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Pope B, Park G, Lau E, Belic J, Lach R, George A, McCoy P, Nguyen A, Grima C, Campbell B, Jung CH, Ditter EJ, Zhao H, Wedge DC, Brewer DS, Lynch AG, Dev H, Gnanpragasam VJ, Rosenfeld N, Hovens CM, Corcoran NM, Massie CE. Ultrasensitive Detection of Circulating Tumour DNA enriches for Patients with a Greater Risk of Recurrence of Clinically Localised Prostate Cancer. Eur Urol 2024; 85:407-410. [PMID: 38378299 DOI: 10.1016/j.eururo.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/17/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Bernard Pope
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia; Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Australia.
| | - Gahee Park
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Edmund Lau
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Jelena Belic
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Radoslaw Lach
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Anne George
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK; Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Patrick McCoy
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Anne Nguyen
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Corrina Grima
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Bethany Campbell
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Emma-Jane Ditter
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hui Zhao
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; Earlham Institute, Norwich, UK
| | - Andy G Lynch
- School of Medicine, University of St. Andrews, St. Andrews, UK; School of Mathematics and Statistics, University of St. Andrews, St. Andrews, UK
| | - Harveer Dev
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Vincent J Gnanpragasam
- Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christopher M Hovens
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Australian Prostate Cancer Research Centre, Melbourne, Australia
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Australia; Victorian Comprehensive Cancer Centre, Parkville, Australia
| | - Charles E Massie
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
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2
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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 Genom 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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [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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Hurst R, Brewer DS, Gihawi A, Wain J, Cooper CS. Cancer invasion and anaerobic bacteria: new insights into mechanisms. J Med Microbiol 2024; 73:001817. [PMID: 38535967 PMCID: PMC10995961 DOI: 10.1099/jmm.0.001817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/27/2024] [Indexed: 04/07/2024] Open
Abstract
There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including Peptoniphilus spp., Porphyromonas spp., Fusobacterium spp., Fenollaria spp., Prevotella spp., Sneathia spp., Veillonella spp. and Anaerococcus spp. linked to multiple cancer types. In this review we explore these pathogenic associations. The mechanisms by which bacteria are known or predicted to interact with human cells are reviewed and we present an overview of the interlinked mechanisms and hypotheses of how multiple intracellular anaerobic bacterial pathogens may act together to cause host cell and tissue microenvironment changes associated with carcinogenesis and cancer cell invasion. These include combined effects on changes in cell signalling, DNA damage, cellular metabolism and immune evasion. Strategies for early detection and eradication of anaerobic cancer-associated bacterial pathogens that may prevent cancer progression are proposed.
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Affiliation(s)
- Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Abraham Gihawi
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- Quadram Institute Biosciences, Colney Lane, Norwich, Norfolk, NR4 7UQ, UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
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Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Major data analysis errors invalidate cancer microbiome findings. mBio 2023; 14:e0160723. [PMID: 37811944 PMCID: PMC10653788 DOI: 10.1128/mbio.01607-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/21/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid.
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Affiliation(s)
- Abraham Gihawi
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Yuchen Ge
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jennifer Lu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amanda Xu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
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5
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Gihawi A, Cooper CS, Brewer DS. Caution regarding the specificities of pan-cancer microbial structure. Microb Genom 2023; 9:mgen001088. [PMID: 37555750 PMCID: PMC10483429 DOI: 10.1099/mgen.0.001088] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
Results published in an article by Poore et al. (Nature. 2020;579:567-574) suggested that machine learning models can almost perfectly distinguish between tumour types based on their microbial composition using machine learning models. Whilst we believe that there is the potential for microbial composition to be used in this manner, we have concerns with the paper that make us question the certainty of the conclusions drawn. We believe there are issues in the areas of the contribution of contamination, handling of batch effects, false positive classifications and limitations in the machine learning approaches used. This makes it difficult to identify whether the authors have identified true biological signal and how robust these models would be in use as clinical biomarkers. We commend Poore et al. on their approach to open data and reproducibility that has enabled this analysis. We hope that this discourse assists the future development of machine learning models and hypothesis generation in microbiome research.
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Affiliation(s)
- Abraham Gihawi
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Colin S. Cooper
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Daniel S. Brewer
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich NR4 7UG, UK
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6
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Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Major data analysis errors invalidate cancer microbiome findings. bioRxiv 2023:2023.07.28.550993. [PMID: 37577699 PMCID: PMC10418105 DOI: 10.1101/2023.07.28.550993] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (1) errors in the genome database and the associated computational methods led to millions of false positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (2) errors in transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well.
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Affiliation(s)
- Abraham Gihawi
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Yuchen Ge
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jennifer Lu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amanda Xu
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, UK
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
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7
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Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H, Cooper CS, Eils R, Ferretti V, Lichter P. Author Correction: The landscape of viral associations in human cancers. Nat Genet 2023:10.1038/s41588-023-01316-y. [PMID: 36944734 DOI: 10.1038/s41588-023-01316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Affiliation(s)
- Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivan Borozan
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Malik Alawi
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nikita Desai
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
- Biomedical Data Science Laboratory, Francis Crick Institute, London, UK
| | - Holger Sültmann
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
| | | | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
- Institute of Cancer Research, London, UK
- University of East Anglia, Norwich, UK
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University and BioQuant Center, Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Vincent Ferretti
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Québec, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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10
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Cardenas R, Prinsley P, Philpott C, Bhutta MF, Wilson E, Brewer DS, Jennings BA. Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma. PLoS One 2023; 18:e0272174. [PMID: 36920900 PMCID: PMC10016674 DOI: 10.1371/journal.pone.0272174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/08/2023] [Indexed: 03/16/2023] Open
Abstract
Cholesteatoma is a rare progressive disease of the middle ear. Most cases are sporadic, but some patients report a positive family history. Identifying functionally important gene variants associated with this disease has the potential to uncover the molecular basis of cholesteatoma pathology with implications for disease prevention, surveillance, or management. We performed an observational WES study of 21 individuals treated for cholesteatoma who were recruited from ten multiply affected families. These family studies were complemented with gene-level mutational burden analysis. We also applied functional enrichment analyses to identify shared properties and pathways for candidate genes and their products. Filtered data collected from pairs and trios of participants within the ten families revealed 398 rare, loss of function (LOF) variants co-segregating with cholesteatoma in 389 genes. We identified six genes DENND2C, DNAH7, NBEAL1, NEB, PRRC2C, and SHC2, for which we found LOF variants in two or more families. The parallel gene-level analysis of mutation burden identified a significant mutation burden for the genes in the DNAH gene family, which encode products involved in ciliary structure. Functional enrichment analyses identified common pathways for the candidate genes which included GTPase regulator activity, calcium ion binding, and degradation of the extracellular matrix. The number of candidate genes identified and the locus heterogeneity that we describe within and between multiply affected families suggest that the genetic architecture for familial cholesteatoma is complex.
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Affiliation(s)
- Ryan Cardenas
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Peter Prinsley
- ENT Department, James Paget University Hospitals NHS Foundation Trust, Great Yarmouth, Norfolk, United Kingdom
| | - Carl Philpott
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Mahmood F. Bhutta
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, United Kingdom
- ENT Department, Royal Sussex County Hospital, Brighton, United Kingdom
| | - Emma Wilson
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (BAJ); (DSB)
| | - Barbara A. Jennings
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
- * E-mail: (BAJ); (DSB)
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11
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Gihawi A, Cardenas R, Hurst R, Brewer DS. Quality Control in Metagenomics Data. Methods Mol Biol 2023; 2649:21-54. [PMID: 37258856 DOI: 10.1007/978-1-0716-3072-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.
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Affiliation(s)
- Abraham Gihawi
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Ryan Cardenas
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rachel Hurst
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Daniel S Brewer
- Bob Champion Research & Education Building, Norwich Medical School, University of East Anglia, Norwich, UK.
- Earlham Institute, Norwich Research Park, Norwich, UK.
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12
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Wardale L, Cardenas R, Gnanapragasam VJ, Cooper CS, Clark J, Brewer DS. Combining Molecular Subtypes with Multivariable Clinical Models Has the Potential to Improve Prediction of Treatment Outcomes in Prostate Cancer at Diagnosis. Curr Oncol 2022; 30:157-170. [PMID: 36661662 PMCID: PMC9857957 DOI: 10.3390/curroncol30010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Clinical management of prostate cancer is challenging because of its highly variable natural history and so there is a need for improved predictors of outcome in non-metastatic men at the time of diagnosis. In this study we calculated the model score from the leading clinical multivariable model, PREDICT prostate, and the poor prognosis DESNT molecular subtype, in a combined expression and clinical dataset that were taken from malignant tissue at prostatectomy (n = 359). Both PREDICT score (p < 0.0001, IQR HR = 1.59) and DESNT score (p < 0.0001, IQR HR = 2.08) were significant predictors for time to biochemical recurrence. A joint model combining the continuous PREDICT and DESNT score (p < 0.0001, IQR HR = 1.53 and 1.79, respectively) produced a significantly improved predictor than either model alone (p < 0.001). An increased probability of mortality after diagnosis, as estimated by PREDICT, was characterised by upregulation of cell-cycle related pathways and the downregulation of metabolism and cholesterol biosynthesis. The DESNT molecular subtype has distinct biological characteristics to those associated with the PREDICT model. We conclude that the inclusion of biological information alongside current clinical prognostic tools has the potential to improve the ability to choose the optimal treatment pathway for a patient.
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Affiliation(s)
- Lewis Wardale
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ryan Cardenas
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vincent J. Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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13
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Buhigas C, Warren AY, Leung WK, Whitaker HC, Luxton HJ, Hawkins S, Kay J, Butler A, Xu Y, Woodcock DJ, Merson S, Frame FM, Sahli A, Abascal F, Martincorena I, Bova GS, Foster CS, Campbell P, Maitland NJ, Neal DE, Massie CE, Lynch AG, Eeles RA, Cooper CS, Wedge DC, Brewer DS. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Mol Cancer 2022; 21:183. [PMID: 36131292 PMCID: PMC9494848 DOI: 10.1186/s12943-022-01644-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/17/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the present study we applied Whole Genome DNA Sequencing (WGS) to a group of morphologically normal tissue (n = 51), including benign prostatic hyperplasia (BPH) and non-BPH samples, from men with and men without prostate cancer. We assess whether the observed genetic changes in morphologically normal tissue are linked to the development of cancer in the prostate. RESULTS Single nucleotide variants (P = 7.0 × 10-03, Wilcoxon rank sum test) and small insertions and deletions (indels, P = 8.7 × 10-06) were significantly higher in morphologically normal samples, including BPH, from men with prostate cancer compared to those without. The presence of subclonal expansions under selective pressure, supported by a high level of mutations, were significantly associated with samples from men with prostate cancer (P = 0.035, Fisher exact test). The clonal cell fraction of normal clones was always higher than the proportion of the prostate estimated as epithelial (P = 5.94 × 10-05, paired Wilcoxon signed rank test) which, along with analysis of primary fibroblasts prepared from BPH specimens, suggests a stromal origin. Constructed phylogenies revealed lineages associated with benign tissue that were completely distinct from adjacent tumour clones, but a common lineage between BPH and non-BPH morphologically normal tissues was often observed. Compared to tumours, normal samples have significantly less single nucleotide variants (P = 3.72 × 10-09, paired Wilcoxon signed rank test), have very few rearrangements and a complete lack of copy number alterations. CONCLUSIONS Cells within regions of morphologically normal tissue (both BPH and non-BPH) can expand under selective pressure by mechanisms that are distinct from those occurring in adjacent cancer, but that are allied to the presence of cancer. Expansions, which are probably stromal in origin, are characterised by lack of recurrent driver mutations, by almost complete absence of structural variants/copy number alterations, and mutational processes similar to malignant tissue. Our findings have implications for treatment (focal therapy) and early detection approaches.
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Affiliation(s)
- Claudia Buhigas
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Wing-Kit Leung
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Hayley C Whitaker
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Hayley J Luxton
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Steve Hawkins
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Molecular Diagnostics and Therapeutics Group, Division of Surgery and Interventional Sciences University College London, London, W1W 7TS, UK
| | - Adam Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Yaobo Xu
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Sue Merson
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - Fiona M Frame
- Cancer Research Unit, Department of Biology, University of York, Heslington, YO10 5DD, North Yorkshire, UK
| | - Atef Sahli
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33014, Tampere, FI, Finland
| | | | - Peter Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, CB10 1RQ, UK
| | - Norman J Maitland
- Cancer Research Unit, Department of Biology, University of York, Heslington, YO10 5DD, North Yorkshire, UK
| | - David E Neal
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
| | - Charlie E Massie
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge Institute, Cambridge, CB2 0RE, UK
- School of Medicine/School of Mathematics and Statistics, University of St Andrews, St Andrews, KY16 9AJ, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, SM2 5PT, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
- The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Wedge
- Oxford Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
- Earlham Institute, Norwich, NR4 7UZ, UK.
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14
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Burns D, Anokian E, Saunders EJ, Bristow RG, Fraser M, Reimand J, Schlomm T, Sauter G, Brors B, Korbel J, Weischenfeldt J, Waszak SM, Corcoran NM, Jung CH, Pope BJ, Hovens CM, Cancel-Tassin G, Cussenot O, Loda M, Sander C, Hayes VM, Dalsgaard Sorensen K, Lu YJ, Hamdy FC, Foster CS, Gnanapragasam V, Butler A, Lynch AG, Massie CE, Woodcock DJ, Cooper CS, Wedge DC, Brewer DS, Kote-Jarai Z, Eeles RA. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol 2022; 82:201-211. [PMID: 35659150 DOI: 10.1016/j.eururo.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/06/2022] [Accepted: 05/10/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Germline variants explain more than a third of prostate cancer (PrCa) risk, but very few associations have been identified between heritable factors and clinical progression. OBJECTIVE To find rare germline variants that predict time to biochemical recurrence (BCR) after radical treatment in men with PrCa and understand the genetic factors associated with such progression. DESIGN, SETTING, AND PARTICIPANTS Whole-genome sequencing data from blood DNA were analysed for 850 PrCa patients with radical treatment from the Pan Prostate Cancer Group (PPCG) consortium from the UK, Canada, Germany, Australia, and France. Findings were validated using 383 patients from The Cancer Genome Atlas (TCGA) dataset. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS A total of 15,822 rare (MAF <1%) predicted-deleterious coding germline mutations were identified. Optimal multifactor and univariate Cox regression models were built to predict time to BCR after radical treatment, using germline variants grouped by functionally annotated gene sets. Models were tested for robustness using bootstrap resampling. RESULTS AND LIMITATIONS Optimal Cox regression multifactor models showed that rare predicted-deleterious germline variants in "Hallmark" gene sets were consistently associated with altered time to BCR. Three gene sets had a statistically significant association with risk-elevated outcome when modelling all samples: PI3K/AKT/mTOR, Inflammatory response, and KRAS signalling (up). PI3K/AKT/mTOR and KRAS signalling (up) were also associated among patients with higher-grade cancer, as were Pancreas-beta cells, TNFA signalling via NKFB, and Hypoxia, the latter of which was validated in the independent TCGA dataset. CONCLUSIONS We demonstrate for the first time that rare deleterious coding germline variants robustly associate with time to BCR after radical treatment, including cohort-independent validation. Our findings suggest that germline testing at diagnosis could aid clinical decisions by stratifying patients for differential clinical management. PATIENT SUMMARY Prostate cancer patients with particular genetic mutations have a higher chance of relapsing after initial radical treatment, potentially providing opportunities to identify patients who might need additional treatments earlier.
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Affiliation(s)
| | | | | | - Robert G Bristow
- Manchester Cancer Research Centre and CRUK Manchester Institute, The University of Manchester, Manchester, UK
| | - Michael Fraser
- Princess Margaret Cancer Centre/University Health Network, Toronto, Ontario, Canada; Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics & Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Guido Sauter
- University Medical Centre Hamburg - Eppendorf, Hamburg, Germany
| | - Benedikt Brors
- German Cancer Research Center (DKFZ), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jan Korbel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Joachim Weischenfeldt
- Charité - Universitätsmedizin Berlin, Berlin, Germany; Biotech Research & Innovation Centre (BRIC) & Finsen Laboratory, University of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatric Research, Division of Pediatric and Adolescent Medicine, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Victoria, Australia; Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia
| | - Chol-Hee Jung
- The University of Melbourne, Grattan Street, Parkville, Victoria, Australia
| | - Bernard J Pope
- Department of Surgery, The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; Royal Melbourne Hospital, Melbourne, Parwille, Victoria, Australia
| | - Chris M Hovens
- Melbourne Bioinformatics, The University of Melbourne, Grattan Street, Victoria, Australia; The University of Melbourne, Grattan Street, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, The Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Géraldine Cancel-Tassin
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Olivier Cussenot
- CeRePP, Hopital Tenon, Paris, France; Sorbonne Universite, GRC n°5 Predictive Onco-Urology, APHP, Tenon Hospital, Paris, France
| | - Massimo Loda
- Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia; School of Medical Sciences, University of Sydney, Charles Perkins Centre, Camperdown, NSW, Australia
| | - Karina Dalsgaard Sorensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Yong-Jie Lu
- Centre for Biomarker and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | | | | | - Adam Butler
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Andy G Lynch
- School of Medicine, University of St Andrews, St Andrews, Fife, UK; School of Mathematics & Statistics, St Andrews, Fife, UK
| | - Charlie E Massie
- CRUK Cambridge Institute, Hutchison MRC Research Centre, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
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- CR-UK/Prostate Cancer UK, ICGC, The Pan Prostate Cancer Group, UK
| | - Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - David C Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; The Royal Marsden NHS Foundation Trust, London, UK
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Jakobsdottir GM, Brewer DS, Cooper C, Green C, Wedge DC. APOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types. BMC Biol 2022; 20:117. [PMID: 35597990 PMCID: PMC9124393 DOI: 10.1186/s12915-022-01316-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes are activated in response to viral infection, and have been associated with increased mutation burden and TP53 mutation. In addition to this, it has been suggested that APOBEC3 activity may be responsible for mutations that do not fall into the classical APOBEC3 signatures (SBS2 and SBS13), through generation of double strand breaks.Previous work has mainly focused on the effects of APOBEC3 within individual tumour types using exome sequencing data. Here, we use whole genome sequencing data from 2451 primary tumours from 39 different tumour types in the Pan-Cancer Analysis of Whole Genomes (PCAWG) data set to investigate the relationship between APOBEC3 and genomic instability (GI). RESULTS AND CONCLUSIONS We found that the number of classical APOBEC3 signature mutations correlates with increased mutation burden across different tumour types. In addition, the number of APOBEC3 mutations is a significant predictor for six different measures of GI. Two GI measures (INDELs attributed to INDEL signatures ID6 and ID8) strongly suggest the occurrence and error prone repair of double strand breaks, and the relationship between APOBEC3 mutations and GI remains when SNVs attributed to kataegis are excluded.We provide evidence that supports a model of cancer genome evolution in which APOBEC3 acts as a causative factor in the development of diverse and widespread genomic instability through the generation of double strand breaks. This has important implications for treatment approaches for cancers that carry APOBEC3 mutations, and challenges the view that APOBECs only act opportunistically at sites of single stranded DNA.
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Affiliation(s)
- G Maria Jakobsdottir
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK
| | - Daniel S Brewer
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Colin Cooper
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Catherine Green
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
- Manchester Cancer Research Centre, University of Manchester, Wilmslow Road, Manchester, M20 4GJ, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, OX4 2PG, UK.
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Hurst R, Meader E, Gihawi A, Rallapalli G, Clark J, Kay GL, Webb M, Manley K, Curley H, Walker H, Kumar R, Schmidt K, Crossman L, Eeles RA, Wedge DC, Lynch AG, Massie CE, Yazbek-Hanna M, Rochester M, Mills RD, Mithen RF, Traka MH, Ball RY, O'Grady J, Brewer DS, Wain J, Cooper CS. Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups. Eur Urol Oncol 2022; 5:412-419. [PMID: 35450835 DOI: 10.1016/j.euo.2022.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/08/2022] [Accepted: 03/29/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been reported. OBJECTIVE To provide improved characterisation of the prostate and urine microbiome and to investigate the prognostic potential of the bacteria present. DESIGN, SETTING, AND PARTICIPANTS Microbiome profiles were interrogated in sample collections of patient urine (sediment microscopy: n = 318, 16S ribosomal amplicon sequencing: n = 46; and extracellular vesicle RNA-seq: n = 40) and cancer tissue (n = 204). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Microbiomes were assessed using anaerobic culture, population-level 16S analysis, RNA-seq, and whole genome DNA sequencing. RESULTS AND LIMITATIONS We demonstrate an association between the presence of bacteria in urine sediments and higher D'Amico risk prostate cancer (discovery, n = 215 patients, p < 0.001; validation, n = 103, p < 0.001, χ2 test for trend). Characterisation of the bacterial community led to the (1) identification of four novel bacteria (Porphyromonas sp. nov., Varibaculum sp. nov., Peptoniphilus sp. nov., and Fenollaria sp. nov.) that were frequently found in patient urine, and (2) definition of a patient subgroup associated with metastasis development (p = 0.015, log-rank test). The presence of five specific anaerobic genera, which includes three of the novel isolates, was associated with cancer risk group, in urine sediment (p = 0.045, log-rank test), urine extracellular vesicles (p = 0.039), and cancer tissue (p = 0.035), with a meta-analysis hazard ratio for disease progression of 2.60 (95% confidence interval: 1.39-4.85; p = 0.003; Cox regression). A limitation is that functional links to cancer development are not yet established. CONCLUSIONS This study characterises prostate and urine microbiomes, and indicates that specific anaerobic bacteria genera have prognostic potential. PATIENT SUMMARY In this study, we investigated the presence of bacteria in patient urine and the prostate. We identified four novel bacteria and suggest a potential prognostic utility for the microbiome in prostate cancer.
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Affiliation(s)
- Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Emma Meader
- Microbiology Department, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Abraham Gihawi
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | | | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Gemma L Kay
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Quadram Institute Biosciences, Norwich, UK
| | - Martyn Webb
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Kate Manley
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Helen Curley
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Helen Walker
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Ravi Kumar
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK
| | - Katarzyna Schmidt
- Microbiology Department, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Lisa Crossman
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Quadram Institute Biosciences, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK; University of Manchester, Manchester, UK
| | - Andy G Lynch
- School of Medicine, University of St Andrews, St Andrews, UK; School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Charlie E Massie
- Hutchison/MRC Research Centre, Cambridge University, Cambridge, UK
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- The CRUK-ICGC Prostate Group, UK
| | - Marcelino Yazbek-Hanna
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Mark Rochester
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Robert D Mills
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Richard F Mithen
- Quadram Institute Biosciences, Norwich, UK; Liggins Institute, University of Auckland, Grafton, Auckland, New Zealand
| | | | - Richard Y Ball
- Norfolk and Waveney Cellular Pathology Service, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Quadram Institute Biosciences, Norwich, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Earlham Institute, Norwich Research Park Innovation Centre, Norwich, UK
| | - John Wain
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK; Quadram Institute Biosciences, Norwich, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, UK.
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17
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Ball RY, Cardenas R, Winterbone MS, Hanna MY, Parker C, Hurst R, Brewer DS, D’Sa L, Mills R, Cooper CS, Clark J. The Urine Biomarker PUR-4 Is Positively Associated with the Amount of Gleason 4 in Human Prostate Cancers. Life (Basel) 2021; 11:life11111172. [PMID: 34833048 PMCID: PMC8622091 DOI: 10.3390/life11111172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
The Prostate Urine Risk (PUR) biomarker is a four-group classifier for predicting outcome in patients prior to biopsy and for men on active surveillance. The four categories correspond to the probabilities of the presence of normal tissue (PUR-1), D’Amico low-risk (PUR-2), intermediate-risk (PUR-3), and high-risk (PUR-4) prostate cancer. In the current study we investigate how the PUR-4 status is linked to Gleason grade, prostate volume, and tumor volume as assessed from biopsy (n = 215) and prostatectomy (n = 9) samples. For biopsy data PUR-4 status alone was linked to Gleason Grade group (GG) (Spearman’s, ρ = 0.58, p < 0.001 trend). To assess the impact of tumor volume each GG was dichotomized into Small and Large volume cancers relative to median volume. For GG1 (Gleason Pattern 3 + 3) cancers volume had no impact on PUR-4 status. In contrast for GG2 (3 + 4) and GG3 (4 + 3) cancers PUR-4 levels increased in large volume cancers with statistical significance observed for GG2 (p = 0.005; Games-Howell). These data indicated that PUR-4 status is linked to the presence of Gleason Pattern 4. To test this observation tumor burden and Gleason Pattern were assessed in nine surgically removed and sectioned prostates allowing reconstruction of 3D maps. PUR-4 was not correlated with Gleason Pattern 3 amount, total tumor volume or prostate size. A strong correlation was observed between amount of Gleason Pattern 4 tumor and PUR-4 signature (r = 0.71, p = 0.034, Pearson’s). These observations shed light on the biological significance of the PUR biomarker and support its use as a non-invasive means of assessing the presence of clinically significant prostate cancer.
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Affiliation(s)
- Richard Y. Ball
- Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich NR4 7UY, UK; (R.Y.B.); (L.D.); (R.M.)
| | - Ryan Cardenas
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
| | - Mark S. Winterbone
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
| | - Marcelino Y. Hanna
- Urology Department Castle Hill, Hull University Teaching Hospital, Castle Rd, Cottingham HU16 5JQ, UK;
| | - Chris Parker
- Institute of Cancer Research, Sutton SM2 5NG, UK;
- Royal Marsden Hospital, Sutton SM2 5PT, UK
| | - Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
- Earlham Institute, Norwich NR4 7UZ, UK
| | - Lauren D’Sa
- Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich NR4 7UY, UK; (R.Y.B.); (L.D.); (R.M.)
| | - Rob Mills
- Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich NR4 7UY, UK; (R.Y.B.); (L.D.); (R.M.)
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK; (R.C.); (M.S.W.); (R.H.); (D.S.B.); (C.S.C.)
- Correspondence:
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18
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Connell SP, Mills R, Pandha H, Morgan R, Cooper CS, Clark J, Brewer DS. Integration of Urinary EN2 Protein & Cell-Free RNA Data in the Development of a Multivariable Risk Model for the Detection of Prostate Cancer Prior to Biopsy. Cancers (Basel) 2021; 13:cancers13092102. [PMID: 33925381 PMCID: PMC8123800 DOI: 10.3390/cancers13092102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Prostate cancer is a disease responsible for a large proportion of all male cancer deaths but there is a high chance that a patient will die with the disease rather than from. Therefore, there is a desperate need for improvements in diagnosing and predicting outcomes for prostate cancer patients to minimise overdiagnosis and overtreatment whilst appropriately treating men with aggressive disease, especially if this can be done without taking an invasive biopsy. In this work we develop a test that predicts whether a patient has prostate cancer and how aggressive the disease is from a urine sample. This model combines the measurement of a protein-marker called EN2 and the levels of 10 genes measured in urine and proves that integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy. Abstract The objective is to develop a multivariable risk model for the non-invasive detection of prostate cancer prior to biopsy by integrating information from clinically available parameters, Engrailed-2 (EN2) whole-urine protein levels and data from urinary cell-free RNA. Post-digital-rectal examination urine samples collected as part of the Movember Global Action Plan 1 study which has been analysed for both cell-free-RNA and EN2 protein levels were chosen to be integrated with clinical parameters (n = 207). A previously described robust feature selection framework incorporating bootstrap resampling and permutation was applied to the data to generate an optimal feature set for use in Random Forest models for prediction. The fully integrated model was named ExoGrail, and the out-of-bag predictions were used to evaluate the diagnostic potential of the risk model. ExoGrail risk (range 0–1) was able to determine the outcome of an initial trans-rectal ultrasound guided (TRUS) biopsy more accurately than clinical standards of care, predicting the presence of any cancer with an area under the receiver operator curve (AUC) = 0.89 (95% confidence interval(CI): 0.85–0.94), and discriminating more aggressive Gleason ≥ 3 + 4 disease returning an AUC = 0.84 (95% CI: 0.78–0.89). The likelihood of more aggressive disease being detected significantly increased as ExoGrail risk score increased (Odds Ratio (OR) = 2.21 per 0.1 ExoGrail increase, 95% CI: 1.91–2.59). Decision curve analysis of the net benefit of ExoGrail showed the potential to reduce the numbers of unnecessary biopsies by 35% when compared to current standards of care. Integration of information from multiple, non-invasive biomarker sources has the potential to greatly improve how patients with a clinical suspicion of prostate cancer are risk-assessed prior to an invasive biopsy.
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Affiliation(s)
- Shea P. Connell
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Robert Mills
- Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, Norfolk NR4 7UY, UK;
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, The University of Surrey, Guildford GU2 7XH, UK;
| | - Richard Morgan
- School of Pharmacy and Medical Sciences, University of Bradford, Bradford BD7 1DP, UK;
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (C.S.C.); (J.C.)
- The Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
- Correspondence: ; Tel.: +44-(0)-1603-593761
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19
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Hägnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature 2020; 584:E18. [PMID: 32728210 DOI: 10.1038/s41586-020-2581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000, Leuven, Belgium.,Cancer Research UK London Research Institute, London, WC2A3LY, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Daniel S Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,The Genome Analysis Centre, Norwich, NR4 7UH, UK
| | - Heini M L Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Gunilla Hägnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Sarah O'Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kevin J Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, 21287, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Maryland, 20892, USA.,Avoneaux Medical Institute, Oxford, Maryland, 21654, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Christopher Foster
- University of Liverpool andHCA Pathology Laboratories, London, WC1E6JA, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB18RN, UK
| | - Hayley C Whitaker
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK
| | | | - David E Neal
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK.,Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Colin S Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK.,Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; and, Sutton, SM2 5PT, UK
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - G Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
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20
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Luca BA, Moulton V, Ellis C, Connell SP, Brewer DS, Cooper CS. Convergence of Prognostic Gene Signatures Suggests Underlying Mechanisms of Human Prostate Cancer Progression. Genes (Basel) 2020; 11:genes11070802. [PMID: 32708551 PMCID: PMC7397325 DOI: 10.3390/genes11070802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/27/2020] [Accepted: 07/10/2020] [Indexed: 12/25/2022] Open
Abstract
The highly heterogeneous clinical course of human prostate cancer has prompted the development of multiple RNA biomarkers and diagnostic tools to predict outcome for individual patients. Biomarker discovery is often unstable with, for example, small changes in discovery dataset configuration resulting in large alterations in biomarker composition. Our hypothesis, which forms the basis of this current study, is that highly significant overlaps occurring between gene signatures obtained using entirely different approaches indicate genes fundamental for controlling cancer progression. For prostate cancer, we found two sets of signatures that had significant overlaps suggesting important genes (p < 10−34 for paired overlaps, hypergeometrical test). These overlapping signatures defined a core set of genes linking hormone signalling (HES6-AR), cell cycle progression (Prolaris) and a molecular subgroup of patients (PCS1) derived by Non Negative Matrix Factorization (NNMF) of control pathways, together designated as SIG-HES6. The second set (designated SIG-DESNT) consisted of the DESNT diagnostic signature and a second NNMF signature PCS3. Stratifications using SIG-HES6 (HES6, PCS1, Prolaris) and SIG-DESNT (DESNT) classifiers frequently detected the same individual high-risk cancers, indicating that the underlying mechanisms associated with SIG-HES6 and SIG-DESNT may act together to promote aggressive cancer development. We show that the use of combinations of a SIG-HES6 signature together with DESNT substantially increases the ability to predict poor outcome, and we propose a model for prostate cancer development involving co-operation between the SIG-HES6 and SIG-DESNT pathways that has implication for therapeutic design.
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Affiliation(s)
- Bogdan-Alexandru Luca
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.-A.L.); (V.M.); (C.E.)
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (D.S.B.)
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.-A.L.); (V.M.); (C.E.)
| | - Christopher Ellis
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (B.-A.L.); (V.M.); (C.E.)
| | - Shea P. Connell
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (D.S.B.)
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (D.S.B.)
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (S.P.C.); (D.S.B.)
- Correspondence:
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21
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Connell SP, O'Reilly E, Tuzova A, Webb M, Hurst R, Mills R, Zhao F, Bapat B, Cooper CS, Perry AS, Clark J, Brewer DS. Development of a multivariable risk model integrating urinary cell DNA methylation and cell-free RNA data for the detection of significant prostate cancer. Prostate 2020; 80:547-558. [PMID: 32153047 PMCID: PMC7383590 DOI: 10.1002/pros.23968] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/17/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Prostate cancer exhibits severe clinical heterogeneity and there is a critical need for clinically implementable tools able to precisely and noninvasively identify patients that can either be safely removed from treatment pathways or those requiring further follow up. Our objectives were to develop a multivariable risk prediction model through the integration of clinical, urine-derived cell-free messenger RNA (cf-RNA) and urine cell DNA methylation data capable of noninvasively detecting significant prostate cancer in biopsy naïve patients. METHODS Post-digital rectal examination urine samples previously analyzed separately for both cellular methylation and cf-RNA expression within the Movember GAP1 urine biomarker cohort were selected for a fully integrated analysis (n = 207). A robust feature selection framework, based on bootstrap resampling and permutation, was utilized to find the optimal combination of clinical and urinary markers in a random forest model, deemed ExoMeth. Out-of-bag predictions from ExoMeth were used for diagnostic evaluation in men with a clinical suspicion of prostate cancer (PSA ≥ 4 ng/mL, adverse digital rectal examination, age, or lower urinary tract symptoms). RESULTS As ExoMeth risk score (range, 0-1) increased, the likelihood of high-grade disease being detected on biopsy was significantly greater (odds ratio = 2.04 per 0.1 ExoMeth increase, 95% confidence interval [CI]: 1.78-2.35). On an initial TRUS biopsy, ExoMeth accurately predicted the presence of Gleason score ≥3 + 4, area under the receiver-operator characteristic curve (AUC) = 0.89 (95% CI: 0.84-0.93) and was additionally capable of detecting any cancer on biopsy, AUC = 0.91 (95% CI: 0.87-0.95). Application of ExoMeth provided a net benefit over current standards of care and has the potential to reduce unnecessary biopsies by 66% when a risk threshold of 0.25 is accepted. CONCLUSION Integration of urinary biomarkers across multiple assay methods has greater diagnostic ability than either method in isolation, providing superior predictive ability of biopsy outcomes. ExoMeth represents a more holistic view of urinary biomarkers and has the potential to result in substantial changes to how patients suspected of harboring prostate cancer are diagnosed.
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Affiliation(s)
- Shea P. Connell
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Eve O'Reilly
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Alexandra Tuzova
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Martyn Webb
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Rachel Hurst
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Robert Mills
- Department of UrologyNorfolk and Norwich University Hospitals NHS Foundation TrustNorfolkUK
| | - Fang Zhao
- Division of Urology, University Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - Bharati Bapat
- Division of Urology, University Health NetworkUniversity of TorontoTorontoOntarioCanada
| | - Colin S. Cooper
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Antoinette S. Perry
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
- Cancer Biology and Therapeutics Laboratory, Conway InstituteUniversity CollegeDublinIreland
| | - Jeremy Clark
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
| | - Daniel S. Brewer
- Norwich Medical SchoolUniversity of East AngliaNorwich Research ParkNorwichUK
- Science DivisionThe Earlham InstituteNorwich Research ParkNorwichNorfolkUK
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22
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Luca BA, Moulton V, Ellis C, Edwards DR, Campbell C, Cooper RA, Clark J, Brewer DS, Cooper CS. A novel stratification framework for predicting outcome in patients with prostate cancer. Br J Cancer 2020; 122:1467-1476. [PMID: 32203215 PMCID: PMC7217762 DOI: 10.1038/s41416-020-0799-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/05/2020] [Accepted: 02/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background Unsupervised learning methods, such as Hierarchical Cluster Analysis, are commonly used for the analysis of genomic platform data. Unfortunately, such approaches ignore the well-documented heterogeneous composition of prostate cancer samples. Our aim is to use more sophisticated analytical approaches to deconvolute the structure of prostate cancer transcriptome data, providing novel clinically actionable information for this disease. Methods We apply an unsupervised model called Latent Process Decomposition (LPD), which can handle heterogeneity within individual cancer samples, to genome-wide expression data from eight prostate cancer clinical series, including 1,785 malignant samples with the clinical endpoints of PSA failure and metastasis. Results We show that PSA failure is correlated with the level of an expression signature called DESNT (HR = 1.52, 95% CI = [1.36, 1.7], P = 9.0 × 10−14, Cox model), and that patients with a majority DESNT signature have an increased metastatic risk (X2 test, P = 0.0017, and P = 0.0019). In addition, we develop a stratification framework that incorporates DESNT and identifies three novel molecular subtypes of prostate cancer. Conclusions These results highlight the importance of using more complex approaches for the analysis of genomic data, may assist drug targeting, and have allowed the construction of a nomogram combining DESNT with other clinical factors for use in clinical management.
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Affiliation(s)
- Bogdan-Alexandru Luca
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Christopher Ellis
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Dylan R Edwards
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, UK
| | - Rosalin A Cooper
- Department of Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.,The Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK.
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23
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Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H, Cooper CS, Eils R, Ferretti V, Lichter P. The landscape of viral associations in human cancers. Nat Genet 2020; 52:320-330. [PMID: 32025001 PMCID: PMC8076016 DOI: 10.1038/s41588-019-0558-9] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 11/22/2019] [Indexed: 12/30/2022]
Abstract
Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
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Affiliation(s)
- Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ivan Borozan
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Borstel-Lübeck-Riems, Hamburg, Germany
| | - Malik Alawi
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nikita Desai
- Bioinformatics Group, Department of Computer Science, University College London, London, UK
- Biomedical Data Science Laboratory, Francis Crick Institute, London, UK
| | - Holger Sültmann
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
- Institute of Cancer Research, London, UK
- University of East Anglia, Norwich, UK
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University and BioQuant Center, Heidelberg, Germany
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Vincent Ferretti
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, Québec, Canada
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
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24
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Webb M, Manley K, Olivan M, Guldvik I, Palczynska M, Hurst R, Connell SP, Mills IG, Brewer DS, Mills R, Cooper CS, Clark J. Methodology for the at-home collection of urine samples for prostate cancer detection. Biotechniques 2020; 68:65-71. [DOI: 10.2144/btn-2019-0092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Urine from patients with prostate cancer (PCa) contains gene transcripts that have been used for PCa diagnosis and prognosis. Historically, patient urine samples have been collected after a digital rectal examination of the prostate, which was thought necessary to boost the levels of prostatic secretions in the urine. We herein describe methodology that allows urine to be collected by patients at home and then posted to a laboratory for analysis. RNA yields and quality were comparable to those for post digital rectal examination urine, and there was improved sensitivity for the detection of TMPRSS2:ERG transcripts by RT-PCR. The At-Home collection protocol has opened up the potential to perform large-scale PCa studies without the inconvenience, cost, discomfort and expense of patients having to visit the clinic.
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Affiliation(s)
- Martyn Webb
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kate Manley
- Norwich Medical School, University of East Anglia, Norwich, UK
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Mireia Olivan
- Group of Biomedical Research in Urology, Vall d'Hebron Research Institute & Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ingrid Guldvik
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway, University of Oslo & Oslo University Hospital, Oslo, Norway
- Department of Tumour Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Shea P Connell
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Ian G Mills
- School of Medicine, Dentistry & Biomedical Sciences, Institute for Health Sciences, Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - Robert Mills
- Norfolk & Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, UK
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Gihawi A, Rallapalli G, Hurst R, Cooper CS, Leggett RM, Brewer DS. SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines. Genome Biol 2019; 20:208. [PMID: 31639030 PMCID: PMC6805339 DOI: 10.1186/s13059-019-1819-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of pathogens is being recognized, for example, Helicobacter pylori and human papillomavirus in the cases of gastric non-cardia and cervical carcinomas, respectively. As of yet, no benchmark has been carried out on the performance of computational approaches for bacterial and viral detection within host-dominated sequence data. RESULTS We present the results of benchmarking over 70 distinct combinations of tools and parameters on 100 simulated cancer datasets spiked with realistic proportions of bacteria. mOTUs2 and Kraken are the highest performing individual tools achieving median genus-level F1 scores of 0.90 and 0.91, respectively. mOTUs2 demonstrates a high performance in estimating bacterial proportions. Employing Kraken on unassembled sequencing reads produces a good but variable performance depending on post-classification filtering parameters. These approaches are investigated on a selection of cervical and gastric cancer whole genome sequences where Alphapapillomavirus and Helicobacter are detected in addition to a variety of other interesting genera. CONCLUSIONS We provide the top-performing pipelines from this benchmark in a unifying tool called SEPATH, which is amenable to high throughput sequencing studies across a range of high-performance computing clusters. SEPATH provides a benchmarked and convenient approach to detect pathogens in tissue sequence data helping to determine the relationship between metagenomics and disease.
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Affiliation(s)
- Abraham Gihawi
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, NR4 7UQ UK
| | - Ghanasyam Rallapalli
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, NR4 7UQ UK
| | - Rachel Hurst
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, NR4 7UQ UK
| | - Colin S. Cooper
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, NR4 7UQ UK
- Functional Crosscutting Genomics England Clinical Interpretation Partnership (GeCIP) Domain Lead, 100,000 Genomes Project, Genomics England, London, UK
| | | | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Bob Champion Research and Education Building, Norwich, NR4 7UQ UK
- Norwich Research Park, Earlham Institute, Norwich, NR4 7UZ UK
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Magiorkinis G, Matthews PC, Wallace SE, Jeffery K, Dunbar K, Tedder R, Mbisa JL, Hannigan B, Vayena E, Simmonds P, Brewer DS, Gihawi A, Rallapalli G, Lahnstein L, Fowler T, Patch C, Maleady-Crowe F, Lucassen A, Cooper C. Potential for diagnosis of infectious disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for reporting results. Wellcome Open Res 2019; 4:155. [PMID: 32055707 PMCID: PMC6993825 DOI: 10.12688/wellcomeopenres.15499.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/30/2022] Open
Abstract
The identification of microbiological infection is usually a diagnostic investigation, a complex process that is firstly initiated by clinical suspicion. With the emergence of high-throughput sequencing (HTS) technologies, metagenomic analysis has unveiled the power to identify microbial DNA/RNA from a diverse range of clinical samples (1). Metagenomic analysis of whole human genomes at the clinical/research interface bypasses the steps of clinical scrutiny and targeted testing and has the potential to generate unexpected findings relating to infectious and sometimes transmissible disease. There is no doubt that microbial findings that may have a significant impact on a patient’s treatment and their close contacts should be reported to those with clinical responsibility for the sample-donating patient. There are no clear recommendations on how such findings that are incidental, or outside the original investigation, should be handled. Here we aim to provide an informed protocol for the management of incidental microbial findings as part of the 100,000 Genomes Project
which may have broader application in this emerging field. As with any other clinical information, we aim to prioritise the reporting of data that are most likely to be of benefit to the patient and their close contacts. We also set out to minimize risks, costs and potential anxiety associated with the reporting of results that are unlikely to be of clinical significance. Our recommendations aim to support the practice of microbial metagenomics by providing a simplified pathway that can be applied to reporting the identification of potential pathogens from metagenomic datasets. Given that the ambition for UK sequenced human genomes over the next 5 years has been set to reach 5 million and the field of metagenomics is rapidly evolving, the guidance will be regularly reviewed and will likely adapt over time as experience develops.
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Affiliation(s)
- Gkikas Magiorkinis
- Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - Philippa C Matthews
- University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | | | - Katie Jeffery
- University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | | | | | | | - Effy Vayena
- Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | | | - Daniel S Brewer
- University of East Anglia, Norwich, UK.,Earlham Institute, Norwich, UK
| | | | | | | | | | | | | | - Anneke Lucassen
- Faculty of Medicine, University of Southampton, Southampton, UK
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Connell SP, Yazbek‐Hanna M, McCarthy F, Hurst R, Webb M, Curley H, Walker H, Mills R, Ball RY, Sanda MG, Pellegrini KL, Patil D, Perry AS, Schalken J, Pandha H, Whitaker H, Dennis N, Stuttle C, Mills IG, Guldvik I, Parker C, Brewer DS, Cooper CS, Clark J. A four-group urine risk classifier for predicting outcomes in patients with prostate cancer. BJU Int 2019; 124:609-620. [PMID: 31106513 PMCID: PMC6851983 DOI: 10.1111/bju.14811] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVES To develop a risk classifier using urine-derived extracellular vesicle (EV)-RNA capable of providing diagnostic information on disease status prior to biopsy, and prognostic information for men on active surveillance (AS). PATIENTS AND METHODS Post-digital rectal examination urine-derived EV-RNA expression profiles (n = 535, multiple centres) were interrogated with a curated NanoString panel. A LASSO-based continuation ratio model was built to generate four prostate urine risk (PUR) signatures for predicting the probability of normal tissue (PUR-1), D'Amico low-risk (PUR-2), intermediate-risk (PUR-3), and high-risk (PUR-4) prostate cancer. This model was applied to a test cohort (n = 177) for diagnostic evaluation, and to an AS sub-cohort (n = 87) for prognostic evaluation. RESULTS Each PUR signature was significantly associated with its corresponding clinical category (P < 0.001). PUR-4 status predicted the presence of clinically significant intermediate- or high-risk disease (area under the curve = 0.77, 95% confidence interval [CI] 0.70-0.84). Application of PUR provided a net benefit over current clinical practice. In an AS sub-cohort (n = 87), groups defined by PUR status and proportion of PUR-4 had a significant association with time to progression (interquartile range hazard ratio [HR] 2.86, 95% CI 1.83-4.47; P < 0.001). PUR-4, when used continuously, dichotomized patient groups with differential progression rates of 10% and 60% 5 years after urine collection (HR 8.23, 95% CI 3.26-20.81; P < 0.001). CONCLUSION Urine-derived EV-RNA can provide diagnostic information on aggressive prostate cancer prior to biopsy, and prognostic information for men on AS. PUR represents a new and versatile biomarker that could result in substantial alterations to current treatment of patients with prostate cancer.
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Affiliation(s)
| | | | | | - Rachel Hurst
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Martyn Webb
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Helen Curley
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Helen Walker
- Norfolk and Norwich University Hospitals NHS Foundation TrustNorwichUK
| | - Rob Mills
- Norfolk and Norwich University Hospitals NHS Foundation TrustNorwichUK
| | - Richard Y. Ball
- Norfolk and Norwich University Hospitals NHS Foundation TrustNorwichUK
| | - Martin G. Sanda
- Department of UrologyWinship Cancer InstituteEmory University School of MedicineAtlantaGAUSA
| | - Kathryn L. Pellegrini
- Department of UrologyWinship Cancer InstituteEmory University School of MedicineAtlantaGAUSA
| | - Dattatraya Patil
- Department of UrologyWinship Cancer InstituteEmory University School of MedicineAtlantaGAUSA
| | - Antoinette S. Perry
- School of Biology and Environmental ScienceScience WestUniversity College DublinDublin 4Ireland
| | - Jack Schalken
- Nijmegen Medical CentreRadboud University Medical CentreNijmegenThe Netherlands
| | - Hardev Pandha
- Faculty of Health and Medical SciencesThe University of SurreyGuildfordUK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics GroupUniversity College LondonLondonUK
| | | | | | - Ian G. Mills
- School of MedicineDentistry and Biomedical SciencesInstitute for Health SciencesCentre for Cancer Research and Cell BiologyQueen's University BelfastBelfastUK,Centre for Molecular MedicineUniversity of OsloOsloNorway,Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Ingrid Guldvik
- Centre for Molecular MedicineUniversity of OsloOsloNorway
| | | | | | - Daniel S. Brewer
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,Earlham InstituteNorwichUK
| | | | - Jeremy Clark
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
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O'Reilly E, Tuzova AV, Walsh AL, Russell NM, O'Brien O, Kelly S, Dhomhnallain ON, DeBarra L, Dale CM, Brugman R, Clarke G, Schmidt O, O'Meachair S, Patil D, Pellegrini KL, Fleshner N, Garcia J, Zhao F, Finn S, Mills R, Hanna MY, Hurst R, McEvoy E, Gallagher WM, Manecksha RP, Cooper CS, Brewer DS, Bapat B, Sanda MG, Clark J, Perry AS. epiCaPture: A Urine DNA Methylation Test for Early Detection of Aggressive Prostate Cancer. JCO Precis Oncol 2019; 2019. [PMID: 30801051 PMCID: PMC6383793 DOI: 10.1200/po.18.00134] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose Liquid biopsies that noninvasively detect molecular correlates of aggressive prostate cancer (PCa) could be used to triage patients, reducing the burdens of unnecessary invasive prostate biopsy and enabling early detection of high-risk disease. DNA hypermethylation is among the earliest and most frequent aberrations in PCa. We investigated the accuracy of a six-gene DNA methylation panel (Epigenetic Cancer of the Prostate Test in Urine [epiCaPture]) at detecting PCa, high-grade (Gleason score greater than or equal to 8) and high-risk (D’Amico and Cancer of the Prostate Risk Assessment] PCa from urine. Patients and Methods Prognostic utility of epiCaPture genes was first validated in two independent prostate tissue cohorts. epiCaPture was assessed in a multicenter prospective study of 463 men undergoing prostate biopsy. epiCaPture was performed by quantitative methylation-specific polymerase chain reaction in DNA isolated from prebiopsy urine sediments and evaluated by receiver operating characteristic and decision curves (clinical benefit). The epiCaPture score was developed and validated on a two thirds training set to one third test set. Results Higher methylation of epiCaPture genes was significantly associated with increasing aggressiveness in PCa tissues. In urine, area under the receiver operating characteristic curve was 0.64, 0.86, and 0.83 for detecting PCa, high-grade PCa, and high-risk PCa, respectively. Decision curves revealed a net benefit across relevant threshold probabilities. Independent analysis of two epiCaPture genes in the same clinical cohort provided analytical validation. Parallel epiCaPture analysis in urine and matched biopsy cores showed added value of a liquid biopsy. Conclusion epiCaPture is a urine DNA methylation test for high-risk PCa. Its tumor specificity out-performs that of prostate-specific antigen (greater than 3 ng/mL). Used as an adjunct to prostate-specific antigen, epiCaPture could aid patient stratification to determine need for biopsy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Fang Zhao
- University of Toronto, Toronto, Ontario, Canada
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30
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Luca BA, Brewer DS, Edwards DR, Edward S, Whitaker HC, Merson S, Dennis N, Cooper RA, Hazell S, Warren AY, Eeles R, Lynch AG, Ross-Adams H, Lamb AD, Neal DE, Sethia K, Mills RD, Ball RY, Curley H, Clark J, Moulton V, Cooper CS. DESNT: A Poor Prognosis Category of Human Prostate Cancer. Eur Urol Focus 2018; 4:842-850. [PMID: 28753852 PMCID: PMC5669460 DOI: 10.1016/j.euf.2017.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND A critical problem in the clinical management of prostate cancer is that it is highly heterogeneous. Accurate prediction of individual cancer behaviour is therefore not achievable at the time of diagnosis leading to substantial overtreatment. It remains an enigma that, in contrast to breast cancer, unsupervised analyses of global expression profiles have not currently defined robust categories of prostate cancer with distinct clinical outcomes. OBJECTIVE To devise a novel classification framework for human prostate cancer based on unsupervised mathematical approaches. DESIGN, SETTING, AND PARTICIPANTS Our analyses are based on the hypothesis that previous attempts to classify prostate cancer have been unsuccessful because individual samples of prostate cancer frequently have heterogeneous compositions. To address this issue, we applied an unsupervised Bayesian procedure called Latent Process Decomposition to four independent prostate cancer transcriptome datasets obtained using samples from prostatectomy patients and containing between 78 and 182 participants. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Biochemical failure was assessed using log-rank analysis and Cox regression analysis. RESULTS AND LIMITATIONS Application of Latent Process Decomposition identified a common process in all four independent datasets examined. Cancers assigned to this process (designated DESNT cancers) are characterized by low expression of a core set of 45 genes, many encoding proteins involved in the cytoskeleton machinery, ion transport, and cell adhesion. For the three datasets with linked prostate-specific antigen failure data following prostatectomy, patients with DESNT cancer exhibited poor outcome relative to other patients (p=2.65×10-5, p=4.28×10-5, and p=2.98×10-8). When these three datasets were combined the independent predictive value of DESNT membership was p=1.61×10-7 compared with p=1.00×10-5 for Gleason sum. A limitation of the study is that only prediction of prostate-specific antigen failure was examined. CONCLUSIONS Our results demonstrate the existence of a novel poor prognosis category of human prostate cancer and will assist in the targeting of therapy, helping avoid treatment-associated morbidity in men with indolent disease. PATIENT SUMMARY Prostate cancer, unlike breast cancer, does not have a robust classification framework. We propose that this failure has occurred because prostate cancer samples selected for analysis frequently have heterozygous compositions (individual samples are made up of many different parts that each have different characteristics). Applying a mathematical approach that can overcome this problem we identify a novel poor prognosis category of human prostate cancer called DESNT.
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Affiliation(s)
- Bogdan-Alexandru Luca
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
- The Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - Dylan R Edwards
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sandra Edward
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Hayley C Whitaker
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Nening Dennis
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
| | - Rosalin A Cooper
- Department of Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - The CancerMap Group
- A list of participants and their affiliations appears in the Supplemental Information
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, Sutton, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Andy G Lynch
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Helen Ross-Adams
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Alastair D Lamb
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - David E Neal
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Krishna Sethia
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Robert D Mills
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Richard Y Ball
- Department of Histopathology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
| | - Helen Curley
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
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31
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - 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
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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32
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Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet 2017; 13:e1007001. [PMID: 28945760 PMCID: PMC5628936 DOI: 10.1371/journal.pgen.1007001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/05/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.
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Affiliation(s)
- Niedzica Camacho
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Sandra Edwards
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Jonathan D. Kay
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Lucy Matthews
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Nening Dennis
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sarah Thomas
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Barbara Kremeyer
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jorge Zamora
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Gunes Gundem
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Hayley Luxton
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Mohammed Ghori
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Luke Marsden
- Department of Physiology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Adam Lambert
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
| | - Katalin Karaszi
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Gill Pelvender
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Charlie E. Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- CRUK Cambridge Centre, Early Detection Programme, Urological Malignancies Programme, Hutchison-MRC Research Centre, Cambridge, Cambridgeshire, United Kingdom
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - William J. Howat
- Histopathology and in situ hybridization Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Steven Hazell
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Naomi Livni
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Cyril Fisher
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher Ogden
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Pardeep Kumar
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alan Thompson
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Nicol
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erik Mayer
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Tim Dudderidge
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Yongwei Yu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Nimish C. Shah
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - Vincent J. Gnanapragasam
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | | | - William Isaacs
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tapio Visakorpi
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Freddie Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Dan Berney
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology and Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, Oxfordshire, United Kingdom
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - David C. Wedge
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Oxford Big Data Institute & Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, United Kingdom
| | - Andrew G. Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, Fife, Scotland
| | | | - Yong Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - G. Steven Bova
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Hayley C. Whitaker
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David E. Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Colin S. Cooper
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
- Organisms and Ecosystems, The Earlham Institute, Norwich, Norfolk, United Kingdom
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33
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JM, Papaemmanuil E, Brewer DS, Kallio H, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. Abstract 956: The evolutionary history of lethal metastatic prostate cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancers emerge from an on-going Darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. This evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. However, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. Although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and inter-clonal cooperation between multiple subclones. In this study, we sought definitive evidence for the existence of polyclonal seeding in human malignancy and to establish the clonal relationship among different metastases in the context of androgen-deprived metastatic prostate cancer. Using whole genome sequencing, we characterised multiple metastases arising from prostate tumours in ten patients. Integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. Metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. Lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. Our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen deprivation therapy in prostate cancer.
Citation Format: Gunes Gundem, Peter Van Loo, Barbara Kremeyer, Ludmil B. Alexandrov, Jose M.C. Tubio, Elli Papaemmanuil, Daniel S. Brewer, Heini Kallio, Gunilla Högnäs, Matti Annala, Kati Kivinummi, Victoria Goody, Calli Latimer, Sarah O'Meara, Kevin J. Dawson, William Isaacs, Michael R. Emmert-Buck, Matti Nykter, Christopher Foster, Zsofia Kote-Jarai, Douglas Easton, Hayley C. Whitaker, David E. Neal, Colin S. Cooper, Rosalind A. Eeles, Tapio Visakorpi, Peter J. Campbell, Ultan McDermott, David C. Wedge, G. S. Bova. The evolutionary history of lethal metastatic prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 956. doi:10.1158/1538-7445.AM2015-956
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Affiliation(s)
- Gunes Gundem
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Peter Van Loo
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | - Daniel S. Brewer
- 2Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Heini Kallio
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | - Gunilla Högnäs
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | - Matti Annala
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | - Kati Kivinummi
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | - Victoria Goody
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Calli Latimer
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Sarah O'Meara
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | | | - Michael R. Emmert-Buck
- 5Laboratory of Pathology, National Cancer Institute, National Institutes of Health; Avoneaux Medical Institute, Oxford, MD
| | - Matti Nykter
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | - Christopher Foster
- 6University of Liverpool and HCA Pathology Laboratories, London, United Kingdom
| | - Zsofia Kote-Jarai
- 7Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Douglas Easton
- 8Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Hayley C. Whitaker
- 9Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
| | - David E. Neal
- 9Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, United Kingdom
| | - Colin S. Cooper
- 10Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK; and Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Rosalind A. Eeles
- 11Division of Genetics and Epidemiology, The Institute Of Cancer Research; Royal Marsden NHS Foundation Trust, London and Sutton, UK, London, United Kingdom
| | - Tapio Visakorpi
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
| | | | | | - David C. Wedge
- 1Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - G. S. Bova
- 3Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere, Tampere, Finland
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Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai Z, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, Ramakrishna M, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE. Corrigendum: analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet 2015; 47:689. [PMID: 26018901 DOI: 10.1038/ng0615-689b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JM, Papaemmanuil E, Brewer DS, Kallio HM, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. The evolutionary history of lethal metastatic prostate cancer. Nature 2015; 520:353-357. [PMID: 25830880 PMCID: PMC4413032 DOI: 10.1038/nature14347] [Citation(s) in RCA: 954] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/23/2015] [Indexed: 02/07/2023]
Abstract
Cancers emerge from an ongoing Darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. This evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. However, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. Although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and interclonal cooperation between multiple subclones. Here we sought definitive evidence for the existence of polyclonal seeding in human malignancy and to establish the clonal relationship among different metastases in the context of androgen-deprived metastatic prostate cancer. Using whole-genome sequencing, we characterized multiple metastases arising from prostate tumours in ten patients. Integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. Metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. Lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. Our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen-deprivation therapy in prostate cancer.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000 Leuven, Belgium
- Cancer Research UK London Research Institute, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Jose M.C. Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Daniel S. Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, UK
| | - Heini M.L. Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Gunilla Högnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sarah O’Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kevin J. Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, MD, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Christopher Foster
- University of Liverpool and HCA Pathology Laboratories, London, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Hayley C. Whitaker
- Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | | | - David E. Neal
- Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Colin S. Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, UK
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Rosalind A. Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - G. Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
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Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS, Cooper CS, Eeles R, Warren AY, Tavaré S, Neal DE, Lynch AG. HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocr Relat Cancer 2015; 22:131-44. [PMID: 25560400 PMCID: PMC4335379 DOI: 10.1530/erc-14-0454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Revised: 12/18/2014] [Accepted: 01/05/2015] [Indexed: 02/06/2023]
Abstract
Prostate cancer is the most common cancer in men, resulting in over 10 000 deaths/year in the UK. Sequencing and copy number analysis of primary tumours has revealed heterogeneity within tumours and an absence of recurrent founder mutations, consistent with non-genetic disease initiating events. Using methylation profiling in a series of multi-focal prostate tumours, we identify promoter methylation of the transcription factor HES5 as an early event in prostate tumourigenesis. We confirm that this epigenetic alteration occurs in 86-97% of cases in two independent prostate cancer cohorts (n=49 and n=39 tumour-normal pairs). Treatment of prostate cancer cells with the demethylating agent 5-aza-2'-deoxycytidine increased HES5 expression and downregulated its transcriptional target HES6, consistent with functional silencing of the HES5 gene in prostate cancer. Finally, we identify and test a transcriptional module involving the AR, ERG, HES1 and HES6 and propose a model for the impact of HES5 silencing on tumourigenesis as a starting point for future functional studies.
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Affiliation(s)
- Charles E Massie
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Inmaculada Spiteri
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Helen Ross-Adams
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hayley Luxton
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Jonathan Kay
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hayley C Whitaker
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Mark J Dunning
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Alastair D Lamb
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Antonio Ramos-Montoya
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Daniel S Brewer
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Colin S Cooper
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Rosalind Eeles
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Anne Y Warren
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Simon Tavaré
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - David E Neal
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Andy G Lynch
- Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK
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37
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Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai ZS, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet 2015; 47:367-372. [PMID: 25730763 PMCID: PMC4380509 DOI: 10.1038/ng.3221] [Citation(s) in RCA: 316] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.
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Affiliation(s)
- Colin S Cooper
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Department of Biological Sciences University of East Anglia, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Human Genome Laboratory, Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium
- Cancer Research UK London Research Institute, London, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Niedzica Camacho
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - Charlie E Massie
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Jonathan Kay
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Hayley J Luxton
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Sandra Edwards
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | | | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Sarah O'Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Matthews
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rachel Hurst
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Richard Mithen
- Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre-University Health Network, Toronto, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Canada
- Department Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Michael Fraser
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre-University Health Network, Toronto, Canada
| | - Susanna Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Hinton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Laura Mudie
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Claire Hardy
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Olivia Joseph
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ben Robinson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Mark Maddison
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stephen Gamble
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Dan Berney
- Department of Molecular Oncology, Barts Cancer Centre, Barts and the London School of Medicine and Dentistry, London, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Nimish C Shah
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Vincent Gnanapragasam
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | - Hayley C Whitaker
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel S Brewer
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- The Genome Analysis Centre, Norwich, UK
| | - David E Neal
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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Zuo J, Brewer DS, Arlt VM, Cooper CS, Phillips DH. Benzo pyrene-induced DNA adducts and gene expression profiles in target and non-target organs for carcinogenesis in mice. BMC Genomics 2014; 15:880. [PMID: 25297811 PMCID: PMC4209037 DOI: 10.1186/1471-2164-15-880] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/23/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Gene expression changes induced by carcinogens may identify differences in molecular function between target and non-target organs. Target organs for benzo[a]pyrene (BaP) carcinogenicity in mice (lung, spleen and forestomach) and three non-target organs (liver, colon and glandular stomach) were investigated for DNA adducts by 32P-postlabelling, for gene expression changes by cDNA microarray and for miRNA expression changes by miRNA microarray after exposure of animals to BaP. RESULTS BaP-DNA adduct formation occurred in all six organs at levels that did not distinguish between target and non-target. cDNA microarray analysis showed a variety of genes modulated significantly by BaP in the six organs and the overall gene expression patterns were tissue specific. Gene ontology analysis also revealed that BaP-induced bioactivities were tissue specific; eight genes (Tubb5, Fos, Cdh1, Cyp1a1, Apc, Myc, Ctnnb1 and Cav) showed significant expression difference between three target and three non-target organs. Additionally, several gene expression changes, such as in Trp53 activation and Stat3 activity suggested some similarities in molecular mechanisms in two target organs (lung and spleen), which were not found in the other four organs. Changes in miRNA expression were generally tissue specific, involving, in total, 21/54 miRNAs significantly up- or down-regulated. CONCLUSIONS Altogether, these findings showed that DNA adduct levels and early gene expression changes did not fully distinguish target from non-target organs. However, mechanisms related to early changes in p53, Stat3 and Wnt/β-catenin pathways may play roles in defining BaP organotropism.
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Affiliation(s)
- Jie Zuo
- />Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, OX3 9DS UK
| | - Daniel S Brewer
- />School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Volker M Arlt
- />Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment & Health, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Colin S Cooper
- />The Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - David H Phillips
- />Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment & Health, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
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Bailey DM, Erith SJ, Griffin PJ, Dowson A, Brewer DS, Gant N, Williams C. Influence of cold-water immersion on indices of muscle damage following prolonged intermittent shuttle running. J Sports Sci 2007; 25:1163-70. [PMID: 17654228 DOI: 10.1080/02640410600982659] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The aim of this study was to assess the effects of cold-water immersion (cryotherapy) on indices of muscle damage following a bout of prolonged intermittent exercise. Twenty males (mean age 22.3 years, s = 3.3; height 1.80 m, s = 0.05; body mass 83.7 kg, s = 11.9) completed a 90-min intermittent shuttle run previously shown to result in marked muscle damage and soreness. After exercise, participants were randomly assigned to either 10 min cold-water immersion (mean 10 degrees C, s = 0.5) or a non-immersion control group. Ratings of perceived soreness, changes in muscular function and efflux of intracellular proteins were monitored before exercise, during treatment, and at regular intervals up to 7 days post-exercise. Exercise resulted in severe muscle soreness, temporary muscular dysfunction, and elevated serum markers of muscle damage, all peaking within 48 h after exercise. Cryotherapy administered immediately after exercise reduced muscle soreness at 1, 24, and 48 h (P < 0.05). Decrements in isometric maximal voluntary contraction of the knee flexors were reduced after cryotherapy treatment at 24 (mean 12%, s(x) = 4) and 48 h (mean 3%, s(x) = 3) compared with the control group (mean 21%, s(x) = 5 and mean 14%, s(x) = 5 respectively; P < 0.05). Exercise-induced increases in serum myoglobin concentration and creatine kinase activity peaked at 1 and 24 h, respectively (P < 0.05). Cryotherapy had no effect on the creatine kinase response, but reduced myoglobin 1 h after exercise (P < 0.05). The results suggest that cold-water immersion immediately after prolonged intermittent shuttle running reduces some indices of exercise-induced muscle damage.
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Affiliation(s)
- D M Bailey
- Human Muscle Metabolism Research Group, English Institute of Sport, Loughborough University, Loughborough, UK.
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