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Prosz A, Sahgal P, Huffman BM, Sztupinszki Z, Morris CX, Chen D, Börcsök J, Diossy M, Tisza V, Spisak S, Likasitwatanakul P, Rusz O, Csabai I, Cecchini M, Baca Y, Elliott A, Enzinger P, Singh H, Ubellaker J, Lazaro JB, Cleary JM, Szallasi Z, Sethi NS. Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting. NPJ Precis Oncol 2024; 8:87. [PMID: 38589664 PMCID: PMC11001913 DOI: 10.1038/s41698-024-00561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in cancer. HR-deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of HR deficiency in gastric and esophageal adenocarcinoma (GEA) still lacks diagnostic and functional validation. Using whole exome and genome sequencing data, we found that a significant subset of GEA, but very few colorectal adenocarcinomas, show evidence of HR deficiency by mutational signature analysis (HRD score). High HRD gastric cancer cell lines demonstrated functional HR deficiency by RAD51 foci assay and increased sensitivity to platinum chemotherapy and PARP inhibitors. Of clinical relevance, analysis of three different GEA patient cohorts demonstrated that platinum treated HR deficient cancers had better outcomes. A gastric cancer cell line with strong sensitivity to cisplatin showed HR proficiency but exhibited NER deficiency by two photoproduct repair assays. Single-cell RNA-sequencing revealed that, in addition to inducing apoptosis, cisplatin treatment triggered ferroptosis in a NER-deficient gastric cancer, validated by intracellular GSH assay. Overall, our study provides preclinical evidence that a subset of GEAs harbor genomic features of HR and NER deficiency and may therefore benefit from platinum chemotherapy and PARP inhibitors.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Brandon M Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Clare X Morris
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Sandor Spisak
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Michael Cecchini
- Department of Medical Oncology, Center for Gastrointestinal Cancers, Yale Medical Center, New Haven, CT, USA
| | | | | | - Peter Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessalyn Ubellaker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary.
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Szallasi Z, Diossy M, Tisza V, Li H, Sahgal P, Zhou J, Sztupinszki Z, Young D, Nuosome D, Kuo C, Jiang J, Chen Y, Ebner R, Sesterhenn I, Moncur J, Chesnut G, Petrovics G, T Klus G, Valcz G, Nuzzo P, Ribli D, Börcsök J, Prósz A, Krzystanek M, Ried T, Szüts D, Rizwan K, Kaochar S, Pathania S, D'Andrea A, Csabai I, Srivastava S, Freedman M, Dobi A, Spisak S. Increased frequency of CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression without inducing homologous recombination deficiency. Res Sq 2024:rs.3.rs-3995251. [PMID: 38645014 PMCID: PMC11030533 DOI: 10.21203/rs.3.rs-3995251/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
We analyzed genomic data derived from the prostate cancer of African and European American men in order to identify differences that may contribute to racial disparity of outcome and that could also define novel therapeutic strategies. In addition to analyzing patient derived next generation sequencing data, we performed FISH based confirmatory studies of Chromodomain helicase DNA-binding protein 1 (CHD1) loss on prostate cancer tissue microarrays. We created CRISPR edited, CHD1 deficient prostate cancer cell lines for genomic, drug sensitivity and functional homologous recombination (HR) activity analysis. We found that subclonal deletion of CHD1 is nearly three times as frequent in prostate tumors of African American men than in men of European ancestry and it associates with rapid disease progression. We further showed that CHD1 deletion is not associated with homologous recombination deficiency associated mutational signatures in prostate cancer. In prostate cancer cell line models CHD1 deletion did not induce HR deficiency as detected by RAD51 foci formation assay or mutational signatures, which was consistent with the moderate increase of olaparib sensitivity. CHD1 deficient prostate cancer cells, however, showed higher sensitivity to talazoparib. CHD1 loss may contribute to worse outcome of prostate cancer in African American men. A deeper understanding of the interaction between CHD1 loss and PARP inhibitor sensitivity will be needed to determine the optimal use of targeted agents such as talazoparib in the context of castration resistant prostate cancer.
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Affiliation(s)
| | | | - Viktoria Tisza
- Institute of Enzymology, Research Centre for Natural Sciences
| | - Hua Li
- Center for Prostate Cancer Research
| | | | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Denise Young
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Darryl Nuosome
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Claire Kuo
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Jiji Jiang
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yongmei Chen
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department Uniformed Services University of the Health Sciences, Bethesda, MD
| | | | | | - Joel Moncur
- Joint Pathology Center, Silver Spring, Maryland, USA
| | - Gregory Chesnut
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Gyorgy Petrovics
- Computational Health Informatics Program, Boston Children's Hospital, USA, Harvard Medical School, Boston, USA
| | | | - Gábor Valcz
- ELKH Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Pier Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dezso Ribli
- Department of Physics of Complex Systems, Eotvos Lorand University, Budapest, Hungary
| | | | | | | | | | - Dávid Szüts
- HUN-REN Research Centre for Natural Sciences
| | - Kinza Rizwan
- Department of Medicine, Baylor College of Medicine, Houston, USA
| | - Salma Kaochar
- Department of Medicine, Baylor College of Medicine, Houston, USA
| | | | | | | | - Shib Srivastava
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Matthew Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Sandor Spisak
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Mahlow J, Barry M, Albertson DJ, Jo YJ, Balatico M, Seasor T, Gebrael G, Kumar SA, Sayegh N, Tripathi N, Agarwal N, Swami U, Sirohi D. Histologic patterns in prostatic adenocarcinoma are not predictive of mutations in the homologous recombination repair pathway. Hum Pathol 2024; 144:28-33. [PMID: 38278448 DOI: 10.1016/j.humpath.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Somatic or germline homologous recombination repair (HRR) pathway gene mutations are commonly detected in prostate cancer, especially in advanced disease, and are associated with response to poly (ADP-ribose) polymerase (PARP) inhibitors. In this study, we evaluated whether histological patterns are predictive of HRR pathway gene mutations. The study population comprised 130 patients with advanced prostate carcinoma who underwent comprehensive genomic profiling (CGP) of tumor tissue at a CLIA-certified laboratory. HRR genes in the study included BRCA1, BRCA2, ATM, BARD1, BRIP, CHEK2, MRE11A, NBN, PALB2, RAD51C, RAD51D, EMSY, ATR, CHEK1, and FAM175A. Overall, 38 patients had mutations in BRCA1/2, 36 in other HRR genes, and 56 were negative for HRR mutations. All cases were re-reviewed and quantified by two genitourinary pathologists blinded to mutational status for the following histological patterns of prostate carcinoma: cribriform, ductal, intraductal carcinoma (IDC), small cell carcinoma, signet ring-like pattern, and lobular carcinoma-like pattern. Discordances were resolved by consensus review. Histologic patterns were analyzed for any correlation with mutations in HRR pathway genes (grouped as BRCA1/2 mutated or non-BRCA1/2 mutated) compared to tumors without mutations in HRR genes by Chi-square testing. Patterns with >20 % and >30 % of tumor volume were additionally evaluated for correlation with mutational status. We found no significant association between HRR pathway mutations and cribriform pattern, IDC, ductal carcinoma, small cell carcinoma, signet ring-like pattern, or lobular carcinoma-like patterns. Tumors with >20 % or >30 % histologic patterns by volume also demonstrated no significant association with mutational status. This study suggests that histopathologic examination alone is insufficient to distinguish prostate cancer with germline or somatic mutations in HRR pathway genes, highlighting the continuing importance of ancillary molecular diagnostics in guiding therapy selection for prostate cancer patients who may benefit from PARP inhibitors.
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Affiliation(s)
- Jon Mahlow
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Marc Barry
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Daniel J Albertson
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Yeon Jung Jo
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Balatico
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Tori Seasor
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Georges Gebrael
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Shruti A Kumar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nicolas Sayegh
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nishita Tripathi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Umang Swami
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Deepika Sirohi
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT, USA.
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Baston C, Preda A, Iordache A, Olaru V, Surcel C, Sinescu I, Gingu C. How to Integrate Prostate Cancer Biomarkers in Urology Clinical Practice: An Update. Cancers (Basel) 2024; 16:316. [PMID: 38254807 PMCID: PMC10813985 DOI: 10.3390/cancers16020316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Nowadays, the management of prostate cancer has become more and more challenging due to the increasing number of available treatment options, therapeutic agents, and our understanding of its carcinogenesis and disease progression. Moreover, currently available risk stratification systems used to facilitate clinical decision-making have limitations, particularly in providing a personalized and patient-centered management strategy. Although prognosis and prostate cancer-specific survival have improved in recent years, the heterogenous behavior of the disease among patients included in the same risk prognostic group negatively impacts not only our clinical decision-making but also oncological outcomes, irrespective of the treatment strategy. Several biomarkers, along with available tests, have been developed to help clinicians in difficult decision-making scenarios and guide management strategies. In this review article, we focus on the scientific evidence that supports the clinical use of several biomarkers considered by professional urological societies (and included in uro-oncological guidelines) in the diagnosis process and specific difficult management strategies for clinically localized or advanced prostate cancer.
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Affiliation(s)
- Catalin Baston
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.B.); (V.O.); (C.S.); (I.S.); (C.G.)
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Adrian Preda
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Alexandru Iordache
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Vlad Olaru
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.B.); (V.O.); (C.S.); (I.S.); (C.G.)
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Cristian Surcel
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.B.); (V.O.); (C.S.); (I.S.); (C.G.)
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Ioanel Sinescu
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.B.); (V.O.); (C.S.); (I.S.); (C.G.)
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
| | - Constantin Gingu
- Department of Nephrology, Urology, Immunology and Immunology of Transplant, Dermatology, Allergology, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania; (C.B.); (V.O.); (C.S.); (I.S.); (C.G.)
- Center of Uronephrology and Kidney Transplantation, Fundeni Clinical Institute, 258 Fundeni Street, 022328 Bucharest, Romania;
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Elias R, Antonarakis ES. Rucaparib for metastatic castration-resistant prostate cancer: did TRITON3 deliver a trifecta? Transl Cancer Res 2023; 12:2448-2453. [PMID: 37969378 PMCID: PMC10643943 DOI: 10.21037/tcr-23-1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Affiliation(s)
- Roy Elias
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
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Li W, Gao L, Yi X, Shi S, Huang J, Shi L, Zhou X, Wu L, Ying J. Patient Assessment and Therapy Planning Based on Homologous Recombination Repair Deficiency. Genomics Proteomics Bioinformatics 2023; 21:962-975. [PMID: 36791952 PMCID: PMC10928375 DOI: 10.1016/j.gpb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/23/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Defects in genes involved in the DNA damage response cause homologous recombination repair deficiency (HRD). HRD is found in a subgroup of cancer patients for several tumor types, and it has a clinical relevance to cancer prevention and therapies. Accumulating evidence has identified HRD as a biomarker for assessing the therapeutic response of tumor cells to poly(ADP-ribose) polymerase inhibitors and platinum-based chemotherapies. Nevertheless, the biology of HRD is complex, and its applications and the benefits of different HRD biomarker assays are controversial. This is primarily due to inconsistencies in HRD assessments and definitions (gene-level tests, genomic scars, mutational signatures, or a combination of these methods) and difficulties in assessing the contribution of each genomic event. Therefore, we aim to review the biological rationale and clinical evidence of HRD as a biomarker. This review provides a blueprint for the standardization and harmonization of HRD assessments.
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Affiliation(s)
- Wenbin Li
- Department of Pathology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Gao
- Geneplus-Shenzhen, Shenzhen 518000, China; Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Yi
- Geneplus-Beijing, Beijing 102206, China
| | | | - Jie Huang
- National Institutes for Food and Drug Control, Beijing 100050, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center / National Clinical Research Center for Cancer / Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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Brown LC, Zhu J, Mauer E, Thiede SN, Macera L, Stein MM, Taxter T, Raghavan D, Burgess EF. RNA-Based Homologous Recombination Deficiency Signature Detects Homologous Recombination Deficiency-RNA+ Patients With and Without Homologous Recombination Repair Gene Pathogenic Alterations in Men With Prostate Cancer. JCO Precis Oncol 2023; 7:e2300378. [PMID: 38061006 DOI: 10.1200/po.23.00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE Homologous recombination deficiency (HRD) is a well-described phenotype of some prostate cancers; however, current biomarkers for HRD are imperfect and rely on detection of single gene alterations in the homologous recombination repair (HRR) pathway, which may not capture the complexity of HRD biology. RNA signature-based methods of HRD identification present a potentially dynamic assessment of the HRD phenotype; however, its relationship with HRR gene alterations is not well characterized in prostate cancer. METHODS A HRD assay on the basis of an RNA signature associated with biallelic BRCA1/2 loss was applied to a retrospective cohort study of 985 men with prostate cancer analyzed on the Tempus xT platform. HRD status was defined by a binary threshold on a continuous scale. RESULTS In this cohort, of the 126 (13%) patients found to be HRD+ by RNA signature (HRD-RNA+), 100 (79%) had no coexisting HRR gene alteration. Among samples with biallelic BRCA1/2 loss, 78% (7/9) were classified as HRD-RNA+, while 8% (2/25) of samples with BRCA1/2 monoallelic loss were HRD-RNA+. Biallelic and monoallelic ATM loss exhibited HRD-RNA+ at a lower prevalence: 6.7% (1/15) and 7.1% (1/14), respectively, compared with HRD-RNA+ prevalence among samples without any HRR gene loss (13%; 100/782). HRD-RNA+ was associated with a significantly higher prevalence of TP53 and AR gene alterations relative to HRD-RNA- after correction for multiple comparisons, 59% versus 39% (q = 0.003) and 23% versus 12% (q = 0.024), respectively. CONCLUSION Use of an RNA-based HRD signature significantly expands the fraction of patients with prostate cancer who may derive benefit from poly (ADP-ribose) polymerase inhibitors (PARPis) compared with using HRR gene mutations alone. Further studies are needed to evaluate functional HRD significance and inform future usage as a predictive biomarker for PARPi selection.
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Affiliation(s)
| | - Jason Zhu
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | | | | | | | | | | | - Derek Raghavan
- Levine Cancer Institute, Atrium Health, Charlotte, NC
- Veterans Administration Health Care Center, Charlotte, NC
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9
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Domrazek K, Pawłowski K, Jurka P. Usefulness of BRCA and ctDNA as Prostate Cancer Biomarkers: A Meta-Analysis. Cancers (Basel) 2023; 15:3452. [PMID: 37444562 DOI: 10.3390/cancers15133452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Prostate cancer represents the most common male urologic neoplasia. Tissue biopsies are the gold standard in oncology for diagnosing prostate cancer. We conducted a study to find the most reliable and noninvasive diagnostic tool. We performed a systematic review and meta-analysis of two biomarkers which we believe are the most interesting: BRCA (BRCA1 and 2) and ctDNA. Our systematic research yielded 248 articles. Forty-five duplicates were first excluded and, upon further examination, a further 203 articles were excluded on the basis of the inclusion and exclusion criteria, leaving 25 articles. A statistical analysis of the obtained data has been performed. With a collective calculation, BRCA1 was expressed in 2.74% of all cases from 24,212 patients examined and BRCA2 in 1.96% of cases from 20,480 patients. In a total calculation using ctDNA, it was observed that 89% of cases from 1198 patients exhibited high expression of circulating tumor DNA. To date, no ideal PCa biomarker has been found. Although BRCA1 and BRCA2 work well for breast and ovarian cancers, they do not seem to be reliable for prostate cancer. ctDNA seems to be a much better biomarker; however, there are few studies in this area. Further studies need to be performed.
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Affiliation(s)
- Kinga Domrazek
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Karol Pawłowski
- Department of Pathology and Veterinary Diagnostics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Piotr Jurka
- Department of Small Animal Diseases and Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159c, 02-776 Warsaw, Poland
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10
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Yang B, Jiang Y, Yang J, Zhou W, Yang T, Zhang R, Xu J, Guo H. Characterization of metabolism-associated molecular patterns in prostate cancer. BMC Urol 2023; 23:104. [PMID: 37280589 DOI: 10.1186/s12894-023-01275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Metabolism is a hallmark of cancer and it involves in resistance to antitumor treatment. Therefore, the purposes of this study are to classify metabolism-related molecular pattern and to explore the molecular and tumor microenvironment characteristics for prognosis predicting in prostate cancer. METHODS The mRNA expression profiles and the corresponding clinical information for prostate cancer patients from TCGA, cBioPortal, and GEO databases. Samples were classified using unsupervised non-negative matrix factorization (NMF) clustering based on differentially expressed metabolism-related genes (MAGs). The characteristics of disease-free survival (DFS), clinicopathological characteristics, pathways, TME, immune cell infiltration, response to immunotherapy, and sensitivity to chemotherapy between subclusters were explored. A prognostic signature was constructed by LASSO cox regression analysis based on differentially expressed MAGs and followed by the development for prognostic prediction. RESULTS A total of 76 MAGs between prostate cancer samples and non-tumorous samples were found, then 489 patients were divided into two metabolism-related subclusters for prostate cancer. The significant differences in clinical characteristics (age, T/N stage, Gleason) and DFS between two subclusters. Cluster 1 was associated with cell cycle and metabolism-related pathways, and epithelial-mesenchymal transition (EMT), etc., involved in cluster 2. Moreover, lower ESTIMATE/immune/stromal scores, lower expression of HLAs and immune checkpoint-related genes, and lower half-maximal inhibitory concentration (IC50) values in cluster 1 compared with cluster 2. The 10 MAG signature was identified and constructed a risk model for DFS predicting. The patients with high-risk scores showed poorer DFS. The area under the curve (AUC) values for 1-, 3-, 5-year DFS were 0.744, 0.731, 0.735 in TCGA-PRAD dataset, and 0.668, 0.712, 0.809 in GSE70768 dataset, 0.763, 0.802, 0.772 in GSE70769 dataset. Besides, risk score and Gleason score were identified as independent factors for DFS predicting, and the AUC values of risk score and Gleason score were respectively 0.743 and 0.738. The nomogram showed a favorable performance in DFS predicting. CONCLUSION Our data identified two metabolism-related molecular subclusters for prostate cancer that were distinctly characterized in prostate cancer. Metabolism-related risk profiles were also constructed for prognostic prediction.
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Affiliation(s)
- Bowei Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yongming Jiang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jun Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenbo Zhou
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Tongxin Yang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Rongchang Zhang
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jinming Xu
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haixiang Guo
- Department of Urology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.
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11
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Herberts C, Wyatt AW, Nguyen PL, Cheng HH. Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book 2023; 43:e390384. [PMID: 37207301 DOI: 10.1200/edbk_390384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Significant progress has been made in genetic and genomic testing for prostate cancer across the disease spectrum. Molecular profiling is increasingly relevant for routine clinical management, fueled in part by advancements in testing technology and integration of biomarkers into clinical trials. In metastatic prostate cancer, defects in DNA damage response genes are now established predictors of benefit to US Food and Drug Administration-approved poly (ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors, and trials are actively investigating these and other targeted treatment strategies in earlier disease states. Excitingly, opportunities for molecularly informed management beyond DNA damage response genes are also maturing. Germline genetic variants (eg, BRCA2 or MSH2/6) and polygenic germline risk scores are being investigated to inform cancer screening and active surveillance in at-risk carriers. RNA expression tests have recently gained traction in localized prostate cancer, enabling patient risk stratification and tailored treatment intensification via radiotherapy and/or androgen deprivation therapy for localized or salvage treatment. Finally, emerging minimally invasive circulating tumor DNA technology promises to enhance biomarker testing in advanced disease pending additional methodological and clinical validation. Collectively, genetic and genomic tests are rapidly becoming indispensable tools for informing the optimal clinical management of prostate cancer.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul L Nguyen
- Harvard Medical School, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Heather H Cheng
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA
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12
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Gillette CM, Yette GA, Cramer SD, Graham LS. Management of Advanced Prostate Cancer in the Precision Oncology Era. Cancers (Basel) 2023; 15:2552. [PMID: 37174018 PMCID: PMC10177563 DOI: 10.3390/cancers15092552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Prostate cancer (PC) is the second leading cause of cancer death in men in the United States. While diversified and improved treatment options for aggressive PC have improved patient outcomes, metastatic castration-resistant prostate cancer (mCRPC) remains incurable and an area of investigative therapeutic interest. This review will cover the seminal clinical data supporting the indication of new precision oncology-based therapeutics and explore their limitations, present utility, and potential in the treatment of PC. Systemic therapies for high-risk and advanced PC have experienced significant development over the past ten years. Biomarker-driven therapies have brought the field closer to the goal of being able to implement precision oncology therapy for every patient. The tumor agnostic approval of pembrolizumab (a PD-1 inhibitor) marked an important advancement in this direction. There are also several PARP inhibitors indicated for patients with DNA damage repair deficiencies. Additionally, theranostic agents for both imaging and treatment have further revolutionized the treatment landscape for PC and represent another advancement in precision medicine. Radiolabeled prostate-specific membrane antigen (PSMA) PET/CT is rapidly becoming a standard of care for diagnosis, and PSMA-targeted radioligand therapies have gained recent FDA approval for metastatic prostate cancer. These advances in precision-based oncology are detailed in this review.
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Affiliation(s)
- Claire M. Gillette
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.M.G.)
| | - Gabriel A. Yette
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.M.G.)
| | - Scott D. Cramer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (C.M.G.)
| | - Laura S. Graham
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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13
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Valsecchi AA, Dionisio R, Panepinto O, Paparo J, Palicelli A, Vignani F, Di Maio M. Frequency of Germline and Somatic BRCA1 and BRCA2 Mutations in Prostate Cancer: An Updated Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:cancers15092435. [PMID: 37173901 PMCID: PMC10177599 DOI: 10.3390/cancers15092435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/05/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
In prostate cancer (PC), the presence of BRCA somatic and/or germline mutation provides prognostic and predictive information. Meta-analysis aims to estimate the frequency of BRCA mutations in patients with PC (PCp). In November 2022, we reviewed literature searching for all articles testing the proportion of BRCA mutations in PCp, without explicit enrichment for familiar risk. The frequency of germline and somatic BRCA1 and/or BRCA2 mutations was described in three stage disease populations (any/metastatic/metastatic castration-resistant PC, mCRPC). Out of 2253 identified articles, 40 were eligible. Here, 0.73% and 1.20% of any stage PCp, 0.94% and 1.10% of metastatic PCp, and 1.21% and 1.10% of mCRPC patients carried germline and somatic BRCA1 mutation, respectively; 3.25% and 6.29% of any stage PCp, 4.51% and 10.26% of metastatic PCp, and 3.90% and 10.52% of mCRPC patients carried germline and somatic BRCA2 mutation, respectively; and 4.47% and 7.18% of any stage PCp, 5.84% and 10.94% of metastatic PCp, and 5.26% and 11.26% of mCRPC patients carried germline and somatic BRCA1/2 mutation, respectively. Somatic mutations are more common than germline and BRCA2 are more common than BRCA1 mutations; the frequency of mutations is higher in the metastatic setting. Despite that BRCA testing in PC is now standard in clinical practice, several open questions remain.
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Affiliation(s)
- Anna Amela Valsecchi
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
| | - Rossana Dionisio
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
| | - Olimpia Panepinto
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
| | - Jessica Paparo
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
| | - Andrea Palicelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Vignani
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
| | - Massimo Di Maio
- Department of Oncology, University of Turin, Ordine Mauriziano Hospital, 10128 Turin, Italy
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14
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Conway JR, Tewari AK, Camp SY, Han S, Crowdis J, He MX, Nyame YA, AlDubayan SH, Schultz N, Szallasi Z, Pomerantz MM, Freedman ML, Fong L, Nelson PS, Brown M, Salari K, Allen EV. Analysis of evolutionary dynamics and clonal architecture in prostate cancer. bioRxiv 2023:2023.03.23.533974. [PMID: 36993558 PMCID: PMC10055322 DOI: 10.1101/2023.03.23.533974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The extent to which clinical and genomic characteristics associate with prostate cancer clonal architecture, tumor evolution, and therapeutic response remains unclear. Here, we reconstructed the clonal architecture and evolutionary trajectories of 845 prostate cancer tumors with harmonized clinical and molecular data. We observed that tumors from patients who self-reported as Black had more linear and monoclonal architectures, despite these men having higher rates of biochemical recurrence. This finding contrasts with prior observations relating polyclonal architecture to adverse clinical outcomes. Additionally, we utilized a novel approach to mutational signature analysis that leverages clonal architecture to uncover additional cases of homologous recombination and mismatch repair deficiency in primary and metastatic tumors and link the origin of mutational signatures to specific subclones. Broadly, prostate cancer clonal architecture analysis reveals novel biological insights that may be immediately clinically actionable and provide multiple opportunities for subsequent investigation. Statement of significance Tumors from patients who self-reported as Black demonstrate linear and monoclonal evolutionary trajectories yet experience higher rates of biochemical recurrence. In addition, analysis of clonal and subclonal mutational signatures identifies additional tumors with potentially actionable alterations such as deficiencies in mismatch repair and homologous recombination.
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15
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Ritch EJ, Herberts C, Warner EW, Ng SWS, Kwan EM, Bacon JVW, Bernales CQ, Schönlau E, Fonseca NM, Giri VN, Maurice-Dror C, Vandekerkhove G, Jones SJM, Chi KN, Wyatt AW. A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes. NPJ Precis Oncol 2023; 7:27. [PMID: 36914848 PMCID: PMC10011564 DOI: 10.1038/s41698-023-00366-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Specific classes of DNA damage repair (DDR) defect can drive sensitivity to emerging therapies for metastatic prostate cancer. However, biomarker approaches based on DDR gene sequencing do not accurately predict DDR deficiency or treatment benefit. Somatic alteration signatures may identify DDR deficiency but historically require whole-genome sequencing of tumour tissue. We assembled whole-exome sequencing data for 155 high ctDNA fraction plasma cell-free DNA and matched leukocyte DNA samples from patients with metastatic prostate or bladder cancer. Labels for DDR gene alterations were established using deep targeted sequencing. Per sample mutation and copy number features were used to train XGBoost ensemble models. Naive somatic features and trinucleotide signatures were associated with specific DDR gene alterations but insufficient to resolve each class. Conversely, XGBoost-derived models showed strong performance including an area under the curve of 0.99, 0.99 and 1.00 for identifying BRCA2, CDK12, and mismatch repair deficiency in metastatic prostate cancer. Our machine learning approach re-classified several samples exhibiting genomic features inconsistent with original labels, identified a metastatic bladder cancer sample with a homozygous BRCA2 copy loss, and outperformed an existing exome-based classifier for BRCA2 deficiency. We present DARC Sign (DnA Repair Classification SIGNatures); a public machine learning tool leveraging clinically-practical liquid biopsy specimens for simultaneously identifying multiple types of metastatic prostate cancer DDR deficiencies. We posit that it will be useful for understanding differential responses to DDR-directed therapies in ongoing clinical trials and may ultimately enable prospective identification of prostate cancers with phenotypic evidence of DDR deficiency.
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Affiliation(s)
- Elie J Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Evan W Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jack V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elena Schönlau
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Veda N Giri
- Yale School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | | | - Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada. .,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
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16
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Tsujino T, Takai T, Hinohara K, Gui F, Tsutsumi T, Bai X, Miao C, Feng C, Gui B, Sztupinszki Z, Simoneau A, Xie N, Fazli L, Dong X, Azuma H, Choudhury AD, Mouw KW, Szallasi Z, Zou L, Kibel AS, Jia L. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. Nat Commun 2023; 14:252. [PMID: 36650183 PMCID: PMC9845315 DOI: 10.1038/s41467-023-35880-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Prostate cancer harboring BRCA1/2 mutations are often exceptionally sensitive to PARP inhibitors. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibition. Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient prostate cancer cells and identify previously unknown genes whose loss has a profound impact on PARP inhibitor response. Specifically, MMS22L deletion, frequently observed (up to 14%) in prostate cancer, renders cells hypersensitive to PARP inhibitors by disrupting RAD51 loading required for homologous recombination repair, although this response is TP53-dependent. Unexpectedly, loss of CHEK2 confers resistance rather than sensitivity to PARP inhibition through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARP inhibitor resistance caused by CHEK2 loss. Our findings may inform the use of PARP inhibitors beyond BRCA1/2-deficient tumors and support reevaluation of current biomarkers for PARP inhibition in prostate cancer.
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Affiliation(s)
- Takuya Tsujino
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Tomoaki Takai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fu Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Takeshi Tsutsumi
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Xiao Bai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chenkui Miao
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chao Feng
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Bin Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zsofia Sztupinszki
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Antoine Simoneau
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Ning Xie
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Adam S Kibel
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Jia
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
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17
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Huang RH, Hong YK, Du H, Ke WQ, Lin BB, Li YL. A machine learning framework develops a DNA replication stress model for predicting clinical outcomes and therapeutic vulnerability in primary prostate cancer. J Transl Med 2023; 21:20. [PMID: 36635710 PMCID: PMC9835390 DOI: 10.1186/s12967-023-03872-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Recent studies have identified DNA replication stress as an important feature of advanced prostate cancer (PCa). The identification of biomarkers for DNA replication stress could therefore facilitate risk stratification and help inform treatment options for PCa. Here, we designed a robust machine learning-based framework to comprehensively explore the impact of DNA replication stress on prognosis and treatment in 5 PCa bulk transcriptomic cohorts with a total of 905 patients. Bootstrap resampling-based univariate Cox regression and Boruta algorithm were applied to select a subset of DNA replication stress genes that were more clinically relevant. Next, we benchmarked 7 survival-related machine-learning algorithms for PCa recurrence using nested cross-validation. Multi-omic and drug sensitivity data were also utilized to characterize PCa with various DNA replication stress. We found that the hyperparameter-tuned eXtreme Gradient Boosting model outperformed other tuned models and was therefore used to establish a robust replication stress signature (RSS). RSS demonstrated superior performance over most clinical features and other PCa signatures in predicting PCa recurrence across cohorts. Lower RSS was characterized by enriched metabolism pathways, high androgen activity, and a favorable prognosis. In contrast, higher RSS was significantly associated with TP53, RB1, and PTEN deletion, exhibited increased proliferation and DNA replication stress, and was more immune-suppressive with a higher chance of immunotherapy response. In silico screening identified 13 potential targets (e.g. TOP2A, CDK9, and RRM2) from 2249 druggable targets, and 2 therapeutic agents (irinotecan and topotecan) for RSS-high patients. Additionally, RSS-high patients were more responsive to taxane-based chemotherapy and Poly (ADP-ribose) polymerase inhibitors, whereas RSS-low patients were more sensitive to androgen deprivation therapy. In conclusion, a robust machine-learning framework was used to reveal the great potential of RSS for personalized risk stratification and therapeutic implications in PCa.
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Affiliation(s)
- Rong-Hua Huang
- Department of Anesthesiology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
| | - Ying-Kai Hong
- Department of Urology, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, Guangdong, China
| | - Heng Du
- Department of Secretion, Baoji Central Hospital, Baoji, 721008, Shaanxi, China
| | - Wei-Qi Ke
- Department of Anesthesiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515000, Guangdong, China
| | - Bing-Biao Lin
- Department of Urology, Kidney and Urology Center, Pelvic Floor Disorders Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518000, Guangdong, China.
| | - Ya-Lan Li
- Department of Anesthesiology, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China.
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18
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Mouw KW, Choudhury AD. Development of PARP Inhibitors in Targeting Castration-Resistant Prostate Cancer. Cancer Treat Res 2023; 186:103-124. [PMID: 37978133 DOI: 10.1007/978-3-031-30065-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Prostate cancer is a genetically heterogenous disease and a subset of prostate tumors harbor alterations in DNA damage and repair (DDR) genes. Prostate tumor DDR gene alterations can arise via germline or somatic events and are enriched in high-grade and advanced disease. Alterations in genes in the homologous recombination (HR) repair pathway are associated with sensitivity to PARP inhibition in breast and ovarian cancer, and data from recently completed randomized trials also demonstrate benefit of PARP inhibitor therapy in patients with advanced metastatic castration-resistant prostate cancer (mCRPC) and tumor HR gene alterations. PARP inhibitors have been investigated in first-line mCRPC in biomarker-selected and unselected populations, and are currently under study in earlier disease states in patients with DDR gene alterations. This chapter focuses on the current state of PARP inhibitor development in prostate cancer with particular emphasis on biomarkers and combination therapy approaches.
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Affiliation(s)
- Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham & Women's Hospital, Harvard Medical School, 450 Brookline Ave., HIM 328, Boston, MA, 02215, USA.
| | - Atish D Choudhury
- Harvard Medical School, Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave., Dana 930, Boston, MA, 02215, USA
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19
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Abstract
Prostate cancer (PCa) is characterized by profound genomic heterogeneity. Recent advances in personalized treatment entail an increasing need of genomic profiling. For localized PCa, gene expression assays can support clinical decisions regarding active surveillance and adjuvant treatment. In metastatic PCa, homologous recombination deficiency, microsatellite instability-high (MSI-H), and CDK12 deficiency constitute main actionable alterations. Alterations in DNA repair genes confer variable sensitivities to poly(ADP-ribose)polymerase inhibitors, and the use of genomic instability assays as predictive biomarker is still incipient. MSI can be assessed by immunohistochemistry To date there is a lack of consensus as to testing standards.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, Bern 3010, Switzerland
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, 1600 Divisadero Street, Suite H-1031, San Francisco, CA 94115, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St Seattle, WA 98195-7110, USA
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, 3008, Switzerland.
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Shi X, Sun Y, Shen C, Zhang Y, Shi R, Zhang F, Liao T, Lv G, Zhu Z, Jiao L, Li P, Xu T, Qu N, Huang N, Hu J, Zhang T, Gu Y, Qin G, Guan H, Pu W, Li Y, Geng X, Zhang Y, Chen T, Huang S, Zhang Z, Ge S, Wang W, Xu W, Yu P, Lu Z, Wang Y, Guo L, Wang Y, Guo T, Ji Q, Wei W. Integrated proteogenomic characterization of medullary thyroid carcinoma. Cell Discov 2022; 8:120. [DOI: 10.1038/s41421-022-00479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractMedullary thyroid carcinoma (MTC) is a rare neuroendocrine malignancy derived from parafollicular cells (C cells) of the thyroid. Here we presented a comprehensive multi-omics landscape of 102 MTCs through whole-exome sequencing, RNA sequencing, DNA methylation array, proteomic and phosphoproteomic profiling. Integrated analyses identified BRAF and NF1 as novel driver genes in addition to the well-characterized RET and RAS proto-oncogenes. Proteome-based stratification of MTCs revealed three molecularly heterogeneous subtypes named as: (1) Metabolic, (2) Basal and (3) Mesenchymal, which are distinct in genetic drivers, epigenetic modification profiles, clinicopathologic factors and clinical outcomes. Furthermore, we explored putative therapeutic targets of each proteomic subtype, and found that two tenascin family members TNC/TNXB might serve as potential prognostic biomarkers for MTC. Collectively, our study expands the knowledge of MTC biology and therapeutic vulnerabilities, which may serve as an important resource for future investigation on this malignancy.
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Mcnevin CS, Cadoo K, Baird A, Finn SP, Mcdermott R. PARP Inhibitors in Advanced Prostate Cancer in Tumors with DNA Damage Signatures. Cancers (Basel) 2022; 14:4751. [PMID: 36230674 PMCID: PMC9564112 DOI: 10.3390/cancers14194751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary This review paper seeks to summarize the current literature on the role of PARP Inhibitors in Advanced Prostate Cancer in tumors with defects in genes associated with DNA damage repair. It will give particular attention to the role of PARPi in tumors with non-BRCA DNA damage repair genes. The aim of this review is to summarize the literature on PARPi and their activity treating BRCA and non BRCA tumors with DNA damage signatures. Abstract Since 2010, significant progress has been made in the treatment of metastatic castrate resistant prostate cancer (mCRPC). While these advancements have improved survival, mCRPC remains a lethal disease, with a precision medicine framework that is lagging behind compared to other cancers. Poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) studies in prostate cancer (PCa) have focused primarily on the homologous recombination repair (HRR) genes, specifically BRCA1 and BRCA2. While homologous recombination deficiency (HRD) can be prompted by germline or somatic BRCA1/2 genetic mutations, it can also exist in tumors with intact BRCA1/BRCA2 genes. While the sensitivity of PARPi in tumors with non-BRCA DNA damage signatures is not as well established, it has been suggested that genomic alterations in DNA damage repair (DDR) genes other than BRCA may confer synthetic lethality with PARPI in mCRPC. The aim of this review is to summarize the literature on PARPi and their activity treating BRCA and non BRCA tumors with DNA damage signatures.
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Crowdis J, Balch S, Sterlin L, Thomas BS, Camp SY, Dunphy M, Anastasio E, Shah S, Damon AL, Ramos R, Sosa DM, Small IK, Tomson BN, Nguyen CM, Mcgillicuddy M, Chastain PS, He MX, Cheung AT, Wankowicz S, Tewari AK, Kim D, Aldubayan SH, Dowdye A, Zola B, Nowak J, Manarite J, Gunn IH, Olson B, Lander ES, Painter CA, Wagle N, Van Allen EM. A patient-driven clinicogenomic partnership for metastatic prostate cancer. Cell Genomics 2022; 2:100169. [PMID: 36177448 PMCID: PMC9518748 DOI: 10.1016/j.xgen.2022.100169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular profiling studies have enabled discoveries for metastatic prostate cancer (MPC) but have predominantly occurred in academic medical institutions and involved non-representative patient populations. We established the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to involve patients with MPC living anywhere in the US and Canada in molecular research. Here, we present results from our partnership with the first 706 MPCproject participants. While 41% of patient partners live in rural, physician-shortage, or medically underserved areas, the MPCproject has not yet achieved racial diversity, a disparity that demands new initiatives detailed herein. Among molecular data from 333 patient partners (572 samples), exome sequencing of 63 tumor and 19 cell-free DNA (cfDNA) samples recapitulated known findings in MPC, while inexpensive ultra-low-coverage sequencing of 318 cfDNA samples revealed clinically relevant AR amplifications. This study illustrates the power of a growing, longitudinal partnership with patients to generate a more representative understanding of MPC. Crowdis et al. describe the MPCproject (mpcproject.org), a decentralized initiative to partner with patients with metastatic prostate cancer in the US and Canada to accelerate molecular research. The authors describe clinicogenomic results from the first 706 geographically diverse patient partners and lay the foundation for sustained and inclusive partnership in this disease.
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Cresta Morgado P, Mateo J. Clinical implications of homologous recombination repair mutations in prostate cancer. Prostate 2022; 82 Suppl 1:S45-S59. [PMID: 35657156 DOI: 10.1002/pros.24352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/28/2022] [Indexed: 11/06/2022]
Abstract
Prostate cancer is a disease with significant interpatient genomics, with a proportion of patients presenting mutations in key homologous recombination repair (HRR) gene aberrations, particularly in late-stage disease. A better understanding of the genomic landscape of prostate cancer and the prognostic and predictive value of HRR mutations could lead to more precise care for prostate cancer patients. BRCA1/2 mutations are associated with a more aggressive disease course and higher risk of developing lethal prostate cancer, but also identify patients who could benefit from directed therapeutic strategies with PARP inhibitors. Other HRR mutations are also frequent but their prognostic and predictive value for prostate cancer patients is less clear. Moreover, a proportion of these mutations are associated with inherited germline defects, being relevant for the patients' risk of second malignancies but also to inform their relatives' risk of cancer through cascade testing. In this manuscript, we review current knowledge of the prognostic and predictive value for different HHR alterations across the different prostate cancer disease states. Additionally, we assess the challenges to implement genomic testing in clinical practice for prostate cancer patients.
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Affiliation(s)
- Pablo Cresta Morgado
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
| | - Joaquin Mateo
- Medical Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Prostate Cancer Translational Research Group, Barcelona, Spain
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Chiu PKF, Lee EKC, Chan MTY, Chan WHC, Cheung MH, Lam MHC, Ma ESK, Poon DMC. Genetic Testing and Its Clinical Application in Prostate Cancer Management: Consensus Statements from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology. Front Oncol 2022; 12:962958. [PMID: 35924163 PMCID: PMC9339641 DOI: 10.3389/fonc.2022.962958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background In recent years, indications for genetic testing in prostate cancer (PC) have expanded from patients with a family history of prostate and/or related cancers to those with advanced castration-resistant disease, and even to early PC patients for determination of the appropriateness of active surveillance. The current consensus aims to provide guidance to urologists, oncologists and pathologists working with Asian PC patients on who and what to test for in selected populations. Methods A joint consensus panel from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology was convened over a series of 5 physical and virtual meetings. A background literature search on genetic testing in PC was performed in PubMed, ClinicalKey, EBSCOHost, Ovid and ProQuest, and three working subgroups were formed to review and present the relevant evidence. Meeting agendas adopted a modified Delphi approach to ensure that discussions proceed in a structured, iterative and balanced manner, which was followed by an anonymous voting on candidate statements. Of 5 available answer options, a consensus statement was accepted if ≥ 75% of the panelists chose “Accept Completely” (Option A) or “Accept with Some Reservation” (Option B). Results The consensus was structured into three parts: indications for testing, testing methods, and therapeutic implications. A list of 35 candidate statements were developed, of which 31 were accepted. The statements addressed questions on the application of PC genetic testing data and guidelines to Asian patients, including patient selection for germline testing, selection of gene panel and tissue sample, provision of genetic counseling, and use of novel systemic treatments in metastatic castration-resistant PC patients. Conclusion This consensus provides guidance to urologists, oncologists and pathologists working with Asian patients on indications for genetic testing, testing methods and technical considerations, and associated therapeutic implications.
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Affiliation(s)
- Peter K. F. Chiu
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eric K. C. Lee
- Department of Clinical Oncology, Tuen Mun Hospital, Hong Kong SAR, China
| | - Marco T. Y. Chan
- Division of Urology, Department of Surgery, Tuen Mun Hospital, Hong Kong SAR, China
| | - Wilson H. C. Chan
- Division of Urology, Department of Surgery, United Christian Hospital, Hong Kong SAR, China
| | - M. H. Cheung
- Division of Urology, Department of Surgery, Tseung Kwan O Hospital, Hong Kong SAR, China
| | - Martin H. C. Lam
- Department of Oncology, United Christian Hospital, Hong Kong SAR, China
| | - Edmond S. K. Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Darren M. C. Poon
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- Comprehensive Oncology Centre, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
- *Correspondence: Darren M. C. Poon,
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25
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Peng H, Wang Y, Wang P, Huang C, Liu Z, Wu C. A Risk Model Developed Based on Homologous Recombination Deficiency Predicts Overall Survival in Patients With Lower Grade Glioma. Front Genet 2022; 13:919391. [PMID: 35846118 PMCID: PMC9283922 DOI: 10.3389/fgene.2022.919391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
The role of homologous recombination deficiency (HRD) in lower grade glioma (LGG) has not been elucidated, and accurate prognostic prediction is also important for the treatment and management of LGG. The aim of this study was to construct an HRD-based risk model and to explore the immunological and molecular characteristics of this risk model. The HRD score threshold = 10 was determined from 506 LGG samples in The Cancer Genome Atlas cohort using the best cut-off value, and patients with high HRD scores had worse overall survival. A total of 251 HRD-related genes were identified by analyzing differentially expressed genes, 182 of which were associated with survival. A risk score model based on HRD-related genes was constructed using univariate Cox regression, least absolute shrinkage and selection operator regression, and stepwise regression, and patients were divided into high- and low-risk groups using the median risk score. High-risk patients had significantly worse overall survival than low-risk patients. The risk model had excellent predictive performance for overall survival in LGG and was found to be an independent risk factor. The prognostic value of the risk model was validated using an independent cohort. In addition, the risk score was associated with tumor mutation burden and immune cell infiltration in LGG. High-risk patients had higher HRD scores and “hot” tumor immune microenvironment, which could benefit from poly-ADP-ribose polymerase inhibitors and immune checkpoint inhibitors. Overall, this big data study determined the threshold of HRD score in LGG, identified HRD-related genes, developed a risk model based on HRD-related genes, and determined the molecular and immunological characteristics of the risk model. This provides potential new targets for future targeted therapies and facilitates the development of individualized immunotherapy to improve prognosis.
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Affiliation(s)
- Hao Peng
- Department of Neurosurgery, Hainan General Hospital, Haikou, China
- Department of Neurosurgery, The Second People’s Hospital of Hainan Province, Wuzhishan, China
| | - Yibiao Wang
- Department of Neurosurgery, Hainan General Hospital, Haikou, China
| | - Pengcheng Wang
- Department of Neurosurgery, Hainan General Hospital, Haikou, China
| | - Chuixue Huang
- Department of Neurosurgery, Hainan General Hospital, Haikou, China
| | - Zhaohui Liu
- Department of Neurosurgery, Hainan General Hospital, Haikou, China
| | - Changwu Wu
- Institute of Anatomy, University of Leipzig, Leipzig, Germany
- Department of Neurosurgery, Xiangya Hospital, Central-South University, Changsha, China
- *Correspondence: Changwu Wu,
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Gillessen S, Armstrong A, Attard G, Beer TM, Beltran H, Bjartell A, Bossi A, Briganti A, Bristow RG, Bulbul M, Caffo O, Chi KN, Clarke CS, Clarke N, Davis ID, de Bono JS, Duran I, Eeles R, Efstathiou E, Efstathiou J, Ekeke ON, Evans CP, Fanti S, Feng FY, Fizazi K, Frydenberg M, George D, Gleave M, Halabi S, Heinrich D, Higano C, Hofman MS, Hussain M, James N, Jones R, Kanesvaran R, Khauli RB, Klotz L, Leibowitz R, Logothetis C, Maluf F, Millman R, Morgans AK, Morris MJ, Mottet N, Mrabti H, Murphy DG, Murthy V, Oh WK, Ost P, O'Sullivan JM, Padhani AR, Parker C, Poon DMC, Pritchard CC, Rabah DM, Rathkopf D, Reiter RE, Rubin M, Ryan CJ, Saad F, Sade JP, Sartor O, Scher HI, Shore N, Skoneczna I, Small E, Smith M, Soule H, Spratt DE, Sternberg CN, Suzuki H, Sweeney C, Sydes MR, Taplin ME, Tilki D, Tombal B, Türkeri L, Uemura H, Uemura H, van Oort I, Yamoah K, Ye D, Zapatero A, Omlin A. Management of Patients with Advanced Prostate Cancer: Report from the Advanced Prostate Cancer Consensus Conference 2021. Eur Urol 2022; 82:115-141. [PMID: 35450732 DOI: 10.1016/j.eururo.2022.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Innovations in treatments, imaging, and molecular characterisation in advanced prostate cancer have improved outcomes, but various areas of management still lack high-level evidence to inform clinical practice. The 2021 Advanced Prostate Cancer Consensus Conference (APCCC) addressed some of these questions to supplement guidelines that are based on level 1 evidence. OBJECTIVE To present the voting results from APCCC 2021. DESIGN, SETTING, AND PARTICIPANTS The experts identified three major areas of controversy related to management of advanced prostate cancer: newly diagnosed metastatic hormone-sensitive prostate cancer (mHSPC), the use of prostate-specific membrane antigen ligands in diagnostics and therapy, and molecular characterisation of tissue and blood. A panel of 86 international prostate cancer experts developed the programme and the consensus questions. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The panel voted publicly but anonymously on 107 pre-defined questions, which were developed by both voting and non-voting panel members prior to the conference following a modified Delphi process. RESULTS AND LIMITATIONS The voting reflected the opinions of panellists and did not incorporate a standard literature review or formal meta-analysis. The answer options for the consensus questions received varying degrees of support from panellists, as reflected in this article and the detailed voting results reported in the Supplementary material. CONCLUSIONS These voting results from a panel of experts in advanced prostate cancer can help clinicians and patients to navigate controversial areas of management for which high-level evidence is scant. However, diagnostic and treatment decisions should always be individualised according to patient characteristics, such as the extent and location of disease, prior treatment(s), comorbidities, patient preferences, and treatment recommendations, and should also incorporate current and emerging clinical evidence and logistic and economic constraints. Enrolment in clinical trials should be strongly encouraged. Importantly, APCCC 2021 once again identified salient questions that merit evaluation in specifically designed trials. PATIENT SUMMARY The Advanced Prostate Cancer Consensus Conference is a forum for discussing current diagnosis and treatment options for patients with advanced prostate cancer. An expert panel votes on predefined questions focused on the most clinically relevant areas for treatment of advanced prostate cancer for which there are gaps in knowledge. The voting results provide a practical guide to help clinicians in discussing treatment options with patients as part of shared decision-making.
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Affiliation(s)
- Silke Gillessen
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Universita della Svizzera Italiana, Lugano, Switzerland; University of Berne, Berne, Switzerland; Division of Cancer Sciences, University of Manchester, Manchester, UK.
| | - Andrew Armstrong
- Duke Cancer Institute Center for Prostate and Urologic Cancers, Durham, NC, USA
| | - Gert Attard
- University College London Cancer Institute, London, UK
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Himisha Beltran
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anders Bjartell
- Department of Urology, Skåne University Hospital, Malmö, Sweden
| | - Alberto Bossi
- Genitourinary Oncology, Prostate Brachytherapy Unit, Gustave Roussy, Paris, France
| | - Alberto Briganti
- Unit of Urology/Division of Oncology, Urological Research Institute, IRCCS Ospedale San Raffaele, Vita-Salute San Raffaele University, Milan, Italy
| | - Robert G Bristow
- Division of Cancer Sciences, University of Manchester, Manchester, UK; Christie NHS Trust and CRUK Manchester Institute and Cancer Centre, Manchester, UK
| | - Muhammad Bulbul
- Division of Urology, Department of Surgery, American University of Beirut Medical Center, Beirut, Lebanon
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Trento, Italy
| | - Kim N Chi
- BC Cancer, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Caroline S Clarke
- Research Department of Primary Care & Population Health, Royal Free Campus, University College London, London, UK
| | - Noel Clarke
- The Christie and Salford Royal Hospitals, Manchester, UK
| | - Ian D Davis
- Monash University and Eastern Health, Victoria, Australia
| | - Johann S de Bono
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ignacio Duran
- Department of Medical Oncology, Hospital Universitario Marques de Valdecilla, IDIVAL, Santander, Spain
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | | | - Jason Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Onyeanunam Ngozi Ekeke
- Department of Surgery, University of Port Harcourt Teaching Hospital, Port Harcourt, Nigeria
| | | | - Stefano Fanti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Felix Y Feng
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
| | - Karim Fizazi
- Institut Gustave Roussy, University of Paris Saclay, Villejuif, France
| | - Mark Frydenberg
- Department of Surgery, Prostate Cancer Research Program, Monash University, Melbourne, Australia
| | - Dan George
- Departments of Medicine and Surgery, Duke Cancer Institute, Duke University, Durham, NC, USA
| | - Martin Gleave
- Urological Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Susan Halabi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Daniel Heinrich
- Department of Oncology and Radiotherapy, Innlandet Hospital Trust, Gjøvik, Norway
| | | | - Michael S Hofman
- Prostate Cancer Theranostics and Imaging Centre of Excellence, Department of Molecular Imaging and Therapeutic Nuclear Medicine, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Maha Hussain
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Nick James
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Robert Jones
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Raja B Khauli
- Department of Urology and the Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Laurence Klotz
- Division of Urology, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, ON, Canada
| | - Raya Leibowitz
- Oncology Institute, Shamir Medical Center and Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Chris Logothetis
- Department of Genitourinary Medical Oncology, David H. Koch Centre, MD Anderson Cancer Centre, Houston, TX, USA; Department of Clinical Therapeutics, University of Athens Alexandra Hospital, Athens, Greece
| | - Fernando Maluf
- Beneficiência Portuguesa de São Paulo, São Paulo, SP, Brazil; Departamento de Oncologia, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | | | - Alicia K Morgans
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael J Morris
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hind Mrabti
- National Institute of Oncology, Mohamed V University, Rabat, Morocco
| | - Declan G Murphy
- Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | | | - William K Oh
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, NY, USA
| | - Piet Ost
- Department of Radiation Oncology, Iridium Netwerk, Antwerp, Belgium; Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Joe M O'Sullivan
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Northern Ireland Cancer Centre, Belfast City Hospital, Belfast, UK
| | - Anwar R Padhani
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK; Mount Vernon Cancer Centre, London, UK
| | - Chris Parker
- The Institute of Cancer Research, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Darren M C Poon
- Comprehensive Oncology Centre, Hong Kong Sanatorium & Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Danny M Rabah
- The Cancer Research Chair, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Dana Rathkopf
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rob E Reiter
- University of California-Los Angeles, Los Angeles, CA, USA
| | - Mark Rubin
- Bern Center for Precision Medicine and Department for Biomedical Research, Bern, Switzerland
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Fred Saad
- Centre Hospitalier de Université de Montréal, Montreal, Canada
| | - Juan P Sade
- Instituto Alexander Fleming, Buenos Aires, Argentina
| | | | - Howard I Scher
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neal Shore
- Carolina Urologic Research Center, Myrtle Beach, SC, USA
| | - Iwona Skoneczna
- Rafal Masztak Grochowski Hospital and Maria Sklodowska Curie National Research Institute of Oncology, Warsaw, Poland
| | - Eric Small
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, San Francisco, CA, USA
| | - Matthew Smith
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Howard Soule
- Prostate Cancer Foundation, Santa Monica, CA, USA
| | - Daniel E Spratt
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | - Cora N Sternberg
- Englander Institute for Precision Medicine, Weill Cornell Medicine Division of Hematology and Oncology, Meyer Cancer Center, New York Presbyterian Hospital, New York, NY, USA
| | | | - Christopher Sweeney
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew R Sydes
- MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany; Department of Urology, Koc University Hospital, Istanbul, Turkey
| | | | - Levent Türkeri
- Department of Urology, M.A. Aydınlar Acıbadem University, Altunizade Hospital, Istanbul, Turkey
| | - Hiroji Uemura
- Yokohama City University Medical Center, Yokohama, Japan
| | - Hirotsugu Uemura
- Department of Urology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Inge van Oort
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kosj Yamoah
- Department of Radiation Oncology & Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, University of South Florida, Tampa, FL, USA
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Almudena Zapatero
- Department of Radiation Oncology, Hospital Universitario de La Princesa, Health Research Institute, Madrid, Spain
| | - Aurelius Omlin
- Department of Medical Oncology and Haematology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
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Dillon KM, Bekele RT, Sztupinszki Z, Hanlon T, Rafiei S, Szallasi Z, Choudhury AD, Mouw KW. PALB2 or BARD1 loss confers homologous recombination deficiency and PARP inhibitor sensitivity in prostate cancer. NPJ Precis Oncol 2022; 6:49. [PMID: 35768576 PMCID: PMC9242979 DOI: 10.1038/s41698-022-00291-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/08/2022] [Indexed: 12/02/2022] Open
Abstract
PARP inhibitors were recently approved for treatment of molecularly-defined subsets of metastatic castrate-resistant prostate cancer (mCRPC) patients. Although the PARP inhibitor olaparib was approved for use in patients with a mutation in one of fourteen genes, the mutation frequency of the genes varies widely in mCRPC and the impact of the less commonly altered genes on PARP inhibitor sensitivity is uncertain. We used functional approaches to directly test the impact of PALB2 and BARD1 loss on homologous recombination (HR) function and PARP inhibitor sensitivity in prostate cancer cell lines. PALB2 or BARD1 loss led to decreased HR function as measured by loss of radiation-induced Rad51 foci formation as well as decreased HR capacity in a cell-based reporter assay. PALB2 or BARD1 loss also significantly increased sensitivity to the PARP inhibitors olaparib and rucaparib across a panel of prostate cancer cell lines. These data support PALB2 and BARD1 loss as markers of clinically relevant PARP inhibitor sensitivity and highlight the potential to use functional approaches to complement and extend findings from clinical trials of targeted agents.
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Affiliation(s)
- Kasia M Dillon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Raie T Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shahrzad Rafiei
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.,Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.,Second Department of Pathology, SE NAP, Brain Metastasis Research Goup, Semmelweis University, Budapest, Hungary
| | - Atish D Choudhury
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA.
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Kensler KH, Baichoo S, Pathania S, Rebbeck TR. The tumor mutational landscape of BRCA2-deficient primary and metastatic prostate cancer. NPJ Precis Oncol 2022; 6:39. [PMID: 35715489 PMCID: PMC9205939 DOI: 10.1038/s41698-022-00284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/17/2022] [Indexed: 02/08/2023] Open
Abstract
Carriers of germline BRCA2 pathogenic sequence variants have elevated aggressive prostate cancer risk and are candidates for precision oncology treatments. We examined whether BRCA2-deficient (BRCA2d) prostate tumors have distinct genomic alterations compared with BRCA2-intact (BRCA2i) tumors. Among 2536 primary and 899 metastatic prostate tumors from the ICGC, GENIE, and TCGA databases, we identified 138 primary and 85 metastatic BRCA2d tumors. Total tumor mutation burden (TMB) was higher among primary BRCA2d tumors, although pathogenic TMB did not differ by tumor BRCA2 status. Pathogenic and total single nucleotide variant (SNV) frequencies at KMT2D were higher in BRCA2d primary tumors, as was the total SNV frequency at KMT2D in BRCA2d metastatic tumors. Homozygous deletions at NEK3, RB1, and APC were enriched in BRCA2d primary tumors, and RB1 deletions in metastatic BRCA2d tumors as well. TMPRSS2-ETV1 fusions were more common in BRCA2d tumors. These results identify somatic alterations that hallmark etiological and prognostic differences between BRCA2d and BRCA2i prostate tumors.
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Affiliation(s)
- Kevin H. Kensler
- grid.5386.8000000041936877XDepartment of Population Health Sciences, Weill Cornell Medicine, New York, NY USA
| | - Shakuntala Baichoo
- grid.45199.300000 0001 2288 9451Department of Digital Technologies, FoICDT, University of Mauritius, Réduit, Mauritius
| | - Shailja Pathania
- grid.266684.80000 0001 2184 9220Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA USA ,grid.266684.80000 0001 2184 9220Department of Biology, University of Massachusetts, Boston, MA USA
| | - Timothy R. Rebbeck
- grid.65499.370000 0001 2106 9910Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
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Pacheco-Barcia V, Muñoz A, Castro E, Ballesteros AI, Marquina G, González-Díaz I, Colomer R, Romero-Laorden N. The Homologous Recombination Deficiency Scar in Advanced Cancer: Agnostic Targeting of Damaged DNA Repair. Cancers (Basel) 2022; 14:2950. [PMID: 35740616 DOI: 10.3390/cancers14122950] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Tumor-suppressor genes are involved in DNA break repair through the homologous recombination system and are widely known for their role in hereditary cancer. Beyond breast and ovarian cancer, prostate and pancreatic cancer also have targetable homologous recombination deficiency (HRD) beyond the well-known BRCA1 and BRCA2 with relevance that exceeds diagnostic purposes. In this review, we aim to summarize the roles of HRD across tumor types and the treatment landscape to guide the targeting of damaged DNA repair based on the cancer’s genetic features. Abstract BRCA1 and BRCA2 are the most recognized tumor-suppressor genes involved in double-strand DNA break repair through the homologous recombination (HR) system. Widely known for its role in hereditary cancer, HR deficiency (HRD) has turned out to be critical beyond breast and ovarian cancer: for prostate and pancreatic cancer also. The relevance for the identification of these patients exceeds diagnostic purposes, since results published from clinical trials with poly-ADP ribose polymerase (PARP) inhibitors (PARPi) have shown how this type of targeted therapy can modify the long-term evolution of patients with HRD. Somatic aberrations in other HRD pathway genes, but also indirect genomic instability as a sign of this DNA repair impairment (known as HRD scar), have been reported to be relevant events that lead to more frequently than expected HR loss of function in several tumor types, and should therefore be included in the current diagnostic and therapeutic algorithm. However, the optimal strategy to identify HRD and potential PARPi responders in cancer remains undefined. In this review, we summarize the role and prevalence of HRD across tumor types and the current treatment landscape to guide the agnostic targeting of damaged DNA repair. We also discuss the challenge of testing patients and provide a special insight for new strategies to select patients who benefit from PARPi due to HRD scarring.
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Leibowitz BD, Dougherty BV, Bell JSK, Kapilivsky J, Michuda J, Sedgewick AJ, Munson WA, Chandra TA, Dry JR, Beaubier N, Igartua C, Taxter T. Validation of genomic and transcriptomic models of homologous recombination deficiency in a real-world pan-cancer cohort. BMC Cancer 2022; 22:587. [PMID: 35643464 PMCID: PMC9148513 DOI: 10.1186/s12885-022-09669-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/11/2022] [Indexed: 12/14/2022] Open
Abstract
Background With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test. We further developed, validated, and explored the Tempus HRD-RNA model, which uses gene expression data from 16,750 RNA-seq samples to predict HRD status from formalin-fixed paraffin-embedded tumor samples across numerous cancer types. Methods Genomic and transcriptomic profiling was performed using next-generation sequencing from Tempus xT, Tempus xO, Tempus xE, Tempus RS, and Tempus RS.v2 assays on 48,843 samples. Samples were labeled based on their BRCA1, BRCA2 and selected Homologous Recombination Repair pathway gene (CDK12, PALB2, RAD51B, RAD51C, RAD51D) mutational status to train and validate HRD-DNA, a genome-wide loss-of-heterozygosity biomarker, and HRD-RNA, a logistic regression model trained on gene expression. Results In a sample of 2058 breast and 1216 ovarian tumors, BRCA status was predicted by HRD-DNA with F1-scores of 0.98 and 0.96, respectively. Across an independent set of 1363 samples across solid tumor types, the HRD-RNA model was predictive of BRCA status in prostate, pancreatic, and non-small cell lung cancer, with F1-scores of 0.88, 0.69, and 0.62, respectively. Conclusions We predict HRD-positive patients across many cancer types and believe both HRD models may generalize to other mechanisms of HRD outside of BRCA loss. HRD-RNA complements DNA-based HRD detection methods, especially for indications with low prevalence of BRCA alterations. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09669-z.
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Chen T, Yu T, Zhuang S, Geng Y, Xue J, Wang J, Ai L, Chen B, Zhao Z, Li Y, Wang J, Liang H, Xu Y, Gu Y. Upregulation of CXCL1 and LY9 contributes to BRCAness in ovarian cancer and mediates response to PARPi and immune checkpoint blockade. Br J Cancer. [DOI: 10.1038/s41416-022-01836-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/08/2022] Open
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Rodriguez-Calero A, Gallon J, Akhoundova D, Maletti S, Ferguson A, Cyrta J, Amstutz U, Garofoli A, Paradiso V, Tomlins SA, Hewer E, Genitsch V, Fleischmann A, Vassella E, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Ng CKY, Gillessen S, Piscuoglio S, Rubin MA. Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nat Commun 2022; 13:2400. [PMID: 35504881 PMCID: PMC9065149 DOI: 10.1038/s41467-022-30003-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 04/12/2022] [Indexed: 12/31/2022] Open
Abstract
Improved survival rates for prostate cancer through more effective therapies have also led to an increase in the diagnosis of metastases to infrequent locations such as the brain. Here we investigate the repertoire of somatic genetic alterations present in brain metastases from 51 patients with prostate cancer brain metastases (PCBM). We highlight the clonal evolution occurring in PCBM and demonstrate an increased mutational burden, concomitant with an enrichment of the homologous recombination deficiency mutational signature in PCBM compared to non-brain metastases. Focusing on known pathogenic alterations within homologous recombination repair genes, we find 10 patients (19.6%) fulfilling the inclusion criteria used in the PROfound clinical trial, which assessed the efficacy of PARP inhibitors (PARPi) in homologous recombination deficient prostate cancer. Eight (15.7%) patients show biallelic loss of one of the 15 genes included in the trial, while 5 patients (9.8%) harbor pathogenic alterations in BRCA1/2 specifically. Uncovering these molecular features of PCBM may have therapeutic implications, suggesting the need of clinical trial enrollment of PCBM patients when evaluating potential benefit from PARPi.
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Affiliation(s)
- Antonio Rodriguez-Calero
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Sina Maletti
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Alison Ferguson
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Oncology, Ludwig Cancer Centre, University of Lausanne, Lausanne, Switzerland
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, University Paris Sciences et Lettres, Paris, France
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Scott A Tomlins
- Departments of Pathology and Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Rainer Grobholz
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Ingeborg Fischer
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Adeboye O Osunkoya
- Departments of Pathology and Laboratory Medicine, and Urology, Emory University School of Medicine, Atlanta, USA
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - George Thalmann
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Silke Gillessen
- Faculty of Biomedical Sciences, USI, Lugano, Switzerland
- Department of Oncology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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Dalmasso B, Puccini A, Catalano F, Borea R, Iaia ML, Bruno W, Fornarini G, Sciallero S, Rebuzzi SE, Ghiorzo P. Beyond BRCA: The Emerging Significance of DNA Damage Response and Personalized Treatment in Pancreatic and Prostate Cancer Patients. Int J Mol Sci 2022; 23:ijms23094709. [PMID: 35563100 PMCID: PMC9099822 DOI: 10.3390/ijms23094709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/07/2022] Open
Abstract
The BRCA1/2 germline and/or somatic pathogenic variants (PVs) are key players in the hereditary predisposition and therapeutic response for breast, ovarian and, more recently, pancreatic and prostate cancers. Aberrations in other genes involved in homologous recombination and DNA damage response (DDR) pathways are being investigated as promising targets in ongoing clinical trials. However, DDR genes are not routinely tested worldwide. Due to heterogeneity in cohort selection and dissimilar sequencing approaches across studies, neither the burden of PVs in DDR genes nor the prevalence of PVs in genes in common among pancreatic and prostate cancer can be easily quantified. We aim to contextualize these genes, altered in both pancreatic and prostate cancers, in the DDR process, to summarize their hereditary and somatic burden in different studies and harness their deficiency for cancer treatments in the context of currently ongoing clinical trials. We conclude that the inclusion of DDR genes, other than BRCA1/2, shared by both cancers considerably increases the detection rate of potentially actionable variants, which are triplicated in pancreatic and almost doubled in prostate cancer. Thus, DDR alterations are suitable targets for drug development and to improve the outcome in both pancreatic and prostate cancer patients. Importantly, this will increase the detection of germline pathogenic variants, thereby patient referral to genetic counseling.
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Affiliation(s)
- Bruna Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
| | - Alberto Puccini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Fabio Catalano
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Roberto Borea
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Maria Laura Iaia
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - William Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
| | - Giuseppe Fornarini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Stefania Sciallero
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Sara Elena Rebuzzi
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Ospedale San Paolo, Medical Oncology, 17100 Savona, Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Correspondence:
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Abstract
Genetic testing for prostate cancer is rapidly growing and is increasingly being driven by precision medicine. Rates of germline pathogenic variants have been reported in up to 15% of men with prostate cancer, particularly in metastatic disease, and results of genetic testing could uncover options for precision therapy along with a spectrum of hereditary cancer-predisposition syndromes with unique clinical features that have complex management options. Thus, the pre-test discussion, whether delivered by genetic counsellors or by health-care professionals in hybrid models, involves information on hereditary cancer risk, extent of gene testing, purpose of testing, medical history and family history, potential types of results, additional cancer risks that might be uncovered, genetically based management and effect on families. Understanding precision medicine, personalized cancer risk management and syndrome-related cancer risk management is important in order to develop collaborative strategies with genetic counselling for optimal care of patients and their families. In this Review, Russo and Giri describe and discuss germline testing criteria, genetic testing strategies, genetically informed screening, precision management, delivery of genetic counselling or alternative genetic services and special considerations for men with prostate cancer. Germline (hereditary) genetic testing is rising in importance for treatment, screening and risk assessment of prostate cancer. Multiple hereditary cancer syndromes might be associated with prostate cancer, might confer risk of other cancerous and non-cancerous conditions, and can have hereditary cancer implications for family members. The rates of these syndromes can vary based upon the attributed genetic mutations. Multiple aspects of germline testing should be discussed in the pre-test setting for men to make an informed decision, including the purpose of genetic testing, the benefits and risks of testing, hereditary cancer risk, identification of additional cancer risks, familial implications and the state of genetic discrimination protections. Genetic evaluation can be conducted by genetic counsellors or a hybrid model can be employed, in which health-care providers deliver pre-test informed consent for testing, order testing and then determine referral to genetic counselling for appropriate patients. Precision medicine is increasingly driving decisions for germline testing. Poly(ADP-ribose) polymerase (PARP) inhibitors, immune checkpoint inhibitors and various other agents now in clinical trials have clinical activity in patients with certain hereditary cancer gene mutations, such as in DNA repair genes. Patients’ experiences with germline testing can be variable; taking the patient’s current experience into account, considering referral to genetic counselling when needed and offering germline testing for eligible men at repeated intervals if initially declined are important.
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Affiliation(s)
- Jessica Russo
- Cancer Risk Assessment and Clinical Cancer Genetics, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Veda N Giri
- Cancer Risk Assessment and Clinical Cancer Genetics, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA. .,Departments of Medical Oncology, Cancer Biology, and Urology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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Weiner AB, Liu Y, McFarlane M, Bawa PS, Li EV, Zhao X, Li Z, Hammoud T, Hazime M, Karnes RJ, Davicioni E, Reichert ZR, Chinnaiyan AM, Lotan TL, Spratt DE, Schaeffer EM. A transcriptomic model for homologous recombination deficiency in prostate cancer. Prostate Cancer Prostatic Dis 2022; 25:659-665. [PMID: 34226663 DOI: 10.1038/s41391-021-00416-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Tumors with mutations associated with homologous recombination deficiency (HRD) are uncommon in prostate cancer (PCa) and variably responsive to PARP inhibition. To better identify tumors with HRD, we developed a transcriptomic signature for HRD in PCa (HRD-P). METHODS By using an established mutational signature, we created and validated HRD-P in six independent PCa cohorts (primary PCa, n = 8224; metastatic castration-resistant PCa [mCRPC], n = 328). Molecular and clinical features were compared between HRD-P+ tumors and those with single HR-gene mutations. RESULTS HRD-P+ tumors were more common than tumors with single HR-gene mutations in primary (201/491, 41% vs 32/491 6.5%) and mCRPC (126/328, 38% vs 82/328, 25%) cases, and HRD-P+ was more predictive of genomic instability suggestive of HRD. HRD-P+ was associated with a shorter time to recurrence following surgery and shorter overall survival in men with mCRPC. In a prospective trial of mCRPC treated with olaparib (n = 10), all three men with HRD-P+ experienced prolonged (>330 days) PSA progression-free survival. CONCLUSION These results suggest transcriptomics can identify more patients that harbor phenotypic HRD than single HR-gene mutations and support further exploration of transcriptionally defined HRD tumors perhaps in conjunction with genomic markers for therapeutic application.
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Affiliation(s)
- Adam B Weiner
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yang Liu
- Decipher Biosciences, San Diego, CA, USA
| | - Matthew McFarlane
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | | | - Eric V Li
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xin Zhao
- Decipher Biosciences, San Diego, CA, USA
| | - Ziwen Li
- Decipher Biosciences, San Diego, CA, USA
| | - Tanya Hammoud
- University of Michigan College of Literature, Science, and the Arts, Ann Arbor, MI, USA
| | - Munna Hazime
- University of Michigan College of Literature, Science, and the Arts, Ann Arbor, MI, USA
| | - R Jeffrey Karnes
- Department of Urology, Mayo Clinic Rochester, Rochester, MN, USA
| | | | - Zachery R Reichert
- Division of Hematology/Oncology, Department of Internal Medicine, Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Schaeffer
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Liao G, Yang Y, Xie A, Jiang Z, Liao J, Yan M, Zhou Y, Zhu J, Hu J, Zhang Y, Xiao Y, Li X. Applicability of Anticancer Drugs for the Triple-Negative Breast Cancer Based on Homologous Recombination Repair Deficiency. Front Cell Dev Biol 2022; 10:845950. [PMID: 35281113 PMCID: PMC8913497 DOI: 10.3389/fcell.2022.845950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive disease with historically poor outcomes, primarily due to the lack of effective targeted therapies. Here, we established a drug sensitivity prediction model based on the homologous recombination deficiency (HRD) using 83 TNBC patients from TCGA. Through analyzing the effect of HRD status on response efficacy of anticancer drugs and elucidating its related mechanisms of action, we found rucaparib (PARP inhibitor) and doxorubicin (anthracycline) sensitive in HR-deficient patients, while paclitaxel sensitive in the HR-proficient. Further, we identified a HRD signature based on gene expression data and constructed a transcriptomic HRD score, for analyzing the functional association between anticancer drug perturbation and HRD. The results revealed that CHIR99021 (GSK3 inhibitor) and doxorubicin have similar expression perturbation patterns with HRD, and talazoparib (PARP inhibitor) could kill tumor cells by reversing the HRD activity. Genomic characteristics indicated that doxorubicin inhibited tumor cells growth by hindering the process of DNA damage repair, while the resistance of cisplatin was related to the activation of angiogenesis and epithelial-mesenchymal transition. The negative correlation of HRD signature score could interpret the association of doxorubicin pIC50 with worse chemotherapy response and shorter survival of TNBC patients. In summary, these findings explain the applicability of anticancer drugs in TNBC and underscore the importance of HRD in promoting personalized treatment development.
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Affiliation(s)
- Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yiran Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Medical University, Haikou, China
- *Correspondence: Yunpeng Zhang, ; Yun Xiao, ; Xia Li,
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Bieńkowski M, Tomasik B, Braun M, Jassem J. PARP inhibitors for metastatic castration-resistant prostate cancer: Biological rationale and current evidence. Cancer Treat Rev 2022; 104:102359. [DOI: 10.1016/j.ctrv.2022.102359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]
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Zhang H, Zhang Y. Olaparib and paclitaxel in combination with carboplatin in treatment of ovarian cancer: influence on disease control. Am J Transl Res 2022; 14:468-475. [PMID: 35173866 PMCID: PMC8829627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To investigate the efficacy and safety of olaparib and paclitaxel combined with carboplatin in the treatment of ovarian cancer and its impact on disease control. METHODS The medical data of 120 patients with ovarian cancer admitted to our hospital from February 2019 to February 2020 were retrospectively analyzed. According to different treatment methods, the enrolled patients were divided into two groups: a control group (n=60) treated with paclitaxel combined with carboplatin, and an experimental group (n=60) additionally treated with olaparib on the basis of the control group. The short-term efficacy, serum levels of carbohydrate antigen 125 (CA125), tumor necrosis factor (TNF-α), interleukin-6 (IL-6), and human epididymis protein 4 (HE4), and the incidence of adverse effects and tumor metastasis were compared between the two groups. RESULTS There was no difference in the baseline data between the two groups (P>0.05). The objective remission rate (ORR) and disease control rate (DCR) of the experimental group were higher than those of the control group (P<0.05). The experimental group had lower levels of serum CA125, TNF-α, IL-6, and HE4 than the control group after treatment (P<0.05). The two groups showed no significant difference in the incidence of adverse reactions (P>0.05). The one-year follow-up identified a lower tumor metastasis rate in the experimental group compared to the control group (P<0.05). CONCLUSION Olaparib and paclitaxel combined with carboplatin improve the serum indexes of patients with ovarian cancer, enhance the disease control, and reduce the recurrence rate, without extra toxic side effects.
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Affiliation(s)
- Heling Zhang
- Health Examination Center, The Fourth Hospital of ShijiazhuangShijiazhuang, Hebei, China
| | - Ye Zhang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical UniversityHebei, China
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Stewart MD, Merino Vega D, Arend RC, Baden JF, Barbash O, Beaubier N, Collins G, French T, Ghahramani N, Hinson P, Jelinic P, Marton MJ, McGregor K, Parsons J, Ramamurthy L, Sausen M, Sokol ES, Stenzinger A, Stires H, Timms KM, Turco D, Wang I, Williams JA, Wong-Ho E, Allen J. OUP accepted manuscript. Oncologist 2022; 27:167-174. [PMID: 35274707 PMCID: PMC8914493 DOI: 10.1093/oncolo/oyab053] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/05/2021] [Indexed: 11/12/2022] Open
Abstract
Background Homologous recombination deficiency (HRD) is a phenotype that is characterized by the inability of a cell to effectively repair DNA double-strand breaks using the homologous recombination repair (HRR) pathway. Loss-of-function genes involved in this pathway can sensitize tumors to poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors and platinum-based chemotherapy, which target the destruction of cancer cells by working in concert with HRD through synthetic lethality. However, to identify patients with these tumors, it is vital to understand how to best measure homologous repair (HR) status and to characterize the level of alignment in these measurements across different diagnostic platforms. A key current challenge is that there is no standardized method to define, measure, and report HR status using diagnostics in the clinical setting. Methods Friends of Cancer Research convened a consortium of project partners from key healthcare sectors to address concerns about the lack of consistency in the way HRD is defined and methods for measuring HR status. Results This publication provides findings from the group’s discussions that identified opportunities to align the definition of HRD and the parameters that contribute to the determination of HR status. The consortium proposed recommendations and best practices to benefit the broader cancer community. Conclusion Overall, this publication provides additional perspectives for scientist, physician, laboratory, and patient communities to contextualize the definition of HRD and various platforms that are used to measure HRD in tumors.
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Affiliation(s)
- Mark D Stewart
- Corresponding author: Mark D. Stewart, 1800 M Street NW, Suite 1050 South, Washington, DC 20036, USA;
| | | | - Rebecca C Arend
- Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingam, AL, USA
| | | | - Olena Barbash
- Oncology Experimental Medicine Unit, GlaxoSmithKline, Philadelphia, PA, USA
| | | | | | - Tim French
- Global Medical Affairs, Diagnostics, AstraZeneca, Cambridge, UK
| | - Negar Ghahramani
- Molecular Genetic Pathology Regional Laboratory, SCPMG Regional Reference Laboratories, Los Angeles, CA, USA
| | - Patsy Hinson
- Independent Cancer Research Patient Advocate, Charlotte, NC, USA
| | - Petar Jelinic
- Early Clinical Oncology, Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Kimberly McGregor
- Cancer Genomics Research Group, Foundation Medicine, Cambridge, MA, USA
| | | | | | - Mark Sausen
- Translational Medicine, Bristol Myers Squibb, New York, NY, USA
| | - Ethan S Sokol
- Cancer Genomics Research Group, Foundation Medicine, Cambridge, MA, USA
| | | | | | | | - Diana Turco
- Myriad Genetics, Inc., Salt Lake City, UT, USA
| | - Iris Wang
- Global Precision Medicine, Novartis Pharmaceuticals Corporation, New York, NY, USA
| | | | - Elaine Wong-Ho
- Clinical Sequencing Division, Thermo Fisher Scientific, San Francisco, CA, USA
| | - Jeff Allen
- Friends of Cancer Research, Washington, DC, USA
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40
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De Sarkar N, Dasgupta S, Chatterjee P, Coleman I, Ha G, Ang LS, Kohlbrenner EA, Frank SB, Nunez TA, Salipante SJ, Corey E, Morrissey C, Van Allen E, Schweizer MT, Haffner MC, Patel R, Hanratty B, Lucas JM, Dumpit RF, Pritchard CC, Montgomery RB, Nelson PS. Genomic attributes of homology-directed DNA repair deficiency in metastatic prostate cancer. JCI Insight 2021; 6:152789. [PMID: 34877933 PMCID: PMC8675196 DOI: 10.1172/jci.insight.152789] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 01/08/2023] Open
Abstract
Cancers with homology-directed DNA repair (HRR) deficiency exhibit high response rates to poly(ADP-ribose) polymerase inhibitors (PARPi) and platinum chemotherapy. Though mutations disrupting BRCA1 and BRCA2 associate with HRR deficiency (HRRd), patterns of genomic aberrations and mutation signatures may be more sensitive and specific indicators of compromised repair. Here, we evaluated whole-exome sequences from 418 metastatic prostate cancers (mPCs) and determined that one-fifth exhibited genomic characteristics of HRRd that included Catalogue Of Somatic Mutations In Cancer mutation signature 3. Notably, a substantial fraction of tumors with genomic features of HRRd lacked biallelic loss of a core HRR-associated gene, such as BRCA2. In this subset, HRRd associated with loss of chromodomain helicase DNA binding protein 1 but not with mutations in serine-protein kinase ATM, cyclin dependent kinase 12, or checkpoint kinase 2. HRRd genomic status was strongly correlated with responses to PARPi and platinum chemotherapy, a finding that supports evaluating biomarkers reflecting functional HRRd for treatment allocation.
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Affiliation(s)
| | | | | | | | - Gavin Ha
- Divisions of Human Biology.,Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lisa S Ang
- Divisions of Human Biology.,Clinical Research
| | | | | | | | | | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington, USA
| | | | - Michael T Schweizer
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | | | | | | | | | | | - Robert B Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter S Nelson
- Divisions of Human Biology.,Clinical Research.,Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Urology, University of Washington, Seattle, Washington, USA.,Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington, USA
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41
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Li Y, Zhao Z, Ai L, Wang Y, Liu K, Chen B, Chen T, Zhuang S, Xu H, Zou M, Gu Y, Li X. Discovering a qualitative transcriptional signature of homologous recombination defectiveness for prostate cancer. iScience 2021; 24:103135. [PMID: 34622176 PMCID: PMC8482486 DOI: 10.1016/j.isci.2021.103135] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/28/2021] [Accepted: 09/12/2021] [Indexed: 12/17/2022] Open
Abstract
The discovery of homologous recombination deficiency (HRD) biomarkers in prostate cancer is important for patients who will benefit from poly ADP-ribose polymerase inhibitor (PARPi). Here, we developed a transcriptional homologous recombination defectiveness (HRDness) signature, comprising 16 gene pairs (16-GPS), for prostate cancer by a relative expression ordering (REO)-based discovery procedure. Subsequently, two newly subtypes classified by 16-GPS showed a higher significance level in various clinicopathological and HRD features than subtypes obtained by other methods, such as HRDetect. HRDness subtype also displayed more aggressive features and higher genomics scores than non-HRDness in three independent datasets. HRDness prostate cancer cells were more sensitive to PARPi than non-HRDness. Moreover, the HRDness samples showed distinct multi-omics characteristics related to homologous recombination repair function loss. Overall, the newly proposed qualitative signature can robustly determine the HRD status for prostate cancer at the personalized level, and especially be an auxiliary tool for PARPi treatment strategy. 16 gene pairs (16-GPS) could predict HRDness for prostate cancer at individual level HRDness samples classified by 16-GPS showed HRD molecular and clinical features HRDness cells classified by 16-GPS tend to be sensitive to PARPi
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Affiliation(s)
- Yawei Li
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Zhangxiang Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Liqiang Ai
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuquan Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Kaidong Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Tingting Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shuping Zhuang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Huanhuan Xu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Min Zou
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xia Li
- Department of Bioinformatics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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42
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Reardon B, Moore ND, Moore NS, Kofman E, AlDubayan SH, Cheung ATM, Conway J, Elmarakeby H, Imamovic A, Kamran SC, Keenan T, Keliher D, Konieczkowski DJ, Liu D, Mouw KW, Park J, Vokes NI, Dietlein F, Van Allen EM. Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. Nat Cancer 2021; 2:1102-1112. [PMID: 35121878 PMCID: PMC9082009 DOI: 10.1038/s43018-021-00243-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 07/14/2021] [Indexed: 02/08/2023]
Abstract
Tumor molecular profiling of single gene-variant ('first-order') genomic alterations informs potential therapeutic approaches. Interactions between such first-order events and global molecular features (for example, mutational signatures) are increasingly associated with clinical outcomes, but these 'second-order' alterations are not yet accounted for in clinical interpretation algorithms and knowledge bases. We introduce the Molecular Oncology Almanac (MOAlmanac), a paired clinical interpretation algorithm and knowledge base to enable integrative interpretation of multimodal genomic data for point-of-care decision making and translational-hypothesis generation. We benchmarked MOAlmanac to a first-order interpretation method across multiple retrospective cohorts and observed an increased number of clinical hypotheses from evaluation of molecular features and profile-to-cell line matchmaking. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 47% of patients. Overall, we present an open-source computational method for integrative clinical interpretation of individualized molecular profiles.
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Affiliation(s)
- Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael D Moore
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Nicholas S Moore
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Harvard University, Boston, MA, USA
| | - Eric Kofman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alexander T M Cheung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Grossman School of Medicine, New York University, New York, NY, USA
| | - Jake Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Haitham Elmarakeby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of System and Computer Engineering, Al-Azhar University, Cairo, Egypt
| | - Alma Imamovic
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sophia C Kamran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tanya Keenan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Keliher
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Mathematics, Tufts University, Medford, MA, USA
| | - David J Konieczkowski
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women's Hospital, Boston, MA, USA
- Harvard Radiation Oncology Program, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiation Oncology, the Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kent W Mouw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women's Hospital, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Natalie I Vokes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Thoracic/Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Felix Dietlein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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43
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Qing T, Wang X, Jun T, Ding L, Pusztai L, Huang KL. Genomic Determinants of Homologous Recombination Deficiency across Human Cancers. Cancers (Basel) 2021; 13:4572. [PMID: 34572800 PMCID: PMC8472123 DOI: 10.3390/cancers13184572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Germline BRCA1/2 mutations associated with HRD are clinical biomarkers for sensitivity to poly-ADP ribose polymerase inhibitors (PARPi) treatment in breast, ovarian, pancreatic, and prostate cancers. However, it remains unclear whether other mutations may also lead to HRD and PARPi sensitivity across a broader range of cancer types. Our goal was to determine the germline or somatic alterations associated with the HRD phenotype that might therefore confer PARPi sensitivity. Using germline and somatic genomic data from over 9000 tumors representing 32 cancer types, we examined associations between HRD scores and pathogenic germline variants, somatic driver mutations, and copy number deletions in 30 candidate genes involved in homologous recombination. We identified several germline and somatic mutations (e.g., BRCA1/2, PALB2, ATM, and ATR mutations) associated with HRD phenotype in ovarian, breast, pancreatic, stomach, bladder, and lung cancer. The co-occurrence of germline BRCA1 variants and somatic TP53 mutations was significantly associated with increasing HRD in breast cancer. Notably, we also identified multiple somatic copy number deletions associated with HRD. Our study suggests that multiple cancer types include tumor subsets that show HRD phenotype and should be considered in the future clinical studies of PARPi and synthetic lethality strategies exploiting HRD, which can be caused by a large number of genomic alterations.
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Affiliation(s)
- Tao Qing
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT 06511, USA;
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China;
| | - Tomi Jun
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63110, USA;
- Department of Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lajos Pusztai
- Breast Medical Oncology, School of Medicine, Yale University, New Haven, CT 06511, USA;
| | - Kuan-Lin Huang
- Department of Genetics and Genomic Sciences, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Tewari AK, Cheung ATM, Crowdis J, Conway JR, Camp SY, Wankowicz SA, Livitz DG, Park J, Lis RT, Bosma-Moody A, He MX, AlDubayan SH, Zhang Z, McKay RR, Leshchiner I, Brown M, Balk SP, Getz G, Taplin ME, Van Allen EM. Molecular features of exceptional response to neoadjuvant anti-androgen therapy in high-risk localized prostate cancer. Cell Rep 2021; 36:109665. [PMID: 34496240 DOI: 10.1016/j.celrep.2021.109665] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/17/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
High-risk localized prostate cancer (HRLPC) is associated with a substantial risk of recurrence and disease mortality. Recent clinical trials have shown that intensifying anti-androgen therapies administered before prostatectomy can induce pathologic complete responses or minimal residual disease, called exceptional response, although the molecular determinants of these clinical outcomes are largely unknown. Here, we perform whole-exome and transcriptome sequencing on pre-treatment multi-regional tumor biopsies from exceptional responders (ERs) and non-responders (NRs, pathologic T3 or lymph node-positive disease) to intensive neoadjuvant anti-androgen therapies. Clonal SPOP mutation and SPOPL copy-number loss are exclusively observed in ERs, while clonal TP53 mutation and PTEN copy-number loss are exclusively observed in NRs. Transcriptional programs involving androgen signaling and TGF-β signaling are enriched in ERs and NRs, respectively. These findings may guide prospective validation studies of these molecular features in large HRLPC clinical cohorts treated with neoadjuvant anti-androgens to improve patient stratification.
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Affiliation(s)
- Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander T M Cheung
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jett Crowdis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jake R Conway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Bioinformatics and Integrative Genomics, Boston, MA 02115, USA
| | - Sabrina Y Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephanie A Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosina T Lis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alice Bosma-Moody
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Meng Xiao He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Graduate Program in Biophysics, Boston, MA 02115, USA
| | - Saud H AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Zhenwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rana R McKay
- Division of Hematology/Oncology, University of California San Diego, San Diego, CA 92037, USA
| | | | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Steven P Balk
- Division of Cancer Biology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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45
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Liao G, Jiang Z, Yang Y, Zhang C, Jiang M, Zhu J, Xu L, Xie A, Yan M, Zhang Y, Xiao Y, Li X. Combined homologous recombination repair deficiency and immune activation analysis for predicting intensified responses of anthracycline, cyclophosphamide and taxane chemotherapy in triple-negative breast cancer. BMC Med 2021; 19:190. [PMID: 34465315 PMCID: PMC8408988 DOI: 10.1186/s12916-021-02068-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/20/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is a clinically aggressive disease with abundant variants that cause homologous recombination repair deficiency (HRD). Whether TNBC patients with HRD are sensitive to anthracycline, cyclophosphamide and taxane (ACT), and whether the combination of HRD and tumour immunity can improve the recognition of ACT responders are still unknown. METHODS Data from 83 TNBC patients in The Cancer Genome Atlas (TCGA) was used as a discovery cohort to analyse the association between HRD and ACT chemotherapy benefits. The combined effects of HRD and immune activation on ACT chemotherapy were explored at both the genome and the transcriptome levels. Independent cohorts from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and Gene Expression Omnibus (GEO) were adopted to validate our findings. RESULTS HRD was associated with a longer ACT chemotherapy failure-free interval (FFI) with a hazard ratio of 0.16 (P = 0.004) and improved patient prognosis (P = 0.0063). By analysing both HRD status and ACT response, we identified patients with a distinct TNBC subtype (ACT-S&HR-P) that showed higher tumour lymphocyte infiltration, IFN-γ activity and NK cell levels. Patients with ACT-S&HR-P had significantly elevated immune inhibitor levels and presented immune activation associated with the increased activities of both innate immune cells and adaptive immune cells, which suggested treatment with immune checkpoint blockade as an option for this subtype. Our analysis revealed that the combination of HRD and immune activation enhanced the efficiency of identifying responders to ACT chemotherapy (AUC = 0.91, P = 1.06e-04) and synergistically contributed to the clinical benefits of TNBC patients. A transcriptional HRD signature of ACT response-related prognostic factors was identified and independently validated to be significantly associated with improved survival in the GEO cohort (P = 0.0038) and the METABRIC dataset (P < 0.0001). CONCLUSIONS These findings highlight that HR deficiency prolongs FFI and predicts intensified responses in TNBC patients by combining HRD and immune activation, which provides a molecular basis for identifying ACT responders.
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Affiliation(s)
- Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yiran Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Cong Zhang
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, 150010, Heilongjiang, China
| | - Meiting Jiang
- Key Laboratory of University in Heilongjiang Province, Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, 150081, Heilongjiang, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China. .,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, 150081, Heilongjiang, China.
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46
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Sztupinszki Z, Diossy M, Börcsök J, Prosz A, Cornelius N, Kjeldsen MK, Mirza MR, Szallasi Z. Comparative Assessment of Diagnostic Homologous Recombination Deficiency associated mutational signatures in ovarian cancer. Clin Cancer Res 2021; 27:5681-5687. [PMID: 34380641 DOI: 10.1158/1078-0432.ccr-21-0981] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/08/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Homologous recombination (HR) deficiency is one of the key determinants of PARP inhibitor response in ovarian cancer, and its accurate detection in tumor biopsies is expected to improve the efficacy of this therapy. Since HR deficiency induces a wide array of genomic aberrations, mutational signatures may serve as a companion diagnostic to identify PARP inhibitor responsive cases. METHODS From the TCGA whole exome sequencing data we extracted different types of mutational signature-based HR deficiency measures, such as the HRD score, genome-wide LOH and HRDetect trained on ovarian and breast cancer specific sequencing data. We compared their performance to identify BRCA1/2 deficient cases in the TCGA ovarian cancer cohort and predict survival benefit in platinum treated, BRCA1/2 wild type ovarian cancer. RESULTS We found that the HRD score, which is based on large chromosomal alterations alone, performed similarly well to an ovarian cancer specific HRDetect, which incorporates mutations on a finer scale as well (AUC=0.823 versus AUC=0.837). In an independent cohort these two methods were equally accurate predicting long term survival after platinum treatment (AUC=0.787 versus AUC=0.823). We also found that HRDetect trained on ovarian cancer was more accurate than HRDetect trained on breast cancer data (AUC=0.837 versus AUC=0.795, p=0.0072). CONCLUSION When WES data are available, methods that quantify only large chromosomal alterations such as the HRD score and HRDetect that captures a wider array of HR deficiency induced genomic aberrations are equally efficient identifying HR deficient ovarian cancer cases.
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Affiliation(s)
| | - Miklos Diossy
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | - Judit Börcsök
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | - Aurel Prosz
- Translational Cancer Genomics, Danish Cancer Society Research Center
| | | | | | | | - Zoltan Szallasi
- Children's Hospital Informatics Program at the Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School
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47
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McFarland TR, Kessel A, Swami U, Agarwal N. Development of PARP inhibitor combinations for castration resistant prostate cancer unselected for homologous recombination repair mutations. Am J Transl Res 2021; 13:7427-7439. [PMID: 34377227 PMCID: PMC8340210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Genetic instability is a hallmark of cancer and, with the introduction of poly (ADP-ribose) polymerase (PARP) inhibitors, is a targetable feature of many tumors. Currently, two PARP inhibitors, olaparib and rucaparib, have received approval as monotherapy by the Food and Drug Administration for the treatment of men with castration resistant prostate cancer with selected mutations involving the homologous recombination (HR) pathway. However, it is currently debated whether an HR mutation is a prerequisite for response or if patients with HR-proficient mCRPC may also benefit from their use when combined with other targeted or immunotherapeutic agents. Several large phase III trials of PARP inhibitors with novel androgen axis inhibitors in groups of unselected patients are underway. Additionally, there are several early phase trials combining PARP inhibitors with radioligands or immunecheckpoint inhibitors. Here we discuss the currently ongoing or recently concluded trials of PARP inhibitor based combinatorial therapies in unselected patients with mCRPC, the rationale behind these trials, and how these may impact the treatment paradigm in men with mCRPC.
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Affiliation(s)
- Taylor Ryan McFarland
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Salt Lake, UT, USA
| | - Adam Kessel
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Salt Lake, UT, USA
| | - Umang Swami
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Salt Lake, UT, USA
| | - Neeraj Agarwal
- Division of Oncology, Department of Internal Medicine, Huntsman Cancer Institute, University of Utah Salt Lake, UT, USA
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48
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Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst) 2021; 103:103125. [PMID: 33940558 PMCID: PMC8206044 DOI: 10.1016/j.dnarep.2021.103125] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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49
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Qiu B, Kline C, Mueller S. Radiation in Combination With Targeted Agents and Immunotherapies for Pediatric Central Nervous System Tumors - Progress, Opportunities, and Challenges. Front Oncol 2021; 11:674596. [PMID: 34277419 PMCID: PMC8278144 DOI: 10.3389/fonc.2021.674596] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pediatric brain tumors are the most common solid tumors in children and represent a heterogenous group of diagnoses. While some are treatable with current standard of care, relapsed/refractory disease is common and some high-risk diagnoses remain incurable. A growing number of therapy options are under development for treatment of CNS tumors, including targeted therapies that disrupt key tumor promoting processes and immunotherapies that promote anti-tumor immune function. While these therapies hold promise, it is likely that single agent treatments will not be sufficient for most high-risk patients and combination strategies will be necessary. Given the central role for radiotherapy for many pediatric CNS tumors, we review current strategies that combine radiation with targeted therapies or immunotherapies. To promote the ongoing development of rational combination treatments, we highlight 1) mechanistic connections between molecular drivers of tumorigenesis and radiation response, 2) ways in which molecular alterations in tumor cells shape the immune microenvironment, and 3) how radiotherapy affects the host immune system. In addition to discussing strategies to maximize efficacy, we review principles that inform safety of combination therapies.
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Affiliation(s)
- Bo Qiu
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Cassie Kline
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sabine Mueller
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurosurgery, University of California, San Francisco, San Francisco, CA, United States
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50
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Zhou Q, Howard ME, Tu X, Zhu Q, Denbeigh JM, Remmes NB, Herman MG, Beltran CJ, Yuan J, Greipp PT, Boughey JC, Wang L, Johnson N, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. Inhibition of ATM Induces Hypersensitivity to Proton Irradiation by Upregulating Toxic End Joining. Cancer Res 2021; 81:3333-3346. [PMID: 33597272 PMCID: PMC8260463 DOI: 10.1158/0008-5472.can-20-2960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/30/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022]
Abstract
Proton Bragg peak irradiation has a higher ionizing density than conventional photon irradiation or the entrance of the proton beam profile. Whether targeting the DNA damage response (DDR) could enhance vulnerability to the distinct pattern of damage induced by proton Bragg peak irradiation is currently unknown. Here, we performed genetic or pharmacologic manipulation of key DDR elements and evaluated DNA damage signaling, DNA repair, and tumor control in cell lines and xenografts treated with the same physical dose across a radiotherapy linear energy transfer spectrum. Radiotherapy consisted of 6 MV photons and the entrance beam or Bragg peak of a 76.8 MeV spot scanning proton beam. More complex DNA double-strand breaks (DSB) induced by Bragg peak proton irradiation preferentially underwent resection and engaged homologous recombination (HR) machinery. Unexpectedly, the ataxia-telangiectasia mutated (ATM) inhibitor, AZD0156, but not an inhibitor of ATM and Rad3-related, rendered cells hypersensitive to more densely ionizing proton Bragg peak irradiation. ATM inhibition blocked resection and shunted more DSBs to processing by toxic ligation through nonhomologous end-joining, whereas loss of DNA ligation via XRCC4 or Lig4 knockdown rescued resection and abolished the enhanced Bragg peak cell killing. Proton Bragg peak monotherapy selectively sensitized cell lines and tumor xenografts with inherent HR defects, and the repair defect induced by ATM inhibitor coadministration showed enhanced efficacy in HR-proficient models. In summary, inherent defects in HR or administration of an ATM inhibitor in HR-proficient tumors selectively enhances the relative biological effectiveness of proton Bragg peak irradiation. SIGNIFICANCE: Coadministration of an ATM inhibitor rewires DNA repair machinery to render cancer cells uniquely hypersensitive to DNA damage induced by the proton Bragg peak, which is characterized by higher density ionization.See related commentary by Nickoloff, p. 3156.
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Affiliation(s)
- Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Janet M Denbeigh
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Michael G Herman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Chris J Beltran
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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