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Yamaguchi TN, Houlahan KE, Zhu H, Kurganovs N, Livingstone J, Fox NS, Yuan J, Sietsma Penington J, Jung CH, Schwarz T, Jaratlerdsiri W, van Riet J, Georgeson P, Mangiola S, Taraszka K, Lesurf R, Jiang J, Chow K, Heisler LE, Shiah YJ, Ramanand SG, Clarkson MJ, Nguyen A, Espiritu SMG, Stuchbery R, Jovelin R, Huang V, Bell C, O’Connor E, McCoy PJ, Lalansingh CM, Cmero M, Salcedo A, Chan EK, Liu LY, Stricker PD, Bhandari V, Bornman RM, Sendorek DH, Lonie A, Prokopec SD, Fraser M, Peters JS, Foucal A, Mutambirwa SB, Mcintosh L, Orain M, Wakefield M, Picard V, Park DJ, Hovington H, Kerger M, Bergeron A, Sabelnykova V, Seo JH, Pomerantz MM, Zaitlen N, Waszak SM, Gusev A, Lacombe L, Fradet Y, Ryan A, Kishan AU, Lolkema MP, Weischenfeldt J, Têtu B, Costello AJ, Hayes VM, Hung RJ, He HH, McPherson JD, Pasaniuc B, van der Kwast T, Papenfuss AT, Freedman ML, Pope BJ, Bristow RG, Mani RS, Corcoran NM, Reimand J, Hovens CM, Boutros PC. The Germline and Somatic Origins of Prostate Cancer Heterogeneity. Cancer Discov 2025; 15:988-1017. [PMID: 39945744 PMCID: PMC12046336 DOI: 10.1158/2159-8290.cd-23-0882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/06/2024] [Accepted: 02/10/2025] [Indexed: 02/23/2025]
Abstract
SIGNIFICANCE This study uncovered 223 recurrently mutated driver regions using the largest cohort of prostate tumors to date. It reveals associations between germline SNPs, somatic drivers, and tumor aggression, offering significant insights into how prostate tumor evolution is shaped by germline factors and the timing of somatic mutations.
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Affiliation(s)
- Takafumi N. Yamaguchi
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Kathleen E. Houlahan
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Helen Zhu
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Natalie Kurganovs
- Ontario Institute for Cancer Research, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | - Julie Livingstone
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
| | - Natalie S. Fox
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Jiapei Yuan
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
| | | | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
| | - Weerachai Jaratlerdsiri
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Job van Riet
- Department of Medical Oncology, Erasmus University, Rotterdam, the Netherlands
| | - Peter Georgeson
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Stefano Mangiola
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Kodi Taraszka
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California
| | - Robert Lesurf
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Jue Jiang
- Laboratory for Human Comparative and Prostate Cancer Genomics, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Darlinghurst, Australia
| | - Ken Chow
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Division of Urology, Royal Melbourne Hospital, Parkville, Australia
| | | | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Michael J. Clarkson
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | - Anne Nguyen
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | | | - Ryan Stuchbery
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edward O’Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick J. McCoy
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | | | - Marek Cmero
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Adriana Salcedo
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Eva K.F. Chan
- St Vincent’s Clinical School, University of New South Wales, Randwick, Australia
- Department of Urology, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| | - Lydia Y. Liu
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Phillip D. Stricker
- Department of Urology, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
| | - Vinayak Bhandari
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Riana M.S. Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | | | - Andrew Lonie
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | | | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Justin S. Peters
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | - Adrien Foucal
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Lachlan Mcintosh
- Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Michèle Orain
- Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Matthew Wakefield
- Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Valérie Picard
- Division of Urology and Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Daniel J. Park
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Hélène Hovington
- Division of Urology and Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Michael Kerger
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
| | - Alain Bergeron
- Division of Urology and Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | | | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark M. Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sebastian M. Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Genetics, Brigham Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts
| | - Louis Lacombe
- Division of Urology and Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Yves Fradet
- Division of Urology and Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Andrew Ryan
- TissuPath Specialist Pathology Services, Mount Waverley, Australia
| | - Amar U. Kishan
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | - Martijn P. Lolkema
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
- Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bernard Têtu
- Research Centre of CHU de Québec-Université Laval, Québec City, Canada
| | - Anthony J. Costello
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Division of Urology, Royal Melbourne Hospital, Parkville, Australia
| | - Vanessa M. Hayes
- St Vincent’s Clinical School, University of New South Wales, Randwick, Australia
- Department of Urology, St. Vincent’s Hospital Sydney, Darlinghurst, Australia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
- Central Clinical School, University of Sydney, Camperdown, Australia
- Department of Medical Sciences, University of Limpopo, Mankweng, South Africa
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Housheng H. He
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - John D. McPherson
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Bogdan Pasaniuc
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | | | - Anthony T. Papenfuss
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Department of Mathematics and Statistics, University of Melbourne, Parkville, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bernard J. Pope
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
- Department of Medicine, Monash University, Clayton, Australia
| | - Robert G. Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Manchester Cancer Research Centre, Manchester, United Kingdom
| | - Ram S. Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, Texas
- Department of Urology, UT Southwestern Medical Center, Dallas, Texas
| | - Niall M. Corcoran
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
- Division of Urology, Royal Melbourne Hospital, Parkville, Australia
- Department of Urology, Peninsula Health, Frankston, Australia
- The Victorian Comprehensive Cancer Centre, Parkville, Australia
| | - Jüri Reimand
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Christopher M. Hovens
- Australian Prostate Cancer Research Centre Epworth, Richmond, Australia
- Department of Surgery, The University of Melbourne, Parkville, Australia
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, California
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, California
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
- Department of Urology, University of California, Los Angeles, Los Angeles, California
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Tang S, Li J, Tian W, Feng Y, Deng Y, Tan Z, Han Z, He H, Wu Y, Huang C, Ning K, Liu F, Luo H, Cai S, Ye J, Zhong W. Characterization of the Biochemical Recurrence Prediction Ability and Progression Correlation of Peroxiredoxins Family in Prostate Cancer Based on Integrating Single-Cell RNA-Seq and Bulk RNA-Seq Cohorts. Cancer Med 2025; 14:e70855. [PMID: 40281661 PMCID: PMC12031674 DOI: 10.1002/cam4.70855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 03/25/2025] [Accepted: 03/26/2025] [Indexed: 04/29/2025] Open
Abstract
INTRODUCTION The peroxiredoxins (PRDXs) family plays a crucial role in balancing reactive oxygen species (ROS) levels in tumor cells. However, its potential role in prognosis and therapy response of prostate cancer (PCa) remains unknown. METHODS In this study, we utilized 2 public single-cell RNA datasets and 8 bulk-RNA datasets to investigate the clinical value of six PRDXs family members in PCa. Expression comparison, biochemical recurrence analysis, and therapy response analysis were measured. Pathway enrichments were utilized to predict the potential down-stream pathway it may involve. In vitro experiments were used to validate the function of PRDX5 in the progression of castration-resistant prostate cancer (CRPC) cell lines. RESULT Among the PRDXs family, PRDX5 was most related to the advancement of prostate cancer. A nomogram integrating the expression of PRDX5 with clinical features was developed to better predict clinical outcomes in PCa patients compared to 30 published signatures. Immunohistochemistry was used to verify that PRDX5 expression was higher in advanced levels of PCa tissue. Gene Set Enrichment Analysis (GSEA) and pathway predictive analysis revealed that the PRDX5 related genes were mainly relevant to ROS Pathway, Mitochondria-related functions, cellular respiration, and oxidative phosphorylation. In vitro cell proliferation assays, ROS determination assay, and apoptosis assay together revealed that depletion of PRDX5 induces apoptosis via ROS accumulation in CRPC cells. Moreover, the expression of PRDX5 in CRPC cells also affects the sensitivity to the ARSI therapy. CONCLUSION This study offers new evidence for determining that the expression of PRDX5 is associated with advanced tumor grade, poor prognosis, and suboptimal response to multiple therapies in PCa within the PRDXs family. Last but not least, our study provides new insights into precision medicine in PCa and provides a reference for further research on PRDX5.
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Affiliation(s)
- Shan Tang
- Urology DepartmentThe Central Hospital of ShaoyangShaoyangChina
| | - Jinchuang Li
- Department of UrologyGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Weicheng Tian
- Guangdong Provincial Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical UniversityGuangzhouChina
| | - Yuanfa Feng
- Guangdong Provincial Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical UniversityGuangzhouChina
- Guangzhou National LaboratoryGuangzhouChina
| | - Yulin Deng
- Department of UrologyThe First Dongguan Affiliated Hospital, Guangdong Medical UniversityDongguanChina
| | - Zeheng Tan
- Department of UrologyGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Zhaodong Han
- Department of UrologyGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Huichan He
- Guangdong Provincial Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical UniversityGuangzhouChina
| | - Yongding Wu
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Chuyang Huang
- Urology DepartmentThe Central Hospital of ShaoyangShaoyangChina
| | - Keping Ning
- Urology DepartmentThe Central Hospital of ShaoyangShaoyangChina
| | - Feng Liu
- Urology DepartmentThe Central Hospital of ShaoyangShaoyangChina
| | - Hongwei Luo
- Urology DepartmentThe Central Hospital of ShaoyangShaoyangChina
| | - Shanghua Cai
- Guangdong Provincial Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical UniversityGuangzhouChina
- Guangzhou National LaboratoryGuangzhouChina
| | - Jianheng Ye
- Department of UrologyGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
| | - Weide Zhong
- Department of UrologyGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Key Laboratory of Clinical Molecular Medicine and DiagnosticsGuangzhou First People's Hospital, School of Medicine, South China University of TechnologyGuangzhouChina
- Guangdong Provincial Key Laboratory of UrologyThe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical UniversityGuangzhouChina
- Guangzhou National LaboratoryGuangzhouChina
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Arbet J, Yamaguchi TN, Shiah YJ, Hugh-White R, Wiggins A, Oh J, Gebo T, Foucal A, Lesurf R, Jung CH, Dang RMA, Agrawal R, Livingstone J, Salcedo A, Yao CQ, Espiritu SMG, Houlahan KE, Yousif F, Heisler LE, Papenfuss AT, Fraser M, Pope B, Kishan A, Berlin A, Chua MLK, Corcoran NM, van der Kwast T, Hovens CM, Bristow RG, Boutros PC. The Landscape of Prostate Tumour Methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.637178. [PMID: 39990314 PMCID: PMC11844408 DOI: 10.1101/2025.02.07.637178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Prostate cancer is characterized by profound clinical and molecular heterogeneity. While its genomic heterogeneity is well-characterized, its epigenomic heterogeneity remains less understood. We therefore created a compendium of 3,001 multi-ancestry prostate methylomes spanning normal tissue through localized disease of all grades to poly-metastatic disease. A subset of 884 samples had multi-omic DNA and/or RNA characterization. We identify four epigenomic subtypes that risk-stratify patients and reflect distinct evolutionary trajectories. We demonstrate extensive regulatory interplay between DNA ploidy and DNA methylation, with transcriptional consequences that vary across genes and disease stages. We define the epigenetic dysregulation signatures of the 15 most important clinico-molecular features, creating predictive models for each. For example, we identify specific epigenetic features that predict patient outcome and that are synergistic with clinico-genomic prognostic features. These results define a complex interplay between tumour genetics and epigenetics that converges to modify gene-expression programs and clinical presentation.
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Kluge K, Haberl D, Haug A, Kenner L, Kramer G, Shariat S, Kumpf K, Hacker M. Genomic instability is associated with response to [¹⁷⁷Lu]Lu-PSMA-I&T radioligand therapy: an exploratory, preliminary liquid biopsy analysis. Eur J Nucl Med Mol Imaging 2025:10.1007/s00259-025-07280-5. [PMID: 40261406 DOI: 10.1007/s00259-025-07280-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Accepted: 04/07/2025] [Indexed: 04/24/2025]
Abstract
BACKGROUND PSMA-targeted radioligand therapies (PSMA RLT) are an effective and safe option for metastatic castration-resistant prostate cancer, but responsive subtypes and their biomarkers are not fully defined. METHODS Plasma samples for cell-free DNA (cfDNA) analysis were collected from 17 patients undergoing [¹⁷⁷Lu]Lu-PSMA-I&T. CfDNA underwent whole-genome sequencing to establish copy number variation (CNV) profiles and circulating-tumor DNA (ctDNA) levels and compared between prostate-specific antigen (PSA) response- and 1-year overall survival (1YOS) groups. RESULTS Non-responders exhibited higher degrees of cfDNA CNV burden (P = 0.048) and higher ctDNA levels (P = 0.036) than responders. Both markers allowed for the differentiation of responses (AUC: 0.792, 0.806) and 1YOS (AUC: 0.778, 0.847). CONCLUSION Unresponsive patients exhibited higher levels of cfDNA genomic instability and ctDNA levels, warranting genome-wide CNV profiling studies next to targeted approaches for mechanistic radiobiological insights and their value as response biomarkers for PSMA RLTs.
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Affiliation(s)
- Kilian Kluge
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, 1090, Austria
- Christian Doppler Laboratory for Applied Metabolomics (CDL AM), Medical University of Vienna, Vienna, Austria
| | - David Haberl
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, 1090, Austria
| | - Alexander Haug
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, 1090, Austria
- Christian Doppler Laboratory for Applied Metabolomics (CDL AM), Medical University of Vienna, Vienna, Austria
| | - Lukas Kenner
- Christian Doppler Laboratory for Applied Metabolomics (CDL AM), Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Gero Kramer
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Shahrokh Shariat
- Department of Urology, Medical University of Vienna, Vienna, Austria
- Department of Urology and Andrology, University Hospital Krems, Krems, Austria
- Karl Landsteiner Institute of Urology and Andrology, Vienna, Austria
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, USA
- Division of Urology, Department of Special Surgery, The University of Jordan, Amman, Jordan
- Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Urology, Weill Cornell Medical College, New York, USA
| | - Katarina Kumpf
- IT Service and Strategic Information Management, Medical University Vienna, Vienna, Austria
| | - Marcus Hacker
- Department of Biomedical Imaging and Image-Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, Währinger Gürtel 18-20, Vienna, 1090, Austria.
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Lin G, Elkashif A, Saha C, Coulter JA, Dunne NJ, McCarthy HO. Key considerations for a prostate cancer mRNA vaccine. Crit Rev Oncol Hematol 2025; 208:104643. [PMID: 39900315 DOI: 10.1016/j.critrevonc.2025.104643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 01/20/2025] [Accepted: 01/30/2025] [Indexed: 02/05/2025] Open
Abstract
Prostate cancer has the second highest cancer mortality rate in the UK in males. Early prostate cancer is typically asymptomatic, with diagnosis at a locally advanced or metastatic stage. In addition, the inherent heterogeneity of prostate cancer tumours differs significantly in terms of genetic, molecular, and histological features. The successful treatment of prostate cancer is therefore exceedingly challenging. Immunotherapies, particularly therapeutic vaccines, have been widely used in preclinical and clinical studies to treat various cancers. Sipuleucel-T was the first cancer vaccine approved by the FDA for the treatment of asymptomatic or minimally symptomatic metastatic castration-resistant prostate cancer (mCRPC), ushering in a new era of immunotherapy. In this review, the latest immunotherapy strategies for prostate cancer are considered with key tumour-associated antigens (TAA) and tumour-specific antigens (TSA) highlighted. The key components of mRNA vaccines include in vitro transcription, stability, and immunogenicity. Finally, strategies to circumvent in vivo mRNA degradation and approaches to optimise in vitro transcription (IVT) process are also discussed.
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Affiliation(s)
- Guanjie Lin
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Ahmed Elkashif
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Chayanika Saha
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Jonathan A Coulter
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Nicholas J Dunne
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin D09 NA55, Ireland; Centre for Medical Engineering Research, Dublin City University, Dublin D09 NA55, Ireland; Biodesign Europe, Dublin City University, Dublin D09 NA55, Ireland; Tissue, Engineering Research Group, Department of Anatomy and Regenerative Medicine, Royal College of Surgeons in Ireland, Dublin D02 PN40, Ireland; Advanced Manufacturing Research Centre (I-Form), School of Mechanical and Manufacturing Engineering, Dublin City University, Dublin D09 NA55, Ireland; Advanced Processing Technology Research Centre, Dublin City University, Dublin D09 NA55, Ireland; Trinity Centre for Biomedical Engineering, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D02 PN40, Ireland; Advanced Materials and Bioengineering Research Centre (AMBER), Trinity College Dublin, Dublin D02 PN40, Ireland; Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Helen O McCarthy
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK.
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6
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Xu X, Zhu H, Hugh-White R, Livingstone J, Eng S, Zeltser N, Wang Y, Pajdzik K, Chen S, Houlahan KE, Luo W, Liu S, Xu X, Sheng M, Guo WY, Arbet J, Song Y, Wang M, Zeng Y, Wang S, Zhu G, Gao T, Chen W, Ci X, Xu W, Xu K, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Têtu B, Fradet Y, Lupien M, Wei GH, Koritzinsky M, Bristow RG, Fleshner NE, Wu X, Shao Y, He C, Berlin A, van der Kwast T, Leong H, Boutros PC, He HH. The landscape of N 6-methyladenosine in localized primary prostate cancer. Nat Genet 2025; 57:934-948. [PMID: 40128621 PMCID: PMC11985349 DOI: 10.1038/s41588-025-02128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/13/2025] [Indexed: 03/26/2025]
Abstract
N6-methyladenosine (m6A), the most abundant internal RNA modification in humans, regulates most aspects of RNA processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we characterized the m6A landscape of 162 localized prostate tumors with matched DNA, RNA and protein profiling. m6A abundance varied dramatically across tumors, with global patterns emerging via complex germline-somatic cooperative regulation. Individual germline polymorphisms regulated m6A abundance, cooperating with somatic mutation of cancer driver genes and m6A regulators. The resulting complex patterns were associated with prognostic clinical features and established the biomarker potential of global and locus-specific m6A patterns. Tumor hypoxia dysregulates m6A profiles, bridging prior genomic and proteomic observations. Specific m6A sites, such as those in VCAN, drive disease aggression, associating with poor outcomes, tumor growth and metastasis. m6A dysregulation is thus associated with key events in the natural history of prostate cancer: germline risk, microenvironmental dysregulation, somatic mutation and metastasis.
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Affiliation(s)
- Xin Xu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Helen Zhu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Rupert Hugh-White
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie Livingstone
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stefan Eng
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicole Zeltser
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yujuan Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Kinga Pajdzik
- Department of Chemistry, the University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, the University of Chicago, Chicago, IL, USA
| | - Sujun Chen
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- West China School of Public Health, West China Fourth Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Kathleen E Houlahan
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wenqin Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shun Liu
- Department of Chemistry, the University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, the University of Chicago, Chicago, IL, USA
| | - Xi Xu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Minzhi Sheng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Wang Yuan Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Jaron Arbet
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuxi Song
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Miranda Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Yong Zeng
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Shiyan Wang
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Guanghui Zhu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- West China School of Public Health, West China Fourth Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Tingxiao Gao
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wei Chen
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Respiratory and Critical Care Medicine, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xinpei Ci
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Wenjie Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Kexin Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Michele Orain
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Valerie Picard
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Helene Hovington
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Alain Bergeron
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Louis Lacombe
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Bernard Têtu
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Yves Fradet
- Research Centre of CHU de Québec-Université Laval, Québec City, Quebec, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gong-Hong Wei
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
- State Key Laboratory of Common Mechanism Research for Major Disease, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, China
| | - Marianne Koritzinsky
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Robert G Bristow
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Christie NHS Trust and CRUK Manchester Institute and Cancer Centre, Manchester, UK
| | - Neil E Fleshner
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Xue Wu
- Geneseeq Research Institute, Geneseeq Technology lnc., Toronto, Ontario, Canada
| | - Yang Shao
- Geneseeq Research Institute, Geneseeq Technology lnc., Toronto, Ontario, Canada
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuan He
- Department of Chemistry, the University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, the University of Chicago, Chicago, IL, USA
| | - Alejandro Berlin
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | | | - Hon Leong
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
| | - Housheng Hansen He
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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7
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Hofstad M, Woods A, Parra K, Sychev ZE, Mazzagatti A, Huo X, Yu L, Gilbreath C, Chen WM, Davis AJ, Ly P, Drake JM, Kittler R. Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer. Oncogene 2025:10.1038/s41388-025-03343-x. [PMID: 40119228 DOI: 10.1038/s41388-025-03343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 01/31/2025] [Accepted: 03/06/2025] [Indexed: 03/24/2025]
Abstract
In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) gene ataxia telangiectasia mutated (ATM) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues for ATM mutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPC in vitro and in vivo, and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.
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Affiliation(s)
- Mia Hofstad
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Andrea Woods
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Karla Parra
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zoi E Sychev
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Alice Mazzagatti
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofang Huo
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lan Yu
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Collin Gilbreath
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei-Min Chen
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Anthony J Davis
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Justin M Drake
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
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8
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Esentürk E, Sahli A, Haberland V, Ziuboniewicz A, Wirth C, Bova GS, Bristow RG, Brook MN, Brors B, Butler A, Cancel-Tassin G, Cheng KC, Cooper CS, Corcoran NM, Cussenot O, Eeles RA, Favero F, Gerhauser C, Gihawi A, Girma EG, Gnanapragasam VJ, Gruber AJ, Hamid A, Hayes VM, He HH, Hovens CM, Imada EL, Jakobsdottir GM, Jung CH, Khani F, Kote-Jarai Z, Lamy P, Leeman G, Loda M, Lutsik P, Marchionni L, Molania R, Papenfuss AT, Pellegrina D, Pope B, Queiroz LR, Rausch T, Reimand J, Robinson B, Schlomm T, Sørensen KD, Uhrig S, Weischenfeldt J, Xu Y, Yamaguchi TN, Zanettini C, Lynch AG, Wedge DC, Brewer DS, Woodcock DJ. Causes of evolutionary divergence in prostate cancer. ARXIV 2025:arXiv:2503.13189v1. [PMID: 40166741 PMCID: PMC11957227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Cancer progression involves the sequential accumulation of genetic alterations that cumulatively shape the tumour phenotype. In prostate cancer, tumours can follow divergent evolutionary trajectories that lead to distinct subtypes, but the causes of this divergence remain unclear. While causal inference could elucidate the factors involved, conventional methods are unsuitable due to the possibility of unobserved confounders and ambiguity in the direction of causality. Here, we propose a method that circumvents these issues and apply it to genomic data from 829 prostate cancer patients. We identify several genetic alterations that drive divergence as well as others that prevent this transition, locking tumours into one trajectory. Further analysis reveals that these genetic alterations may cause each other, implying a positive-feedback loop that accelerates divergence. Our findings provide insights into how cancer subtypes emerge and offer a foundation for genomic surveillance strategies aimed at monitoring the progression of prostate cancer.
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Affiliation(s)
- Emre Esentürk
- Nuffield Department of Medicine, University of Oxford, UK
| | - Atef Sahli
- Manchester Cancer Research Centre, The University of Manchester, UK
| | | | | | | | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Robert G Bristow
- Manchester Cancer Research Centre and Cancer Research UK Manchester Institute, The University of Manchester, UK
- Christie NHS Foundation Trust, UK
- Div Cancer Sciences, Faculty of Biology, Medicine & Health, University of Manchester, UK
| | | | - Benedikt Brors
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Germany
- German Cancer Consortium (DKTK), Core Center Heidelberg, and National Center for Tumor Diseases (NCT), Germany
- Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, Germany
| | | | - Géraldine Cancel-Tassin
- CeRePP (Centre de Recherche sur les Pathologies Prostatiques et Urologiques), France
- Sorbonne Université, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, France
| | - Kevin Cl Cheng
- Computational Biology Program, Ontario Institute for Cancer Research, Canada
- Department of Medical Biophysics, University of Toronto, Canada
| | | | - Niall M Corcoran
- Department of Urology, Royal Melbourne Hospital, Australia
- Department of Surgery, The University of Melbourne, Australia
- Department of Urology, Western Health, Australia
| | - Olivier Cussenot
- CeRePP (Centre de Recherche sur les Pathologies Prostatiques et Urologiques), France
| | - Ros A Eeles
- The Institute of Cancer Research, UK
- The Royal Marsden NHS Foundation Trust, London & Sutton
| | - Francesco Favero
- Biotech Research & Innovation Centre (BRIC) - University of Copenhagen, Denmark
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Denmark
| | - Clarissa Gerhauser
- Division Cancer Epigenomics, German Cancer Research Center (DKFZ), Germany
| | | | - Etsehiwot G Girma
- Biotech Research & Innovation Centre (BRIC) - University of Copenhagen, Denmark
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Denmark
| | - Vincent J Gnanapragasam
- Department of Surgery, Urology, University of Cambridge & Cambridge University Hospitals NHS Trust, Cambridge Urology Translational Research and Clinical Trials (Office), Cambridge Biomedical Campus, Addenbrooke's Hospital Site, S Wards Building, UK
| | | | - Anis Hamid
- Department of Surgery, The University of Melbourne, Australia
| | - Vanessa M Hayes
- School of Medical Sciences, University of Sydney, Faculty of Medicine & Health, Australia
- School of Health Systems & Public Health, University of Pretoria, South Africa
- Manchester Cancer Research Centre, University of Manchester, UK
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network; Department of Medical Biophysics, University of Toronto, Canada
| | - Christopher M Hovens
- Department of Surgery, The Collaborative Centre for Genomic Cancer Medicine, The University of Melbourne, Australia
| | - Eddie Luidy Imada
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - G Maria Jakobsdottir
- Division of Cancer Sciences, The University of Manchester, UK
- Christie Hospital, The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, UK
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Australia
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - Zsofia Kote-Jarai
- The Institute of Cancer Research, UK
- The Royal Marsden NHS Foundation Trust, London & Sutton
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | | | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
- Nuffield Department of Surgical Sciences, University of Oxford, UK
| | - Pavlo Lutsik
- Division Cancer Epigenomics, German Cancer Research Center (DKFZ), Germany
- Department of Oncology, KU Leuven, Belgium
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - Ramyar Molania
- Walter and Eliza Hall Institute of Medical Research, Australia
- Department of Medical Biology, The University of Melbourne, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Australia
- Department of Medical Biology, The University of Melbourne, Australia
| | - Diogo Pellegrina
- Computational Biology Program, Ontario Institute for Cancer Research, Canada
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Australia
- Australian BioCommons, The University of Melbourne, Australia
- Department of Surgery, The University of Melbourne, Australia
| | - Lucio R Queiroz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - Tobias Rausch
- Genome Biology, European Molecular Biology Laboratory (EMBL), Germany
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Canada
- Department of Molecular Genetics, University of Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Canada
| | - Brian Robinson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - Thorsten Schlomm
- Department of Urology, Charité - Universitätsmedizin Berlin, Germany
| | - Karina D Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Sebastian Uhrig
- Division Applied Bioinformatics, German Cancer Research Center (DKFZ), Germany
| | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC) - University of Copenhagen, Denmark
- Finsen Laboratory, Copenhagen University Hospital - Rigshospitalet, Denmark
- Department of Urology, Charité - Universitätsmedizin Berlin, Germany
| | | | - Takafumi N Yamaguchi
- Jonsson Comprehensive Cancer Center, University of California - Los Angeles, USA
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, USA
| | - Andy G Lynch
- School of Medicine, School of Mathematics & Statistics, University of St Andrews, UK
| | - David C Wedge
- Manchester Cancer Research Centre, The University of Manchester, UK
| | - Daniel S Brewer
- Metabolic Health research centre, Norwich Medical School, University of East Anglia, UK
- The Earlham Institute, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, UK
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9
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Suvac A, Ashton J, Bristow RG. Tumour hypoxia in driving genomic instability and tumour evolution. Nat Rev Cancer 2025; 25:167-188. [PMID: 39875616 DOI: 10.1038/s41568-024-00781-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2024] [Indexed: 01/30/2025]
Abstract
Intratumour hypoxia is a feature of all heterogenous solid tumours. Increased levels or subregions of tumour hypoxia are associated with an adverse clinical prognosis, particularly when this co-occurs with genomic instability. Experimental evidence points to the acquisition of DNA and chromosomal alterations in proliferating hypoxic cells secondary to inhibition of DNA repair pathways such as homologous recombination, base excision repair and mismatch repair. Cell adaptation and selection in repair-deficient cells give rise to a model whereby novel single-nucleotide mutations, structural variants and copy number alterations coexist with altered mitotic control to drive chromosomal instability and aneuploidy. Whole-genome sequencing studies support the concept that hypoxia is a critical microenvironmental cofactor alongside the driver mutations in MYC, BCL2, TP53 and PTEN in determining clonal and subclonal evolution in multiple tumour types. We propose that the hypoxic tumour microenvironment selects for unstable tumour clones which survive, propagate and metastasize under reduced immune surveillance. These aggressive features of hypoxic tumour cells underpin resistance to local and systemic therapies and unfavourable outcomes for patients with cancer. Possible ways to counter the effects of hypoxia to block tumour evolution and improve treatment outcomes are described.
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Affiliation(s)
- Alexandru Suvac
- Translational Oncogenomics Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jack Ashton
- Translational Oncogenomics Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Robert G Bristow
- Translational Oncogenomics Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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10
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Qian X, Sun D, Ma Y, Qiu L, Wu J. Exploring Mechanisms and Biomarkers of Breast Cancer Invasion and Migration: An Explainable Gene-Pathway-Compounds Neural Network. Cancer Med 2025; 14:e70769. [PMID: 40095726 PMCID: PMC11912184 DOI: 10.1002/cam4.70769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 02/18/2025] [Accepted: 03/06/2025] [Indexed: 03/19/2025] Open
Abstract
BACKGROUNDS Exploring the molecular features that drive breast cancer invasion and migration remains an important biological and clinical challenge. In recent years, the use of interpretable machine learning models has enhanced our understanding of the underlying mechanisms of disease progression. METHODS In this study, we present a novel gene-pathway-compound-related sparse deep neural network (GPC-Net) for investigating breast cancer invasion and migration. The GPC-Net is an interpretable neural network model that utilizes molecular data to predict cancer status. It visually represents genes, pathways, and associated compounds involved in these pathways. RESULTS Compared with other modeling methods, GPC-Net demonstrates superior performance. Our research identifies key genes, such as ADCY8, associated with invasive breast cancer and verifies their expression in breast cancer cells. In addition, we conducted a preliminary exploration of several pathways. CONCLUSION GPC-Net is among the pioneering deep neural networks that incorporate pathways and compounds, aiming to balance interpretability and performance. It is expected to offer a more convenient approach for future biomedical research.
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Affiliation(s)
- Xia Qian
- Department of Laboratory MedicinePeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
| | - Dandan Sun
- Department of Laboratory MedicinePeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
| | - Yichen Ma
- Department of Laboratory MedicinePeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
| | - Ling Qiu
- Department of Laboratory MedicinePeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
- State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
| | - Jie Wu
- Department of Laboratory MedicinePeking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical ScienceBeijingPeople's Republic of China
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11
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Ding CKC, Greenland NY, Sirohi D, Lotan TL. Molecular Landscape of Aggressive Histologic Subtypes of Localized Prostate Cancer. Surg Pathol Clin 2025; 18:1-12. [PMID: 39890297 DOI: 10.1016/j.path.2024.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2025]
Abstract
Despite incredible progress in describing the molecular underpinnings of prostate cancer over the last decades, pathologic examination remains indispensable for predicting aggressive behavior in the localized setting. Beyond pathologic grade, specific histologic findings have emerged as critical prognostic or predictive indicators. Here, the authors review molecular correlates of aggressive histologic subtypes of prostate cancer in the localized setting, demonstrating that many of the signature molecular alterations found in metastatic disease-such as tumor suppressor gene loss and DNA repair defects-are enriched in primary disease with adverse histologic features, presaging aggressive behavior, and presenting opportunities for earlier germline screening or targeted therapies.
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Affiliation(s)
- Chien-Kuang C Ding
- Department of Pathology, University of California, San Francisco (UCSF), 1825 4th Street, M2370, San Francisco, CA 94158, USA
| | - Nancy Y Greenland
- Department of Pathology, University of California, San Francisco (UCSF), 1825 4th Street, M2370, San Francisco, CA 94158, USA
| | - Deepika Sirohi
- Department of Pathology, University of California, San Francisco (UCSF), 1825 4th Street, M2370, San Francisco, CA 94158, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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12
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Morgan RA, Hazard ES, Savage SJ, Halbert CH, Gattoni-Celli S, Hardiman G. Unveiling Racial Disparities in Localized Prostate Cancer: A Systems-Level Exploration of the lncRNA Landscape. Genes (Basel) 2025; 16:229. [PMID: 40004558 PMCID: PMC11855151 DOI: 10.3390/genes16020229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 01/17/2025] [Accepted: 01/22/2025] [Indexed: 02/27/2025] Open
Abstract
BACKGROUND/OBJECTIVES Prostate cancer (PC) is the most common non-cutaneous cancer in men globally, and one which displays significant racial disparities. Men of African descent (AF) are more likely to develop PC and face higher mortality compared to men of European descent (EU). The biological mechanisms underlying these differences remain unclear. Long non-coding RNAs (lncRNAs), recognized as key regulators of gene expression and immune processes, have emerged as potential contributors to these disparities. This study aimed to investigate the regulatory role of lncRNAs in localized PC in AF men relative to those of EU and assess their involvement in immune response and inflammation. METHODS A systems biology approach was employed to analyze differentially expressed (DE) lncRNAs and their roles in prostate cancer (PC). Immune-related pathways were investigated through over-representation analysis of lncRNA-mRNA networks. The study also examined the effects of vitamin D supplementation on lncRNA expression in African descent (AF) PC patients, highlighting their potential regulatory roles in immune response and inflammation. RESULTS Key lncRNAs specific to AF men were identified, with several being implicated for immune response and inflammatory processes. Notably, 10 out of the top 11 ranked lncRNAs demonstrated strong interactions with immune-related genes. Pathway analysis revealed their regulatory influence on antigen processing and presentation, chemokine signaling, and ribosome pathways, suggesting their critical roles in immune regulation. CONCLUSIONS These findings highlight the pivotal role of lncRNAs in PC racial disparities, particularly through immune modulation. The identified lncRNAs may serve as potential biomarkers or therapeutic targets to address racial disparities in PC outcomes.
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Affiliation(s)
- Rebecca A. Morgan
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Queen’s University Belfast (QUB), Belfast BT9 5DL, UK;
| | - E. Starr Hazard
- Academic Affairs Faculty, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA;
| | - Stephen J. Savage
- Department of Urology, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA;
- Ralph H. Johnson VA Health Care System (VAHCS) Medical Center, Charleston, SC 29425, USA;
| | - Chanita Hughes Halbert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA;
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Sebastiano Gattoni-Celli
- Ralph H. Johnson VA Health Care System (VAHCS) Medical Center, Charleston, SC 29425, USA;
- Department of Radiation Oncology, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA
| | - Gary Hardiman
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Institute for Global Food Security (IGFS), Queen’s University Belfast (QUB), Belfast BT9 5DL, UK;
- Department of Medicine, Medical University of South Carolina (MUSC), Charleston, SC 29425, USA
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13
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He Q, Xiong Y, Yang X, Yu Y, Chen Z. Molecular subtyping combined with multiomics analysis to study correlation between TACE refractoriness and tumor stemness in hepatocellular carcinoma. Discov Oncol 2025; 16:197. [PMID: 39961903 PMCID: PMC11832877 DOI: 10.1007/s12672-025-01955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Accepted: 02/07/2025] [Indexed: 02/20/2025] Open
Abstract
BACKGROUND Transarterial chemoembolization (TACE) refractoriness is a significant challenge in treating intermediate to advanced-stage hepatocellular carcinoma (HCC). A few studies suggest that liver cancer stem cells (LCSCs) may be associated with TACE refractoriness. This study aims to explore the potential correlation between TACE refractoriness and HCC stemness, highlighting its clinical significance. METHODS This research encompassed the analysis of diverse HCC datasets, including RNA-sequencing, microarray, single-cell RNA-sequencing, and clinical cohorts. We identified common genes between TACE refractoriness and tumor stemness (TSGs). Unsupervised clustering was employed to classify HCC patients into different clusters based on TSGs (TRS clusters). The study explored the differences in clinical prognosis, biological characteristics, genomic variations, immune landscapes, and treatment responses among the TRS clusters. RESULTS Patients with TACE-refractoriness demonstrated significantly higher tumor stemness. Our study identified 33 TSGs and established two TRS clusters, including C1 and C2. C1 was associated with TACE refractoriness, elevated tumor stemness, and poorer prognosis. Genomic alterations were found to be significantly different between the TRS clusters. The C1 exhibited signs of immunosuppression and lower activity of immune effector cells, while the C2 had a more robust immune response and higher level of immune cell presence. Single-cell RNA-seq revealed distinct cell type characteristics in each subtypes, with the C1 showing a higher proportion of stem cells and malignant cells. CONCLUSION Our findings establish a connection between TACE refractoriness and tumor stemness in HCC, proposing a novel subtype classification to guide personalized treatment. Insights gained may facilitate overcoming TACE refractoriness and the development of innovative therapies.
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Affiliation(s)
- Qifan He
- Department of Radiology, Haining People's Hospital, No.2 Qianjiang West Road, Haining, 314400, China
| | - Yue Xiong
- Department of Radiology, Haining People's Hospital, No.2 Qianjiang West Road, Haining, 314400, China
| | - Xiaoyu Yang
- Department of Radiology, Haining People's Hospital, No.2 Qianjiang West Road, Haining, 314400, China
| | - Yihui Yu
- Department of Radiology, Haining People's Hospital, No.2 Qianjiang West Road, Haining, 314400, China
| | - Zhonghua Chen
- Department of Radiology, Haining People's Hospital, No.2 Qianjiang West Road, Haining, 314400, China.
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14
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Pedrani M, Barizzi J, Salfi G, Nepote A, Testi I, Merler S, Castelo-Branco L, Mestre RP, Turco F, Tortola L, Theurillat JP, Gillessen S, Vogl U. The Emerging Predictive and Prognostic Role of Aggressive-Variant-Associated Tumor Suppressor Genes Across Prostate Cancer Stages. Int J Mol Sci 2025; 26:318. [PMID: 39796175 PMCID: PMC11719667 DOI: 10.3390/ijms26010318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 12/23/2024] [Accepted: 12/31/2024] [Indexed: 01/13/2025] Open
Abstract
Aggressive variant prostate cancer (AVPC) is characterized by a molecular signature involving combined defects in TP53, RB1, and/or PTEN (AVPC-TSGs), identifiable through immunohistochemistry or genomic analysis. The reported prevalence of AVPC-TSG alterations varies widely, reflecting differences in assay sensitivity, treatment pressure, and disease stage evolution. Although robust clinical evidence is still emerging, the study of AVPC-TSG alterations in prostate cancer (PCa) is promising. Alterations in TP53, RB1, and PTEN, as well as the combined loss of AVPC-TSGs, may have significant implications for prognosis and treatment. These biomarkers might help predict responses to various therapies, including hormonal treatments, cytotoxic agents, radiotherapy, and targeted therapies. Understanding the impact of these molecular alterations in patients with PCa is crucial for personalized management. In this review, we provide a comprehensive overview of the emerging prognostic and predictive roles of AVPC-TSG alterations across PCa stages. Moreover, we discuss the implications of different methods used for detecting AVPC-TSG alterations and summarize factors influencing their prevalence. As our comprehension of the genomic landscape of PCa disease deepens, incorporating genomic profiling into clinical decision making will become increasingly important for improving patient outcomes.
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Affiliation(s)
- Martino Pedrani
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, 20122 Milan, Italy
| | - Jessica Barizzi
- Istituto Cantonale di Patologia, Ente Ospedaliero Cantonale (EOC), 6600 Locarno, Switzerland
| | - Giuseppe Salfi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland;
| | - Alessandro Nepote
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland;
- AOU San Luigi Gonzaga, Department of Oncology, University of Torino, 10124 Torino, Italy
| | - Irene Testi
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - Sara Merler
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland;
- Section of Innovation Biomedicine—Oncology Area, Department of Engineering for Innovation Medicine, University of Verona and Verona University Hospital Trust, 37126 Verona, Italy
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Luis Castelo-Branco
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
| | - Ricardo Pereira Mestre
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland;
| | - Fabio Turco
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
| | - Luigi Tortola
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
| | - Jean-Philippe Theurillat
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland;
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Silke Gillessen
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Ursula Vogl
- Oncology Institute of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), 6500 Bellinzona, Switzerland; (M.P.); (A.N.); (S.M.); (R.P.M.); (F.T.); (S.G.)
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15
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Agostini M, Giacobbi E, Servadei F, Bishof J, Funke L, Sica G, Rovella V, Carilli M, Iacovelli V, Shi Y, Hou J, Candi E, Melino G, Cervelli G, Scimeca M, Mauriello A, Bove P. Unveiling the molecular profile of a prostate carcinoma: implications for personalized medicine. Biol Direct 2024; 19:146. [PMID: 39741346 PMCID: PMC11686862 DOI: 10.1186/s13062-024-00492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 01/02/2025] Open
Abstract
BACKGROUND Prostate cancer is the most common diagnosed tumor and the fifth cancer related death among men in Europe. Although several genetic alterations such as ERG-TMPRSS2 fusion, MYC amplification, PTEN deletion and mutations in p53 and BRCA2 genes play a key role in the pathogenesis of prostate cancer, specific gene alteration signature that could distinguish indolent from aggressive prostate cancer or may aid in patient stratification for prognosis and/or clinical management of patients with prostate cancer is still missing. Therefore, here, by a multi-omics approach we describe a prostate cancer carrying the fusion of TMPRSS2 with ERG gene and deletion of 16q chromosome arm. RESULTS We have observed deletion of KDM6A gene, which may represent an additional genomic alteration to be considered for patient stratification. The cancer hallmarks gene signatures highlight intriguing molecular aspects that characterize the biology of this tumor by both a high hypoxia and immune infiltration scores. Moreover, our analysis showed a slight increase in the Tumoral Mutational Burden, as well as an over-expression of the immune checkpoints. The omics profiling integrating hypoxia, ROS and the anti-cancer immune response, optimizes therapeutic strategies and advances personalized care for prostate cancer patients. CONCLUSION The here data reported can lay the foundation for predicting a poor prognosis for the studied prostate cancer, as well as the possibility of targeted therapies based on the modulation of hypoxia, ROS, and the anti-cancer immune response.
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Affiliation(s)
- Massimiliano Agostini
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Erica Giacobbi
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Francesca Servadei
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Julia Bishof
- Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | - Likas Funke
- Indivumed GmbH, Falkenried, 88 Building D, 20251, Hamburg, Germany
| | - Giuseppe Sica
- Department of Surgical Science, University Tor Vergata, Viale Oxford 81, 00133, Rome, Italy
| | - Valentina Rovella
- Department of System Medicine, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Marco Carilli
- Urology Unit, Department of Surgery, Tor Vergata University of Rome, Rome, Italy
| | - Valerio Iacovelli
- Urology Unit, Department of Surgery, Tor Vergata University of Rome, Rome, Italy
| | - Yufang Shi
- Institutes for Translational Medicine, The Fourth Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215000, China
| | - Jianquan Hou
- Institutes for Translational Medicine, The Fourth Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215000, China
| | - Eleonora Candi
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Giulio Cervelli
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Manuel Scimeca
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Alessandro Mauriello
- Department of Experimental Medicine, TOR, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Pierluigi Bove
- Urology Unit, Department of Surgery, Tor Vergata University of Rome, Rome, Italy.
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16
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Agrawal R, Al-Hiyari S, Hugh-White R, Hromas R, Patel Y, Williamson EA, Mootor MFE, Gonzalez A, Fu J, Haas R, Jordan M, Wickes BL, Mohammed G, Tian M, Doris MJ, Jobin C, Wernke KM, Pan Y, Yamaguchi TN, Herzon SB, Boutros PC, Liss MA. Colibactin Exerts Androgen-dependent and -independent Effects on Prostate Cancer. Eur Urol Oncol 2024:S2588-9311(24)00245-1. [PMID: 39547899 PMCID: PMC12075626 DOI: 10.1016/j.euo.2024.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/23/2024] [Accepted: 10/26/2024] [Indexed: 11/17/2024]
Abstract
BACKGROUND AND OBJECTIVE The etiology of prostate cancer (PC) is multifactorial and poorly understood. It has been suggested that colibactin-producing Escherichia coli positive for the pathogenicity island pks (pks+) initiate cancers via induction of genomic instability. In PC, androgens promote oncogenic translocations. Our aim was to investigate the association of pks+E. coli with PC diagnosis and molecular architecture, and its relationship with androgens. METHODS We quantified the association of pks+E. coli with PC diagnosis in a volunteer-sampled 235-person cohort from two institutional practices (UT San Antonio). We then used colibactin 742 and DNA/RNA sequencing to evaluate the effects of colibactin 742, dihydrotestosterone (DHT), and their combination in vitro. KEY FINDINGS AND LIMITATIONS Colibactin exposure was positively associated with PC diagnosis (p = 0.04) in our clinical cohort, and significantly increased replication fork stalling and fusions in vitro (p < 0.01). Combined in vitro exposure to colibactin 742 and DHT induced more somatic mutations of all types than exposure to either alone. The combination also elicited kataegis, with a higher density of somatic point mutations. Laboratory analyses were conducted using a single cell line, which limited our ability to fully recapitulate the complexity of PC etiology. CONCLUSIONS AND CLINICAL IMPLICATIONS Our findings are consistent with synergistic induction of genome instability and kataegis by colibactin 742 and DHT in cell culture. Colibactin-producing pks+ E. coli may plausibly contribute to PC etiology. PATIENT SUMMARY We investigated whether a bacterial toxin that is linked to colon cancer can also cause prostate cancer. Our results support this idea by showing a link between the toxin and prostate cancer diagnosis in a large patient population. We also found that this toxin causes genetic dysfunction in prostate cancer cells when combined with testosterone.
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Affiliation(s)
- Raag Agrawal
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Sarah Al-Hiyari
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Rupert Hugh-White
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Yash Patel
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Mohammed F E Mootor
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Alfredo Gonzalez
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Jianmin Fu
- Department of Microbiology and Immunology, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Roni Haas
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Madison Jordan
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Brian L Wickes
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas, San Antonia, TC, USA
| | - Ghouse Mohammed
- Office of Health Informatics and Analytics, University of California-Los Angeles, Los Angeles, CA, USA
| | - Mao Tian
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA
| | - Molly J Doris
- Department of Urology, University of Texas Health-San Antonio, San Antonio, TX, USA
| | - Christian Jobin
- Departments of Medicine, Infectious Diseases and Immunology, and Anatomy and Cell Physiology, University of Florida, Gainesville, FL, USA
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Pan
- Office of Health Informatics and Analytics, University of California-Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA; Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California-Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California-Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California-Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California-Los Angeles, Los Angeles, CA, USA; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Michael A Liss
- Department of Urology, University of Texas Health-San Antonio, San Antonio, TX, USA.
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17
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Li Q, Wang Y, Chen J, Zeng K, Wang C, Guo X, Hu Z, Hu J, Liu B, Xiao J, Zhou P. Machine learning based androgen receptor regulatory gene-related random forest survival model for precise treatment decision in prostate cancer. Heliyon 2024; 10:e37256. [PMID: 39296076 PMCID: PMC11407950 DOI: 10.1016/j.heliyon.2024.e37256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/29/2024] [Accepted: 08/29/2024] [Indexed: 09/21/2024] Open
Abstract
Background It has been demonstrated that aberrant androgen receptor (AR) signaling contributes to the pathogenesis of prostate cancer (PCa). To date, the most efficacious strategy for the treatment of PCa remains to target the AR signaling axis. However, numerous PCa patients still face the issue of overtreatment or undertreatment. The establishment of a precise risk prediction model is urgently needed to distinguish patients with high-risk and select appropriate treatment modalities. Methods In this study, a consensus AR regulatory gene-related signature (ARS) was developed by integrating a total of 101 algorithm combinations of 10 machine learning algorithms. We evaluated the value of ARS in predicting patient prognosis and the therapeutic effects of the various treatments. Additionally, we conducted a screening of therapeutic targets and agents for high-risk patients, followed by the verification in vitro and in vivo. Results ARS was an independent risk factor for biochemical recurrence and distant metastasis in PCa patients. The enhanced and consistent prognostic predictive capability of ARS across various platforms was confirmed when compared with 44 previously published signatures. More importantly, PCa patients in the ARShigh group benefit more from PARP inhibitors and immunotherapy, while chemotherapy, radiotherapy, and AR-targeted therapy are more effective for ARSlow patients. The results of in silico screening suggest that AURKB could potentially serve as a promising therapeutic target for ARShigh patients. Conclusions Collectively, this prediction model based on AR regulatory genes holds great clinical translational potential to solve the dilemma of treatment choice and identify potential novel therapeutic targets in PCa.
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Affiliation(s)
- Qinyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yanan Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Junjie Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Kai Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chengwei Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Xiangdong Guo
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhiquan Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jia Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Bo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Jun Xiao
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Peng Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
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18
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Fernandez-Mateos J, Cresswell GD, Trahearn N, Webb K, Sakr C, Lampis A, Stuttle C, Corbishley CM, Stavrinides V, Zapata L, Spiteri I, Heide T, Gallagher L, James C, Ramazzotti D, Gao A, Kote-Jarai Z, Acar A, Truelove L, Proszek P, Murray J, Reid A, Wilkins A, Hubank M, Eeles R, Dearnaley D, Sottoriva A. Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer. NATURE CANCER 2024; 5:1334-1351. [PMID: 38997466 PMCID: PMC11424488 DOI: 10.1038/s43018-024-00787-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/23/2024] [Indexed: 07/14/2024]
Abstract
Cancer evolution lays the groundwork for predictive oncology. Testing evolutionary metrics requires quantitative measurements in controlled clinical trials. We mapped genomic intratumor heterogeneity in locally advanced prostate cancer using 642 samples from 114 individuals enrolled in clinical trials with a 12-year median follow-up. We concomitantly assessed morphological heterogeneity using deep learning in 1,923 histological sections from 250 individuals. Genetic and morphological (Gleason) diversity were independent predictors of recurrence (hazard ratio (HR) = 3.12 and 95% confidence interval (95% CI) = 1.34-7.3; HR = 2.24 and 95% CI = 1.28-3.92). Combined, they identified a group with half the median time to recurrence. Spatial segregation of clones was also an independent marker of recurrence (HR = 2.3 and 95% CI = 1.11-4.8). We identified copy number changes associated with Gleason grade and found that chromosome 6p loss correlated with reduced immune infiltration. Matched profiling of relapse, decades after diagnosis, confirmed that genomic instability is a driving force in prostate cancer progression. This study shows that combining genomics with artificial intelligence-aided histopathology leads to the identification of clinical biomarkers of evolution.
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Affiliation(s)
- Javier Fernandez-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Katharine Webb
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Chirine Sakr
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Lampis
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Christine Stuttle
- The Royal Marsden NHS Foundation Trust, London, UK
- Oncogenetics Team, The Institute of Cancer Research, London, UK
| | - Catherine M Corbishley
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
- St. George's Hospital Healthcare NHS Trust, London, UK
| | | | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Lewis Gallagher
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Chela James
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | | | - Annie Gao
- Bob Champion Cancer Unit, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | | | - Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Lesley Truelove
- Bob Champion Cancer Unit, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Paula Proszek
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Julia Murray
- The Royal Marsden NHS Foundation Trust, London, UK
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Alison Reid
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Anna Wilkins
- The Royal Marsden NHS Foundation Trust, London, UK
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Michael Hubank
- Molecular Pathology Section, The Institute of Cancer Research, London, UK
- Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Ros Eeles
- The Royal Marsden NHS Foundation Trust, London, UK
- Oncogenetics Team, The Institute of Cancer Research, London, UK
| | - David Dearnaley
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK.
- Academic Urology Unit, The Royal Marsden NHS Foundation Trust, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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19
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Kim S, Yang H, Cho S, Jang Y, Han IO, Oh ES. Correlation of syndecan gene amplification with metastatic potential and clinical outcomes in carcinomas. Am J Physiol Cell Physiol 2024; 327:C380-C386. [PMID: 38953842 DOI: 10.1152/ajpcell.00270.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 07/04/2024]
Abstract
Cell surface receptors play crucial roles in cellular responses to extracellular ligands, helping to modulate the functions of a cell based on information coming from outside the cell. Syndecan refers to a family of cell adhesion receptors that regulate both extracellular and cytosolic events. Alteration of syndecan expression disrupts regulatory mechanisms in a cell type-specific fashion, often leading to serious diseases, notably cancer. Given the multifaceted functions and distinct tissue distributions of syndecan, it will be important to unravel the gene-level intricacies of syndecan expression and thereby further understand its involvement in various carcinogenic processes. Although accumulating evidence indicates that the protein expression patterns of syndecan family members are significantly altered in cancer cells, the underlying gene-level mechanisms remain largely unknown. This review endeavors to explore syndecan gene expression levels across different cancer types by scrutinizing extensive cancer genome datasets using tools such as cBioPortal. Our analysis unveils that somatic mutations in SDC genes are rare occurrences, whereas copy number alterations are frequently observed across diverse cancers, particularly in SDC2 and SDC4. Notably, amplifications of SDC2 and SDC4 correlate with heightened metastatic potential and dismal prognosis. This underscores the recurrent nature of SDC2 and SDC4 amplifications during carcinogenesis and sheds light on their role in promoting cancer activity through augmented protein expression. The identification of these amplifications not only enriches our understanding of carcinogenic mechanisms but also hints at the potential therapeutic avenue of targeting SDC2 and SDC4 to curb cancer cell proliferation and metastasis.
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Affiliation(s)
- Sewoon Kim
- Institute of Sensor Technology, Easytem Co., Ltd., Seoul, Republic of Korea
| | - Hyeonju Yang
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Subin Cho
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Yunjung Jang
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Inn-Oc Han
- Department of Biomedical Science, Program in Biomedical Science and Engineering, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Eok-Soo Oh
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
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20
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Marlin R, Loger JS, Joachim C, Ebring C, Robert-Siegwald G, Pennont S, Rose M, Raguette K, Suez-Panama V, Ulric-Gervaise S, Lusbec S, Bera O, Vallard A, Aline-Fardin A, Colomba E, Jean-Laurent M. Copy number signatures and CCNE1 amplification reveal the involvement of replication stress in high-grade endometrial tumors oncogenesis. Cell Oncol (Dordr) 2024; 47:1441-1457. [PMID: 38564163 PMCID: PMC11322381 DOI: 10.1007/s13402-024-00942-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Managing high-grade endometrial cancer in Martinique poses significant challenges. The diversity of copy number alterations in high-grade endometrial tumors, often associated with a TP53 mutation, is a key factor complicating treatment. Due to the high incidence of high-grade tumors with poor prognosis, our study aimed to characterize the molecular signature of these tumors within a cohort of 25 high-grade endometrial cases. METHODS We conducted a comprehensive pangenomic analysis to categorize the copy number alterations involved in these tumors. Whole-Exome Sequencing (WES) and Homologous Recombination (HR) analysis were performed. The alterations obtained from the WES were classified into various signatures using the Copy Number Signatures tool available in COSMIC. RESULTS We identified several signatures that correlated with tumor stage and disctinct prognoses. These signatures all seem to be linked to replication stress, with CCNE1 amplification identified as the primary driver of oncogenesis in over 70% of tumors analyzed. CONCLUSION The identification of CCNE1 amplification, which is currently being explored as a therapeutic target in clinical trials, suggests new treatment strategies for high-grade endometrial cancer. This finding holds particular significance for Martinique, where access to care is challenging.
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Affiliation(s)
- Regine Marlin
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique.
| | - Jean-Samuel Loger
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Clarisse Joachim
- General Cancer Registry of Martinique, University Hospital of Martinique, Fort-de-France, Martinique
| | - Coralie Ebring
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Guillaume Robert-Siegwald
- MitoVasc Unit, SFR ICAT, Mitolab Team, UMR CNRS 6015 INSERM U1083, University of Angers, Angers, France
| | - Sabrina Pennont
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Mickaelle Rose
- Martinique Regional Oncology Platform, University Hospital of Martinique, Fort-de-France, Martinique
| | - Kevin Raguette
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Valerie Suez-Panama
- Biological Resource Center, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylviane Ulric-Gervaise
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Sylvie Lusbec
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
| | - Odile Bera
- Department of Cancer Molecular Genetics, University Hospital of Martinique, Fort-de-France, Martinique
| | - Alexis Vallard
- Department of Oncology Hematology Urology, University Hospital of Martinique, Fort-de-France, Martinique
| | | | - Emeline Colomba
- Department of Cancer Medicine, Institut Gustave Roussy, University of Paris Saclay, Gif-sur-Yvette, France
| | - Mehdi Jean-Laurent
- Department of Gynecological and Breast Surgery, University Hospital of Martinique, Fort-de-France, Martinique
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21
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Hofstad M, Woods A, Parra K, Sychev ZE, Mazzagatti A, Yu L, Gilbreath C, Ly P, Drake JM, Kittler R. Dual inhibition of ATR and DNA-PKcs radiosensitizes ATM-mutant prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602941. [PMID: 39026771 PMCID: PMC11257504 DOI: 10.1101/2024.07.10.602941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
In advanced castration resistant prostate cancer (CRPC), mutations in the DNA damage response (DDR) gene ataxia telangiectasia mutated ( ATM ) are common. While poly(ADP-ribose) polymerase inhibitors are approved in this context, their clinical efficacy remains limited. Thus, there is a compelling need to identify alternative therapeutic avenues for ATM mutant prostate cancer patients. Here, we generated matched ATM-proficient and ATM-deficient CRPC lines to elucidate the impact of ATM loss on DDR in response to DNA damage via irradiation. Through unbiased phosphoproteomic screening, we unveiled that ATM-deficient CRPC lines maintain dependence on downstream ATM targets through activation of ATR and DNA-PKcs kinases. Dual inhibition of ATR and DNA-PKcs effectively inhibited downstream γH2AX foci formation in response to irradiation and radiosensitized ATM-deficient lines to a greater extent than either ATM-proficient controls or single drug treatment. Further, dual inhibition abrogated residual downstream ATM pathway signaling and impaired replication fork dynamics. To circumvent potential toxicity, we leveraged the RUVBL1/2 ATPase inhibitor Compound B, which leads to the degradation of both ATR and DNA-PKcs kinases. Compound B effectively radiosensitized ATM-deficient CRPC in vitro and in vivo , and impacted replication fork dynamics. Overall, dual targeting of both ATR and DNA-PKcs is necessary to block DDR in ATM-deficient CRPC, and Compound B could be utilized as a novel therapy in combination with irradiation in these patients.
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22
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Carceles-Cordon M, Orme JJ, Domingo-Domenech J, Rodriguez-Bravo V. The yin and yang of chromosomal instability in prostate cancer. Nat Rev Urol 2024; 21:357-372. [PMID: 38307951 PMCID: PMC11156566 DOI: 10.1038/s41585-023-00845-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 02/04/2024]
Abstract
Metastatic prostate cancer remains an incurable lethal disease. Studies indicate that prostate cancer accumulates genomic changes during disease progression and displays the highest levels of chromosomal instability (CIN) across all types of metastatic tumours. CIN, which refers to ongoing chromosomal DNA gain or loss during mitosis, and derived aneuploidy, are known to be associated with increased tumour heterogeneity, metastasis and therapy resistance in many tumour types. Paradoxically, high CIN levels are also proposed to be detrimental to tumour cell survival, suggesting that cancer cells must develop adaptive mechanisms to ensure their survival. In the context of prostate cancer, studies indicate that CIN has a key role in disease progression and might also offer a therapeutic vulnerability that can be pharmacologically targeted. Thus, a comprehensive evaluation of the causes and consequences of CIN in prostate cancer, its contribution to aggressive advanced disease and a better understanding of the acquired CIN tolerance mechanisms can translate into new tumour classifications, biomarker development and therapeutic strategies.
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Affiliation(s)
| | - Jacob J Orme
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Josep Domingo-Domenech
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
| | - Veronica Rodriguez-Bravo
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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23
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Saxena A, Andrews J, Bryce AH, Riaz IB. Optimal systemic therapy in men with low-volume prostate cancer. Curr Opin Urol 2024; 34:183-197. [PMID: 38445371 DOI: 10.1097/mou.0000000000001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
PURPOSE OF REVIEW Low-volume prostate cancer is an established prognostic category of metastatic hormone-sensitive prostate cancer. However, the term is often loosely used to reflect the low burden of disease across different prostate cancer states. This review explores the definitions of low-volume prostate cancer, biology, and current evidence for treatment. We also explore future directions, including the impact of advanced imaging modalities, particularly prostate-specific membrane antigen (PSMA) positron emission tomography (PET) scans, on refining patient subgroups and treatment strategies for patients with low-volume prostate cancer. RECENT FINDINGS Recent investigations have attempted to redefine low-volume disease, incorporating factors beyond metastatic burden. Advanced imaging, especially PSMA PET, offers enhanced accuracy in detecting metastases, potentially challenging the conventional definition of low volume. The prognosis and treatment of low-volume prostate cancer may vary by the timing of metastatic presentation. Biomarker-directed consolidative therapy, metastases-directed therapy, and de-escalation of systemic therapies will be increasingly important, especially in patients with metachronous low-volume disease. SUMMARY In the absence of validated biomarkers, the management of low-volume prostate cancer as defined by CHAARTED criteria may be guided by the timing of metastatic presentation. For metachronous low-volume disease, we recommend novel hormonal therapy (NHT) doublets with or without consolidative metastasis-directed therapy (MDT), and for synchronous low-volume disease, NHT doublets with or without consolidative MDT and prostate-directed radiation. Docetaxel triplets may be a reasonable alternative in some patients with synchronous presentation. There is no clear role of docetaxel doublets in patients with low-volume disease. In the future, a small subset of low-volume diseases with oligometastases selected by genomics and advanced imaging like PSMA PET may achieve long-term remission with MDT with no systemic therapy.
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Affiliation(s)
| | | | - Alan Haruo Bryce
- Department of Oncology, City of Hope Cancer Center, Goodyear, Arizona, USA
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24
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Orman MV, Sreekanth V, Laajala TD, Cramer SD, Costello JC. ProstaMine: a bioinformatics tool for identifying subtype-specific co-alterations associated with aggressiveness in prostate cancer. Front Pharmacol 2024; 15:1360352. [PMID: 38751776 PMCID: PMC11094266 DOI: 10.3389/fphar.2024.1360352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/13/2024] [Indexed: 05/18/2024] Open
Abstract
Background Prostate cancer is a leading cause of cancer-related deaths among men, marked by heterogeneous clinical and molecular characteristics. The complexity of the molecular landscape necessitates tools for identifying multi-gene co-alteration patterns that are associated with aggressive disease. The identification of such gene sets will allow for deeper characterization of the processes underlying prostate cancer progression and potentially lead to novel strategies for treatment. Methods We developed ProstaMine to systematically identify co-alterations associated with aggressiveness in prostate cancer molecular subtypes defined by high-fidelity alterations in primary prostate cancer. ProstaMine integrates genomic, transcriptomic, and clinical data from five primary and one metastatic prostate cancer cohorts to prioritize co-alterations enriched in metastatic disease and associated with disease progression. Results Integrated analysis of primary tumors defined a set of 17 prostate cancer alterations associated with aggressive characteristics. We applied ProstaMine to NKX3-1-loss and RB1-loss tumors and identified subtype-specific co-alterations associated with metastasis and biochemical relapse in these molecular subtypes. In NKX3-1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations known to regulate prostate cancer signaling pathways including MAPK, NF-kB, p53, PI3K, and Sonic hedgehog. In RB1-loss prostate cancer, ProstaMine identified novel subtype-specific co-alterations involved in p53, STAT6, and MHC class I antigen presentation. Co-alterations impacting autophagy were noted in both molecular subtypes. Conclusion ProstaMine is a method to systematically identify novel subtype-specific co-alterations associated with aggressive characteristics in prostate cancer. The results from ProstaMine provide insights into potential subtype-specific mechanisms of prostate cancer progression which can be formed into testable experimental hypotheses. ProstaMine is publicly available at: https://bioinformatics.cuanschutz.edu/prostamine.
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Affiliation(s)
- Michael V. Orman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Teemu D. Laajala
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Scott D. Cramer
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - James C. Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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25
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He X, Hu S, Wang C, Yang Y, Li Z, Zeng M, Song G, Li Y, Lu Q. Predicting prostate cancer recurrence: Introducing PCRPS, an advanced online web server. Heliyon 2024; 10:e28878. [PMID: 38623253 PMCID: PMC11016622 DOI: 10.1016/j.heliyon.2024.e28878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Background Prostate cancer (PCa) is one of the leading causes of cancer death in men. About 30% of PCa will develop a biochemical recurrence (BCR) following initial treatment, which significantly contributes to prostate cancer-related deaths. In clinical practice, accurate prediction of PCa recurrence is crucial for making informed treatment decisions. However, the development of reliable models and biomarkers for predicting PCa recurrence remains a challenge. In this study, the aim is to establish an effective and reliable tool for predicting the recurrence of PCa. Methods We systematically screened and analyzed potential datasets to predict PCa recurrence. Through quality control analysis, low-quality datasets were removed. Using meta-analysis, differential expression analysis, and feature selection, we identified key genes associated with recurrence. We also evaluated 22 previously published signatures for PCa recurrence prediction. To assess prediction performance, we employed nine machine learning algorithms. We compared the predictive capabilities of models constructed using clinical variables, expression data, and their combinations. Subsequently, we implemented these machine learning models into a user-friendly web server freely accessible to all researchers. Results Based on transcriptomic data derived from eight multicenter studies consisting of 733 PCa patients, we screened 23 highly influential genes for predicting prostate cancer recurrence. These genes were used to construct the Prostate Cancer Recurrence Prediction Signature (PCRPS). By comparing with 22 published signatures and four important clinicopathological features, the PCRPS exhibited a robust and significantly improved predictive capability. Among the tested algorithms, Random Forest demonstrated the highest AUC value of 0.72 in predicting PCa recurrence in the testing dataset. To facilitate access and usage of these machine learning models by all researchers and clinicians, we also developed an online web server (https://urology1926.shinyapps.io/PCRPS/) where the PCRPS model can be freely utilized. The tool can also be used to (1) predict the PCa recurrence by clinical information or expression data with high accuracy. (2) provide the possibility of PCa recurrence by nine machine learning algorithms. Furthermore, using the PCRPS scores, we predicted the sensitivity of 22 drugs from GDSC2 and 95 drugs from CTRP2 to the samples. These predictions provide valuable insights into potential drug sensitivities related to the PCRPS score groups. Conclusion Overall, our study provides an attractive tool to further guide the clinical management and individualized treatment for PCa.
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Affiliation(s)
| | | | - Chen Wang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yongjun Yang
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Zhuo Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Mingqiang Zeng
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Guangqing Song
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Yuanwei Li
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
| | - Qiang Lu
- Department of Urology, Hunan Provincial People's Hospital (The 1st Affiliated Hospital of Hunan Normal University), China
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26
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Imodoye SO, Adedokun KA, Bello IO. From complexity to clarity: unravelling tumor heterogeneity through the lens of tumor microenvironment for innovative cancer therapy. Histochem Cell Biol 2024; 161:299-323. [PMID: 38189822 DOI: 10.1007/s00418-023-02258-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/09/2024]
Abstract
Despite the tremendous clinical successes recorded in the landscape of cancer therapy, tumor heterogeneity remains a formidable challenge to successful cancer treatment. In recent years, the emergence of high-throughput technologies has advanced our understanding of the variables influencing tumor heterogeneity beyond intrinsic tumor characteristics. Emerging knowledge shows that drivers of tumor heterogeneity are not only intrinsic to cancer cells but can also emanate from their microenvironment, which significantly favors tumor progression and impairs therapeutic response. Although much has been explored to understand the fundamentals of the influence of innate tumor factors on cancer diversity, the roles of the tumor microenvironment (TME) are often undervalued. It is therefore imperative that a clear understanding of the interactions between the TME and other tumor intrinsic factors underlying the plastic molecular behaviors of cancers be identified to develop patient-specific treatment strategies. This review highlights the roles of the TME as an emerging factor in tumor heterogeneity. More particularly, we discuss the role of the TME in the context of tumor heterogeneity and explore the cutting-edge diagnostic and therapeutic approaches that could be used to resolve this recurring clinical conundrum. We conclude by speculating on exciting research questions that can advance our understanding of tumor heterogeneity with the goal of developing customized therapeutic solutions.
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Affiliation(s)
- Sikiru O Imodoye
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Kamoru A Adedokun
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Ibrahim O Bello
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry, King Saud University, Riyadh, Saudi Arabia.
- Department of Pathology, University of Helsinki, Haartmaninkatu 3, 00014, Helsinki, Finland.
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27
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Ma T, Wang J. GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network. Bioinformatics 2024; 40:btae165. [PMID: 38530778 PMCID: PMC11007237 DOI: 10.1093/bioinformatics/btae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
MOTIVATION Studying the molecular heterogeneity of cancer is essential for achieving personalized therapy. At the same time, understanding the biological processes that drive cancer development can lead to the identification of valuable therapeutic targets. Therefore, achieving accurate and interpretable clinical predictions requires paramount attention to thoroughly characterizing patients at both the molecular and biological pathway levels. RESULTS Here, we present GraphPath, a biological knowledge-driven graph neural network with multi-head self-attention mechanism that implements the pathway-pathway interaction network. We train GraphPath to classify the cancer status of patients with prostate cancer based on their multi-omics profiling. Experiment results show that our method outperforms P-NET and other baseline methods. Besides, two external cohorts are used to validate that the model can be generalized to unseen samples with adequate predictive performance. We reduce the dimensionality of latent pathway embeddings and visualize corresponding classes to further demonstrate the optimal performance of the model. Additionally, since GraphPath's predictions are interpretable, we identify target cancer-associated pathways that significantly contribute to the model's predictions. Such a robust and interpretable model has the potential to greatly enhance our understanding of cancer's biological mechanisms and accelerate the development of targeted therapies. AVAILABILITY AND IMPLEMENTATION https://github.com/amazingma/GraphPath.
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Affiliation(s)
- Teng Ma
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 41083, Hunan, China
| | - Jianxin Wang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 41083, Hunan, China
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28
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Zeng PYF, Prokopec SD, Lai SY, Pinto N, Chan-Seng-Yue MA, Clifton-Bligh R, Williams MD, Howlett CJ, Plantinga P, Cecchini MJ, Lam AK, Siddiqui I, Wang J, Sun RX, Watson JD, Korah R, Carling T, Agrawal N, Cipriani N, Ball D, Nelkin B, Rooper LM, Bishop JA, Garnis C, Berean K, Nicolson NG, Weinberger P, Henderson YC, Lalansingh CM, Tian M, Yamaguchi TN, Livingstone J, Salcedo A, Patel K, Vizeacoumar F, Datti A, Xi L, Nikiforov YE, Smallridge R, Copland JA, Marlow LA, Hyrcza MD, Delbridge L, Sidhu S, Sywak M, Robinson B, Fung K, Ghasemi F, Kwan K, MacNeil SD, Mendez A, Palma DA, Khan MI, Shaikh M, Ruicci KM, Wehrli B, Winquist E, Yoo J, Mymryk JS, Rocco JW, Wheeler D, Scherer S, Giordano TJ, Barrett JW, Faquin WC, Gill AJ, Clayman G, Boutros PC, Nichols AC. The genomic and evolutionary landscapes of anaplastic thyroid carcinoma. Cell Rep 2024; 43:113826. [PMID: 38412093 PMCID: PMC11077417 DOI: 10.1016/j.celrep.2024.113826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.
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Affiliation(s)
- Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Stephenie D Prokopec
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole Pinto
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | | | - Roderick Clifton-Bligh
- Division of Endocrinology, Royal North Shore Hospital, and University of Sydney, Sydney, NSW, Australia
| | - Michelle D Williams
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Paul Plantinga
- Department of Pathology, Western University, London, ON, Canada
| | - Matthew J Cecchini
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Alfred K Lam
- Department of Pathology, School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Iram Siddiqui
- Department of Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jianxin Wang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ren X Sun
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - John D Watson
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Reju Korah
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Tobias Carling
- Department of Surgery, Yale University, New Haven, CT, USA
| | - Nishant Agrawal
- Department of Otolaryngology - Head and Neck Surgery, University of Chicago, Chicago, IL, USA
| | - Nicole Cipriani
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Douglas Ball
- Division of Endocrinology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Barry Nelkin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Lisa M Rooper
- Division of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin A Bishop
- Department of Pathology, University of Texas Southwestern, Dallas, TX, USA
| | | | | | | | - Paul Weinberger
- Department of Otolaryngology - Head and Neck Surgery, Louisiana State University Health Sciences Center, Shreveport, LA, USA; Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Ying C Henderson
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Mao Tian
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Takafumi N Yamaguchi
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie Livingstone
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Salcedo
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Krupal Patel
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada; Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Liu Xi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Robert Smallridge
- Division of Endocrinology, Department of Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Laura A Marlow
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Martin D Hyrcza
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Leigh Delbridge
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Stan Sidhu
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Mark Sywak
- Department of Surgery, Royal North Shore Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NWS, Australia
| | - Bruce Robinson
- University of Sydney, Sydney, NWS, Australia; Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Farhad Ghasemi
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Keith Kwan
- Department of Pathology, Western University, London, ON, Canada
| | - S Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - David A Palma
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Mohammed I Khan
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Mushfiq Shaikh
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Kara M Ruicci
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - Bret Wehrli
- Department of Pathology, Western University, London, ON, Canada
| | - Eric Winquist
- London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - James W Rocco
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University, Columbus, OH, USA
| | - David Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steve Scherer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Anthony J Gill
- University of Sydney, Sydney, NWS, Australia; Cancer Diagnosis and Pathology Group, Kolling Institute of Medicine, Royal North Shore Hospital, Sydney, NSW, Australia; NSW Health Pathology, Department of Anatomical Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Gary Clayman
- The Clayman Thyroid Surgery and Thyroid Cancer Center, The Thyroid Institute, Tampa General Hospital, Tampa, FL, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, Western University, London, ON, Canada; London Regional Cancer Program, London, ON, Canada; Lawson Health Research Institute, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada.
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29
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Woodcock DJ, Sahli A, Teslo R, Bhandari V, Gruber AJ, Ziubroniewicz A, Gundem G, Xu Y, Butler A, Anokian E, Pope BJ, Jung CH, Tarabichi M, Dentro SC, Farmery JHR, Van Loo P, Warren AY, Gnanapragasam V, Hamdy FC, Bova GS, Foster CS, Neal DE, Lu YJ, Kote-Jarai Z, Fraser M, Bristow RG, Boutros PC, Costello AJ, Corcoran NM, Hovens CM, Massie CE, Lynch AG, Brewer DS, Eeles RA, Cooper CS, Wedge DC. Genomic evolution shapes prostate cancer disease type. CELL GENOMICS 2024; 4:100511. [PMID: 38428419 PMCID: PMC10943594 DOI: 10.1016/j.xgen.2024.100511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/11/2021] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
The development of cancer is an evolutionary process involving the sequential acquisition of genetic alterations that disrupt normal biological processes, enabling tumor cells to rapidly proliferate and eventually invade and metastasize to other tissues. We investigated the genomic evolution of prostate cancer through the application of three separate classification methods, each designed to investigate a different aspect of tumor evolution. Integrating the results revealed the existence of two distinct types of prostate cancer that arise from divergent evolutionary trajectories, designated as the Canonical and Alternative evolutionary disease types. We therefore propose the evotype model for prostate cancer evolution wherein Alternative-evotype tumors diverge from those of the Canonical-evotype through the stochastic accumulation of genetic alterations associated with disruptions to androgen receptor DNA binding. Our model unifies many previous molecular observations, providing a powerful new framework to investigate prostate cancer disease progression.
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Affiliation(s)
- Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Atef Sahli
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | | | - Vinayak Bhandari
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Andreas J Gruber
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Aleksandra Ziubroniewicz
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK; Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yaobo Xu
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Bernard J Pope
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia; Department of Medicine, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, Australia
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK; Institute of Interdisciplinary Research (IRIBHM), Universite Libre de Bruxelles, Brussels, Belgium
| | - Stefan C Dentro
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK
| | - J Henry R Farmery
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent Gnanapragasam
- Cambridge Urology Translational Research and Clinical Trials Office, Addenbrooke's Hospital, Cambridge, UK; Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | | | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, UK; Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Michael Fraser
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK; The Christie NHS Foundation Trust, Manchester, UK; CRUK Manchester Institute, University of Manchester, Manchester, UK; Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Departments of Human Genetics and Urology, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anthony J Costello
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Niall M Corcoran
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christopher M Hovens
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, UK; Early Detection Programme and Urological Malignancies Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Andy G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK; School of Medicine/School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; Earlham Institute, Norwich, UK.
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK.
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK; Norwich Medical School, University of East Anglia, Norwich, UK.
| | - David C Wedge
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK; Manchester Cancer Research Centre, University of Manchester, Manchester, UK; Oxford NIHR Biomedical Research Centre, Oxford, UK; Manchester NIHR Biomedical Research Centre, Manchester, UK.
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30
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Tyagi N, Roy S, Vengadesan K, Gupta D. Multi-omics approach for identifying CNV-associated lncRNA signatures with prognostic value in prostate cancer. Noncoding RNA Res 2024; 9:66-75. [PMID: 38075203 PMCID: PMC10700122 DOI: 10.1016/j.ncrna.2023.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/21/2023] [Accepted: 10/03/2023] [Indexed: 03/28/2025] Open
Abstract
BACKGROUND Prostate cancer, the second most prevalent malignancy among men, poses a significant threat to affected patients' well-being due to its poor prognosis. Novel biomarkers are required to enhance clinical outcomes and tailor personalized treatments. Herein, we describe our research to explore the prognostic value of long non-coding RNAs (lncRNAs) deregulated by copy number variations (CNVs) in prostate cancer. METHODS The study employed an integrative multi-omics data analysis of the prostate cancer transcriptomic, CNV and methylation datasets to identify prognosis-related subtypes. Subtype-specific expression profiles of protein-coding genes (PCGs) and lncRNAs were determined. We analysed CNV patterns of lncRNAs across the genome to identify subtype-specific lncRNAs with CNV changes. LncRNAs exhibiting significant amplification or deletion and a positive correlation were designated CNV-deregulated lncRNAs. A prognostic risk score model was subsequently developed using these CNV-driven lncRNAs. RESULTS Six molecular subtypes of prostate cancer were identified, demonstrating significant differences in prognosis (P = 0.034). The CNV profiles of subtype-specific lncRNAs were examined, revealing their correlation with CNV amplification or deletion. Six lncRNAs (CCAT2, LINC01593, LINC00276, GACAT2, LINC00457, LINC01343) were selected based on significant CNV amplifications or deletions using a rigorous univariate Cox proportional risk regression model. A robust risk score model was developed, stratifying patients into high-risk and low-risk categories. Notably, our prognostic model based on these six lncRNAs exhibited exceptional predictive capabilities for recurrence-free survival (RFS) in prostate cancer patients (P = 0.024). CONCLUSIONS Our study successfully identified a prognostic risk score model comprising six CNV-driven lncRNAs that could potentially be prognostic biomarkers for prostate cancer. These lncRNA signatures are closely associated with RFS, providing promising prospects for improved patient prognostication and personalized therapeutic strategies for novel prostate cancer treatment.
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Affiliation(s)
- Neetu Tyagi
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Shikha Roy
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | | | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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31
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Wang S, Wu CY, He MM, Yong JX, Chen YX, Qian LM, Zhang JL, Zeng ZL, Xu RH, Wang F, Zhao Q. Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer. Nat Commun 2024; 15:1515. [PMID: 38373991 PMCID: PMC10876971 DOI: 10.1038/s41467-024-45479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
The clinical implications of extrachromosomal DNA (ecDNA) in cancer therapy remain largely elusive. Here, we present a comprehensive analysis of ecDNA amplification spectra and their association with clinical and molecular features in multiple cohorts comprising over 13,000 pan-cancer patients. Using our developed computational framework, GCAP, and validating it with multifaceted approaches, we reveal a consistent pan-cancer pattern of mutual exclusivity between ecDNA amplification and microsatellite instability (MSI). In addition, we establish the role of ecDNA amplification as a risk factor and refine genomic subtypes in a cohort from 1015 colorectal cancer patients. Importantly, our investigation incorporates data from four clinical trials focused on anti-PD-1 immunotherapy, demonstrating the pivotal role of ecDNA amplification as a biomarker for guiding checkpoint blockade immunotherapy in gastrointestinal cancer. This finding represents clinical evidence linking ecDNA amplification to the effectiveness of immunotherapeutic interventions. Overall, our study provides a proof-of-concept of identifying ecDNA amplification from cancer whole-exome sequencing (WES) data, highlighting the potential of ecDNA amplification as a valuable biomarker for facilitating personalized cancer treatment.
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Affiliation(s)
- Shixiang Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chen-Yi Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Ming-Ming He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jia-Xin Yong
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yan-Xing Chen
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Mei Qian
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jin-Ling Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhao-Lei Zeng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, China.
| | - Feng Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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32
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O'Malley DE, Raspin K, Melton PE, Burdon KP, Dickinson JL, FitzGerald LM. Acquired copy number variation in prostate tumours: a review of common somatic copy number alterations, how they are formed and their clinical utility. Br J Cancer 2024; 130:347-357. [PMID: 37945750 PMCID: PMC10844642 DOI: 10.1038/s41416-023-02485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men and unfortunately, disease will progress in up to a third of patients despite primary treatment. Currently, there is a significant lack of prognostic tests that accurately predict disease course; however, the acquisition of somatic chromosomal variation in the form of DNA copy number variants may help understand disease progression. Notably, studies have found that a higher burden of somatic copy number alterations (SCNA) correlates with more aggressive disease, recurrence after surgery and metastasis. Here we will review the literature surrounding SCNA formation, including the roles of key tumour suppressors and oncogenes (PTEN, BRCA2, NKX3.1, ERG and AR), and their potential to inform diagnostic and prognostic clinical testing to improve predictive value. Ultimately, SCNAs, or inherited germline alterations that predispose to SCNAs, could have significant clinical utility in diagnostic and prognostic tests, in addition to guiding therapeutic selection.
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Affiliation(s)
- Dannielle E O'Malley
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- School of Population and Global Health, The University of Western Australia, Crawley, WA, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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33
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Salachan PV, Ulhøi BP, Borre M, Sørensen KD. Association between copy number alterations estimated using low-pass whole genome sequencing of formalin-fixed paraffin-embedded prostate tumor tissue and cancer-specific clinical parameters. Sci Rep 2023; 13:22445. [PMID: 38105358 PMCID: PMC10725894 DOI: 10.1038/s41598-023-49811-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Copy number alterations (CNAs) are frequently observed in early-stage prostate cancer and are associated with disease recurrence and tumor aggressiveness. Cost-effective assessment of CNAs could enhance clinical utility of CNAs. Here, we combined the cost-effectiveness of low-pass (low coverage) whole genome sequencing (LPWGS) and the routine availability of formalin-fixed paraffin-embedded (FFPE) tumor tissue for assessing CNAs in a cohort of 187 men with early-stage localised prostate cancer. We detected well known CNAs in 8p, 8q, 13q and 16q and recurrent gains of the oncogene MYC and losses of the tumor suppressor genes NKX3-1, PTEN and RB1, indicating assay reliability. The estimated burden of CNAs was significantly associated with Gleason score, pathological T stage, surgical margin status and biochemical recurrence. Further, genomic losses or gains in specific chromosomal arms were significantly associated with worse BCR-free survival. Copy number signatures extracted from the LPWGS data showed potential for risk stratifying patients, where signatures S1 and S2 showed significant association to worse BCR-free survival compared to S3. Our study provides clinical validation of the associations between CNAs and tumor aggressiveness in an independent and representative RP cohort, while demonstrating the feasibility of performing LPWGS of FFPE tumor tissue for cost-effective assessment of CNAs.
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Affiliation(s)
- Paul Vinu Salachan
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark
| | | | - Michael Borre
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus N, Denmark.
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Marino-Enriquez A, Novotny JP, Gulhan DC, Klooster I, Tran AV, Kasbo M, Lundberg MZ, Ou WB, Tao DL, Pilco-Janeta DF, Mao VY, Zenke FT, Leeper BA, Gokhale PC, Cowley GS, Baker LH, Ballman KV, Root DE, Albers J, Park PJ, George S, Fletcher JA. Hyper-Dependence on NHEJ Enables Synergy between DNA-PK Inhibitors and Low-Dose Doxorubicin in Leiomyosarcoma. Clin Cancer Res 2023; 29:5128-5139. [PMID: 37773632 PMCID: PMC10841464 DOI: 10.1158/1078-0432.ccr-23-0998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE Leiomyosarcoma (LMS) is an aggressive sarcoma for which standard chemotherapies achieve response rates under 30%. There are no effective targeted therapies against LMS. Most LMS are characterized by chromosomal instability (CIN), resulting in part from TP53 and RB1 co-inactivation and DNA damage repair defects. We sought to identify therapeutic targets that could exacerbate intrinsic CIN and DNA damage in LMS, inducing lethal genotoxicity. EXPERIMENTAL DESIGN We performed clinical targeted sequencing in 287 LMS and genome-wide loss-of-function screens in 3 patient-derived LMS cell lines, to identify LMS-specific dependencies. We validated candidate targets by biochemical and cell-response assays in vitro and in seven mouse models. RESULTS Clinical targeted sequencing revealed a high burden of somatic copy-number alterations (median fraction of the genome altered =0.62) and demonstrated homologous recombination deficiency signatures in 35% of LMS. Genome-wide short hairpin RNA screens demonstrated PRKDC (DNA-PKcs) and RPA2 essentiality, consistent with compensatory nonhomologous end joining (NHEJ) hyper-dependence. DNA-PK inhibitor combinations with unconventionally low-dose doxorubicin had synergistic activity in LMS in vitro models. Combination therapy with peposertib and low-dose doxorubicin (standard or liposomal formulations) inhibited growth of 5 of 7 LMS mouse models without toxicity. CONCLUSIONS Combinations of DNA-PK inhibitors with unconventionally low, sensitizing, doxorubicin dosing showed synergistic effects in LMS in vitro and in vivo models, without discernable toxicity. These findings underscore the relevance of DNA damage repair alterations in LMS pathogenesis and identify dependence on NHEJ as a clinically actionable vulnerability in LMS.
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Affiliation(s)
- Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jan Philipp Novotny
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Doga C. Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Isabella Klooster
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Antuan V. Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Macy Kasbo
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meijun Z. Lundberg
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Wen-Bin Ou
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Derrick L. Tao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel F. Pilco-Janeta
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Translational Research Laboratory, Vall d’Hebron Institute of Oncology, Autonomous University of Barcelona, Barcelona, Spain
| | - Victor Y. Mao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Frank T. Zenke
- Research Unit Oncology, the healthcare business of Merck KGaA, Darmstadt, Germany
| | - Brittaney A. Leeper
- Experimental Therapeutics Core and the Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and the Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Karla V. Ballman
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, New York
| | - David E. Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joachim Albers
- Research Unit Oncology, the healthcare business of Merck KGaA, Darmstadt, Germany
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Suzanne George
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jonathan A. Fletcher
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Turpin A, Delliaux C, Parent P, Chevalier H, Escudero-Iriarte C, Bonardi F, Vanpouille N, Flourens A, Querol J, Carnot A, Leroy X, Herranz N, Lanel T, Villers A, Olivier J, Touzet H, de Launoit Y, Tian TV, Duterque-Coquillaud M. Fascin-1 expression is associated with neuroendocrine prostate cancer and directly suppressed by androgen receptor. Br J Cancer 2023; 129:1903-1914. [PMID: 37875732 PMCID: PMC10703930 DOI: 10.1038/s41416-023-02449-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/11/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Neuroendocrine prostate cancer (NEPC) is an aggressive form of prostate cancer, arising from resistance to androgen-deprivation therapies. However, the molecular mechanisms associated with NEPC development and invasiveness are still poorly understood. Here we investigated the expression and functional significance of Fascin-1 (FSCN1), a pro-metastasis actin-bundling protein associated with poor prognosis of several cancers, in neuroendocrine differentiation of prostate cancer. METHODS Differential expression analyses using Genome Expression Omnibus (GEO) database, clinical samples and cell lines were performed. Androgen or antagonist's cellular treatments and knockdown experiments were used to detect changes in cell morphology, molecular markers, migration properties and in vivo tumour growth. Chromatin immunoprecipitation-sequencing (ChIP-Seq) data and ChIP assays were analysed to decipher androgen receptor (AR) binding. RESULTS We demonstrated that FSCN1 is upregulated during neuroendocrine differentiation of prostate cancer in vitro, leading to phenotypic changes and NEPC marker expression. In human prostate cancer samples, FSCN1 expression is restricted to NEPC tumours. We showed that the androgen-activated AR downregulates FSCN1 expression and works as a transcriptional repressor to directly suppress FSCN1 expression. AR antagonists alleviate this repression. In addition, FSCN1 silencing further impairs in vivo tumour growth. CONCLUSION Collectively, our findings identify FSCN1 as an AR-repressed gene. Particularly, it is involved in NEPC aggressiveness. Our results provide the rationale for the future clinical development of FSCN1 inhibitors in NEPC patients.
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Affiliation(s)
- Anthony Turpin
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Department of Medical Oncology, Lille University Hospital, F-59000, Lille, France
| | - Carine Delliaux
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Pauline Parent
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Department of Medical Oncology, Lille University Hospital, F-59000, Lille, France
| | - Hortense Chevalier
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Department of Medical Oncology, Centre Oscar Lambret, 3, rue Frederic Combemale, 59000, Lille, France
| | | | - Franck Bonardi
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Nathalie Vanpouille
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Anne Flourens
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Aurélien Carnot
- Department of Medical Oncology, Centre Oscar Lambret, 3, rue Frederic Combemale, 59000, Lille, France
| | - Xavier Leroy
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Institut de Pathologie, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | - Nicolás Herranz
- Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Tristan Lanel
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Institut de Pathologie, CHU Lille, Avenue Oscar Lambret, F-59000, Lille, France
| | - Arnauld Villers
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Department of Urology, Hospital Claude Huriez, CHU Lille, Lille, France
| | - Jonathan Olivier
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
- Department of Urology, Hospital Claude Huriez, CHU Lille, Lille, France
| | - Hélène Touzet
- University Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000, Lille, France
| | - Yvan de Launoit
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), 08035, Barcelona, Spain
| | - Martine Duterque-Coquillaud
- University Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000, Lille, France.
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36
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Creighton CJ, Zhang F, Zhang Y, Castro P, Hu R, Islam M, Ghosh S, Ittmann M, Kwabi-Addo B. Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer. Epigenetics 2023; 18:2180585. [PMID: 37279148 PMCID: PMC9980641 DOI: 10.1080/15592294.2023.2180585] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
African American (AA) men have the highest incidence and mortality rate from Prostate cancer (PCa) than any other racial/ethnic group. To date, PCa genomic studies have largely under-represented tumour samples from AA men. We measured genome-wide DNA methylation in benign and tumor prostate tissues from AA men using the Illumina Infunium 850 K EPIC array. mRNA expression database from a subset of the AA biospecimen were used to assess correlation of transcriptome and methylation datasets. Genome-wide methylation analysis identified 11,460 probes that were significant (p < 0.01) and differentially methylated in AA PCa compared to normal prostate tissues and showed significant (p < 0.01) inverse-correlation with mRNA expression. Ingenuity pathway analysis and Gene Ontology analysis in our AA dataset compared with TCGA dataset showed similarities in methylation patterns: top candidate genes with significant hypermethylation and corresponding down-regulated gene expression were associated with biological pathways in hemidesmosome assembly, mammary gland development, epidermis development, hormone biosynthesis, and cell communication. In addition, top candidate genes with significant hypomethylation and corresponding up-regulated gene expression were associated with biological pathways in macrophage differentiation, cAMP-dependent protein kinase activity, protein destabilization, transcription co-repression, and fatty acid biosynthesis. In contrast, differences in genome-wide methylation in our AA dataset compared with TCGA dataset were enriched for genes in steroid signalling, immune signalling, chromatin structure remodelling and RNA processing. Overall, differential methylation of AMIGO3, IER3, UPB1, GRM7, TFAP2C, TOX2, PLSCR2, ZNF292, ESR2, MIXL1, BOLL, and FGF6 were significant and uniquely associated with PCa progression in our AA cohort.
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Affiliation(s)
- Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Flora Zhang
- Center for Women’s Studies, Colgate University, Hamilton, New York, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Patricia Castro
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Rong Hu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Md Islam
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Somiranjan Ghosh
- Department of Biology, Howard University, Washington, Columbia, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, Howard University, Washington, Columbia, USA
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Zhang M, Ceyhan Y, Mei S, Hirz T, Sykes DB, Agoulnik IU. Regulation of EZH2 Expression by INPP4B in Normal Prostate and Primary Prostate Cancer. Cancers (Basel) 2023; 15:5418. [PMID: 38001678 PMCID: PMC10670027 DOI: 10.3390/cancers15225418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
The phosphatases INPP4B and PTEN are tumor suppressors that are lost in nearly half of advanced metastatic cancers. The loss of PTEN in prostate epithelium initially leads to an upregulation of several tumor suppressors that slow the progression of prostate cancer in mouse models. We tested whether the loss of INPP4B elicits a similar compensatory response in prostate tissue and whether this response is distinct from the one caused by the loss of PTEN. Knockdown of INPP4B but not PTEN in human prostate cancer cell lines caused a decrease in EZH2 expression. In Inpp4b-/- mouse prostate epithelium, EZH2 levels were decreased, as were methylation levels of histone H3. In contrast, Ezh2 levels were increased in the prostates of Pten-/- male mice. Contrary to PTEN, there was a positive correlation between INPP4B and EZH2 expression in normal human prostates and early-stage prostate tumors. Analysis of single-cell transcriptomic data demonstrated that a subset of EZH2-positive cells expresses INPP4B or PTEN, but rarely both, consistent with their opposing correlation with EZH2 expression. Unlike PTEN, INPP4B did not affect the levels of SMAD4 protein expression or Pml mRNA expression. Like PTEN, p53 protein expression and phosphorylation of Akt in Inpp4b-/- murine prostates were elevated. Taken together, the loss of INPP4B in the prostate leads to overlapping and distinct changes in tumor suppressor and oncogenic downstream signaling.
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Affiliation(s)
- Manqi Zhang
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, NC 27708, USA;
| | - Yasemin Ceyhan
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA;
| | - Shenglin Mei
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Taghreed Hirz
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David B. Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (S.M.); (T.H.); (D.B.S.)
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Irina U. Agoulnik
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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38
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Rehman K, Iqbal Z, Zhiqin D, Ayub H, Saba N, Khan MA, Yujie L, Duan L. Analysis of genetic biomarkers, polymorphisms in ADME-related genes and their impact on pharmacotherapy for prostate cancer. Cancer Cell Int 2023; 23:247. [PMID: 37858151 PMCID: PMC10585889 DOI: 10.1186/s12935-023-03084-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
Prostate cancer (PCa) is a non-cutaneous malignancy in males with wide variation in incidence rates across the globe. It is the second most reported cause of cancer death. Its etiology may have been linked to genetic polymorphisms, which are not only dominating cause of malignancy casualties but also exerts significant effects on pharmacotherapy outcomes. Although many therapeutic options are available, but suitable candidates identified by useful biomarkers can exhibit maximum therapeutic efficacy. The single-nucleotide polymorphisms (SNPs) reported in androgen receptor signaling genes influence the effectiveness of androgen receptor pathway inhibitors and androgen deprivation therapy. Furthermore, SNPs located in genes involved in transport, drug metabolism, and efflux pumps also influence the efficacy of pharmacotherapy. Hence, SNPs biomarkers provide the basis for individualized pharmacotherapy. The pharmacotherapeutic options for PCa include hormonal therapy, chemotherapy (Docetaxel, Mitoxantrone, Cabazitaxel, and Estramustine, etc.), and radiotherapy. Here, we overview the impact of SNPs reported in various genes on the pharmacotherapy for PCa and evaluate current genetic biomarkers with an emphasis on early diagnosis and individualized treatment strategy in PCa.
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Affiliation(s)
- Khurram Rehman
- Faculty of Pharmacy, Gomal University, D.I.Khan, Pakistan
| | - Zoya Iqbal
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Deng Zhiqin
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China
| | - Hina Ayub
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | - Naseem Saba
- Department of Gynae, Gomal Medical College, D.I.Khan, Pakistan
| | | | - Liang Yujie
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen Mental Health Center, Shenzhen, 518035, Guangdong, China.
| | - Li Duan
- Department of Orthopedics, The First Affiliated Hospital of Shenzhen University, Second People's Hospital, ShenzhenShenzhen, 518035, Guangdong, China.
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People's Hospital, Shenzhen, 518035, Guangdong, China.
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39
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Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med 2023; 15:82. [PMID: 37828555 PMCID: PMC10571458 DOI: 10.1186/s13073-023-01242-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical trials do not include evolution as an essential feature. Whether or not analysis of genomic data in an evolutionary context in primary prostate cancer can provide unique added value in the research and clinical domains remains an open question. METHODS We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high-risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones. RESULTS In patient GP5, CDK12 inactivation was among the first mutations, leading to a PrCa tandem duplicator phenotype and initiating the cancer around age 50, followed by rapid cancer evolution after age 57, and metastasis around age 59, 5 years prior to prostatectomy. In patient GP12, accelerated cancer progression was detected after age 54, and metastasis occurred around age 56, 3 years prior to prostatectomy. Multiple metastasis-originating events were identified in each patient and tracked anatomically. Metastasis from prostate to lymph nodes occurred strictly ipsilaterally in all 12 detected events. In this pilot, metastatic subclone content analysis appears to substantially enhance the identification of key drivers. Evolutionary analysis' potential impact on therapy selection appears positive in these pilot cases. CONCLUSIONS PrCa evolutionary analysis allows tracking of anatomic site of origin, timing of cancer origin and spread, and distinction of metastatic-capable from non-metastatic subclones. This enables better identification of actionable targets for therapy. If extended to larger cohorts, it appears likely that similar analyses could add substantial biological insight and clinically relevant value.
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Affiliation(s)
- Anssi Nurminen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Serafiina Jaatinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tom Lesluyes
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Kerstin Haase
- The Francis Crick Institute, London, NW1 1AT, UK
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany
| | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland
| | - Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Jenni Kesäniemi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tiia Nikupaavola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Irina Rinta-Kiikka
- Imaging Centre, Department of Radiology, Tampere University Hospital, Tampere, Finland
| | - Jarno Riikonen
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antti Kaipia
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teemu Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, M20 4GJ, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.
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Wei Y, Zhang T, Wang B, Pan J, Jin S, Fang B, Gu W, Qin X, Dai B, Lin G, Gan H, Wu J, Ye D, Zhu Y. Prospective clinical sequencing of 1016 Chinese prostate cancer patients: uncovering genomic characterization and race disparity. Mol Oncol 2023; 17:2183-2199. [PMID: 37584393 PMCID: PMC10552897 DOI: 10.1002/1878-0261.13511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023] Open
Abstract
Although there is a well-known disparity in prostate cancer (PC) incidence and mortality between Chinese and Western patients, the underlying genomic differences have been investigated only sparsely. This clinicogenomic study was conducted to reveal the genomic mutations contributing to the PC disparity across ethnicities and investigate the mutational profile of Chinese PC patients. A total of 1016 Chinese PC patients were prospectively enrolled and subjected to targeted sequencing, resulting in usable sequencing data for 41 genes from 859 patients. Genomic data retrieved from The Cancer Genome Atlas (TCGA; locoregional PC), Memorial Sloan Kettering Cancer Center [MSKCC; metastatic castration-sensitive PC (mCSPC)], and Stand Up To Cancer [SU2C; metastatic castration-resistant PC (mCRPC)] cohorts were used as comparators representing Western men. Genomic mutations were analyzed using an integrated bioinformatic strategy. A comparison of the disease stages revealed that mutations in tumor protein 53 (TP53), androgen receptor (AR), forkhead box A1 (FOXA1), and genes involved in the cell cycle pathway were enriched in mCRPC. Mutations in adenomatous polyposis coli (APC) gene were found to be more prevalent in patients with visceral metastasis. Genomic differences between Western and Chinese men were mainly observed in castration-sensitive PC, with tumors from Chinese men having more FOXA1 (11.4% vs. 4.2%) but fewer TP53 (4.8% vs. 13%) mutations in locoregional PC and harboring fewer TP53 (11% vs. 29.2%), phosphatase and tensin homolog (PTEN; 2.5% vs. 10.3%), and APC (1.7% vs. 7.4%) mutations in the mCSPC stage than those of Western men. Patients of both ethnicities with mCRPC had similar mutational spectra. Furthermore, FOXA1 class-2 was less common than FOXA1 class-1 and showed no enrichment in metastasis, contrary to the findings in the Western cohort. Our study provides a valuable resource for a better understanding of PC in China and reveals the genomic alterations associated with PC disparity across races.
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Affiliation(s)
- Yu Wei
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Tingwei Zhang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Beihe Wang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Jian Pan
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Shengming Jin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Bangwei Fang
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Weijie Gu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Xiaojian Qin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Bo Dai
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Guowen Lin
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Hualei Gan
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterChina
| | - Junlong Wu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Dingwei Ye
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
| | - Yao Zhu
- Department of UrologyFudan University Shanghai Cancer CenterChina
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina
- Shanghai Genitourinary Cancer InstituteChina
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He H, Ma H, Chen Z, Chen J, Wu D, Lv X, Zhu J. Chromosomal Copy Number Variation Predicts EGFR-TKI Response and Prognosis for Patients with Non-Small Cell Lung Cancer. Pharmgenomics Pers Med 2023; 16:835-846. [PMID: 37724294 PMCID: PMC10505391 DOI: 10.2147/pgpm.s418320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023] Open
Abstract
Purpose Chromosomal abnormalities represent genomic signatures linked to cancer prognosis and responses to chemotherapy, immunotherapy, and drug resistance. This study aimed to investigate the impact of chromosome copy number variants (CNVs) on the efficacy of tyrosine kinase inhibitors (TKIs) in EGFR-mutated non-small cell lung cancer (NSCLC) patients, as well as its prognostic implications for progression-free survival (PFS) and overall survival (OS) in EGFR wild-type patients. Methods A total of 110 patients with advanced NSCLC were enrolled in this study and categorized into EGFR-mutated and wild-type groups. Utilizing next-generation sequencing (NGS) technology, we assessed 24 genes and chromosome CNVs associated with lung cancer pathways in patients' tissue samples. Results Within the EGFR-mutated group, patients with a gain in Chr 1p13.3-p13.1 exhibited poor TKI responses, a high relapse rate, and shortened PFS (P = 0.002). Conversely, EGFR-mutated patients with a gain in 14q31.1-q31.3 demonstrated favorable TKI responses and relatively extended PFS (P = 0.005). Among EGFR wild-type patients, the presence of 7q31.1-q31.31 CNV emerged as an independent factor influencing both PFS and OS (P = 0.013, P = 0.004). Notably, patients with a gain in 7q31.1-q31.31 exhibited prolonged PFS and OS. Additionally, independent prognostic significance for OS in EGFR wild-type patients was observed for CNVs in 9q21.31-q22.2 and 11p11.11-q12.1 regions (P = 0.001). Patients with gains in these regions experienced extended OS, while losses were predictive of poorer outcomes. Conclusion Our results suggested that chromosomal copy number variation is a practical indicator for predicting the response of EGFR-targeted therapy and prognosis for NSCLC patients.
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Affiliation(s)
- Haiyan He
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Hang Ma
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Zhuo Chen
- Department of Invasive Technology, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Jingliang Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Dandan Wu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Xuedong Lv
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
| | - Jie Zhu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nantong University, Nantong First People’s Hospital, Nantong, Jiangsu, 226001, People’s Republic of China
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Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
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Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
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Yang X, Zhang Q, Li S, Devarajan R, Luo B, Tan Z, Wang Z, Giannareas N, Wenta T, Ma W, Li Y, Yang Y, Manninen A, Wu S, Wei GH. GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression. J Exp Clin Cancer Res 2023; 42:198. [PMID: 37550764 PMCID: PMC10408074 DOI: 10.1186/s13046-023-02745-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/30/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Aberrant somatic genomic alteration including copy number amplification is a hallmark of cancer genomes. We previously profiled genomic landscapes of prostate cancer (PCa), yet the underlying causal genes with prognostic potential has not been defined. It remains unclear how a somatic genomic event cooperates with inherited germline variants contribute to cancer predisposition and progression. METHODS We applied integrated genomic and clinical data, experimental models and bioinformatic analysis to identify GATA2 as a highly prevalent metastasis-associated genomic amplification in PCa. Biological roles of GATA2 in PCa metastasis was determined in vitro and in vivo. Global chromatin co-occupancy and co-regulation of GATA2 and SMAD4 was investigated by coimmunoprecipitation, ChIP-seq and RNA-seq assays. Tumor cellular assays, qRT-PCR, western blot, ChIP, luciferase assays and CRISPR-Cas9 editing methods were performed to mechanistically understand the cooperation of GATA2 with SMAD4 in promoting TGFβ1 and AR signaling and mediating inherited PCa risk and progression. RESULTS In this study, by integrated genomics and experimental analysis, we identified GATA2 as a prevalent metastasis-associated genomic amplification to transcriptionally augment its own expression in PCa. Functional experiments demonstrated that GATA2 physically interacted and cooperated with SMAD4 for genome-wide chromatin co-occupancy and co-regulation of PCa genes and metastasis pathways like TGFβ signaling. Mechanistically, GATA2 was cooperative with SMAD4 to enhance TGFβ and AR signaling pathways, and activated the expression of TGFβ1 via directly binding to a distal enhancer of TGFβ1. Strinkingly, GATA2 and SMAD4 globally mediated inherited PCa risk and formed a transcriptional complex with HOXB13 at the PCa risk-associated rs339331/6q22 enhancer, leading to increased expression of the PCa susceptibility gene RFX6. CONCLUSIONS Our study prioritizes causal genomic amplification genes with prognostic values in PCa and reveals the pivotal roles of GATA2 in transcriptionally activating the expression of its own and TGFβ1, thereby co-opting to TGFβ1/SMAD4 signaling and RFX6 at 6q22 to modulate PCa predisposition and progression.
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Affiliation(s)
- Xiayun Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Shuxuan Li
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Raman Devarajan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Binjie Luo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zixian Wang
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Nikolaos Giannareas
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tomasz Wenta
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Wenlong Ma
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuqing Li
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China
| | - Yuehong Yang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Song Wu
- Institute of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China.
- Institute of Urology, South China Hospital of Shenzhen University, Shenzhen, China.
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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Laajala TD, Sreekanth V, Soupir AC, Creed JH, Halkola AS, Calboli FCF, Singaravelu K, Orman MV, Colin-Leitzinger C, Gerke T, Fridley BL, Tyekucheva S, Costello JC. A harmonized resource of integrated prostate cancer clinical, -omic, and signature features. Sci Data 2023; 10:430. [PMID: 37407670 PMCID: PMC10322899 DOI: 10.1038/s41597-023-02335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Genomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical outcomes and to test hypotheses across multiple, independent patient cohorts. In addition, derived features, such as estimates of cell composition, risk scores, and androgen receptor (AR) scores, can be used to develop novel hypotheses leveraging existing multi-omic datasets. The full potential of such data is yet to be realized as independent datasets exist in different repositories, have been processed using different pipelines, and derived and clinical features are often not provided or not standardized. Here, we present the curatedPCaData R package, a harmonized data resource representing >2900 primary tumor, >200 normal tissue, and >500 metastatic PCa samples across 19 datasets processed using standardized pipelines with updated gene annotations. We show that meta-analysis across harmonized studies has great potential for robust and clinically meaningful insights. curatedPCaData is an open and accessible community resource with code made available for reproducibility.
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Affiliation(s)
- Teemu D Laajala
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Varsha Sreekanth
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alex C Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jordan H Creed
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Anni S Halkola
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Federico C F Calboli
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
- Natural Resources Institute Finland (Luke), F-31600, Jokioinen, Finland
| | | | - Michael V Orman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Travis Gerke
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Svitlana Tyekucheva
- Department of Data Science, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Ravindran F, Jain A, Desai S, Menon N, Srivastava K, Bawa PS, Sateesh K, Srivatsa N, Raghunath SK, Srinivasan S, Choudhary B. Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ. J Cancer Res Clin Oncol 2023; 149:2451-2462. [PMID: 35737091 DOI: 10.1007/s00432-022-04111-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/03/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Prostate cancer is the second most common cancer diagnosed worldwide and the third most common cancer among men in India. This study's objective was to characterise the mutational landscape of Indian prostate cancer using whole-exome sequencing to identify population-specific polymorphisms. METHODS Whole-exome sequencing was performed of 58 treatment-naive primary prostate tumors of Indian origin. Multiple computational and statistical analyses were used to profile the known common mutations, other deleterious mutations, driver genes, prognostic biomarkers, and gene signatures unique to each clinical parameter. Cox analysis was performed to validate survival-associated genes. McNemar test identified genes significant to recurrence and receiver-operating characteristic (ROC) analysis was conducted to determine its accuracy. OncodriveCLUSTL algorithm was used to deduce driver genes. The druggable target identified was modeled with its known inhibitor using Autodock. RESULTS TP53 was the most commonly mutated gene in our cohort. Three novel deleterious variants unique to the Indian prostate cancer subtype were identified: POLQ, FTHL17, and OR8G1. COX regression analysis identified ACSM5, a mitochondrial gene responsible for survival. CYLC1 gene, which encodes for sperm head cytoskeletal protein, was identified as an unfavorable prognostic biomarker indicative of recurrence. The novel POLQ mutant, also identified as a driver gene, was evaluated as the druggable target in this study. POLQ, a DNA repair enzyme implicated in various cancer types, is overexpressed and is associated with a poor prognosis. The mutant POLQ was subjected to structural analysis and modeled with its known inhibitor novobiocin resulting in decreased binding efficiency necessitating the development of a better drug. CONCLUSION In this pilot study, the molecular profiling using multiple computational and statistical analyses revealed distinct polymorphisms in the Indian prostate cancer cohort. The mutational signatures identified provide a valuable resource for prognostic stratification and targeted treatment strategies for Indian prostate cancer patients. The DNA repair enzyme, POLQ, was identified as the druggable target in this study.
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Affiliation(s)
- Febina Ravindran
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Anika Jain
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
- Manipal Academy of Higher Education, Manipal, India
| | - Navjoth Menon
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Kriti Srivastava
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Pushpinder Singh Bawa
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - K Sateesh
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - N Srivatsa
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - S K Raghunath
- Healthcare Global Enterprises Ltd, Cancer Centre, Bangalore, India
| | - Subhashini Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronic City Phase 1, Bangalore, Karnataka, India.
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Ebrahimizadeh W, Guérard KP, Rouzbeh S, Scarlata E, Brimo F, Patel PG, Jamaspishvili T, Hamel L, Aprikian AG, Lee AY, Berman DM, Bartlett JMS, Chevalier S, Lapointe J. A DNA copy number alteration classifier as a prognostic tool for prostate cancer patients. Br J Cancer 2023; 128:2165-2174. [PMID: 37037938 PMCID: PMC10241891 DOI: 10.1038/s41416-023-02236-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Distinguishing between true indolent and potentially life-threatening prostate cancer is challenging in tumours displaying clinicopathologic features associated with low or intermediate risk of relapse. Several somatic DNA copy number alterations (CNAs) have been identified as potential prognostic biomarkers, but the standard cytogenetic method to assess them has a limited multiplexing capability. METHODS Multiplex ligation-dependent probe amplification (MLPA) targeting 14 genes was optimised to survey 448 tumours of patients with low or intermediate risk (Grade Group 1-3, Gleason score ≤7) who underwent radical prostatectomy. A 6-gene CNA classifier was developed using random survival forest and Cox proportional hazard modelling to predict biochemical recurrence. RESULTS The classifier score was significantly associated with biochemical recurrence after adjusting for standard clinicopathologic variables and the known prognostic index CAPRA-S score with a hazard ratio of 2.17 and 1.80, respectively (n = 406, P < 0.01). The prognostic value of this classifier was externally validated in published CNA data from three radical prostatectomy cohorts and one radiation therapy pre-treatment biopsy cohort. CONCLUSION The 6-gene CNA classifier generated by a single MLPA assay compatible with the small quantities of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue specimens has the potential to improve the clinical management of patients with low or intermediate risk disease.
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Affiliation(s)
- Walead Ebrahimizadeh
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
- Current affiliation: IMV Inc., Dartmouth, Canada
| | - Karl-Philippe Guérard
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Shaghayegh Rouzbeh
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Eleonora Scarlata
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Fadi Brimo
- Department of Pathology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Palak G Patel
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Tamara Jamaspishvili
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, ON, Canada
- Department of Pathology & Laboratory Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Lucie Hamel
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Armen G Aprikian
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Anna Y Lee
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - David M Berman
- Department of Pathology & Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - John M S Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Simone Chevalier
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada
| | - Jacques Lapointe
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre (RI MUHC), Montreal, QC, Canada.
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47
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Mohamed S, Bertolaccini L, Galetta D, Petrella F, Casiraghi M, de Marinis F, Spaggiari L. The Role of Immunotherapy or Immuno-Chemotherapy in Non-Small Cell Lung Cancer: A Comprehensive Review. Cancers (Basel) 2023; 15:cancers15092476. [PMID: 37173943 PMCID: PMC10177497 DOI: 10.3390/cancers15092476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Many new treatment modalities for non-small-cell carcinoma (NSCLC) have been described in the last two decades. Surgical resections remain the gold standard for early stages and may be considered for locally advanced tumors. Medical treatment has changed drastically in recent years, especially for advanced stages, for which the development of immunotherapy and molecular targeted therapy significantly increased survival and quality of life. The addition of radical surgical resection following immunotherapy or immuno-chemotherapy is feasible and safe with low surgical-related mortality and morbidity in selected patients with initially unresectable NSCLC. However, data from multiple ongoing trials with overall survival as the primary endpoint should be awaited before this strategy is introduced into the standard of care.
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Affiliation(s)
- Shehab Mohamed
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Luca Bertolaccini
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Domenico Galetta
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Francesco Petrella
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Monica Casiraghi
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Filippo de Marinis
- Department of Thoracic Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Lorenzo Spaggiari
- Department of Thoracic Surgery, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
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48
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Alfahed A, Ebili HO, Almoammar NE, Alasiri G, AlKhamees OA, Aldali JA, Al Othaim A, Hakami ZH, Abdulwahed AM, Waggiallah HA. Prognostic Values of Gene Copy Number Alterations in Prostate Cancer. Genes (Basel) 2023; 14:genes14050956. [PMID: 37239316 DOI: 10.3390/genes14050956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Whilst risk prediction for individual prostate cancer (PCa) cases is of a high priority, the current risk stratification indices for PCa management have severe limitations. This study aimed to identify gene copy number alterations (CNAs) with prognostic values and to determine if any combination of gene CNAs could have risk stratification potentials. Clinical and genomic data of 500 PCa cases from the Cancer Genome Atlas stable were retrieved from the Genomic Data Commons and cBioPortal databases. The CNA statuses of a total of 52 genetic markers, including 21 novel markers and 31 previously identified potential prognostic markers, were tested for prognostic significance. The CNA statuses of a total of 51/52 genetic markers were significantly associated with advanced disease at an odds ratio threshold of ≥1.5 or ≤0.667. Moreover, a Kaplan-Meier test identified 27/52 marker CNAs which correlated with disease progression. A Cox Regression analysis showed that the amplification of MIR602 and deletions of MIR602, ZNF267, MROH1, PARP8, and HCN1 correlated with a progression-free survival independent of the disease stage and Gleason prognostic group grade. Furthermore, a binary logistic regression analysis identified twenty-two panels of markers with risk stratification potentials. The best model of 7/52 genetic CNAs, which included the SPOP alteration, SPP1 alteration, CCND1 amplification, PTEN deletion, CDKN1B deletion, PARP8 deletion, and NKX3.1 deletion, stratified the PCa cases into a localised and advanced disease with an accuracy of 70.0%, sensitivity of 85.4%, specificity of 44.9%, positive predictive value of 71.67%, and negative predictive value of 65.35%. This study validated prognostic gene level CNAs identified in previous studies, as well as identified new genetic markers with CNAs that could potentially impact risk stratification in PCa.
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Affiliation(s)
- Abdulaziz Alfahed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Henry Okuchukwu Ebili
- Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye P.M.B. 2002, Nigeria
| | - Nasser Eissa Almoammar
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Glowi Alasiri
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud University, Riyadh 13317, Saudi Arabia
| | - Osama A AlKhamees
- Department of Pharmacology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Jehad A Aldali
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317, Saudi Arabia
| | - Ayoub Al Othaim
- Department of Medical Laboratories, College of Applied Medical Sciences, Majmaah University, Al-Majmaah 11952, Saudi Arabia
| | - Zaki H Hakami
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 82817, Saudi Arabia
| | - Abdulhadi M Abdulwahed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Hisham Ali Waggiallah
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
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49
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Tao Z, Wang S, Wu C, Wu T, Zhao X, Ning W, Wang G, Wang J, Chen J, Diao K, Chen F, Liu XS. The repertoire of copy number alteration signatures in human cancer. Brief Bioinform 2023; 24:7048898. [PMID: 36806386 PMCID: PMC10025440 DOI: 10.1093/bib/bbad053] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/01/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes WGS samples, and further validated with 10 851 the cancer genome atlas SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients' prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution and etiology.
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Affiliation(s)
- Ziyu Tao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shixiang Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Bioinformatics Platform, Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Chenxu Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Xiangyu Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Wei Ning
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Guangshuai Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jinyu Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Jing Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Kaixuan Diao
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
| | - Fuxiang Chen
- Department of Clinical Immunology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, People's Republic of China
| | - Xue-Song Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
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50
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Preclinical models of prostate cancer - modelling androgen dependency and castration resistance in vitro, ex vivo and in vivo. Nat Rev Urol 2023:10.1038/s41585-023-00726-1. [PMID: 36788359 DOI: 10.1038/s41585-023-00726-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 02/16/2023]
Abstract
Prostate cancer is well known to be dependent on the androgen receptor (AR) for growth and survival. Thus, AR is the main pharmacological target to treat this disease. However, after an initially positive response to AR-targeting therapies, prostate cancer will eventually evolve to castration-resistant prostate cancer, which is often lethal. Tumour growth was initially thought to become androgen-independent following treatments; however, results from molecular studies have shown that most resistance mechanisms involve the reactivation of AR. Consequently, tumour cells become resistant to castration - the blockade of testicular androgens - and not independent of AR per se. However, confusion still remains on how to properly define preclinical models of prostate cancer, including cell lines. Most cell lines were isolated from patients for cell culture after evolution of the tumour to castration-resistant prostate cancer, but not all of these cell lines are described as castration resistant. Moreover, castration refers to the blockade of testosterone production by the testes; thus, even the concept of "castration" in vitro is questionable. To ensure maximal transfer of knowledge from scientific research to the clinic, understanding the limitations and advantages of preclinical models, as well as how these models recapitulate cancer cell androgen dependency and can be used to study castration resistance mechanisms, is essential.
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