-10; 310 patients [40.9%] with de novo metastatic disease). Median (IQR) follow-up from mCRPC was 26.6 (14.2-44.7) months. Blood-based molecular testing was more common in Black men (111 men [48.7%]) than White men (317 men [36.4%]; P < .001). Rates of actionable alterations were similar between groups (65 Black men [32.8%]; 215 White men [29.1%]; P = .35), but MMRD or MSI-H was more common in Black men (18 men [9.1]) than White men (36 men [4.9%]; P = .04). PTEN alterations were less frequent in Black men than White men (31 men [15.7%] vs 194 men [26.3%]; P = .003), as were TMPRSS alterations (14 men [7.1%] vs 155 men [21.0%]; P < .001). No other differences were seen in the 15 most frequently altered genes, including TP53, AR, CDK12, RB1, and PIK3CA. Matched targeted therapy was given less frequently in Black men than White men (22 men [33.5%] vs 115 men [53.5%]; P = .008). There were no differences in response to targeted therapy or survival between the two cohorts. Conclusions and Relevance This cohort study of men with mCRPC found higher frequency of MMRD or MSI-H and lower frequency of PTEN and TMPRSS alterations in Black men compared with White men. Although Black men received targeted therapy less frequently than White men, no differences were observed in clinical outcomes.
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Affiliation(s)
| | | | | | - Brandon Holland
- Wayne State University School of Medicine, Detroit, Michigan
| | - Frank C. Cackowski
- Wayne State University School of Medicine, Detroit, Michigan
- Karmanos Cancer Institute, Detroit, Michigan
| | | | | | - Shoshana Rothstein
- Wayne State University School of Medicine, Detroit, Michigan
- Karmanos Cancer Institute, Detroit, Michigan
| | - Matthew Labriola
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancer, Duke University, Durham, North Carolina
| | | | | | | | | | | | | | - Bicky Thapa
- Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | | | | | - Vadim S. Koshkin
- University of California San Francisco, San Francisco, California
| | - Erik Hernandez
- University of California San Francisco, San Francisco, California
| | | | - Andrew J. Armstrong
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute Center for Prostate and Urologic Cancer, Duke University, Durham, North Carolina
| | - Rana R. McKay
- University of California San Diego, La Jolla, California
| | | | | | - Pedro C. Barata
- Tulane University, New Orleans, Louisiana
- University Hospitals Seidman Cancer Center, Cleveland, Ohio
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12
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Austin BK, Firooz A, Valafar H, Blenda AV. An Updated Overview of Existing Cancer Databases and Identified Needs. BIOLOGY 2023; 12:1152. [PMID: 37627037 PMCID: PMC10452211 DOI: 10.3390/biology12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Our search of existing cancer databases aimed to assess the current landscape and identify key needs. We analyzed 71 databases, focusing on genomics, proteomics, lipidomics, and glycomics. We found a lack of cancer-related lipidomic and glycomic databases, indicating a need for further development in these areas. Proteomic databases dedicated to cancer research were also limited. To assess overall progress, we included human non-cancer databases in proteomics, lipidomics, and glycomics for comparison. This provided insights into advancements in these fields over the past eight years. We also analyzed other types of cancer databases, such as clinical trial databases and web servers. Evaluating user-friendliness, we used the FAIRness principle to assess findability, accessibility, interoperability, and reusability. This ensured databases were easily accessible and usable. Our search summary highlights significant growth in cancer databases while identifying gaps and needs. These insights are valuable for researchers, clinicians, and database developers, guiding efforts to enhance accessibility, integration, and usability. Addressing these needs will support advancements in cancer research and benefit the wider cancer community.
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Affiliation(s)
- Brittany K. Austin
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
| | - Ali Firooz
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Homayoun Valafar
- Department of Computer Science and Engineering, College of Engineering and Computing, University of South Carolina, Columbia, SC 29208, USA;
| | - Anna V. Blenda
- Department of Biomedical Sciences, School of Medicine Greenville, University of South Carolina, Greenville, SC 29605, USA;
- Prisma Health Cancer Institute, Prisma Health, Greenville, SC 29605, USA
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13
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Li Z, Wang M, Peng D, Liu J, Xie Y, Dai Z, Zou X. Identification of Chemical-Disease Associations Through Integration of Molecular Fingerprint, Gene Ontology and Pathway Information. Interdiscip Sci 2022; 14:683-696. [PMID: 35391615 DOI: 10.1007/s12539-022-00511-5] [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: 10/28/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The identification of chemical-disease association types is helpful not only to discovery lead compounds and study drug repositioning, but also to treat disease and decipher pathomechanism. It is very urgent to develop computational method for identifying potential chemical-disease association types, since wet methods are usually expensive, laborious and time-consuming. In this study, molecular fingerprint, gene ontology and pathway are utilized to characterize chemicals and diseases. A novel predictor is proposed to recognize potential chemical-disease associations at the first layer, and further distinguish whether their relationships belong to biomarker or therapeutic relations at the second layer. The prediction performance of current method is assessed using the benchmark dataset based on ten-fold cross-validation. The practical prediction accuracies of the first layer and the second layer are 78.47% and 72.07%, respectively. The recognition ability for lead compounds, new drug indications, potential and true chemical-disease association pairs has also been investigated and confirmed by constructing a variety of datasets and performing a series of experiments. It is anticipated that the current method can be considered as a powerful high-throughput virtual screening tool for drug researches and developments.
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Affiliation(s)
- Zhanchao Li
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangzhou, 510006, People's Republic of China.
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of Traditional Chinese Medicine, Guangzhou, 510006, People's Republic of China.
| | - Mengru Wang
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Dongdong Peng
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China
| | - Yun Xie
- HuiZhou University, Huizhou, 516007, People's Republic of China
| | - Zong Dai
- School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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14
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Keegan NM, Vasselman SE, Barnett ES, Nweji B, Carbone EA, Blum A, Morris MJ, Rathkopf DE, Slovin SF, Danila DC, Autio KA, Scher HI, Kantoff PW, Abida W, Stopsack KH. Clinical annotations for prostate cancer research: Defining data elements, creating a reproducible analytical pipeline, and assessing data quality. Prostate 2022; 82:1107-1116. [PMID: 35538298 PMCID: PMC9246896 DOI: 10.1002/pros.24363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/04/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Routine clinical data from clinical charts are indispensable for retrospective and prospective observational studies and clinical trials. Their reproducibility is often not assessed. We developed a prostate cancer-specific database for clinical annotations and evaluated data reproducibility. METHODS For men with prostate cancer who had clinical-grade paired tumor-normal sequencing at a comprehensive cancer center, we performed team-based retrospective data collection from the electronic medical record using a defined source hierarchy. We developed an open-source R package for data processing. With blinded repeat annotation by a reference medical oncologist, we assessed data completeness, reproducibility of team-based annotations, and impact of measurement error on bias in survival analyses. RESULTS Data elements on demographics, diagnosis and staging, disease state at the time of procuring a genomically characterized sample, and clinical outcomes were piloted and then abstracted for 2261 patients (with 2631 samples). Completeness of data elements was generally high. Comparing to the repeat annotation by a medical oncologist blinded to the database (100 patients/samples), reproducibility of annotations was high; T stage, metastasis date, and presence and date of castration resistance had lower reproducibility. Impact of measurement error on estimates for strong prognostic factors was modest. CONCLUSIONS With a prostate cancer-specific data dictionary and quality control measures, manual clinical annotations by a multidisciplinary team can be scalable and reproducible. The data dictionary and the R package for reproducible data processing are freely available to increase data quality and efficiency in clinical prostate cancer research.
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Affiliation(s)
- Niamh M. Keegan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ethan S. Barnett
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barbara Nweji
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily A. Carbone
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander Blum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael J. Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Dana E. Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Susan F Slovin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Daniel C. Danila
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Karen A. Autio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Howard I. Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Philip W. Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Correspondence: Wassim Abida and Konrad Stopsack, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; Phone (646) 422-4633, and
| | - Konrad H. Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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15
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Ethnic Pharmacogenomic Differences in the Management of Asian Patients with Metastatic Prostate Cancer. Cancers (Basel) 2022; 14:cancers14020407. [PMID: 35053569 PMCID: PMC8773846 DOI: 10.3390/cancers14020407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/16/2022] Open
Abstract
Progression to metastatic disease occurs in about half of all men who develop prostate cancer (PC), one of the most common cancers in men worldwide. Androgen deprivation therapy has been the mainstay therapy for patients with metastatic PC (mPC) since the 1940s. In the last decade, there has been unprecedented advancement in systemic therapies, e.g., taxane, androgen-signalling pathway inhibitors, and biomarker-driven targeted therapies for various stages of disease, resulting in overall survival improvement. Adding to ongoing controversies over how best to treat these patients is the recognition that ethnicity may influence prognosis and outcomes. This review discusses recent evidence for the impacts of Asian ethnicity specifically, which includes environmental, sociocultural, and genetic factors, on the approach to pharmacological management of mPC. Clear inter-ethnic differences in drug tolerability, serious adverse events (AEs), and genetic heterogeneity must all be considered when dosing and scheduling for treatment, as well as designing future precision studies in PC.
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16
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Freeman MN, Jang A, Zhu J, Sanati F, Nandagopal L, Ravindranathan D, Desai A, Phone A, Nussenzveig R, Jaeger E, Caputo SA, Koshkin VS, Swami U, Basu A, Bilen MA, Agarwal N, Sartor O, Burgess EF, Barata PC. OUP accepted manuscript. Oncologist 2022; 27:220-227. [PMID: 35274720 PMCID: PMC8914485 DOI: 10.1093/oncolo/oyab057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background The outcomes of metastatic hormone-sensitive prostate cancer (mHSPC) have significantly improved through treatment intensification, yet Black representation in those studies is suboptimal. Methods A multi-institutional, retrospective analysis of Black men with mHSPC was conducted, focusing on baseline demographics, treatment patterns, genomic profiles, clinical outcomes including prostate-specific antigen response, time to castrate-resistant prostate cancer (CRPC), and subsequent treatments. Results A total of 107 patients, median age 64 years, 62% with de novo metastases at diagnosis and 64% with high-volume disease, were included. Twenty-nine patients (27%) were treated with androgen deprivation therapy (ADT) with and without first generation anti-androgens, while 20%, 38% and 5% received chemotherapy, abiraterone, and enzalutamide, respectively. At time of data cut-off, 57 (54%) patients had developed CRPC, with a median time to CRPC of 25.4 months (95% CI 20.3-30.4). The median time to CRPC was 46.3 months (18.9-73.7) and 23.4 months (18.6-28.2) for patients who received ADT with or without first-generation anti-androgens and treatment intensification, respectively. The 2-year survival rate was 93.3%, and estimated median overall survival of was 74.9 months (95% CI, 68.7-81.0). Most patients (90%) underwent germline testing; the most frequent known alterations were found within the DNA repair group of genes. Somatic testing revealed pathogenic alterations of interest, notably TP53 (24%) and CDK12 (12%). Conclusion In our cohort, Black men with mHSPC presented with a high proportion of de novo metastases and high-volume disease. Treatment outcomes were very favorable with ADT-based regimens. The genomic landscape suggests different molecular profile relative to White patients with potential therapeutic implications.
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Affiliation(s)
| | | | - Jason Zhu
- Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Farhad Sanati
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | | | | | - Arpita Desai
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Audrey Phone
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Roberto Nussenzveig
- Huntsman Cancer Institute-University of Utah Health Care, Salt Lake City, UT, USA
| | - Ellen Jaeger
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sydney A Caputo
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Vadim S Koshkin
- University of California San Francisco, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Umang Swami
- Huntsman Cancer Institute-University of Utah Health Care, Salt Lake City, UT, USA
| | - Arnab Basu
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mehmet A Bilen
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Neeraj Agarwal
- Huntsman Cancer Institute-University of Utah Health Care, Salt Lake City, UT, USA
| | - Oliver Sartor
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Pedro C Barata
- Corresponding author: Pedro C. Barata, Department of Medicine, Tulane University Medical School, 131 S. Robertson Building, 131 S. Robertson Street, New Orleans, LA 70112, USA. Tel: 504-988-1236,
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17
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Fougner V, Hasselbalch B, Lassen U, Weischenfeldt J, Poulsen HS, Urup T. Implementing targeted therapies in the treatment of glioblastoma: Previous shortcomings, future promises, and a multimodal strategy recommendation. Neurooncol Adv 2022; 4:vdac157. [PMID: 36325372 PMCID: PMC9616055 DOI: 10.1093/noajnl/vdac157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023] Open
Abstract
The introduction of targeted therapies to the field of oncology has prolonged the survival of several tumor types. Despite extensive research and numerous trials, similar outcomes have unfortunately not been realized for glioblastoma. For more than 15 years, the standard treatment of glioblastoma has been unchanged. This review walks through the elements that have challenged the success of previous trials and highlight some future promises. Concurrently, this review describes how institutions, through a multimodal and comprehensive strategy with 4 essential components, may increase the probability of finding a meaningful role for targeted therapies in the treatment of glioblastoma. These components are (1) prudent trial designs, (2) considered drug and target selection, (3) harnessed real-world clinical and molecular evidence, and (4) incorporation of translational research.
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Affiliation(s)
- Vincent Fougner
- Department for Cancer Treatment, DCCC—Brain Tumor Center, Rigshospitalet, Copenhagen, Capitol Region of Denmark, Denmark
| | - Benedikte Hasselbalch
- Department for Cancer Treatment, DCCC—Brain Tumor Center, Rigshospitalet, Copenhagen, Capitol Region of Denmark, Denmark
| | - Ulrik Lassen
- Department for Cancer Treatment, DCCC—Brain Tumor Center, Rigshospitalet, Copenhagen, Capitol Region of Denmark, Denmark
| | - Joachim Weischenfeldt
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Hans Skovgaard Poulsen
- Department for Cancer Treatment, DCCC—Brain Tumor Center, Rigshospitalet, Copenhagen, Capitol Region of Denmark, Denmark
| | - Thomas Urup
- Department for Cancer Treatment, DCCC—Brain Tumor Center, Rigshospitalet, Copenhagen, Capitol Region of Denmark, Denmark
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