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Wu B, Lu X, Shen H, Yuan X, Wang X, Yin N, Sun L, Shen P, Hu C, Jiang H, Wang D. Intratumoral heterogeneity and genetic characteristics of prostate cancer. Int J Cancer 2020; 146:3369-3378. [PMID: 32159858 DOI: 10.1002/ijc.32961] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023]
Abstract
Prostate cancer is a heterogeneous disease and optimum gene targeting treatment is often impermissible. We aim to determine the intratumoral genomic heterogeneity of prostate cancer and explore candidate genes for targeted therapy. Exome sequencing was performed on 37 samples from 16 patients with prostate cancer. Somatic variant analysis, copy number variant (CNV) analysis, clonal evolution analysis and variant spectrum analysis were used to study the intratumoral genomic heterogeneity and genetic characteristics of metastatic prostate cancer. Our study confirmed the high intratumoral genetic heterogeneity of prostate cancer in many aspects, including number of shared variants, tumor mutation burden (TMB), variant genes, CNV burden, weighted genome instability index (wGII), CNV profiles, clonal evolutionary process, variant spectrum and mutational signatures. Moreover, we identified several common genetic characteristics of prostate cancer. Alterations of DNA damage repair genes, RTK/RAS pathway associated gene RASGRF1 and autophagy gene EPG5 may be involved in tumorigenesis in prostate cancer. CNV burden and DNA damage repair (DDR) genes may be associated with metastasis of prostate cancer.
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Affiliation(s)
- Bo Wu
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.,First College of Clinical Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xin Lu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Haibo Shen
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaobin Yuan
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xin Wang
- First College of Clinical Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Nan Yin
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Libin Sun
- First College of Clinical Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Pengliang Shen
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Caoyang Hu
- Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huanrong Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Dongwen Wang
- First College of Clinical Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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Abida W, Cyrta J, Heller G, Prandi D, Armenia J, Coleman I, Cieslik M, Benelli M, Robinson D, Van Allen EM, Sboner A, Fedrizzi T, Mosquera JM, Robinson BD, De Sarkar N, Kunju LP, Tomlins S, Wu YM, Nava Rodrigues D, Loda M, Gopalan A, Reuter VE, Pritchard CC, Mateo J, Bianchini D, Miranda S, Carreira S, Rescigno P, Filipenko J, Vinson J, Montgomery RB, Beltran H, Heath EI, Scher HI, Kantoff PW, Taplin ME, Schultz N, deBono JS, Demichelis F, Nelson PS, Rubin MA, Chinnaiyan AM, Sawyers CL. Genomic correlates of clinical outcome in advanced prostate cancer. Proc Natl Acad Sci U S A 2019; 116:11428-11436. [PMID: 31061129 PMCID: PMC6561293 DOI: 10.1073/pnas.1902651116] [Citation(s) in RCA: 823] [Impact Index Per Article: 164.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Heterogeneity in the genomic landscape of metastatic prostate cancer has become apparent through several comprehensive profiling efforts, but little is known about the impact of this heterogeneity on clinical outcome. Here, we report comprehensive genomic and transcriptomic analysis of 429 patients with metastatic castration-resistant prostate cancer (mCRPC) linked with longitudinal clinical outcomes, integrating findings from whole-exome, transcriptome, and histologic analysis. For 128 patients treated with a first-line next-generation androgen receptor signaling inhibitor (ARSI; abiraterone or enzalutamide), we examined the association of 18 recurrent DNA- and RNA-based genomic alterations, including androgen receptor (AR) variant expression, AR transcriptional output, and neuroendocrine expression signatures, with clinical outcomes. Of these, only RB1 alteration was significantly associated with poor survival, whereas alterations in RB1, AR, and TP53 were associated with shorter time on treatment with an ARSI. This large analysis integrating mCRPC genomics with histology and clinical outcomes identifies RB1 genomic alteration as a potent predictor of poor outcome, and is a community resource for further interrogation of clinical and molecular associations.
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Affiliation(s)
- Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Joanna Cyrta
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021
- Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Glenn Heller
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Davide Prandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ilsa Coleman
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Matteo Benelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Dan Robinson
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Broad Institute, Cambridge, MA 02142
| | - Andrea Sboner
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021
| | - Tarcisio Fedrizzi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Juan Miguel Mosquera
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021
| | - Brian D Robinson
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021
| | - Navonil De Sarkar
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109
| | - Lakshmi P Kunju
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Scott Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Yi Mi Wu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel Nava Rodrigues
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Massimo Loda
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Colin C Pritchard
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109
| | - Joaquin Mateo
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Diletta Bianchini
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Susana Miranda
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Suzanne Carreira
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Pasquale Rescigno
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Julie Filipenko
- Prostate Cancer Clinical Trials Consortium, New York, NY 10065
| | - Jacob Vinson
- Prostate Cancer Clinical Trials Consortium, New York, NY 10065
| | | | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Medicine, Weill Medical College of Cornell University, New York, NY 10021
| | - Elisabeth I Heath
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201
- Department of Oncology, Barbara Ann Karmanos Cancer Institute, Detroit, MI 48201
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Johann S deBono
- Institute of Cancer Research, London SW7 3RP, United Kingdom
- The Royal Marsden National Health Service Foundation Trust, London SM2 5NG, United Kingdom
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Peter S Nelson
- Fred Hutchinson Cancer Center, University of Washington, Seattle, WA 98109;
| | - Mark A Rubin
- Department of Pathology, Weill Medical College of Cornell University, New York, NY 10021;
- Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109;
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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