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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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Sushentsev N, Hamm G, Richings J, McLean MA, Menih IH, Ayyappan V, Mills IG, Warren AY, Gnanapragasam VJ, Barry ST, Goodwin RJA, Gallagher FA, Barrett T. Imaging tumor lactate is feasible for identifying intermediate-risk prostate cancer patients with postsurgical biochemical recurrence. Proc Natl Acad Sci U S A 2023; 120:e2312261120. [PMID: 38011568 PMCID: PMC10710070 DOI: 10.1073/pnas.2312261120] [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: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 11/29/2023] Open
Abstract
While radical prostatectomy remains the mainstay of prostate cancer (PCa) treatment, 20 to 40% of patients develop postsurgical biochemical recurrence (BCR). A particularly challenging clinical cohort includes patients with intermediate-risk disease whose risk stratification would benefit from advanced approaches that complement standard-of-care diagnostic tools. Here, we show that imaging tumor lactate using hyperpolarized 13C MRI and spatial metabolomics identifies BCR-positive patients in two prospective intermediate-risk surgical cohorts. Supported by spatially resolved tissue analysis of established glycolytic biomarkers, this study provides the rationale for multicenter trials of tumor metabolic imaging as an auxiliary tool to support PCa treatment decision-making.
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Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
| | - Gregory Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research & Development, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Jack Richings
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research & Development, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Mary A. McLean
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
| | - Ines Horvat Menih
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
| | - Vinay Ayyappan
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
| | - Ian G. Mills
- Patrick G. Johnston Centre for Cancer Research, Genito-Urinary and Prostate Focus Group, Queen’s University Belfast, BelfastBT9 7AE, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, OxfordOX3 7DQ, United Kingdom
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen5021, Norway
| | - Anne Y. Warren
- Department of Pathology, Cambridge University Hospitals National Health Service Foundation Trust, CB2 0QQCambridge, United Kingdom
| | - Vincent J. Gnanapragasam
- Department of Urology, Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
- Cambridge Urology Translational Research and Clinical Trials Office, Cambridge Biomedical Campus, Addenbrooke’s Hospital, CambridgeCB2 0QQ, United Kingdom
| | - Simon T. Barry
- Bioscience, Discovery, Oncology Research & Development, AstraZeneca, CambridgeCB20AA, United Kingdom
| | - Richard J. A. Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research & Development, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Ferdia A. Gallagher
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
| | - Tristan Barrett
- Department of Radiology, Addenbrooke’s Hospital and University of Cambridge, Cambridge Biomedical Campus, CB2 0QQCambridge, United Kingdom
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Wesolowski L, Ge J, Castillon L, Sesia D, Dyas A, Hirosue S, Caraffini V, Warren AY, Rodrigues P, Ciriello G, Patel SA, Vanharanta S. The SWI/SNF complex member SMARCB1 supports lineage fidelity in kidney cancer. iScience 2023; 26:107360. [PMID: 37554444 PMCID: PMC10405256 DOI: 10.1016/j.isci.2023.107360] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/22/2023] [Accepted: 07/07/2023] [Indexed: 08/10/2023] Open
Abstract
Lineage switching can induce therapy resistance in cancer. Yet, how lineage fidelity is maintained and how it can be lost remain poorly understood. Here, we have used CRISPR-Cas9-based genetic screening to demonstrate that loss of SMARCB1, a member of the SWI/SNF chromatin remodeling complex, can confer an advantage to clear cell renal cell carcinoma (ccRCC) cells upon inhibition of the renal lineage factor PAX8. Lineage factor inhibition-resistant ccRCC cells formed tumors with morphological features, but not molecular markers, of neuroendocrine differentiation. SMARCB1 inactivation led to large-scale loss of kidney-specific epigenetic programs and restoration of proliferative capacity through the adoption of new dependencies on factors that represent rare essential genes across different cancers. We further developed an analytical approach to systematically characterize lineage fidelity using large-scale CRISPR-Cas9 data. An understanding of the rules that govern lineage switching could aid the development of more durable lineage factor-targeted and other cancer therapies.
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Affiliation(s)
- Ludovic Wesolowski
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
| | - Jianfeng Ge
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Leticia Castillon
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
| | - Debora Sesia
- Department of Computational Biology, University of Lausanne (UNIL), 1015 Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Anna Dyas
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Shoko Hirosue
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
| | - Veronica Caraffini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), 1015 Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Saroor A. Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Box 197, Cambridge CB2 0XZ, UK
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
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4
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Vasudev NS, Scelo G, Glennon KI, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Cartledge J, Soomro N, Adeyoju A, Patel PM, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE. Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma. Clin Cancer Res 2023; 29:1220-1231. [PMID: 36815791 PMCID: PMC10068441 DOI: 10.1158/1078-0432.ccr-22-1936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/12/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023]
Abstract
PURPOSE Patients with resected localized clear-cell renal cell carcinoma (ccRCC) remain at variable risk of recurrence. Incorporation of biomarkers may refine risk prediction and inform adjuvant treatment decisions. We explored the role of tumor genomics in this setting, leveraging the largest cohort to date of localized ccRCC tissues subjected to targeted gene sequencing. EXPERIMENTAL DESIGN The somatic mutation status of 12 genes was determined in 943 ccRCC cases from a multinational cohort of patients, and associations to outcomes were examined in a Discovery (n = 469) and Validation (n = 474) framework. RESULTS Tumors containing a von-Hippel Lindau (VHL) mutation alone were associated with significantly improved outcomes in comparison with tumors containing a VHL plus additional mutations. Within the Discovery cohort, those with VHL+0, VHL+1, VHL+2, and VHL+≥3 tumors had disease-free survival (DFS) rates of 90.8%, 80.1%, 68.2%, and 50.7% respectively, at 5 years. This trend was replicated in the Validation cohort. Notably, these genomically defined groups were independent of tumor mutational burden. Amongst patients eligible for adjuvant therapy, those with a VHL+0 tumor (29%) had a 5-year DFS rate of 79.3% and could, therefore, potentially be spared further treatment. Conversely, patients with VHL+2 and VHL+≥3 tumors (32%) had equivalent DFS rates of 45.6% and 35.3%, respectively, and should be prioritized for adjuvant therapy. CONCLUSIONS Genomic characterization of ccRCC identified biologically distinct groups of patients with divergent relapse rates. These groups account for the ∼80% of cases with VHL mutations and could be used to personalize adjuvant treatment discussions with patients as well as inform future adjuvant trial design.
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Affiliation(s)
- Naveen S. Vasudev
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Ghislaine Scelo
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Kate I. Glennon
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Michelle Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Louis Letourneau
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Robert Eveleigh
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Nazanin Nourbehesht
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Madeleine Arseneault
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Antoine Paccard
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Edgars Celms
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sharon M. Jackson
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Behnoush Abedi-Ardekani
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, United Kingdom
| | - Peter J. Selby
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Sebastian Trainor
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Michael Kimuli
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Jon Cartledge
- Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, Lincoln Wing, St James's University Hospital, Leeds, United Kingdom
| | - Naeem Soomro
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Poulam M. Patel
- Division of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Magdalena B. Wozniak
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Ivana Holcatova
- Charles University in Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | | | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Estelle Chanudet
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - David Zaridze
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Anush Moukeria
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Oxana Shangina
- N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucuresti, Romania
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Prof. Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Ljiljana Bogdanovic
- Institute of Pathology, School of Medicine Belgrade, University of Belgrade, Belgrade, Serbia
| | - Bozidar Kovacevic
- Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade, Serbia
| | - Anne Cambon-Thomsen
- Institut National de la Santé et de la Recherche Médicale (INSERM) and Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | - Guillaume Bourque
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Alvis Brazma
- European Bioinformatics Institute, European Molecular Biology Laboratory, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jörg Tost
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie Francois Jacob, University Paris Saclay, Evry, France
| | - Paul Brennan
- World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Mark Lathrop
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Yasser Riazalhosseini
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Rosamonde E. Banks
- Leeds Institute of Medical Research at St James's, University of Leeds, St James's University Hospital, Leeds, United Kingdom
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Sushentsev N, Rundo L, Abrego L, Li Z, Nazarenko T, Warren AY, Gnanapragasam VJ, Sala E, Zaikin A, Barrett T, Blyuss O. Time series radiomics for the prediction of prostate cancer progression in patients on active surveillance. Eur Radiol 2023; 33:3792-3800. [PMID: 36749370 PMCID: PMC10182165 DOI: 10.1007/s00330-023-09438-x] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Serial MRI is an essential assessment tool in prostate cancer (PCa) patients enrolled on active surveillance (AS). However, it has only moderate sensitivity for predicting histopathological tumour progression at follow-up, which is in part due to the subjective nature of its clinical reporting and variation among centres and readers. In this study, we used a long short-term memory (LSTM) recurrent neural network (RNN) to develop a time series radiomics (TSR) predictive model that analysed longitudinal changes in tumour-derived radiomic features across 297 scans from 76 AS patients, 28 with histopathological PCa progression and 48 with stable disease. Using leave-one-out cross-validation (LOOCV), we found that an LSTM-based model combining TSR and serial PSA density (AUC 0.86 [95% CI: 0.78-0.94]) significantly outperformed a model combining conventional delta-radiomics and delta-PSA density (0.75 [0.64-0.87]; p = 0.048) and achieved comparable performance to expert-performed serial MRI analysis using the Prostate Cancer Radiologic Estimation of Change in Sequential Evaluation (PRECISE) scoring system (0.84 [0.76-0.93]; p = 0.710). The proposed TSR framework, therefore, offers a feasible quantitative tool for standardising serial MRI assessment in PCa AS. It also presents a novel methodological approach to serial image analysis that can be used to support clinical decision-making in multiple scenarios, from continuous disease monitoring to treatment response evaluation. KEY POINTS: •LSTM RNN can be used to predict the outcome of PCa AS using time series changes in tumour-derived radiomic features and PSA density. •Using all available TSR features and serial PSA density yields a significantly better predictive performance compared to using just two time points within the delta-radiomics framework. •The concept of TSR can be applied to other clinical scenarios involving serial imaging, setting out a new field in AI-driven radiology research.
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Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK.
| | - Leonardo Rundo
- Department of Radiology, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
- Department of Information and Electrical Engineering and Applied Mathematics (DIEM), University of Salerno, Fisciano, SA, Italy
| | - Luis Abrego
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Zonglun Li
- Department of Mathematics, University College London, London, UK
| | - Tatiana Nazarenko
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
- Department of Mathematics, University College London, London, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent J Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials Office, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Evis Sala
- Department of Radiology, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alexey Zaikin
- Department of Women's Cancer, Institute for Women's Health, University College London, London, UK
- Department of Mathematics, University College London, London, UK
| | - Tristan Barrett
- Department of Radiology, School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge Biomedical Campus, Box 218, Cambridge, CB2 0QQ, UK
| | - Oleg Blyuss
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
- Center of Photonics, Lobachevsky University, Nizhny Novgorod, Russian Federation
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6
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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 K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, 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, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, 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, Antonello D, von Mering C, 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, 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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. 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, 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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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8
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Sciacovelli M, Dugourd A, Jimenez LV, Yang M, Nikitopoulou E, Costa ASH, Tronci L, Caraffini V, Rodrigues P, Schmidt C, Ryan DG, Young T, Zecchini VR, Rossi SH, Massie C, Lohoff C, Masid M, Hatzimanikatis V, Kuppe C, Von Kriegsheim A, Kramann R, Gnanapragasam V, Warren AY, Stewart GD, Erez A, Vanharanta S, Saez-Rodriguez J, Frezza C. Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression. Nat Commun 2022; 13:7830. [PMID: 36539415 PMCID: PMC9767928 DOI: 10.1038/s41467-022-35036-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/16/2022] [Indexed: 12/24/2022] Open
Abstract
Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related clear cell renal cancer cells (ccRCC) grown in physiological media to identify key stage-specific metabolic vulnerabilities. We show that a VHL loss-dependent reprogramming of branched-chain amino acid catabolism sustains the de novo biosynthesis of aspartate and arginine enabling tumor cells with the flexibility of partitioning the nitrogen of the amino acids depending on their needs. Importantly, we identify the epigenetic reactivation of argininosuccinate synthase (ASS1), a urea cycle enzyme suppressed in primary ccRCC, as a crucial event for metastatic renal cancer cells to acquire the capability to generate arginine, invade in vitro and metastasize in vivo. Overall, our study uncovers a mechanism of metabolic flexibility occurring during ccRCC progression, paving the way for the development of novel stage-specific therapies.
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Affiliation(s)
- Marco Sciacovelli
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- Department of Molecular and Clinical Cancer Medicine; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GE, UK
| | - Aurelien Dugourd
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Lorea Valcarcel Jimenez
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine-University Hospital Cologne, 50931, Cologne, Germany
| | - Ming Yang
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine-University Hospital Cologne, 50931, Cologne, Germany
| | - Efterpi Nikitopoulou
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Ana S H Costa
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- Matterworks, Somerville, MA, 02143, USA
| | - Laura Tronci
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Veronica Caraffini
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Paulo Rodrigues
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Christina Schmidt
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- CECAD Research Center, Faculty of Medicine-University Hospital Cologne, 50931, Cologne, Germany
| | - Dylan Gerard Ryan
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Timothy Young
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Vincent R Zecchini
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Sabrina H Rossi
- Early Detection Programme, CRUK Cambridge Centre, Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Charlie Massie
- Early Detection Programme, CRUK Cambridge Centre, Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Caroline Lohoff
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Maria Masid
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Department of Oncology, Lausanne University Hospital (CHUV), University of Lausanne, CH-1011, Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Alex Von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, Edinburgh, EH4 2XR, UK
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Vincent Gnanapragasam
- Department of Surgery, University of Cambridge and Cambridge University Hospitals NHS Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y Warren
- Department of Histopathology-Cambridge University Hospitals NHS, Box 235 Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Department of Surgery, University of Cambridge and Cambridge University Hospitals NHS Cambridge Biomedical Campus, Cambridge, UK
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sakari Vanharanta
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK
- Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg University, Heidelberg, Germany.
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197 Biomedical Campus, Cambridge, CB2 0XZ, UK.
- CECAD Research Center, Faculty of Medicine-University Hospital Cologne, 50931, Cologne, Germany.
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9
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Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, Mamanova L, Neves JB, Bolt L, Fasouli ES, Lawson ARJ, Young MD, Hooks Y, Oliver TRW, Butler TM, Armitage JN, Aho T, Riddick ACP, Gnanapragasam V, Welsh SJ, Meyer KB, Warren AY, Tran MGB, Stewart GD, Cortés-Ciriano I, Behjati S, Clatworthy MR, Campbell PJ, Teichmann SA, Mitchell TJ. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 2022; 40:1583-1599.e10. [PMID: 36423636 PMCID: PMC9767677 DOI: 10.1016/j.ccell.2022.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/12/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
Tumor behavior is intricately dependent on the oncogenic properties of cancer cells and their multi-cellular interactions. To understand these dependencies within the wider microenvironment, we studied over 270,000 single-cell transcriptomes and 100 microdissected whole exomes from 12 patients with kidney tumors, prior to validation using spatial transcriptomics. Tissues were sampled from multiple regions of the tumor core, the tumor-normal interface, normal surrounding tissues, and peripheral blood. We find that the tissue-type location of CD8+ T cell clonotypes largely defines their exhaustion state with intra-tumoral spatial heterogeneity that is not well explained by somatic heterogeneity. De novo mutation calling from single-cell RNA-sequencing data allows us to broadly infer the clonality of stromal cells and lineage-trace myeloid cell development. We report six conserved meta-programs that distinguish tumor cell function, and find an epithelial-mesenchymal transition meta-program highly enriched at the tumor-normal interface that co-localizes with IL1B-expressing macrophages, offering a potential therapeutic target.
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Affiliation(s)
- Ruoyan Li
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Georgina S Bowyer
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sean Laidlaw
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Joana B Neves
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK; Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Liam Bolt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eirini S Fasouli
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew R J Lawson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew D Young
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvette Hooks
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Thomas R W Oliver
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Timothy M Butler
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Tev Aho
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Antony C P Riddick
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Vincent Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah J Welsh
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Kerstin B Meyer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK; Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Menna R Clatworthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Thomas J Mitchell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
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10
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Sushentsev N, McLean MA, Warren AY, Brodie C, Jones J, Gallagher FA, Barrett T. The potential of hyperpolarised 13C-MRI to target glycolytic tumour core in prostate cancer. Eur Radiol 2022; 32:7155-7162. [PMID: 35731287 PMCID: PMC9474577 DOI: 10.1007/s00330-022-08929-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022]
Abstract
Hyperpolarised [1-13C]pyruvate MRI (HP-13C-MRI) is an emerging metabolic imaging technique that has shown promise for evaluating prostate cancer (PCa) aggressiveness. Accurate tumour delineation on HP-13C-MRI is vital for quantitative assessment of the underlying tissue metabolism. However, there is no consensus on the optimum method for segmenting HP-13C-MRI, and whole-mount pathology (WMP) as the histopathological gold-standard is only available for surgical patients. Although proton MRI can be used for tumour delineation, this approach significantly underestimates tumour volume, and metabolic tumour segmentation based on HP-13C-MRI could provide an important functional metric of tumour volume. In this study, we quantified metabolism using HP-13C-MRI and segmentation approaches based on WMP maps, 1H-MRI-derived T2-weighted imaging (T2WI), and HP-13C-MRI-derived total carbon signal-to-noise ratio maps (TC-SNR) with an SNR threshold of 5.0. 13C-labelled pyruvate SNR, lactate SNR, TC-SNR, and the pyruvate-to-lactate exchange rate constant (kPL) were significantly higher when measured using the TC-SNR-guided approach, which also corresponded to a significantly higher tumour epithelial expression on RNAscope imaging of the enzyme catalysing pyruvate-to-lactate metabolism (lactate dehydrogenase (LDH)). However, linear regression and Bland-Altman analyses demonstrated a strong linear relationship between all three segmentation approaches, which correlated significantly with RNA-scope-derived epithelial LDH expression. These results suggest that standard-of-care T2WI and TC-SNR maps could be used as clinical reference tools for segmenting localised PCa on HP-13C-MRI in the absence of the WMP gold standard. The TC-SNR-guided approach could be used clinically to target biopsies towards highly glycolytic tumour areas and therefore to sample aggressive disease with higher precision. KEY POINTS: • T2WI- and TC-SNR-guided segmentations can be used in all PCa patients and do not explicitly require WMP maps. • Agreement between the three segmentation approaches is biologically validated by their strong relationship with epithelial LDH mRNA expression. • The TC-SNR-guided approach can potentially be used to identify occult disease on 1H-MRI and target the most glycolytically active regions.
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Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge School of Clinical Medicine, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
| | - Mary A McLean
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge School of Clinical Medicine, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Cara Brodie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Julia Jones
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ferdia A Gallagher
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge School of Clinical Medicine, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge School of Clinical Medicine, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
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11
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Stewart GD, Welsh SJ, Ursprung S, Gallagher FA, Jones JO, Shields J, Smith CG, Mitchell TJ, Warren AY, Bex A, Boleti E, Carruthers J, Eisen T, Fife K, Hamid A, Laird A, Leung S, Malik J, Mendichovszky IA, Mumtaz F, Oades G, Priest AN, Riddick ACP, Venugopal B, Welsh M, Riddle K, Hopcroft LEM, Jones RJ. A Phase II study of neoadjuvant axitinib for reducing the extent of venous tumour thrombus in clear cell renal cell cancer with venous invasion (NAXIVA). Br J Cancer 2022; 127:1051-1060. [PMID: 35739300 PMCID: PMC9470559 DOI: 10.1038/s41416-022-01883-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Surgery for renal cell carcinoma (RCC) with venous tumour thrombus (VTT) extension into the renal vein (RV) and/or inferior vena cava (IVC) has high peri-surgical morbidity/mortality. NAXIVA assessed the response of VTT to axitinib, a potent tyrosine kinase inhibitor. METHODS NAXIVA was a single-arm, multi-centre, Phase 2 study. In total, 20 patients with resectable clear cell RCC and VTT received upto 8 weeks of pre-surgical axitinib. The primary endpoint was percentage of evaluable patients with VTT improvement by Mayo level on MRI. Secondary endpoints were percentage change in surgical approach and VTT length, response rate (RECISTv1.1) and surgical morbidity. RESULTS In all, 35% (7/20) patients with VTT had a reduction in Mayo level with axitinib: 37.5% (6/16) with IVC VTT and 25% (1/4) with RV-only VTT. No patients had an increase in Mayo level. In total, 75% (15/20) of patients had a reduction in VTT length. Overall, 41.2% (7/17) of patients who underwent surgery had less invasive surgery than originally planned. Non-responders exhibited lower baseline microvessel density (CD31), higher Ki67 and exhausted or regulatory T-cell phenotype. CONCLUSIONS NAXIVA provides the first Level II evidence that axitinib downstages VTT in a significant proportion of patients leading to reduction in the extent of surgery. CLINICAL TRIAL REGISTRATION NCT03494816.
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Affiliation(s)
- Grant D Stewart
- University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Sarah J Welsh
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ferdia A Gallagher
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - James O Jones
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | - Jacqui Shields
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | | | - Thomas J Mitchell
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Anne Y Warren
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Axel Bex
- Royal Free London NHS Foundation Trust, London, UK
| | | | - Jade Carruthers
- Scottish Clinical Trials Research Unit, Public Health Scotland, Edinburgh, UK
| | - Tim Eisen
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kate Fife
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Alexander Laird
- Western General Hospital, Edinburgh, UK
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | | | - Iosif A Mendichovszky
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Faiz Mumtaz
- Royal Free London NHS Foundation Trust, London, UK
| | | | - Andrew N Priest
- University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Balaji Venugopal
- NHS Greater Glasgow and Clyde, Glasgow, UK
- University of Glasgow, Glasgow, UK
| | - Michelle Welsh
- Scottish Clinical Trials Research Unit, Public Health Scotland, Edinburgh, UK
| | - Kathleen Riddle
- Scottish Clinical Trials Research Unit, Public Health Scotland, Edinburgh, UK
| | - Lisa E M Hopcroft
- Scottish Clinical Trials Research Unit, Public Health Scotland, Edinburgh, UK
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Robert J Jones
- NHS Greater Glasgow and Clyde, Glasgow, UK
- University of Glasgow, Glasgow, UK
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12
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Rossi SH, Newsham I, Pita S, Brennan K, Park G, Smith CG, Lach RP, Mitchell T, Huang J, Babbage A, Warren AY, Leppert JT, Stewart GD, Gevaert O, Massie CE, Samarajiwa SA. Accurate detection of benign and malignant renal tumor subtypes with MethylBoostER: An epigenetic marker-driven learning framework. Sci Adv 2022; 8:eabn9828. [PMID: 36170366 PMCID: PMC9519038 DOI: 10.1126/sciadv.abn9828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Current gold standard diagnostic strategies are unable to accurately differentiate malignant from benign small renal masses preoperatively; consequently, 20% of patients undergo unnecessary surgery. Devising a more confident presurgical diagnosis is key to improving treatment decision-making. We therefore developed MethylBoostER, a machine learning model leveraging DNA methylation data from 1228 tissue samples, to classify pathological subtypes of renal tumors (benign oncocytoma, clear cell, papillary, and chromophobe RCC) and normal kidney. The prediction accuracy in the testing set was 0.960, with class-wise ROC AUCs >0.988 for all classes. External validation was performed on >500 samples from four independent datasets, achieving AUCs >0.89 for all classes and average accuracies of 0.824, 0.703, 0.875, and 0.894 for the four datasets. Furthermore, consistent classification of multiregion samples (N = 185) from the same patient demonstrates that methylation heterogeneity does not limit model applicability. Following further clinical studies, MethylBoostER could facilitate a more confident presurgical diagnosis to guide treatment decision-making in the future.
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Affiliation(s)
- Sabrina H. Rossi
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Sara Pita
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kevin Brennan
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Gahee Park
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher G. Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Cancer Research UK Major Centre, Cambridge, UK
| | - Radoslaw P. Lach
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Mitchell
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Junfan Huang
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Babbage
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y. Warren
- Department of Histopathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - John T. Leppert
- Department of Urology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Urology Surgical Service, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Olivier Gevaert
- Stanford Centre for Biomedical Informatics Research, Department of Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Charles E. Massie
- Department of Oncology, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Early Cancer Institute, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Shamith A. Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison–MRC Research Centre, Cambridge Biomedical Campus, Cambridge, 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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Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T, Neville MDC, Leongamornlert D, Sanders MA, Hooks Y, Cagan A, Mitchell TJ, Cortes-Ciriano I, Warren AY, Wedge DC, Heer R, Coleman N, Murray MJ, Campbell PJ, Rahbari R, Behjati S. Clonal diversification and histogenesis of malignant germ cell tumours. Nat Commun 2022; 13:4272. [PMID: 35953478 PMCID: PMC9372159 DOI: 10.1038/s41467-022-31375-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 12/21/2022] Open
Abstract
Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.
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Affiliation(s)
- Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | | | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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15
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Glennon KI, Vasudev NS, Scelo G, Wilson M, Letourneau L, Eveleigh R, Nourbehesht N, Arseneault M, Paccard A, Egevad L, Viksna J, Celms E, Jackson SM, Abedi-Ardekani B, Warren AY, Selby PJ, Trainor S, Kimuli M, Soomro N, Adeyoju A, Patel P, Wozniak MB, Holcatova I, Brisuda A, Janout V, Chanudet E, Zaridze D, Moukeria A, Shangina O, Foretova L, Navratilova M, Mates D, Jinga V, Bogdanovic L, Kovacevic B, Cambon-Thomsen A, Bourque G, Brazma A, Tost J, Brennan P, Lathrop M, Riazalhosseini Y, Banks RE. Abstract LB113: Genomic classification to refine prognosis in clear cell renal cell carcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb113] [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
Renal cell carcinomas (RCC) are characterized by their heterogenous clinical outcomes, and due to their indeterminate behavior and the absence of routine biomarkers, it is difficult to identify patients who are at high-risk for relapse after curative nephrectomy. To identify genomic biomarkers for clear cell RCC (ccRCC) risk-stratification we interrogated somatic mutation status of 12 RCC-relevant genes using next-generation sequencing (NGS) in tumor-normal pairs from 943 patients with matched follow up data from the Cancer Genomics of the Kidney (CAGEKID) study. We examined associations between genomically-defined patient groups, explained below, and disease-free as well as RCC-specific survival independently in two cohorts of patients (N=469 for cohort 1; 474 for cohort 2). We used the Kaplan-Meier method with log-rank tests to compare survival functions, and Cox proportional hazards models to stratify for patient stage and age to estimate association of each group with survival. RCC-specific survival was assessed with a competing-risks method to include deaths from other causes. Within these cohorts, 76.4% of patients harbored somatic mutations in VHL, the most common driver gene in ccRCC. The most commonly mutated genes within VHL-mutated tumors were PBRM1 (39.7%), SETD2 (19%), BAP1 (14.3%), and KDM5C (8.3%). Less frequently mutated genes included ATM, COL11A1, DMD, TP53, and TRRAP (~3-5%).Among VHL-driven tumors, we identified a new genomic classifier on the basis of the number of mutations in additional RCC driver genes in the panel examined. Patients were classified based on the presence of mutations only in VHL (VHL+0), those with mutations in VHL and one other driver gene (VHL+1), two other driver genes (VHL+2), and 3 or more other driver genes (VHL≥3). We observed within both cohorts that both the risk of disease recurrence as well as RCC-specific death were associated with an increased number of mutations within this classification. When stratified for patient stage and age, the hazard-ratio for 5-year disease-free survival for VHL≥3 patients was 6.69 (p=0.000212), 4.31 for VHL+2 (p=0.000862), and 2.43 for VHL+1 (p=0.035662), compared to patients with only mutations in VHL. These observations were replicated in the second patient cohort, with hazards ratios of 4.55, 2.49, and 1.40, for VHL≥3, VHL+2, and VHL+1 classified patients respectively, indicating that risk of disease recurrence increases with the number of driver mutations. Notably, tumor mutational burden (TMB) was not significantly different between the aforementioned groups, demonstrating that our classifier is independent of TMB. We created a model based on a set of 12 RCC-relevant genes, which can predict risk of relapse for the ~80% of patients with ccRCC that are VHL-driven. This classification can be defined based on a small panel of genes, making it easily applicable to the clinic, in the context of tumor or liquid biopsy analysis.
Citation Format: Kate I. Glennon, Naveen S. Vasudev, Ghislaine Scelo, Michelle Wilson, Louis Letourneau, Robert Eveleigh, Nazanin Nourbehesht, Madeleine Arseneault, Antoine Paccard, Lars Egevad, Juris Viksna, Edgars Celms, Sharon M. Jackson, Behnoush Abedi-Ardekani, Anne Y. Warren, Peter J. Selby, Sebastian Trainor, Michael Kimuli, Naeem Soomro, Adebanji Adeyoju, Poulam Patel, Magdalena B. Wozniak, Ivana Holcatova, Antonin Brisuda, Vladimir Janout, Estelle Chanudet, David Zaridze, Anush Moukeria, Oxana Shangina, Lenka Foretova, Marie Navratilova, Dana Mates, Viorel Jinga, Ljiljana Bogdanovic, Bozidar Kovacevic, Anne Cambon-Thomsen, Guillaume Bourque, Alvis Brazma, Jörg Tost, Paul Brennan, Mark Lathrop, Yasser Riazalhosseini, Rosamonde E. Banks. Genomic classification to refine prognosis in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB113.
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Affiliation(s)
| | - Naveen S. Vasudev
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Ghislaine Scelo
- 3Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Michelle Wilson
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | | | | | | | | | | | - Lars Egevad
- 4Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juris Viksna
- 5Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Edgars Celms
- 5Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Sharon M. Jackson
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Behnoush Abedi-Ardekani
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Anne Y. Warren
- 7Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Peter J. Selby
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Sebastian Trainor
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
| | - Michael Kimuli
- 8Pyrah Department of Urology, Leeds Teaching Hospitals NHS Trust, St James’s University Hospital, Leeds, United Kingdom
| | - Naeem Soomro
- 9Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Poulam Patel
- 11Divison of Cancer & Stem Cells, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Magdalena B. Wozniak
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Ivana Holcatova
- 12Charles University in Prague, First Faculty of Medicine, Institute of Hygiene and Epidemiology, Prague, Czech Republic
| | | | - Vladimir Janout
- 14Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Estelle Chanudet
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - David Zaridze
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Anush Moukeria
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Oxana Shangina
- 15N.N. Blokhin National Medical Research Centre of Oncology, Moscow, Russian Federation
| | - Lenka Foretova
- 16Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Marie Navratilova
- 16Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Dana Mates
- 17National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- 18Carol Davila University of Medicine and Pharmacy, Burghele Clinical Hospital, Bucharest, Romania
| | - Ljiljana Bogdanovic
- 19Institute of Pathology, School of Medicine Belgrade, University of Belgrade, Belgrade
| | - Bozidar Kovacevic
- 20Institute of Pathology and Forensic Medicine, Military Medical Academy, Belgrade
| | - Anne Cambon-Thomsen
- 21Institut National de la Santé et de la Recherche Médicale (INSERM) and Université Toulouse III Paul Sabatier (UPS), Toulouse, France
| | | | - Alvis Brazma
- 22European Bioinformatics Institute, European Molecular Biology Laboratory, EMBL- EBI, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Jörg Tost
- 23Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie Francois Jacob, University Paris Saclay, Evry, France
| | - Paul Brennan
- 6World Health Organisation (WHO), International Agency for Research on Cancer (IARC), The Genomic Epidemiology Branch, Lyon, France
| | - Mark Lathrop
- 1McGill University Genome Centre, Montreal, Quebec, Canada
| | | | - Rosamonde E. Banks
- 2Leeds Institute of Medical Research at St James’s, University of Leeds, St James’s University Hospital, Leeds, United Kingdom
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16
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Sushentsev N, Barrett T, Warren AY, Gnanapragasam VJ. How and when should radiologists report T-staging on MRI in patients with prostate cancer? BJU Int 2022; 130:434-436. [PMID: 35696280 DOI: 10.1111/bju.15824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.,Translational Prostate Cancer Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.,Translational Prostate Cancer Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Translational Prostate Cancer Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.,Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent J Gnanapragasam
- Translational Prostate Cancer Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.,Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK.,Cambridge Urology Translational Research and Clinical Trials Office, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, UK
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17
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Patel SA, Hirosue S, Rodrigues P, Vojtasova E, Richardson EK, Ge J, Syafruddin SE, Speed A, Papachristou EK, Baker D, Clarke D, Purvis S, Wesolowski L, Dyas A, Castillon L, Caraffini V, Bihary D, Yong C, Harrison DJ, Stewart GD, Machiela MJ, Purdue MP, Chanock SJ, Warren AY, Samarajiwa SA, Carroll JS, Vanharanta S. The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer. Nature 2022; 606:999-1006. [PMID: 35676472 PMCID: PMC9242860 DOI: 10.1038/s41586-022-04809-8] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/27/2022] [Indexed: 12/12/2022]
Abstract
Large-scale human genetic data1-3 have shown that cancer mutations display strong tissue-selectivity, but how this selectivity arises remains unclear. Here, using experimental models, functional genomics and analyses of patient samples, we demonstrate that the lineage transcription factor paired box 8 (PAX8) is required for oncogenic signalling by two common genetic alterations that cause clear cell renal cell carcinoma (ccRCC) in humans: the germline variant rs7948643 at 11q13.3 and somatic inactivation of the von Hippel-Lindau tumour suppressor (VHL)4-6. VHL loss, which is observed in about 90% of ccRCCs, can lead to hypoxia-inducible factor 2α (HIF2A) stabilization6,7. We show that HIF2A is preferentially recruited to PAX8-bound transcriptional enhancers, including a pro-tumorigenic cyclin D1 (CCND1) enhancer that is controlled by PAX8 and HIF2A. The ccRCC-protective allele C at rs7948643 inhibits PAX8 binding at this enhancer and downstream activation of CCND1 expression. Co-option of a PAX8-dependent physiological programme that supports the proliferation of normal renal epithelial cells is also required for MYC expression from the ccRCC metastasis-associated amplicons at 8q21.3-q24.3 (ref. 8). These results demonstrate that transcriptional lineage factors are essential for oncogenic signalling and that they mediate tissue-specific cancer risk associated with somatic and inherited genetic variants.
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Affiliation(s)
- Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Shoko Hirosue
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Emma K Richardson
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Jianfeng Ge
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Malaysia
| | - Alyson Speed
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | | | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - David Clarke
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Stephenie Purvis
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ludovic Wesolowski
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anna Dyas
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Leticia Castillon
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Veronica Caraffini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Dóra Bihary
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Cissy Yong
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Grant D Stewart
- Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
- Translational Cancer Medicine Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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18
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Caglic I, Sushentsev N, Colarieti A, Warren AY, Shah N, Lamb BW, Barrett T. Value of the capsular enhancement sign on dynamic contrast-enhanced prostate multiparametric MRI for the detection of extracapsular extension. Eur J Radiol 2022; 150:110275. [DOI: 10.1016/j.ejrad.2022.110275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 01/10/2023]
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Andreou A, Yngvadottir B, Bassaganyas L, Clark G, Martin E, Whitworth J, Cornish AJ, Houlston RS, Rich P, Egan C, Hodgson SV, Warren AY, Snape K, Maher ER. Elongin C (ELOC/TCEB1)-associated von Hippel-Lindau disease. Hum Mol Genet 2022; 31:2728-2737. [PMID: 35323939 PMCID: PMC9402235 DOI: 10.1093/hmg/ddac066] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Around 95% of patients with clinical features that meet the diagnostic criteria for von Hippel-Lindau disease (VHL) have a detectable inactivating germline variant in VHL. The VHL protein (pVHL) functions as part of the E3 ubiquitin ligase complex comprising pVHL, elongin C, elongin B, cullin 2 and ring box 1 (VCB-CR complex), which plays a key role in oxygen sensing and degradation of hypoxia-inducible factors. To date, only variants in VHL have been shown to cause VHL disease. We undertook trio analysis by whole-exome sequencing in a proband with VHL disease but without a detectable VHL mutation. Molecular studies were also performed on paired DNA extracted from the proband's kidney tumour and blood and bioinformatics analysis of sporadic renal cell carcinoma (RCC) dataset was undertaken. A de novo pathogenic variant in ELOC NM_005648.4(ELOC):c.236A>G (p.Tyr79Cys) gene was identified in the proband. ELOC encodes elongin C, a key component [C] of the VCB-CR complex. The p.Tyr79Cys substitution is a mutational hotspot in sporadic VHL-competent RCC and has previously been shown to mimic the effects of pVHL deficiency on hypoxic signalling. Analysis of an RCC from the proband showed similar findings to that in somatically ELOC-mutated RCC (expression of hypoxia-responsive proteins, no somatic VHL variants and chromosome 8 loss). These findings are consistent with pathogenic ELOC variants being a novel cause for VHL disease and suggest that genetic testing for ELOC variants should be performed in individuals with suspected VHL disease with no detectable VHL variant.
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Affiliation(s)
- Avgi Andreou
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bryndis Yngvadottir
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Laia Bassaganyas
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Graeme Clark
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ezequiel Martin
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK,Stratified Medicine Core Laboratory NGS Hub, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | | | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Philip Rich
- Department of Neuroradiology, St. George’s University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Catherine Egan
- NIHR Biomedical Research Center at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Shirley V Hodgson
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust, Cambridge CB2 OQQ, UK
| | - Katie Snape
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK,St George's University of London, UK
| | - Eamonn R Maher
- To whom correspondence should be addressed at: Department of Medical Genetics, University of Cambridge, Box 238, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. Tel: +44 01223746715; Fax: +44 01223746777;
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20
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Sushentsev N, McLean MA, Warren AY, Benjamin AJV, Brodie C, Frary A, Gill AB, Jones J, Kaggie JD, Lamb BW, Locke MJ, Miller JL, Mills IG, Priest AN, Robb FJL, Shah N, Schulte RF, Graves MJ, Gnanapragasam VJ, Brindle KM, Barrett T, Gallagher FA. Author Correction: Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer. Nat Commun 2022; 13:1274. [PMID: 35256616 PMCID: PMC8901739 DOI: 10.1038/s41467-022-28979-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Mary A McLean
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Arnold J V Benjamin
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Cara Brodie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Amy Frary
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Andrew B Gill
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Julia Jones
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joshua D Kaggie
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Benjamin W Lamb
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- School of Allied Health, Anglia Ruskin University, Cambridge, UK
| | - Matthew J Locke
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Jodi L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ian G Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Andrew N Priest
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | | | - Nimish Shah
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Martin J Graves
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials Office, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
| | - Ferdia A Gallagher
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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21
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Caglic I, Sushentsev N, Shah N, Warren AY, Lamb BW, Barrett T. Integration of Prostate Biopsy Results with Pre-Biopsy Multiparametric Magnetic Resonance Imaging Findings Improves Local Staging of Prostate Cancer. Can Assoc Radiol J 2022; 73:515-523. [PMID: 35199583 DOI: 10.1177/08465371211073158] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To assess the added value of histological information for local staging of prostate cancer (PCa) by comparing the accuracy of multiparametric MRI alone (mpMRI) and mpMRI with biopsy Gleason grade (mpMRI+Bx). METHODS 133 consecutive patients who underwent preoperative 3T-MRI and subsequent radical prostatectomy for PCa were included in this single-centre retrospective study. mpMRI imaging was reviewed independently by two uroradiologists for the presence of extracapsular extension (ECE) and seminal vesicle invasion (SVI) on a 5-point Likert scale. For second reads, the radiologists received results of targeted fused MR/US biopsy (mpMRI+Bx) prior to re-staging. RESULTS The median patient age was 63 years (interquartile range (IQR) 58-67 years) and median PSA was 6.5 ng/mL (IQR 5.0-10.0 ng/mL). Extracapsular extension was present in 85/133 (63.9%) patients and SVI was present in 22/133 (16.5%) patients. For ECE prediction, mpMRI showed sensitivity and specificity of 63.5% and 81.3%, respectively, compared to 77.7% and 81.3% achieved by mpMRI+Bx. At an optimal cut-off value of Likert score ≥ 3, areas under the curves (AUCs) was .85 for mpMRI+Bx and .78 for mpMRI, P < .01. For SVI prediction, AUC was .95 for mpMRI+Bx compared to .92 for mpMRI; P = .20. Inter-reader agreement for ECE and SVI prediction was substantial for mpMRI (k range, .78-.79) and mpMRI+Bx (k range, .74-.79). CONCLUSIONS MpMRI+Bx showed superior diagnostic performance with an increased sensitivity for ECE prediction but no significant difference for SVI prediction. Inter-reader agreement was substantial for both protocols. Integration of biopsy information adds value when staging prostate mpMRI.
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Affiliation(s)
- Iztok Caglic
- CamPARI Prostate Cancer Group, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Faculty of Medicine, University of Ljubljana, Slovenia
| | - Nikita Sushentsev
- Department of Radiology, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nimish Shah
- CamPARI Prostate Cancer Group, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Urology, 573020Addenbrooke's Hospital, Cambridge, UK
| | - Anne Y Warren
- CamPARI Prostate Cancer Group, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Pathology, 573020Addenbrooke's Hospital, Cambridge, UK
| | - Benjamin W Lamb
- CamPARI Prostate Cancer Group, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Urology, 573020Addenbrooke's Hospital, Cambridge, UK
| | - Tristan Barrett
- CamPARI Prostate Cancer Group, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, 573020Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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22
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Sushentsev N, McLean MA, Warren AY, Benjamin AJV, Brodie C, Frary A, Gill AB, Jones J, Kaggie JD, Lamb BW, Locke MJ, Miller JL, Mills IG, Priest AN, Robb FJL, Shah N, Schulte RF, Graves MJ, Gnanapragasam VJ, Brindle KM, Barrett T, Gallagher FA. Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer. Nat Commun 2022; 13:466. [PMID: 35075123 PMCID: PMC8786834 DOI: 10.1038/s41467-022-28069-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/02/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperpolarised magnetic resonance imaging (HP 13C-MRI) is an emerging clinical technique to detect [1-13C]lactate production in prostate cancer (PCa) following intravenous injection of hyperpolarised [1-13C]pyruvate. Here we differentiate clinically significant PCa from indolent disease in a low/intermediate-risk population by correlating [1-13C]lactate labelling on MRI with the percentage of Gleason pattern 4 (%GP4) disease. Using immunohistochemistry and spatial transcriptomics, we show that HP 13C-MRI predominantly measures metabolism in the epithelial compartment of the tumour, rather than the stroma. MRI-derived tumour [1-13C]lactate labelling correlated with epithelial mRNA expression of the enzyme lactate dehydrogenase (LDHA and LDHB combined), and the ratio of lactate transporter expression between the epithelial and stromal compartments (epithelium-to-stroma MCT4). We observe similar changes in MCT4, LDHA, and LDHB between tumours with primary Gleason patterns 3 and 4 in an independent TCGA cohort. Therefore, HP 13C-MRI can metabolically phenotype clinically significant disease based on underlying metabolic differences in the epithelial and stromal tumour compartments.
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Affiliation(s)
- Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Mary A McLean
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Arnold J V Benjamin
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Cara Brodie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Amy Frary
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Andrew B Gill
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Julia Jones
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joshua D Kaggie
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Benjamin W Lamb
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- School of Allied Health, Anglia Ruskin University, Cambridge, UK
| | - Matthew J Locke
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Jodi L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ian G Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
- Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Andrew N Priest
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | | | - Nimish Shah
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Martin J Graves
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials Office, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge, UK
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
| | - Ferdia A Gallagher
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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23
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Ursprung S, Woitek R, McLean MA, Priest AN, Crispin-Ortuzar M, Brodie CR, Gill AB, Gehrung M, Beer L, Riddick ACP, Field-Rayner J, Grist JT, Deen SS, Riemer F, Kaggie JD, Zaccagna F, Duarte JAG, Locke MJ, Frary A, Aho TF, Armitage JN, Casey R, Mendichovszky IA, Welsh SJ, Barrett T, Graves MJ, Eisen T, Mitchell TJ, Warren AY, Brindle KM, Sala E, Stewart GD, Gallagher FA. Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell Carcinoma-A Proof of Principle Study. Cancers (Basel) 2022; 14:335. [PMID: 35053497 PMCID: PMC8773685 DOI: 10.3390/cancers14020335] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 11/15/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
Differentiating aggressive clear cell renal cell carcinoma (ccRCC) from indolent lesions is challenging using conventional imaging. This work prospectively compared the metabolic imaging phenotype of renal tumors using carbon-13 MRI following injection of hyperpolarized [1-13C]pyruvate (HP-13C-MRI) and validated these findings with histopathology. Nine patients with treatment-naïve renal tumors (6 ccRCCs, 1 liposarcoma, 1 pheochromocytoma, 1 oncocytoma) underwent pre-operative HP-13C-MRI and conventional proton (1H) MRI. Multi-regional tissue samples were collected using patient-specific 3D-printed tumor molds for spatial registration between imaging and molecular analysis. The apparent exchange rate constant (kPL) between 13C-pyruvate and 13C-lactate was calculated. Immunohistochemistry for the pyruvate transporter (MCT1) from 44 multi-regional samples, as well as associations between MCT1 expression and outcome in the TCGA-KIRC dataset, were investigated. Increasing kPL in ccRCC was correlated with increasing overall tumor grade (ρ = 0.92, p = 0.009) and MCT1 expression (r = 0.89, p = 0.016), with similar results acquired from the multi-regional analysis. Conventional 1H-MRI parameters did not discriminate tumor grades. The correlation between MCT1 and ccRCC grade was confirmed within a TCGA dataset (p < 0.001), where MCT1 expression was a predictor of overall and disease-free survival. In conclusion, metabolic imaging using HP-13C-MRI differentiates tumor aggressiveness in ccRCC and correlates with the expression of MCT1, a predictor of survival. HP-13C-MRI may non-invasively characterize metabolic phenotypes within renal cancer.
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Affiliation(s)
- Stephan Ursprung
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Ramona Woitek
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Mary A. McLean
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Andrew N. Priest
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
- Department of Radiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Mireia Crispin-Ortuzar
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
| | - Cara R. Brodie
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
| | - Andrew B. Gill
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Marcel Gehrung
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
| | - Lucian Beer
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Antony C. P. Riddick
- Department of Urology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.C.P.R.); (T.F.A.); (J.N.A.)
| | - Johanna Field-Rayner
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - James T. Grist
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Surrin S. Deen
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
- Department of Radiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Frank Riemer
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Joshua D. Kaggie
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Fulvio Zaccagna
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Joao A. G. Duarte
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Matthew J. Locke
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Amy Frary
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Tevita F. Aho
- Department of Urology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.C.P.R.); (T.F.A.); (J.N.A.)
| | - James N. Armitage
- Department of Urology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.C.P.R.); (T.F.A.); (J.N.A.)
| | - Ruth Casey
- Department of Endocrinology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Iosif A. Mendichovszky
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
- Department of Radiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Sarah J. Welsh
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Oncology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tristan Barrett
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Martin J. Graves
- Department of Radiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK;
| | - Tim Eisen
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Oncology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Thomas J. Mitchell
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Urology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.C.P.R.); (T.F.A.); (J.N.A.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | - Anne Y. Warren
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Pathology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Kevin M. Brindle
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
| | - Evis Sala
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
| | - Grant D. Stewart
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Urology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.C.P.R.); (T.F.A.); (J.N.A.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ferdia A. Gallagher
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (S.U.); (R.W.); (M.A.M.); (M.C.-O.); (C.R.B.); (A.B.G.); (M.G.); (L.B.); (J.F.-R.); (S.S.D.); (F.R.); (J.D.K.); (F.Z.); (J.A.G.D.); (M.J.L.); (A.F.); (I.A.M.); (S.J.W.); (T.B.); (T.E.); (T.J.M.); (A.Y.W.); (K.M.B.); (E.S.); (G.D.S.)
- Department of Radiology, University of Cambridge, Cambridge CB2 0QQ, UK; (A.N.P.); (J.T.G.)
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24
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Tuong ZK, Loudon KW, Berry B, Richoz N, Jones J, Tan X, Nguyen Q, George A, Hori S, Field S, Lynch AG, Kania K, Coupland P, Babbage A, Grenfell R, Barrett T, Warren AY, Gnanapragasam V, Massie C, Clatworthy MR. Resolving the immune landscape of human prostate at a single-cell level in health and cancer. Cell Rep 2021; 37:110132. [PMID: 34936871 PMCID: PMC8721283 DOI: 10.1016/j.celrep.2021.110132] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 09/01/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
The prostate gland produces prostatic fluid, high in zinc and citrate and essential for the maintenance of spermatozoa. Prostate cancer is a common condition with limited treatment efficacy in castration-resistant metastatic disease, including with immune checkpoint inhibitors. Using single-cell RNA-sequencing to perform an unbiased assessment of the cellular landscape of human prostate, we identify a subset of tumor-enriched androgen receptor-negative luminal epithelial cells with increased expression of cancer-associated genes. We also find a variety of innate and adaptive immune cells in normal prostate that were transcriptionally perturbed in prostate cancer. An exception is a prostate-specific, zinc transporter-expressing macrophage population (MAC-MT) that contributes to tissue zinc accumulation in homeostasis but shows enhanced inflammatory gene expression in tumors, including T cell-recruiting chemokines. Remarkably, enrichment of the MAC-MT signature in cancer biopsies is associated with improved disease-free survival, suggesting beneficial antitumor functions.
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Affiliation(s)
- Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Brendan Berry
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Xiao Tan
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quan Nguyen
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Anne George
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Early Detection Programme, CRUK Cambridge Centre, Cambridge, UK
| | - Satoshi Hori
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK
| | | | - Andy G Lynch
- CRUK Cambridge Institute, Cambridge, UK; School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, UK
| | | | | | - Anne Babbage
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Tristan Barrett
- Department of Radiology, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent Gnanapragasam
- 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 Biomedical Campus, Cambridge, UK
| | - Charlie Massie
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; CRUK Cambridge Institute, Cambridge, UK; Early Detection Programme, CRUK Cambridge Centre, Cambridge, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK; NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Diseases, Cambridge, UK.
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25
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Ursprung S, Mossop H, Gallagher FA, Sala E, Skells R, Sipple JAN, Mitchell TJ, Chhabra A, Fife K, Matakidou A, Young G, Walker A, Thomas MG, Ortuzar MC, Sullivan M, Protheroe A, Oades G, Venugopal B, Warren AY, Stone J, Eisen T, Wason J, Welsh SJ, Stewart GD. The WIRE study a phase II, multi-arm, multi-centre, non-randomised window-of-opportunity clinical trial platform using a Bayesian adaptive design for proof-of-mechanism of novel treatment strategies in operable renal cell cancer - a study protocol. BMC Cancer 2021; 21:1238. [PMID: 34794412 PMCID: PMC8600815 DOI: 10.1186/s12885-021-08965-4] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/04/2021] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Window-of-opportunity trials, evaluating the engagement of drugs with their biological target in the time period between diagnosis and standard-of-care treatment, can help prioritise promising new systemic treatments for later-phase clinical trials. Renal cell carcinoma (RCC), the 7th commonest solid cancer in the UK, exhibits targets for multiple new systemic anti-cancer agents including DNA damage response inhibitors, agents targeting vascular pathways and immune checkpoint inhibitors. Here we present the trial protocol for the WIndow-of-opportunity clinical trial platform for evaluation of novel treatment strategies in REnal cell cancer (WIRE). METHODS WIRE is a Phase II, multi-arm, multi-centre, non-randomised, proof-of-mechanism (single and combination investigational medicinal product [IMP]), platform trial using a Bayesian adaptive design. The Bayesian adaptive design leverages outcome information from initial participants during pre-specified interim analyses to determine and minimise the number of participants required to demonstrate efficacy or futility. Patients with biopsy-proven, surgically resectable, cT1b+, cN0-1, cM0-1 clear cell RCC and no contraindications to the IMPs are eligible to participate. Participants undergo diagnostic staging CT and renal mass biopsy followed by treatment in one of the treatment arms for at least 14 days. Initially, the trial includes five treatment arms with cediranib, cediranib + olaparib, olaparib, durvalumab and durvalumab + olaparib. Participants undergo a multiparametric MRI before and after treatment. Vascularised and de-vascularised tissue is collected at surgery. A ≥ 30% increase in CD8+ T-cells on immunohistochemistry between the screening and nephrectomy is the primary endpoint for durvalumab-containing arms. Meanwhile, a reduction in tumour vascular permeability measured by Ktrans on dynamic contrast-enhanced MRI by ≥30% is the primary endpoint for other arms. Secondary outcomes include adverse events and tumour size change. Exploratory outcomes include biomarkers of drug mechanism and treatment effects in blood, urine, tissue and imaging. DISCUSSION WIRE is the first trial using a window-of-opportunity design to demonstrate pharmacological activity of novel single and combination treatments in RCC in the pre-surgical space. It will provide rationale for prioritising promising treatments for later phase trials and support the development of new biomarkers of treatment effect with its extensive translational agenda. TRIAL REGISTRATION ClinicalTrials.gov: NCT03741426 / EudraCT: 2018-003056-21 .
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Affiliation(s)
| | - Helen Mossop
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Ferdia A Gallagher
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Evis Sala
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Richard Skells
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- AstraZeneca, Cambridge, UK
| | - Jamal A N Sipple
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Thomas J Mitchell
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Anita Chhabra
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kate Fife
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Athena Matakidou
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gemma Young
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Amanda Walker
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin G Thomas
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Mark Sullivan
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Andrew Protheroe
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Grenville Oades
- Department of Urology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Balaji Venugopal
- Institute of Cancer Sciences, University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - Anne Y Warren
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Tim Eisen
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - James Wason
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Sarah J Welsh
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Grant D Stewart
- CRUK Cambridge Centre, University of Cambridge, Cambridge, UK.
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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26
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Ursprung S, Priest AN, Zaccagna F, Qian W, Machin A, Stewart GD, Warren AY, Eisen T, Welsh SJ, Gallagher FA, Barrett T. Multiparametric MRI for assessment of early response to neoadjuvant sunitinib in renal cell carcinoma. PLoS One 2021; 16:e0258988. [PMID: 34699525 PMCID: PMC8547646 DOI: 10.1371/journal.pone.0258988] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To detect early response to sunitinib treatment in metastatic clear cell renal cancer (mRCC) using multiparametric MRI. METHOD Participants with mRCC undergoing pre-surgical sunitinib therapy in the prospective NeoSun clinical trial (EudraCtNo: 2005-004502-82) were imaged before starting treatment, and after 12 days of sunitinib therapy using morphological MRI sequences, advanced diffusion-weighted imaging, measurements of R2* (related to hypoxia) and dynamic contrast-enhanced imaging. Following nephrectomy, participants continued treatment and were followed-up with contrast-enhanced CT. Changes in imaging parameters before and after sunitinib were assessed with the non-parametric Wilcoxon signed-rank test and the log-rank test was used to assess effects on survival. RESULTS 12 participants fulfilled the inclusion criteria. After 12 days, the solid and necrotic tumor volumes decreased by 28% and 17%, respectively (p = 0.04). However, tumor-volume reduction did not correlate with progression-free or overall survival (PFS/OS). Sunitinib therapy resulted in a reduction in median solid tumor diffusivity D from 1298x10-6 to 1200x10-6mm2/s (p = 0.03); a larger decrease was associated with a better RECIST response (p = 0.02) and longer PFS (p = 0.03) on the log-rank test. An increase in R2* from 19 to 28s-1 (p = 0.001) was observed, paralleled by a decrease in Ktrans from 0.415 to 0.305min-1 (p = 0.01) and a decrease in perfusion fraction from 0.34 to 0.19 (p<0.001). CONCLUSIONS Physiological imaging confirmed efficacy of the anti-angiogenic agent 12 days after initiating therapy and demonstrated response to treatment. The change in diffusivity shortly after starting pre-surgical sunitinib correlated to PFS in mRCC undergoing nephrectomy, however, no parameter predicted OS. TRIAL REGISTRATION EudraCtNo: 2005-004502-82.
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Affiliation(s)
- Stephan Ursprung
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
| | - Andrew N. Priest
- University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Wendi Qian
- University of Cambridge, Cambridge, United Kingdom
- Cambridge Cancer Trial Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrea Machin
- University of Cambridge, Cambridge, United Kingdom
- Cambridge Cancer Trial Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Grant D. Stewart
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Anne Y. Warren
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Timothy Eisen
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Sarah J. Welsh
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Ferdia A. Gallagher
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
| | - Tristan Barrett
- University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, United Kingdom
- Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
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27
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Moore L, Cagan A, Coorens THH, Neville MDC, Sanghvi R, Sanders MA, Oliver TRW, Leongamornlert D, Ellis P, Noorani A, Mitchell TJ, Butler TM, Hooks Y, Warren AY, Jorgensen M, Dawson KJ, Menzies A, O'Neill L, Latimer C, Teng M, van Boxtel R, Iacobuzio-Donahue CA, Martincorena I, Heer R, Campbell PJ, Fitzgerald RC, Stratton MR, Rahbari R. The mutational landscape of human somatic and germline cells. Nature 2021; 597:381-386. [PMID: 34433962 DOI: 10.1038/s41586-021-03822-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [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: 11/23/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.
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Affiliation(s)
- Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D C Neville
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rashesh Sanghvi
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Thomas R W Oliver
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata, Cambridge, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mabel Teng
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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28
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Abedi-Ardekani B, Nasrollahzadeh D, Egevad L, Banks RE, Vasudev N, Holcatova I, Povysil C, Foretova L, Janout V, Mates D, Jinga V, Petrescu A, Milosavljevic S, Ognjanovic M, Ognjanovic S, Viksna J, Warren AY, Lathrop M, Riazalhosseini Y, Carreira C, Chanudet E, McKay J, Brennan P, Scélo G. Morphological findings in frozen non-neoplastic kidney tissues of patients with kidney cancer from large-scale multicentric studies on renal cancer. Virchows Arch 2021; 478:1099-1107. [PMID: 33403511 PMCID: PMC8203524 DOI: 10.1007/s00428-020-02986-3] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/11/2020] [Accepted: 12/03/2020] [Indexed: 11/23/2022]
Abstract
There are unexplained geographical variations in the incidence of kidney cancer with the high rates reported in Baltic countries, as well as eastern and central Europe. Having access to a large and well-annotated collection of "tumor/non-tumor" pairs of kidney cancer patients from the Czech Republic, Romania, Serbia, UK, and Russia, we aimed to analyze the morphology of non-neoplastic renal tissue in nephrectomy specimens. By applying digital pathology, we performed a microscopic examination of 1012 frozen non-neoplastic kidney tissues from patients with renal cell carcinoma. Four components of renal parenchyma were evaluated and scored for the intensity of interstitial inflammation and fibrosis, tubular atrophy, glomerulosclerosis, and arterial wall thickening, globally called chronic renal parenchymal changes. Moderate or severe changes were observed in 54 (5.3%) of patients with predominance of occurrence in Romania (OR = 2.67, CI 1.07-6.67) and Serbia (OR = 4.37, CI 1.20-15.96) in reference to those from Russia. Further adjustment for comorbidities, tumor characteristics, and stage did not change risk estimates. In multinomial regression model, relative probability of non-glomerular changes was 5.22 times higher for Romania and Serbia compared to Russia. Our findings show that the frequency of chronic renal parenchymal changes, with the predominance of chronic interstitial nephritis pattern, in kidney cancer patients varies by country, significantly more frequent in countries located in central and southeastern Europe where the incidence of kidney cancer has been reported to be moderate to high. The observed association between these pathological features and living in certain geographic areas requires a larger population-based study to confirm this association on a large scale.
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Affiliation(s)
- Behnoush Abedi-Ardekani
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France.
| | - Dariush Nasrollahzadeh
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rosamonde E Banks
- Leeds Institute of Medical Research @ St James's, University of Leeds, Leeds, UK
| | - Naveen Vasudev
- Leeds Institute of Medical Research @ St James's, University of Leeds, Leeds, UK
| | - Ivana Holcatova
- First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ctibor Povysil
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Vladimir Janout
- Centre of Science and Research, Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Viorel Jinga
- Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Amelia Petrescu
- Pathology Department, Professor Dr. Th. Burghele Clinical Hospital, Bucharest, Romania
| | - Sasa Milosavljevic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - Miodrag Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - Simona Ognjanovic
- International Organization for Cancer Prevention and Research, Belgrade, Serbia
| | - Juris Viksna
- Institute of Mathematics and Computer Science, University of Latvia, Riga, Latvia
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Yasser Riazalhosseini
- McGill University and Génome Québec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Christine Carreira
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
| | - Estelle Chanudet
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
| | - Ghislaine Scélo
- International Agency for Research on Cancer, World Health Organization, 150 Cours Albert Thomas, 69372, Lyon Cedex 8, France
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Caglic I, Sushentsev N, Shah N, Warren AY, Lamb BW, Barrett T. Comparison of biparametric versus multiparametric prostate MRI for the detection of extracapsular extension and seminal vesicle invasion in biopsy naïve patients. Eur J Radiol 2021; 141:109804. [PMID: 34062473 DOI: 10.1016/j.ejrad.2021.109804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/09/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022]
Abstract
PURPOSE To compare biparametric MRI (bpMRI) with multiparametric MRI (mpMRI) staging accuracy in assessing extracapsular extension (ECE) and seminal vesicle invasion (SVI). METHOD Biopsy-naïve patients undergoing 3 T-MRI before radical prostatectomy for clinically significant prostate cancer were included in this single-centre retrospective study. Two uroradiologists separately evaluated bpMRI and mpMRI for presence of ECE and SVI using a 5-point Likert scale (1: ECE/SVI highly unlikely, 5: ECE/SVI highly likely). RESULTS 110 men of median age 63 years and PSA 8.5 ng/mL were included. ECE and SVI was confirmed histologically in 71/110 (64.5 %) and 18/110 (16.4 %) patients, respectively. Sensitivity and specificity of bpMRI versus mpMRI for predicting ECE was 59.1 % and 87.2 % versus 66.2 % and 84.6 %, respectively. For SVI detection, the sensitivity and specificity for bpMRI versus mpMRI was 66.7 % and 92.4 % versus 83.3 % and 97.8 %, respectively. At an optimal cut-off Likert score ≥3 for ECE prediction, mpMRI area under the receiver operating curve (AUC) was 0.80 (95 % confidence interval (CI) 0.72-0.87) versus 0.78 (95 % CI 0.69-0.86) for bpMRI (p = 0.52) and for SVI, mpMRI AUC was 0.91 (95 % CI 0.84-0.96) versus 0.86 (95 % CI 0.78-0.92) for bpMRI (p = 0.02), respectively. Inter-reader agreement for both ECE and SVI prediction was substantial, with a marginally higher k-value for mpMRI (k range, 0.67-0.75) than bpMRI (k range, 0.65-0.69). CONCLUSIONS Diagnostic performance of bpMRI and mpMRI was comparable for detection of ECE, however, mpMRI with contrast was superior for SVI detection and improved the inter-reader agreement.
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Affiliation(s)
- Iztok Caglic
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
| | - Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
| | - Nimish Shah
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Urology, Addenbrooke's Hospital, Cambridge, UK.
| | - Anne Y Warren
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Pathology, Addenbrooke's Hospital, Cambridge, UK.
| | - Benjamin W Lamb
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Urology, Addenbrooke's Hospital, Cambridge, UK.
| | - Tristan Barrett
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
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30
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Caglic I, Sushentsev N, Gnanapragasam VJ, Sala E, Shaida N, Koo BC, Kozlov V, Warren AY, Kastner C, Barrett T. MRI-derived PRECISE scores for predicting pathologically-confirmed radiological progression in prostate cancer patients on active surveillance. Eur Radiol 2021; 31:2696-2705. [PMID: 33196886 PMCID: PMC8043947 DOI: 10.1007/s00330-020-07336-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/16/2020] [Accepted: 07/23/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To assess the predictive value and correlation to pathological progression of the Prostate Cancer Radiological Estimation of Change in Sequential Evaluation (PRECISE) scoring system in the follow-up of prostate cancer (PCa) patients on active surveillance (AS). METHODS A total of 295 men enrolled on an AS programme between 2011 and 2018 were included. Baseline multiparametric magnetic resonance imaging (mpMRI) was performed at AS entry to guide biopsy. The follow-up mpMRI studies were prospectively reported by two sub-specialist uroradiologists with 10 years and 13 years of experience. PRECISE scores were dichotomized at the cut-off value of 4, and the sensitivity, specificity, positive predictive value and negative predictive value were calculated. Diagnostic performance was further quantified by using area under the receiver operating curve (AUC) which was based on the results of targeted MRI-US fusion biopsy. Univariate analysis using Cox regression was performed to assess which baseline clinical and mpMRI parameters were related to disease progression on AS. RESULTS Progression rate of the cohort was 13.9% (41/295) over a median follow-up of 52 months. With a cut-off value of category ≥ 4, the PRECISE scoring system showed sensitivity, specificity, PPV and NPV for predicting progression on AS of 0.76, 0.89, 0.52 and 0.96, respectively. The AUC was 0.82 (95% CI = 0.74-0.90). Prostate-specific antigen density (PSA-D), Likert lesion score and index lesion size were the only significant baseline predictors of progression (each p < 0.05). CONCLUSION The PRECISE scoring system showed good overall performance, and the high NPV may help limit the number of follow-up biopsies required in patients on AS. KEY POINTS • PRECISE scores 1-3 have high NPV which could reduce the need for re-biopsy during active surveillance. • PRECISE scores 4-5 have moderate PPV and should trigger either close monitoring or re-biopsy. • Three baseline predictors (PSA density, lesion size and Likert score) have a significant impact on the progression-free survival (PFS) time.
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Affiliation(s)
- Iztok Caglic
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nikita Sushentsev
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge, Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Evis Sala
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nadeem Shaida
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Brendan C Koo
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Vasily Kozlov
- Department of Public Health and Healthcare Organisation, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Anne Y Warren
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Christof Kastner
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Tristan Barrett
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
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31
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Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA, Bareham B, Butler TM, Harvey LMR, Cagan A, Menzies A, Moore L, Colquhoun AJ, Turner W, Thomas B, Gnanapragasam V, Williams N, Rassl DM, Vöhringer H, Zumalave S, Nangalia J, Tubío JMC, Gerstung M, Saeb-Parsy K, Stratton MR, Campbell PJ, Mitchell TJ, Martincorena I. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 2020; 370:75-82. [PMID: 33004514 DOI: 10.1126/science.aba8347] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [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: 01/09/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
The extent of somatic mutation and clonal selection in the human bladder remains unknown. We sequenced 2097 bladder microbiopsies from 20 individuals using targeted (n = 1914 microbiopsies), whole-exome (n = 655), and whole-genome (n = 88) sequencing. We found widespread positive selection in 17 genes. Chromatin remodeling genes were frequently mutated, whereas mutations were absent in several major bladder cancer genes. There was extensive interindividual variation in selection, with different driver genes dominating the clonal landscape across individuals. Mutational signatures were heterogeneous across clones and individuals, which suggests differential exposure to mutagens in the urine. Evidence of APOBEC mutagenesis was found in 22% of the microbiopsies. Sequencing multiple microbiopsies from five patients with bladder cancer enabled comparisons with cancer-free individuals and across histological features. This study reveals a rich landscape of mutational processes and selection in normal urothelium with large heterogeneity across clones and individuals.
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Affiliation(s)
- Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam 3015 GD, Netherlands
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Krishnaa T A Mahbubani
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bethany Bareham
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alexandra J Colquhoun
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - William Turner
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Benjamin Thomas
- The Royal Melbourne Hospital, Parkville, Victoria 3010, Australia
- Department of Surgery, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Vincent Gnanapragasam
- Academic Urology Group, Department of Surgery and Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge CB2 0QQ, UK
| | - Nicholas Williams
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Doris M Rassl
- Department of Pathology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK
| | - Harald Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jyoti Nangalia
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - José M C Tubío
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- The Biomedical Research Centre (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
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32
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Smith PS, West H, Whitworth J, Castle B, Sansbury FH, Warren AY, Woodward ER, Tischkowitz M, Maher ER. Pathogenic germline variants in patients with features of hereditary renal cell carcinoma: Evidence for further locus heterogeneity. Genes Chromosomes Cancer 2020; 60:5-16. [PMID: 32830346 DOI: 10.1002/gcc.22893] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 08/19/2020] [Indexed: 11/08/2022] Open
Abstract
Inherited renal cell carcinoma (RCC) is associated with multiple familial cancer syndromes but most individuals with features of non-syndromic inherited RCC do not harbor variants in the most commonly tested renal cancer predisposition genes (CPGs). We investigated whether undiagnosed cases might harbor mutations in CPGs that are not routinely tested for by testing 118 individuals with features suggestive of inherited RCC (family history of RCC, two or more primary RCC aged <60 years, or early onset RCC ≤46 years) for the presence of pathogenic variants in a large panel of CPGs. All individuals had been prescreened for pathogenic variants in the major RCC genes. We detected pathogenic or likely pathogenic (P/LP) variants of potential clinical relevance in 16.1% (19/118) of individuals, including P/LP variants in BRIP1 (n = 4), CHEK2 (n = 3), MITF (n = 1), and BRCA1 (n = 1). Though the power to detect rare variants was limited by sample size the frequency of truncating variants in BRIP1, 4/118, was significantly higher than in controls (P = 5.92E-03). These findings suggest that the application of genetic testing for larger inherited cancer gene panels in patients with indicators of a potential inherited RCC can increase the diagnostic yield for P/LP variants. However, the clinical utility of such a diagnostic strategy requires validation and further evaluation and in particular, confirmation of rarer RCC genotype-phenotype associations is required.
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Affiliation(s)
- Philip S Smith
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Hannah West
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Bruce Castle
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital (Heavitree), Exeter, UK University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Francis H Sansbury
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital (Heavitree), Exeter, UK University of Exeter Medical School, University of Exeter, Exeter, UK.,All Wales Medical Genomics Service, Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust and Cancer Research UK Cambridge Centre, Cambridge, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University Hospitals NHS Foundation Trust, and Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health Innovation Manchester, Manchester, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
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Crispin-Ortuzar M, Gehrung M, Ursprung S, Gill AB, Warren AY, Beer L, Gallagher FA, Mitchell TJ, Mendichovszky IA, Priest AN, Stewart GD, Sala E, Markowetz F. Three-Dimensional Printed Molds for Image-Guided Surgical Biopsies: An Open Source Computational Platform. JCO Clin Cancer Inform 2020; 4:736-748. [PMID: 32804543 PMCID: PMC7469624 DOI: 10.1200/cci.20.00026] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Spatial heterogeneity of tumors is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood because it relies on the accurate coregistration of medical images and tissue biopsies. Tumor molds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumor heterogeneity data. METHODS We have developed an open-source computational framework to automatically produce patient-specific 3-dimensional-printed molds that can be used in the clinical setting. Our approach achieves accurate coregistration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging, and pathology workflows. RESULTS We applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalized molds for 6 patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.96 for tumor regions and between 0.70 and 0.76 for healthy kidneys. The framework required minimal manual intervention, producing the final mold design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes. CONCLUSION Our work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumor heterogeneity on multiple spatial scales.
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Affiliation(s)
- Mireia Crispin-Ortuzar
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Marcel Gehrung
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stephan Ursprung
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew B. Gill
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Lucian Beer
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University Vienna, Vienna, Austria
| | | | - Thomas J. Mitchell
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Iosif A. Mendichovszky
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Andrew N. Priest
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Grant D. Stewart
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Evis Sala
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Radiology, University of Cambridge, Cambridge, United Kingdom
| | - Florian Markowetz
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
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Zawaideh JP, Sala E, Pantelidou M, Shaida N, Koo B, Caglic I, Warren AY, Carmisciano L, Saeb-Parsy K, Gnanapragasam VJ, Kastner C, Barrett T. Comparison of Likert and PI-RADS version 2 MRI scoring systems for the detection of clinically significant prostate cancer. Br J Radiol 2020; 93:20200298. [PMID: 32479105 DOI: 10.1259/bjr.20200298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE To compare the performance of Likert and Prostate Imaging-Reporting and Data System (PI-RADS) multiparametric (mp) MRI scoring systems for detecting clinically significant prostate cancer (csPCa). METHODS 199 biopsy-naïve males undergoing prostate mpMRI were prospectively scored with Likert and PI-RADS systems by four experienced radiologists. A binary cut-off (threshold score ≥3) was used to analyze histological results by three groups: negative, insignificant disease (Gleason 3 + 3; iPCa), and csPCa (Gleason ≥3 +4). Lesion-level results and prostate zonal location were also compared. RESULTS 129/199 (64.8%) males underwent biopsy, 96 with Likert or PI-RADS score ≥3, and 21 with negative MRI. A further 12 patients were biopsied during follow-up (mean 507 days). Prostate cancer was diagnosed in 87/199 (43.7%) patients, 65 with (33.6%) csPCa. 30/92 (32.6%) patients with negative MRI were biopsied, with an NPV of 83.3% for cancer and 86.7% for csPCa. Likert and PI-RADS score differences were observed in 92 patients (46.2%), but only for 16 patients (8%) at threshold score ≥3. Likert scoring had higher specificity than PI-RADS (0.77 vs 0.66), higher area under the curve (0.92 vs 0.87, p = 0.002) and higher PPV (0.66 vs 0.58); NPV and sensitivity were the same. Likert had more five score results (58%) compared to PI-RADS (36%), but with similar csCPa detection (81.0 and 80.6% respectively). Likert demonstrated lower proportion of false positive in the predominately AFMS-involving lesions. CONCLUSION Likert and PI-RADS systems both demonstrate high cancer detection rates. Likert scoring had a higher AUC with moderately higher specificity and lower positive call rate and could potentially help to reduce the number of unnecessary biopsies performed. ADVANCES IN KNOWLEDGE This paper illustrates that the Likert scoring system has potential to help urologists reduce the number of prostate biopsies performed.
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Affiliation(s)
- Jeries P Zawaideh
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Evis Sala
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Maria Pantelidou
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nadeem Shaida
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Brendan Koo
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Iztok Caglic
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Luca Carmisciano
- Department of health Sciences (DISSAL), Biostatistics section, University of Genoa, Genoa, Italy
| | - Kasra Saeb-Parsy
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Vincent J Gnanapragasam
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Christof Kastner
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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Tran MGB, Bibby BAS, Yang L, Lo F, Warren AY, Shukla D, Osborne M, Hadfield J, Carroll T, Stark R, Scott H, Ramos-Montoya A, Massie C, Maxwell P, West CML, Mills IG, Neal DE. Independence of HIF1a and androgen signaling pathways in prostate cancer. BMC Cancer 2020; 20:469. [PMID: 32450824 PMCID: PMC7249645 DOI: 10.1186/s12885-020-06890-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 02/06/2020] [Accepted: 04/22/2020] [Indexed: 01/27/2023] Open
Abstract
Background Therapeutic targeting of the androgen signaling pathway is a mainstay treatment for prostate cancer. Although initially effective, resistance to androgen targeted therapies develops followed by disease progression to castrate-resistant prostate cancer (CRPC). Hypoxia and HIF1a have been implicated in the development of resistance to androgen targeted therapies and progression to CRCP. The interplay between the androgen and hypoxia/HIF1a signaling axes was investigated. Methods In vitro stable expression of HIF1a was established in the LNCaP cell line by physiological induction or retroviral transduction. Tumor xenografts with stable expression of HIF1a were established in castrated and non-castrated mouse models. Gene expression analysis identified transcriptional changes in response to androgen treatment, hypoxia and HIF1a. The binding sites of the AR and HIF transcription factors were identified using ChIP-seq. Results Androgen and HIF1a signaling promoted proliferation in vitro and enhanced tumor growth in vivo. The stable expression of HIF1a in vivo restored tumor growth in the absence of endogenous androgens. Hypoxia reduced AR binding sites whereas HIF binding sites were increased with androgen treatment under hypoxia. Gene expression analysis identified seven genes that were upregulated both by AR and HIF1a, of which six were prognostic. Conclusions The oncogenic AR, hypoxia and HIF1a pathways support prostate cancer development through independent signaling pathways and transcriptomic profiles. AR and hypoxia/HIF1a signaling pathways independently promote prostate cancer progression and therapeutic targeting of both pathways simultaneously is warranted.
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Affiliation(s)
- Maxine G B Tran
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK.,UCL division of Surgery and Interventional Science, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Becky A S Bibby
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Trust, M20 4BX, Manchester, UK
| | - Lingjian Yang
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Trust, M20 4BX, Manchester, UK
| | - Franklin Lo
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Anne Y Warren
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, UK
| | - Deepa Shukla
- Division of Medicine, University College London, London, UK
| | - Michelle Osborne
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - James Hadfield
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Thomas Carroll
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Rory Stark
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Helen Scott
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Antonio Ramos-Montoya
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK
| | - Charlie Massie
- Uro-oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, CB02 0RE, UK.,Department of Oncology, University of Cambridge, London, CB2 0XZ, UK
| | - Patrick Maxwell
- Cambridge Institute of Medical Research, Cambridge Biomedical Campus, Cambridge, CB2 0SP, UK
| | - Catharine M L West
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Christie Hospital NHS Trust, M20 4BX, Manchester, UK.,Manchester Biomedical Research Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Ian G Mills
- Patrick G Johnston Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, BT9 7AE, UK. .,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK.
| | - David E Neal
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX3 9DU, UK.,Academic Urology Group, University of Cambridge, Cambridge, UK
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Al-Lamki RS, Hudson NJ, Bradley JR, Warren AY, Eisen T, Welsh SJ, Riddick ACP, O’Mahony FC, Turnbull A, Powles T, Reverter A, Harrison DJ, Stewart GD. The Efficacy of Sunitinib Treatment of Renal Cancer Cells Is Associated with the Protein PHAX In Vitro. Biology (Basel) 2020; 9:E74. [PMID: 32272660 PMCID: PMC7236799 DOI: 10.3390/biology9040074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 02/02/2023]
Abstract
Anti-angiogenic agents, such as the multi-tyrosine kinase inhibitor sunitinib, are key first line therapies for metastatic clear cell renal cell carcinoma (ccRCC), but their mechanism of action is not fully understood. Here, we take steps towards validating a computational prediction based on differential transcriptome network analysis that phosphorylated adapter RNA export protein (PHAX) is associated with sunitinib drug treatment. The regulatory impact factor differential network algorithm run on patient tissue samples suggests PHAX is likely an important regulator through changes in genome-wide network connectivity. Immunofluorescence staining of patient tumours showed strong localisation of PHAX to the microvasculature consistent with the anti-angiogenic effect of sunitinib. In normal kidney tissue, PHAX protein abundance was low but increased with tumour grade (G1 vs. G3/4; p < 0.01), consistent with a possible role in cancer progression. In organ culture, ccRCC cells had higher levels of PHAX protein expression than normal kidney cells, and sunitinib increased PHAX protein expression in a dose dependent manner (untreated vs. 100 µM; p < 0.05). PHAX knockdown in a ccRCC organ culture model impacted the ability of sunitinib to cause cancer cell death (p < 0.0001 untreated vs. treated), suggesting a role for PHAX in mediating the efficacy of sunitinib.
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Affiliation(s)
- Rafia S. Al-Lamki
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Nicholas J. Hudson
- School of Agriculture and Food Sciences, University of Queensland, Gatton, QLD 4343, Australia;
| | - John R. Bradley
- Department of Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; (R.S.A.-L.); (J.R.B.)
| | - Anne Y. Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Department of Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah J. Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Antony C. P. Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
| | - Fiach C. O’Mahony
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Arran Turnbull
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Thomas Powles
- Bart’s Cancer Institute, Charterhouse Square, London EC1M 6BE, UK;
| | - SCOTRRCC Collaborative
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia;
| | - David J. Harrison
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- School of Medicine, University of St. Andrews, St. Andrews KY16 9TF, UK
| | - Grant D. Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (A.Y.W.); (T.E.); (S.J.W.); (A.C.P.R.)
- Scottish Collaboration on Translational Research into Renal Cell Cancer (SCOTRRCC); fiach.o' (F.C.O.); (A.T.); (D.J.H.)
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
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Bryant RJ, Oxley J, Young GJ, Lane JA, Metcalfe C, Davis M, Turner EL, Martin RM, Goepel JR, Varma M, Griffiths DF, Grigor K, Mayer N, Warren AY, Bhattarai S, Dormer J, Mason M, Staffurth J, Walsh E, Rosario DJ, Catto JW, Neal DE, Donovan JL, Hamdy FC. The ProtecT trial: analysis of the patient cohort, baseline risk stratification and disease progression. BJU Int 2020; 125:506-514. [PMID: 31900963 PMCID: PMC7187290 DOI: 10.1111/bju.14987] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To test the hypothesis that the baseline clinico-pathological features of the men with localized prostate cancer (PCa) included in the ProtecT (Prostate Testing for Cancer and Treatment) trial who progressed (n = 198) at a 10-year median follow-up were different from those of men with stable disease (n = 1409). PATIENTS AND METHODS We stratified the study participants at baseline according to risk of progression using clinical disease stage, pathological grade and PSA level, using Cox proportional hazard models. RESULTS The findings showed that 34% of participants (n = 505) had intermediate- or high-risk PCa, and 66% (n = 973) had low-risk PCa. Of 198 participants who progressed, 101 (51%) had baseline International Society of Urological Pathology Grade Group 1, 59 (30%) Grade Group 2, and 38 (19%) Grade Group 3 PCa, compared with 79%, 17% and 5%, respectively, for 1409 participants without progression (P < 0.001). In participants with progression, 38% and 62% had baseline low- and intermediate-/high-risk disease, compared with 69% and 31% of participants with stable disease (P < 0.001). Treatment received, age (65-69 vs 50-64 years), PSA level, Grade Group, clinical stage, risk group, number of positive cores, tumour length and perineural invasion were associated with time to progression (P ≤ 0.005). Men progressing after surgery (n = 19) were more likely to have a higher Grade Group and pathological stage at surgery, larger tumours, lymph node involvement and positive margins. CONCLUSIONS We demonstrate that one-third of the ProtecT cohort consists of people with intermediate-/high-risk disease, and the outcomes data at an average of 10 years' follow-up are generalizable beyond men with low-risk PCa.
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Affiliation(s)
- Richard J. Bryant
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Jon Oxley
- Department of Cellular PathologyNorth Bristol NHS TrustBristolUK
| | - Grace J. Young
- Bristol Medical SchoolUniversity of BristolBristolUK
- The Bristol Randomised Trials CollaborationUniversity of BristolBristolUK
| | - Janet A. Lane
- Bristol Medical SchoolUniversity of BristolBristolUK
- The Bristol Randomised Trials CollaborationUniversity of BristolBristolUK
| | - Chris Metcalfe
- Bristol Medical SchoolUniversity of BristolBristolUK
- The Bristol Randomised Trials CollaborationUniversity of BristolBristolUK
| | - Michael Davis
- Bristol Medical SchoolUniversity of BristolBristolUK
| | | | | | - John R. Goepel
- Department of PathologyRoyal Hallamshire HospitalSheffieldUK
| | - Murali Varma
- Department of PathologyUniversity Hospital of WalesCardiffUK
| | | | - Ken Grigor
- Department of PathologyWestern General HospitalEdinburghUK
| | - Nick Mayer
- Department of PathologyUniversity of LeicesterLeicesterUK
| | - Anne Y. Warren
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Selina Bhattarai
- Department of PathologyLeeds Teaching Hospitals NHS TrustLeedsUK
| | - John Dormer
- Department of PathologyUniversity of LeicesterLeicesterUK
| | | | - John Staffurth
- Division of Cancer and GeneticsSchool of MedicineCardiff UniversityCardiffUK
| | - Eleanor Walsh
- Bristol Medical SchoolUniversity of BristolBristolUK
| | | | | | - David E. Neal
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
- Academic Urology GroupUniversity of CambridgeCambridgeUK
| | - Jenny L. Donovan
- Bristol Medical SchoolUniversity of BristolBristolUK
- National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care WestUniversity Hospitals Bristol NHS Foundation TrustBristolUK
| | - Freddie C. Hamdy
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
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Zawaideh JP, Sala E, Shaida N, Koo B, Warren AY, Carmisciano L, Saeb-Parsy K, Gnanapragasam VJ, Kastner C, Barrett T. Diagnostic accuracy of biparametric versus multiparametric prostate MRI: assessment of contrast benefit in clinical practice. Eur Radiol 2020; 30:4039-4049. [PMID: 32166495 DOI: 10.1007/s00330-020-06782-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [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: 10/02/2019] [Revised: 02/16/2020] [Accepted: 02/27/2020] [Indexed: 01/28/2023]
Abstract
PURPOSE To assess the added value of dynamic contrast-enhanced (DCE) in prostate MR in clinical practice. METHODS Two hundred sixty-four patients underwent prostate MRI, with T2 and DWI sequences initially interpreted, prior to full multiparametric magnetic resonance imaging (mpMRI) interpretation using a Likert 1-5 scale. A prospective opinion was given on likely benefit of contrast prior to review of the DCE sequence, and retrospectively following full mpMRI review. The final histology result following targeted and/or systematic biopsy of the prostate was used for outcome purposes. RESULTS Biparametric magnetic resonance imaging (bpMRI) and mpMRI were assigned the same score in 86% of cases; when dichotomising to a negative or positive MRI (Likert score ≥ 3), concordance increased to 92.8%. At Likert score ≥ 3 bpMRI detected 89.9% of all cancers and 93.5% clinically significant prostate cancers (csPCa) and mpMRI 90.7% and 94.6%, respectively. mpMRI had fewer false positives than bpMRI (11.4% vs 18.9%) and a lower Likert 3 rate (8.3% vs 17%), conferring higher specificity (74% vs 67%), but similar sensitivity (95% versus 94%) and ROC-AUC (90% vs 89%). At a positive MRI threshold of Likert ≥ 4, mpMRI had a higher sensitivity than bpMRI (89% versus 80%) and detected more csPCa (89.2% versus 79.6%). DCE was prospectively considered of potential benefit in 27.3%, but readers would only recall 11% of patients for DCE sequences, mainly to assess score 3 peripheral zone lesions. Following full mpMRI review, DCE was considered helpful in 28.4% of cases; in 23/75 (30.6%) of these cases this only became apparent after reviewing the sequence, reasons included increased confidence, presence of "safety-net" lesions or inflammatory lesions. CONCLUSION BpMRI has equivalent cancer detection rates to mpMRI; however, mpMRI had fewer Likert 3 call rates and increased specificity and was subjectively considered of benefit by readers in 28.4% of cases. KEY POINTS • bpMRI has similar cancer detection rates to the full mpMRI protocol at a positive MRI threshold of Likert 3. • mpMRI had fewer intermediate category 3 calls (8.3%) than bpMRI (17%) and fewer false positives than bpMRI (11.4% vs 18.9%), conferring higher specificity (74% vs 67%). • Readers considered DCE beneficial in 28.4% of cases, but in a relatively high number (30.6%) this only became apparent after reviewing the sequence.
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Affiliation(s)
- Jeries P Zawaideh
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK. .,Department of Health Sciences (DISSAL), Radiology Section, University of Genoa, Genoa, Italy.
| | - Evis Sala
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nadeem Shaida
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Brendan Koo
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | - Luca Carmisciano
- Department of Health Sciences (DISSAL), Biostatistics Section, University of Genoa, Genoa, Italy
| | - Kasra Saeb-Parsy
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Vincent J Gnanapragasam
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Christof Kastner
- CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Prostate Cancer Group, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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Smith CG, Moser T, Mouliere F, Field-Rayner J, Eldridge M, Riediger AL, Chandrananda D, Heider K, Wan JCM, Warren AY, Morris J, Hudecova I, Cooper WN, Mitchell TJ, Gale D, Ruiz-Valdepenas A, Klatte T, Ursprung S, Sala E, Riddick ACP, Aho TF, Armitage JN, Perakis S, Pichler M, Seles M, Wcislo G, Welsh SJ, Matakidou A, Eisen T, Massie CE, Rosenfeld N, Heitzer E, Stewart GD. Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors. Genome Med 2020; 12:23. [PMID: 32111235 PMCID: PMC7048087 DOI: 10.1186/s13073-020-00723-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 09/19/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established. METHODS Here, a combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n = 91) with various renal tumor subtypes, were used to determine ctDNA content in plasma and urine. RESULTS Our data revealed lower plasma ctDNA levels in RCC relative to other cancers of similar size and stage, with untargeted detection in 27.5% of patients from both cohorts. A sensitive personalized approach, applied to plasma and urine from select patients (n = 22) improved detection to ~ 50%, including in patients with early-stage disease and even benign lesions. Detection in plasma, but not urine, was more frequent amongst patients with larger tumors and in those patients with venous tumor thrombus. With data from one extensively characterized patient, we observed that plasma and, for the first time, urine ctDNA may better represent tumor heterogeneity than a single tissue biopsy. Furthermore, in a subset of patients (n = 16), longitudinal sampling revealed that ctDNA can track disease course and may pre-empt radiological identification of minimal residual disease or disease progression on systemic therapy. Additional datasets will be required to validate these findings. CONCLUSIONS These data highlight RCC as a ctDNA-low malignancy. The biological reasons for this are yet to be determined. Nonetheless, our findings indicate potential clinical utility in the management of patients with renal tumors, provided improvement in isolation and detection approaches.
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Affiliation(s)
- Christopher G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Tina Moser
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Florent Mouliere
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - Johanna Field-Rayner
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anja L Riediger
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Irena Hudecova
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andrea Ruiz-Valdepenas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tobias Klatte
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Urology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Stephan Ursprung
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Evis Sala
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Antony C P Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Tevita F Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Samantha Perakis
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine Graz, Austria Division of Oncology, Medical University of Graz, Graz, Austria
| | - Maximilian Seles
- Department of Urology, Medical University of Graz, Graz, Austria
| | - Gabriel Wcislo
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Sarah J Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Athena Matakidou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Charles E Massie
- Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ellen Heitzer
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Grant D Stewart
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
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Smith PS, Whitworth J, West H, Cook J, Gardiner C, Lim DHK, Morrison PJ, Hislop RG, Murray E, Tischkowitz M, Warren AY, Woodward ER, Maher ER. Characterization of renal cell carcinoma-associated constitutional chromosome abnormalities by genome sequencing. Genes Chromosomes Cancer 2020; 59:333-347. [PMID: 31943436 PMCID: PMC7187337 DOI: 10.1002/gcc.22833] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/21/2022] Open
Abstract
Constitutional translocations, typically involving chromosome 3, have been recognized as a rare cause of inherited predisposition to renal cell carcinoma (RCC) for four decades. However, knowledge of the molecular basis of this association is limited. We have characterized the breakpoints by genome sequencing (GS) of constitutional chromosome abnormalities in five individuals who presented with RCC. In one individual with constitutional t(10;17)(q11.21;p11.2), the translocation breakpoint disrupted two genes: the known renal tumor suppressor gene (TSG) FLCN (and clinical features of Birt‐Hogg‐Dubé syndrome were detected) and RASGEF1A. In four cases, the rearrangement breakpoints did not disrupt known inherited RCC genes. In the second case without chromosome 3 involvement, the translocation breakpoint in an individual with a constitutional t(2;17)(q21.1;q11.2) mapped 12 Kb upstream of NLK. Interestingly, NLK has been reported to interact indirectly with FBXW7 and a previously reported RCC‐associated translocation breakpoint disrupted FBXW7. In two cases of constitutional chromosome 3 translocations, no candidate TSGs were identified in the vicinity of the breakpoints. However, in an individual with a constitutional chromosome 3 inversion, the 3p breakpoint disrupted the FHIT TSG (which has been reported previously to be disrupted in two apparently unrelated families with an RCC‐associated t(3;8)(p14.2;q24.1). These findings (a) expand the range of constitutional chromosome rearrangements that may be associated with predisposition to RCC, (b) confirm that chromosome rearrangements not involving chromosome 3 can predispose to RCC, (c) suggest that a variety of molecular mechanisms are involved the pathogenesis of translocation‐associated RCC, and (d) demonstrate the utility of GS for investigating such cases.
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Affiliation(s)
- Philip S Smith
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Hannah West
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Jacqueline Cook
- Department of Clinical Genetics, Sheffield Children's Hospital, Sheffield, UK
| | - Carol Gardiner
- West of Scotland Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Derek H K Lim
- West Midlands Regional Genetics Service, Birmingham Women's and Children's National Health Service (NHS) Foundation Trust, Birmingham, UK
| | - Patrick J Morrison
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast, UK
| | - R Gordon Hislop
- East of Scotland Regional Genetics Service, Ninewells Hospital, Dundee, UK
| | - Emily Murray
- East of Scotland Regional Genetics Service, Ninewells Hospital, Dundee, UK
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- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust and Cancer Research UK Cambridge Centre, Cambridge, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University Hospitals NHS Foundation Trust, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health Innovation Manchester, Manchester, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, UK
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Bradley JR, Wang J, Pacey S, Warren AY, Pober JS, Al‐Lamki RS. Tumor necrosis factor receptor-2 signaling pathways promote survival of cancer stem-like CD133 + cells in clear cell renal carcinoma. FASEB Bioadv 2020; 2:126-144. [PMID: 32123862 PMCID: PMC7003657 DOI: 10.1096/fba.2019-00071] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 08/25/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) contains cancer stem-like cells (CSCs) that express CD133 (ccRCC-CD133+). CSCs are rarely in cell cycle and, as nonproliferating cells, resist most chemotherapeutic agents. Previously, we reported that tumor necrosis factor receptor-2 (TNFR2) signaling promotes the cell cycle entry of ccRCC-CD133+CSCs, rendering them susceptible to cell-cycle-dependent chemotherapeutics. Here, we describe a TNFR2-activated signaling pathway in ccRCC-CD133+CSCs that is required for cell survival. Wild-type (wt)TNF or R2TNF but not R1TNF (TNF muteins that selectively bind to TNFR2 and TNFR1) induces phosphorylation of signal transducer and activator of transcription 3 (STAT3) on serine727 but not tyrosine705, resulting in pSTAT3Ser727 translocation to and colocalization with TNFR2 in mitochondria. R2TNF signaling activates a kinase cascade involving the phosphorylation of VEGFR2, PI-3K, Akt, and mTORC. Inhibition of any of the kinases or siRNA knockdown of TNFR2 or STAT3 promotes cell death associated with mitochondrial morphological changes, cytochrome c release, generation of reactive oxygen species, and TUNEL+cells expressing phosphorylated mixed lineage kinase-like (MLKL). Pretreatment with necrostatin-1 is more protective than z-VAD.fmk, suggesting that most death is necroptotic and TNFR2 signaling promotes cell survival by preventing mitochondrial-mediated necroptosis. These data suggest that a TNFR2 selective agonist may offer a potential therapeutic strategy for ccRCC.
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Affiliation(s)
- John R. Bradley
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Jun Wang
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Simon Pacey
- Department of OncologyNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
| | - Anne Y. Warren
- Department of HistopathologyAddenbrooke's Hospital and University of CambridgeCambridgeUK
| | | | - Rafia S. Al‐Lamki
- Department of MedicineNIHR Cambridge Biomedical Research CentreUniversity of CambridgeCambridgeUK
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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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Casey RT, McLean MA, Challis BG, McVeigh TP, Warren AY, Mendil L, Houghton R, De Sanctis S, Kosmoliaptsis V, Sandford RN, Gallagher FA, Maher ER. Fumarate Metabolic Signature for the Detection of Reed Syndrome in Humans. Clin Cancer Res 2020; 26:391-396. [PMID: 31636096 DOI: 10.1158/1078-0432.ccr-19-1729] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/30/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Inherited pathogenic variants in genes encoding the metabolic enzymes succinate dehydrogenase (SDH) and fumarate hydratase predispose to tumor development through accumulation of oncometabolites (succinate and fumarate, respectively; ref. 1). Noninvasive in vivo detection of tumor succinate by proton magnetic resonance spectroscopy (1H-MRS) has been reported in SDH-deficient tumors, but the potential utility of this approach in the management of patients with hereditary leiomyomatosis and renal cell cancer syndrome or Reed syndrome is unknown. EXPERIMENTAL DESIGN Magnetic resonance spectroscopy (1H-MRS) was performed on three cases and correlated with germline genetic results and tumor IHC when available. RESULTS Here, we have demonstrated a proof of principle that 1H-MRS can provide a noninvasive diagnosis of hereditary leiomyomatosis and renal cell cancer syndrome or Reed syndrome through detection of fumarate accumulation in vivo. CONCLUSIONS This study demonstrates that in vivo detection of fumarate could be employed as a functional biomarker.
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Affiliation(s)
- Ruth T Casey
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge, United Kingdom.
- Department of Endocrinology, Cambridge University NHS Foundation Trust, Cambridge, United Kingdom
| | - Mary A McLean
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Benjamin G Challis
- Department of Endocrinology, Cambridge University NHS Foundation Trust, Cambridge, United Kingdom
| | - Terri P McVeigh
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Anne Y Warren
- Department of Histopathology, Cambridge University NHS Foundation Trust and Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Lee Mendil
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Richard Houghton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Stefano De Sanctis
- Department of Histopathology, Cambridge University NHS Foundation Trust and Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Richard N Sandford
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Ferdia A Gallagher
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
- Department of Radiology, Cambridge University NHS Foundation Trust, Cambridge, United Kingdom
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
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Barrett T, Riemer F, McLean MA, Kaggie JD, Robb F, Warren AY, Graves MJ, Gallagher FA. Molecular imaging of the prostate: Comparing total sodium concentration quantification in prostate cancer and normal tissue using dedicated 13 C and 23 Na endorectal coils. J Magn Reson Imaging 2020; 51:90-97. [PMID: 31081564 DOI: 10.1002/jmri.26788] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/30/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND There has been recent interest in nonproton MRI including hyperpolarized carbon-13 (13 C) imaging. Prostate cancer has been shown to have a higher tissue sodium concentration (TSC) than normal tissue. Sodium (23 Na) and 13 C nuclei have a frequency difference of only 1.66 MHz at 3T, potentially enabling 23 Na imaging with a 13 C-tuned coil and maximizing the metabolic information obtained from a single study. PURPOSE To compare TSC measurements from a 13 C-tuned endorectal coil to those quantified with a dedicated 23 Na-tuned coil. STUDY TYPE Prospective. POPULATION Eight patients with biopsy-proven, intermediate/high risk prostate cancer imaged prior to prostatectomy. SEQUENCE 3T MRI with separate dual-tuned 1 H/23 Na and 1 H/13 C endorectal receive coils to quantify TSC. ASSESSMENT Regions-of-interest for TSC quantification were defined for normal peripheral zone (PZ), normal transition zone (TZ), and tumor, with reference to histopathology maps. STATISTICAL TESTS Two-sided Wilcoxon rank sum with additional measures of correlation, coefficient of variation, and Bland-Altman plots to assess for between-test differences. RESULTS Mean TSC for normal PZ and TZ were 39.2 and 33.9 mM, respectively, with the 23 Na coil and 40.1 and 36.3 mM, respectively, with the 13 C coil (P = 0.22 and P = 0.11 for the intercoil comparison, respectively). For tumor tissue, there was no statistical difference between the overall mean tumor TSC measured with the 23 Na coil (41.8 mM) and with the 13 C coil (46.6 mM; P = 0.38). Bland-Altman plots showed good repeatability for tumor TSC measurements between coils, with a reproducibility coefficient of 9 mM; the coefficient of variation between the coils was 12%. The Pearson correlation coefficient for TSC between coils for all measurements was r = 0.71 (r2 = 0.51), indicating a strong positive linear relationship. The mean TSC within PZ tumors was significantly higher compared with normal PZ for both the 23 Na coil (45.4 mM; P = 0.02) and the 13 C coil (49.4 mM; P = 0.002). DATA CONCLUSION We demonstrated the feasibility of using a carbon-tuned coil to quantify TSC, enabling dual metabolic information from a single coil. This approach could make the acquisition of both 23 Na-MRI and 13 C-MRI feasible in a single clinical imaging session. LEVEL OF EVIDENCE 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;51:90-97.
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Affiliation(s)
- Tristan Barrett
- Department of Radiology, University of Cambridge, Cambridge, UK
- Department of Radiology, Cambridge University Hospitals, Cambridge, UK
| | - Frank Riemer
- Department of Radiology, University of Cambridge, Cambridge, UK
| | | | - Joshua D Kaggie
- Department of Radiology, University of Cambridge, Cambridge, UK
| | | | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals and University of Cambridge, Cambridge, UK
| | - Martin J Graves
- Department of Radiology, Cambridge University Hospitals, Cambridge, UK
| | - Ferdia A Gallagher
- Department of Radiology, University of Cambridge, Cambridge, UK
- Department of Radiology, Cambridge University Hospitals, Cambridge, UK
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Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW, Oostveen M, Collord G, Tarpey PS, Cagan A, Hooks Y, Brougham M, Reynolds BC, Barone G, Anderson J, Jorgensen M, Burke GAA, Visser J, Nicholson JC, Smeulders N, Mushtaq I, Stewart GD, Campbell PJ, Wedge DC, Martincorena I, Rampling D, Hook L, Warren AY, Coleman N, Chowdhury T, Sebire N, Drost J, Saeb-Parsy K, Stratton MR, Straathof K, Pritchard-Jones K, Behjati S. Embryonal precursors of Wilms tumor. Science 2019; 366:1247-1251. [PMID: 31806814 PMCID: PMC6914378 DOI: 10.1126/science.aax1323] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/04/2019] [Accepted: 11/06/2019] [Indexed: 12/27/2022]
Abstract
Adult cancers often arise from premalignant clonal expansions. Whether the same is true of childhood tumors has been unclear. To investigate whether Wilms tumor (nephroblastoma; a childhood kidney cancer) develops from a premalignant background, we examined the phylogenetic relationship between tumors and corresponding normal tissues. In 14 of 23 cases studied (61%), we found premalignant clonal expansions in morphologically normal kidney tissues that preceded tumor development. These clonal expansions were defined by somatic mutations shared between tumor and normal tissues but absent from blood cells. We also found hypermethylation of the H19 locus, a known driver of Wilms tumor development, in 58% of the expansions. Phylogenetic analyses of bilateral tumors indicated that clonal expansions can evolve before the divergence of left and right kidney primordia. These findings reveal embryonal precursors from which unilateral and multifocal cancers develop.
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Affiliation(s)
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Reem Al-Saadi
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Suzanne Tugnait
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | | | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Minou Oostveen
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick S Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Mark Brougham
- Department of Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Ben C Reynolds
- Department of Paediatric Nephrology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Giuseppe Barone
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Johannes Visser
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James C Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Naima Smeulders
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | | | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Tanzina Chowdhury
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Neil Sebire
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, 3584 CS Utrecht, Netherlands
| | - Kourosh Saeb-Parsy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Karin Straathof
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Kathy Pritchard-Jones
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Braga FAV, Botting RA, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera MDC, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Behjati S, Clatworthy MR. Spatiotemporal immune zonation of the human kidney. Science 2019; 365:1461-1466. [PMID: 31604275 PMCID: PMC7343525 DOI: 10.1126/science.aat5031] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [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: 03/05/2018] [Revised: 01/31/2019] [Accepted: 09/04/2019] [Indexed: 11/02/2022]
Abstract
Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly or by cross-talk with immune cells. We used single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. We reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, our study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.
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Affiliation(s)
- Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Alexandra M Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Gordon L Frazer
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | - Joy UL Staniforth
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
| | | | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah J Farndon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Charlotte Guzzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Grace Collord
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Tevita Aho
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Antony CP Riddick
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Stephen Farrell
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Johanna Burge
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Marc Bajenoff
- Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Surgery, University of Cambridge, CB2 0QQ, UK
| | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- UCL Great Ormond Street Hospital Institute of Child Health, London WC1N 1E, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Sam Behjati
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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47
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Caglic I, Povalej Brzan P, Warren AY, Bratt O, Shah N, Barrett T. Defining the incremental value of 3D T2-weighted imaging in the assessment of prostate cancer extracapsular extension. Eur Radiol 2019; 29:5488-5497. [PMID: 30887192 PMCID: PMC6719333 DOI: 10.1007/s00330-019-06070-6] [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] [Received: 08/03/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 12/12/2022]
Abstract
Objectives To assess the added value of 3D T2-weighted imaging (T2WI) over conventional 2D T2WI in diagnosing extracapsular extension (ECE). Methods Seventy-five patients undergoing 3-T MRI before radical prostatectomy were included. PI-RADS ≥ 4 lesions were assessed for ECE on 2D T2W images using a 5-point Likert scale (1 = no ECE, 5 = definite ECE) and the length of tumour prostatic capsular contact. A second read using 3D T2W images and reformats evaluated ECE and the maximal 3D capsular contact length and surface. Results One hundred six lesions were identified at MRI. ECE was confirmed by histology in 54% (57/106) of lesions and 64% (48/75) of patients. Sensitivity and specificity for 3D T2 reads were 75.4% versus 64.9% (p = 0.058), respectively, and 83.7% versus 85.7% (p = 0.705) for 2D T2 reads, respectively. 3D T2W reads showed significantly higher mean subjective Likert scores of 3.7 ± 1.4 versus 3.3 ± 1.4 (p = 0.001) in ECE-positive lesions and lower mean Likert score of 1.5 ± 1 versus 1.6 ± 0.9 (p = 0.27) in ECE-negative lesions compared with 2D T2W reads. 3D contact significantly increased sensitivity from 59.6 to 73.7% (p = 0.03), whilst maintaining the same specificity of 87.8% (p = 1). High-grade group tumours (≥ Gleason 4 + 3) showed significantly higher ECE prevalence than low-grade tumours (88% versus 44%, p < 0.001) and a positive predictive value (PPV) for ECE of 90.9% with ≥ 5 mm of contact versus PPV of 90.4% at ≥ 12.5 mm for lower grade tumours. Conclusions 3D T2WI significantly increases sensitivity and confidence in calling ECE. The capsular contact length threshold differed between low- and high-grade cancers. Key Points • 3D capsular contact length and 3D surface contact significantly increased sensitivity in diagnosing ECE. • 3D T2W reads significantly increased reader confidence in calling ECE. • Thresholds for capsular contact length differed between low-grade and high-grade cancers. Electronic supplementary material The online version of this article (10.1007/s00330-019-06070-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iztok Caglic
- Department of Radiology, Norfolk & Norwich University Hospital, Colney Lane, Norwich, Norfolk, NR4 7UY, UK. .,Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK. .,University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia.
| | - Petra Povalej Brzan
- University of Maribor, Faculty of Health Sciences, Maribor, Slovenia.,University of Maribor, Faculty of Electrical Engineering and Computer Science, Maribor, Slovenia
| | - Anne Y Warren
- Department of Histopathology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Ola Bratt
- Department of Urology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Nimish Shah
- Department of Urology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Tristan Barrett
- Department of Radiology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.,CamPARI Clinic, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
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48
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Syafruddin SE, Rodrigues P, Vojtasova E, Patel SA, Zaini MN, Burge J, Warren AY, Stewart GD, Eisen T, Bihary D, Samarajiwa SA, Vanharanta S. A KLF6-driven transcriptional network links lipid homeostasis and tumour growth in renal carcinoma. Nat Commun 2019; 10:1152. [PMID: 30858363 PMCID: PMC6411998 DOI: 10.1038/s41467-019-09116-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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] [Received: 06/29/2018] [Accepted: 02/15/2019] [Indexed: 12/17/2022] Open
Abstract
Transcriptional networks are critical for the establishment of tissue-specific cellular states in health and disease, including cancer. Yet, the transcriptional circuits that control carcinogenesis remain poorly understood. Here we report that Kruppel like factor 6 (KLF6), a transcription factor of the zinc finger family, regulates lipid homeostasis in clear cell renal cell carcinoma (ccRCC). We show that KLF6 supports the expression of lipid metabolism genes and promotes the expression of PDGFB, which activates mTOR signalling and the downstream lipid metabolism regulators SREBF1 and SREBF2. KLF6 expression is driven by a robust super enhancer that integrates signals from multiple pathways, including the ccRCC-initiating VHL-HIF2A pathway. These results suggest an underlying mechanism for high mTOR activity in ccRCC cells. More generally, the link between super enhancer-driven transcriptional networks and essential metabolic pathways may provide clues to the mechanisms that maintain the stability of cell identity-defining transcriptional programmes in cancer. Super enhancers are frequently involved in the dysregulation of gene expression in cancer. Here, in kidney cancer, a super enhancer is shown to drive the expression of KLF6, which alters the expression of lipid metabolism genes and promotes tumorigenesis.
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Affiliation(s)
- Saiful E Syafruddin
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.,UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Paulo Rodrigues
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Erika Vojtasova
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Saroor A Patel
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - M Nazhif Zaini
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Johanna Burge
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Grant D Stewart
- Academic Urology Group, Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Tim Eisen
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK.,Department of Oncology, Addenbrooke's Hospital, Cambridge University Health Partners, Cambridge, CB2 0QQ, UK.,Oncology Early Clinical Development, AstraZeneca, Cambridge, SG8 6EH, UK
| | - Dóra Bihary
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Sakari Vanharanta
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
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49
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Warren AY, Massie CE, Watt K, Luko K, Orafidiya F, Selth LA, Mohammed H, Chohan BS, Menon S, Baridi A, Zhao W, Escriu C, Pungsrinont T, D'Santos C, Yang X, Taylor C, Qureshi A, Zecchini VR, Shaw GL, Dehm SM, Mills IG, Carroll JS, Tilley WD, McEwan IJ, Baniahmad A, Neal DE, Asim M. A reciprocal feedback between the PDZ binding kinase and androgen receptor drives prostate cancer. Oncogene 2019; 38:1136-1150. [PMID: 30237440 PMCID: PMC6514849 DOI: 10.1038/s41388-018-0501-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/16/2018] [Revised: 07/17/2018] [Accepted: 08/16/2018] [Indexed: 12/23/2022]
Abstract
Elucidation of mechanisms underlying the increased androgen receptor (AR) activity and subsequent development of aggressive prostate cancer (PrCa) is pivotal in developing new therapies. Using a systems biology approach, we interrogated the AR-regulated proteome and identified PDZ binding kinase (PBK) as a novel AR-regulated protein that regulates full-length AR and AR variants (ARVs) activity in PrCa. PBK overexpression in aggressive PrCa is associated with early biochemical relapse and poor clinical outcome. In addition to its carboxy terminus ligand-binding domain, PBK directly interacts with the amino terminus transactivation domain of the AR to stabilise it thereby leading to increased AR protein expression observed in PrCa. Transcriptome sequencing revealed that PBK is a mediator of global AR signalling with key roles in regulating tumour invasion and metastasis. PBK inhibition decreased growth of PrCa cell lines and clinical specimen cultured ex vivo. We uncovered a novel interplay between AR and PBK that results in increased AR and ARVs expression that executes AR-mediated growth and progression of PrCa, with implications for the development of PBK inhibitors for the treatment of aggressive PrCa.
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Affiliation(s)
- Anne Y Warren
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, UK
| | - Charlie E Massie
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kate Watt
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Katarina Luko
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Folake Orafidiya
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
- Freemasons Foundation Centre for Men's Health, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, OHSU, Portland, USA
| | - Brinder S Chohan
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, UK
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ajoeb Baridi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wanfeng Zhao
- Department of Pathology, Addenbrooke's Cambridge University Hospital, Cambridge, UK
| | - Carles Escriu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Xiaoping Yang
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Chris Taylor
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Arham Qureshi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Vincent R Zecchini
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Greg L Shaw
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, USA
| | - Ian G Mills
- Prostate Cancer UK/Movember Centre of Excellence, CCRCB, Queens University, Belfast, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
- Freemasons Foundation Centre for Men's Health, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, Australia
| | - Iain J McEwan
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - David E Neal
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Mohammad Asim
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.
- Department of Clinical & Experimental Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK.
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50
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Barrett T, Lawrence EM, Priest AN, Warren AY, Gnanapragasam VJ, Gallagher FA, Sala E. Repeatability of diffusion-weighted MRI of the prostate using whole lesion ADC values, skew and histogram analysis. Eur J Radiol 2019; 110:22-29. [PMID: 30599864 DOI: 10.1016/j.ejrad.2018.11.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 11/02/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/11/2022]
Abstract
PURPOSE To investigate the repeatability of diffusion-weighted imaging parameter including ADC-derived histogram values in prostate cancer. METHODS 10 patients with prostate cancer were prospectively recruited to a retest cohort. 3 T diffusion-weighted MRI of the prostate was acquired consecutively with patient getting off the scanner between studies. Prostatectomy-histopathology defined tumour regions-of-interest were outlined on ADC maps and diffusion-weighted metrics including histograms were calculated. The coefficient of reproducibility (CoR) and Bland-Altman plots were used to assess repeatability. RESULTS 10th centile, 90th centile, and median ADC showed good repeatability with mean difference ranging from -0.005 to -0.025 × 103 mm2s-1, and CoR ranging from 0.271-0.294 × 103 mm2s-1 of scan 1 mean). Two measures of heterogeneity and simplified texture, IQR and mean local range, had only moderate repeatability. IQR had a mean difference of -0.032 × 103 mm2s-1 between scans with CoR 0.181 × 103 mm2s-1 (56% of scan 1 mean). Mean local range had a mean difference -0.008 × 103 mm2s-1 between scans (37% of scan 1 mean). Bland-Altman plots showed good repeatability for test and re-test analysis for median, percentile and mean range values. All ADC values had good reliability regardless of whether the tumour border was included in quantitative analysis. ADC histogram skew had poor repeatability, CoR 0.78 × 103 mm2s-1 (373% of scan 1 mean). CONCLUSION 10th and 90th centile ADC demonstrated sufficient repeatability for clinical use. However, more advanced measures of heterogeneity such as histogram skew, IQR, or mean local range may be limited by their repeatability.
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Affiliation(s)
- Tristan Barrett
- Department of Radiology, University of Cambridge, Cambridge, UK; Department of Radiology, Addenbrooke's Hospital, Cambridge, UK; CamPARI Clinic, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK.
| | - Edward M Lawrence
- Department of Radiology, University of Cambridge, Cambridge, UK; Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, United States of America
| | - Andrew N Priest
- Department of Radiology, Addenbrooke's Hospital, Cambridge, UK
| | - Anne Y Warren
- CamPARI Clinic, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Histopathology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- CamPARI Clinic, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK; Department of Urology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK
| | - Ferdia A Gallagher
- Department of Radiology, University of Cambridge, Cambridge, UK; Department of Radiology, Addenbrooke's Hospital, Cambridge, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Cambridge, UK; Department of Radiology, Addenbrooke's Hospital, Cambridge, UK
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