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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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/11/2021] [Accepted: 02/08/2024] [Indexed: 03/03/2024]
Abstract
The development of cancer is an evolutionary process involving the sequential acquisition of genetic alterations that disrupt normal biological processes, enabling tumor cells to rapidly proliferate and eventually invade and metastasize to other tissues. We investigated the genomic evolution of prostate cancer through the application of three separate classification methods, each designed to investigate a different aspect of tumor evolution. Integrating the results revealed the existence of two distinct types of prostate cancer that arise from divergent evolutionary trajectories, designated as the Canonical and Alternative evolutionary disease types. We therefore propose the evotype model for prostate cancer evolution wherein Alternative-evotype tumors diverge from those of the Canonical-evotype through the stochastic accumulation of genetic alterations associated with disruptions to androgen receptor DNA binding. Our model unifies many previous molecular observations, providing a powerful new framework to investigate prostate cancer disease progression.
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Affiliation(s)
- Dan J Woodcock
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Atef Sahli
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | | | - Vinayak Bhandari
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Andreas J Gruber
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK; Department of Biology, University of Konstanz, Konstanz, Germany
| | - Aleksandra Ziubroniewicz
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK; Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yaobo Xu
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Bernard J Pope
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia; Department of Medicine, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, Australia
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK; Institute of Interdisciplinary Research (IRIBHM), Universite Libre de Bruxelles, Brussels, Belgium
| | - Stefan C Dentro
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK
| | - J Henry R Farmery
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent Gnanapragasam
- Cambridge Urology Translational Research and Clinical Trials Office, Addenbrooke's Hospital, Cambridge, UK; Division of Urology, Department of Surgery, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | | | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, UK; Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Michael Fraser
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK; The Christie NHS Foundation Trust, Manchester, UK; CRUK Manchester Institute, University of Manchester, Manchester, UK; Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada; Departments of Human Genetics and Urology, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anthony J Costello
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Niall M Corcoran
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christopher M Hovens
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia; Department of Urology, Royal Melbourne Hospital, Melbourne, VIC, Australia; Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, UK; Early Detection Programme and Urological Malignancies Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Andy G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK; School of Medicine/School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; Earlham Institute, Norwich, UK.
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK.
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK; Norwich Medical School, University of East Anglia, Norwich, UK.
| | - David C Wedge
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; Big Data Institute, University of Oxford, Oxford, UK; Manchester Cancer Research Centre, University of Manchester, Manchester, UK; Oxford NIHR Biomedical Research Centre, Oxford, UK; Manchester NIHR Biomedical Research Centre, Manchester, UK.
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Kaljunen H, Taavitsainen S, Kaarijärvi R, Takala E, Paakinaho V, Nykter M, Bova GS, Ketola K. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol 2023; 13:1260826. [PMID: 38023254 PMCID: PMC10643534 DOI: 10.3389/fonc.2023.1260826] [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: 07/18/2023] [Accepted: 09/29/2023] [Indexed: 12/01/2023] Open
Abstract
Prostate cancer is one of the leading causes of death among men worldwide, and thus, research on the genetic factors enabling the formation of treatment-resistant cancer cells is crucial for improving patient outcomes. Here, we report a cell line-specific dependence on FANCI and related signaling pathways to counteract the effects of DNA-damaging chemotherapy in prostate cancer. Our results reveal that FANCI depletion results in significant downregulation of Fanconi anemia (FA) pathway members in prostate cancer cells, indicating that FANCI is an important regulator of the FA pathway. Furthermore, we found that FANCI silencing reduces proliferation in p53-expressing prostate cancer cells. This extends the evidence that inactivation of FANCI may convert cancer cells from a resistant state to an eradicable state under the stress of DNA-damaging chemotherapy. Our results also indicate that high expression of FA pathway genes correlates with poorer survival in prostate cancer patients. Moreover, genomic alterations of FA pathway members are prevalent in prostate adenocarcinoma patients; mutation and copy number information for the FA pathway genes in seven patient cohorts (N = 1,732 total tumor samples) reveals that 1,025 (59.2%) tumor samples have an alteration in at least one of the FA pathway genes, suggesting that genomic alteration of the pathway is a prominent feature in patients with the disease.
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Affiliation(s)
- Heidi Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Roosa Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eerika Takala
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med 2023; 15:82. [PMID: 37828555 PMCID: PMC10571458 DOI: 10.1186/s13073-023-01242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical trials do not include evolution as an essential feature. Whether or not analysis of genomic data in an evolutionary context in primary prostate cancer can provide unique added value in the research and clinical domains remains an open question. METHODS We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high-risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones. RESULTS In patient GP5, CDK12 inactivation was among the first mutations, leading to a PrCa tandem duplicator phenotype and initiating the cancer around age 50, followed by rapid cancer evolution after age 57, and metastasis around age 59, 5 years prior to prostatectomy. In patient GP12, accelerated cancer progression was detected after age 54, and metastasis occurred around age 56, 3 years prior to prostatectomy. Multiple metastasis-originating events were identified in each patient and tracked anatomically. Metastasis from prostate to lymph nodes occurred strictly ipsilaterally in all 12 detected events. In this pilot, metastatic subclone content analysis appears to substantially enhance the identification of key drivers. Evolutionary analysis' potential impact on therapy selection appears positive in these pilot cases. CONCLUSIONS PrCa evolutionary analysis allows tracking of anatomic site of origin, timing of cancer origin and spread, and distinction of metastatic-capable from non-metastatic subclones. This enables better identification of actionable targets for therapy. If extended to larger cohorts, it appears likely that similar analyses could add substantial biological insight and clinically relevant value.
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Affiliation(s)
- Anssi Nurminen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Serafiina Jaatinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tom Lesluyes
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Kerstin Haase
- The Francis Crick Institute, London, NW1 1AT, UK
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany
| | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland
| | - Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Jenni Kesäniemi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tiia Nikupaavola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Irina Rinta-Kiikka
- Imaging Centre, Department of Radiology, Tampere University Hospital, Tampere, Finland
| | - Jarno Riikonen
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antti Kaipia
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teemu Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, M20 4GJ, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.
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4
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Sattari M, Kohvakka A, Moradi E, Rauhala H, Urhonen H, Isaacs WB, Nykter M, Murtola TJ, Tammela TLJ, Latonen L, Bova GS, Kesseli J, Visakorpi T. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer 2023:ERC-22-0247. [PMID: 37140987 DOI: 10.1530/erc-22-0247] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Prostate cancer (PCa) is the second-most common cause of male cancer-related death in western industrialized countries, and the emergence of metastases is a key challenge in the treatment of PCa. Accumulating studies have shown that long noncoding RNAs (lncRNAs) play an important role in the regulation of diverse cellular and molecular processes during the development and progression of cancer. Here, we utilized a unique cohort of castration-resistant prostate cancer metastases (mCRPC) and corresponding localized tumors and RNA sequencing (RNA-seq). First, we showed that patient-to-patient variability accounted for most of the variance in lncRNA expression between the samples, suggesting that genomic alterations in the samples are the main drivers of lncRNA expression in PCa metastasis. Subsequently, we identified 27 lncRNAs with differential expression (DE-lncRNAs) between metastases and corresponding primary tumors, suggesting that they are mCRPC-specific lncRNAs. Analyses of potential regulation by transcription factors (TFs) revealed that approximately half of the DE-lncRNAs have at least one binding site for the androgen receptor (AR) in their regulatory regions. In addition, transcription factor enrichment analysis revealed the enrichment of binding sites for PCa-associated TFs, such as FOXA1 and HOXB13, in the regulatory regions of the DE-lncRNAs. In a cohort of prostatectomy-treated prostate tumors, four of the DE-lncRNAs showed association with progression-free time, and two of them (lnc-SCFD2-2, and lnc-R3HCC1L-8) were independent prognostic markers. Our study highlights several mCRPC-specific lncRNAs that might be important in the progression of the disease to the metastatic stage and may also serve as potential biomarkers for aggressive PCa.
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Affiliation(s)
- Mina Sattari
- M Sattari, faculty of medicine and health technology, Tampere University, Tampere, 33014, Finland
| | - Annika Kohvakka
- A Kohvakka, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Elaheh Moradi
- E Moradi, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland - Kuopio Campus, Kuopio, Finland
| | - Hanna Rauhala
- H Rauhala, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henna Urhonen
- H Urhonen, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - William B Isaacs
- W Isaacs, The James Buchanan Brady Urological Institute, Johns Hopkins, Baltimore, United States
| | - Matti Nykter
- M Nykter, Faculty of medicine and health technology, Tays Cancer Center, Tampere, Finland
| | - Teemu J Murtola
- T Murtola, Faculty of Medicine and Health Technology, Tampere Universities, Tampere, Finland
| | - Teuvo L J Tammela
- T Tammela, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Leena Latonen
- L Latonen, Institute of Biomedicine, University of Eastern Finland School of Medicine, Kuopio, Finland
| | - G Steven Bova
- G Bova, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Juha Kesseli
- J Kesseli, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Tapio Visakorpi
- T Visakorpi, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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5
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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, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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. 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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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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8
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Ouellet V, Erickson A, Wiley K, Morrissey C, Berge V, Moreno CS, Tasken KA, Trudel D, True LD, Lewis MS, Svindland A, Ertunc O, Vidal ID, Osunkoya AO, Jones T, Bova GS, Lamminen T, Achtman AH, Buzza M, Kouspou MM, Bigler SA, Zhou X, Freedland SJ, Mes-Masson AM, Garraway IP, Trock BJ, Taimen P, Saad F, Mirtti T, Knudsen BS, De Marzo AM. The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource. Cancer Epidemiol Biomarkers Prev 2022; 31:715-727. [PMID: 35131885 PMCID: PMC9381093 DOI: 10.1158/1055-9965.epi-21-0600] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The need to better understand the molecular underpinnings of the heterogeneous outcomes of patients with prostate cancer is a pressing global problem and a key research priority for Movember. To address this, the Movember Global Action Plan 1 Unique tissue microarray (GAP1-UTMA) project constructed a set of unique and richly annotated tissue microarrays (TMA) from prostate cancer samples obtained from multiple institutions across several global locations. METHODS Three separate TMA sets were built that differ by purpose and disease state. RESULTS The intended use of TMA1 (Primary Matched LN) is to validate biomarkers that help determine which clinically localized prostate cancers with associated lymph node metastasis have a high risk of progression to lethal castration-resistant metastatic disease, and to compare molecular properties of high-risk index lesions within the prostate to regional lymph node metastases resected at the time of prostatectomy. TMA2 (Pre vs. Post ADT) was designed to address questions regarding risk of castration-resistant prostate cancer (CRPC) and response to suppression of the androgen receptor/androgen axis, and characterization of the castration-resistant phenotype. TMA3 (CRPC Met Heterogeneity)'s intended use is to assess the heterogeneity of molecular markers across different anatomic sites in lethal prostate cancer metastases. CONCLUSIONS The GAP1-UTMA project has succeeded in combining a large set of tissue specimens from 501 patients with prostate cancer with rich clinical annotation. IMPACT This resource is now available to the prostate cancer community as a tool for biomarker validation to address important unanswered clinical questions around disease progression and response to treatment.
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Affiliation(s)
- Véronique Ouellet
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
| | - Andrew Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Department of Pathology, Helsinki and Uusimaa Hospital District and Medicum, University of Helsinki, Helsinki, Finland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Kathy Wiley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Viktor Berge
- Department of Urology, Oslo University Hospital, Oslo, Norway
| | - Carlos S. Moreno
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Kristin Austlid Tasken
- Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dominique Trudel
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Pathology and Cellular Biology, Université de Montréal, Montreal, Canada
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Michael S. Lewis
- West Los Angeles Veterans Affairs Medical Center and Departments of Pathology and Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aud Svindland
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Onur Ertunc
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Suleyman Demirel University, Department of Pathology, Training and Research Hospital East Campus, Isparta, Turkey
| | - Igor Damasceno Vidal
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adeboye O. Osunkoya
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
- Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Tracy Jones
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Tarja Lamminen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | | | - Steven A. Bigler
- Department of Pathology, Mississippi Baptist Medical Center, Jackson, Mississippi
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Stephen J. Freedland
- Center for Integrated Research on Cancer and Lifestyle, Cedars-Sinai Medical Center, Los Angeles, California
- Section of Urology, Durham VA Medical Center, Durham, North Carolina
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Medicine, Université de Montréal, Montreal, Canada
| | - Isla P. Garraway
- Department of Urology, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California, Los Angeles, California
- Division of Urology, Greater Los Angeles VA Healthcare System, Los Angeles, California
| | - Bruce J. Trock
- Department of Urology and Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pekka Taimen
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Fred Saad
- Centre de recherche du Centre hospitalier de l'Université de Montréal et Institut du cancer de Montréal, Montreal, Canada
- Department of Surgery, Université de Montréal, Montreal, Canada
| | - Tuomas Mirtti
- HUS Diagnostic Center, Department of Pathology, HUS Helsinki University Hospital, Helsinki, Finland
- Medicum and Research Program In Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Beatrice S. Knudsen
- Digital and Computational Pathology, University of Utah, Salt Lake City, Utah
| | - Angelo M. De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology and Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
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9
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Ketola K, Kaljunen H, Taavitsainen S, Kaarijärvi R, Järvelä E, Rodríguez-Martín B, Haase K, Woodcock DJ, Tubio J, Wedge DC, Nykter M, Bova GS. Subclone Eradication Analysis Identifies Targets for Enhanced Cancer Therapy and Reveals L1 Retrotransposition as a Dynamic Source of Cancer Heterogeneity. Cancer Res 2021; 81:4901-4909. [PMID: 34348967 PMCID: PMC9397610 DOI: 10.1158/0008-5472.can-21-0371] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/03/2021] [Accepted: 08/02/2021] [Indexed: 01/07/2023]
Abstract
Treatment-eradicated cancer subclones have been reported in leukemia and have recently been detected in solid tumors. Here we introduce Differential Subclone Eradication and Resistance (DSER) analysis, a method developed to identify molecular targets for improved therapy by direct comparison of genomic features of eradicated and resistant subclones in pre- and posttreatment samples from a patient with BRCA2-deficient metastatic prostate cancer. FANCI and EYA4 were identified as candidate DNA repair-related targets for converting subclones from resistant to eradicable, and RNAi-mediated depletion of FANCI confirmed it as a potential target. The EYA4 alteration was associated with adjacent L1 transposon insertion during cancer evolution upon treatment, raising questions surrounding the role of therapy in L1 activation. Both carboplatin and enzalutamide turned on L1 transposon machinery in LNCaP and VCaP but not in PC3 and 22Rv1 prostate cancer cell lines. L1 activation in LNCaP and VCaP was inhibited by the antiretroviral drug azidothymidine. L1 activation was also detected postcastration in LuCaP 77 and LuCaP 105 xenograft models and postchemotherapy in previously published time-series transcriptomic data from SCC25 head and neck cancer cells. In conclusion, DSER provides an informative intermediate step toward effective precision cancer medicine and should be tested in future studies, especially those including dramatic but temporary metastatic tumor regression. L1 transposon activation may be a modifiable source of cancer genomic heterogeneity, suggesting the potential of leveraging newly discovered triggers and blockers of L1 activity to overcome therapy resistance. SIGNIFICANCE: Differential analysis of eradicated and resistant subclones following cancer treatment identifies that L1 activity associated with resistance is induced by current therapies and blocked by the antiretroviral drug azidothymidine.
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Affiliation(s)
- Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
| | - Heidi Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Roosa Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Emmi Järvelä
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Bernardo Rodríguez-Martín
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Kerstin Haase
- Experimental and Clinical Research Center, Charité and the Max Delbrück Center for Molecular Medicine, Universitätsmedizin Berlin, Berlin, Germany
| | - Dan J. Woodcock
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Jose Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
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10
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Li QK, Chen J, Hu Y, Höti N, Lih TSM, Thomas SN, Chen L, Roy S, Meeker A, Shah P, Chen L, Bova GS, Zhang B, Zhang H. Proteomic characterization of primary and metastatic prostate cancer reveals reduced proteinase activity in aggressive tumors. Sci Rep 2021; 11:18936. [PMID: 34556748 PMCID: PMC8460832 DOI: 10.1038/s41598-021-98410-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022] Open
Abstract
Prostate cancer (PCa) is a heterogeneous group of tumors with variable clinical courses. In order to improve patient outcomes, it is critical to clinically separate aggressive PCa (AG) from non-aggressive PCa (NAG). Although recent genomic studies have identified a spectrum of molecular abnormalities associated with aggressive PCa, it is still challenging to separate AG from NAG. To better understand the functional consequences of PCa progression and the unique features of the AG subtype, we studied the proteomic signatures of primary AG, NAG and metastatic PCa. 39 PCa and 10 benign prostate controls in a discovery cohort and 57 PCa in a validation cohort were analyzed using a data-independent acquisition (DIA) SWATH-MS platform. Proteins with the highest variances (top 500 proteins) were annotated for the pathway enrichment analysis. Functional analysis of differentially expressed proteins in NAG and AG was performed. Data was further validated using a validation cohort; and was also compared with a TCGA mRNA expression dataset and confirmed by immunohistochemistry (IHC) using PCa tissue microarray (TMA). 4,415 proteins were identified in the tumor and benign control tissues, including 158 up-regulated and 116 down-regulated proteins in AG tumors. A functional analysis of tumor-associated proteins revealed reduced expressions of several proteinases, including dipeptidyl peptidase 4 (DPP4), carboxypeptidase E (CPE) and prostate specific antigen (KLK3) in AG and metastatic PCa. A targeted analysis further identified that the reduced expression of DPP4 was associated with the accumulation of DPP4 substrates and the reduced ratio of DPP4 cleaved peptide to intact substrate peptide. Findings were further validated using an independently-collected tumor cohort, correlated with a TCGA mRNA dataset, and confirmed by immunohistochemical stains of PCa tumor microarray (TMA). Our study is the first large-scale proteomics analysis of PCa tissue using a DIA SWATH-MS platform. It provides not only an interrogative proteomic signature of PCa subtypes, but also indicates the critical roles played by certain proteinases during tumor progression. The spectrum map and protein profile generated in the study can be used to investigate potential biological mechanisms involved in PCa and for the development of a clinical assay to distinguish aggressive from indolent PCa.
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Affiliation(s)
- Qing Kay Li
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA.
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
| | - Jing Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Yingwei Hu
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Naseruddin Höti
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Tung-Shing Mamie Lih
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Stefani N Thomas
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Li Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Sujayita Roy
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Alan Meeker
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Punit Shah
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Lijun Chen
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Bai Zhang
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA
| | - Hui Zhang
- Department of Pathology, The John Hopkins Medical Institutions, 600 N. Wolfe Street, Baltimore, MD, 21224, USA.
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Department of Urology, Sidney Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD, USA.
- Johns Hopkins University, 400 N. Broadway, Smith Bldg Rm 4011, Baltimore, MD, 21287, USA.
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11
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Jasu J, Tolonen T, Antonarakis ES, Beltran H, Halabi S, Eisenberger MA, Carducci MA, Loriot Y, Van der Eecken K, Lolkema M, Ryan CJ, Taavitsainen S, Gillessen S, Högnäs G, Talvitie T, Taylor RJ, Koskenalho A, Ost P, Murtola TJ, Rinta-Kiikka I, Tammela T, Auvinen A, Kujala P, Smith TJ, Kellokumpu-Lehtinen PL, Isaacs WB, Nykter M, Kesseli J, Bova GS. Combined Longitudinal Clinical and Autopsy Phenomic Assessment in Lethal Metastatic Prostate Cancer: Recommendations for Advancing Precision Medicine. EUR UROL SUPPL 2021; 30:47-62. [PMID: 34337548 PMCID: PMC8317817 DOI: 10.1016/j.euros.2021.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Systematic identification of data essential for outcome prediction in metastatic prostate cancer (mPC) would accelerate development of precision oncology. OBJECTIVE To identify novel phenotypes and features associated with mPC outcome, and to identify biomarker and data requirements to be tested in future precision oncology trials. DESIGN SETTING AND PARTICIPANTS We analyzed deep longitudinal clinical, neuroendocrine expression, and autopsy data of 33 men who died from mPC between 1995 and 2004 (PELICAN33), and related findings to mPC biomarkers reported in the literature. INTERVENTION Thirty-three men prospectively consented to participate in an integrated clinical-molecular rapid autopsy study of mPC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Data exploration with correction for multiple testing and survival analysis from the time of diagnosis to time to death and time to first occurrence of severe pain as outcomes were carried out. The effect of seven complications on the modeled probability of dying within 2 yr after presenting with the complication was evaluated using logistic regression. RESULTS AND LIMITATIONS Feature exploration revealed novel phenotypes related to mPC outcome. Four complications (pleural effusion, severe anemia, severe or controlled pain, and bone fracture) predict the likelihood of death within 2 yr. Men with Gleason grade group 5 cancers developed severe pain sooner than those with lower-grade tumors. Surprisingly, neuroendocrine (NE) differentiation was frequently observed in the setting of high serum prostate-specific antigen (PSA) levels (≥30 ng/ml). In 4/33 patients, no controlled (requiring analgesics) or severe pain was detected, and strikingly, 14/15 metastatic sites studied in these men did not express NE markers, suggesting an inverse relationship between NE differentiation and pain in mPC. Intracranial subdural metastasis is common (36%) and is usually clinically undetected. Categorization of "skeletal-related events" complications used in recent studies likely obscures the understanding of spinal cord compression and fracture. Early death from prostate cancer was identified in a subgroup of men with a low longitudinal PSA bandwidth. Cachexia is common (body mass index <0.89 in 24/31 patients) but limited to the last year of life. Biomarker review identified 30 categories of mPC biomarkers in need of winnowing in future trials. All findings require validation in larger cohorts, preferably alongside data from this study. CONCLUSIONS The study identified novel outcome subgroups for future validation and provides "vision for mPC precision oncology 2020-2050" draft recommendations for future data collection and biomarker studies. PATIENT SUMMARY To better understand variation in metastatic prostate cancer behavior, we assembled and analyzed longitudinal clinical and autopsy records in 33 men. We identified novel outcomes, phenotypes, and aspects of disease burden to be tested and refined in future trials.
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Affiliation(s)
- Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Teemu Tolonen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Emmanuel S. Antonarakis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Susan Halabi
- Duke University Medical Center, Department of Biostatistics and Bioinformatics, Durham, NC, USA
| | - Mario A. Eisenberger
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael A. Carducci
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yohann Loriot
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Kim Van der Eecken
- Department of Medical and Forensic Pathology, Ghent University, Ghent, Belgium
| | - Martijn Lolkema
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Charles J. Ryan
- Department of Medicine, Division of Oncology, University of Minnesota, Minneapolis, MN, USA
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Silke Gillessen
- Institute of Oncology of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biosciences, Università della Svizzera Italiana, Lugano, Switzerland
- Faculty of Cancer Science, University of Manchester, UK
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Timo Talvitie
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | | | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Piet Ost
- Department of Radiation Oncology, Iridium Netwerk, Wilrijk (Antwerp), Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Teemu J. Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Urology, Tampere, Finland
| | - Irina Rinta-Kiikka
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Radiology, Tampere, Finland
| | - Teuvo Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Urology, Tampere, Finland
| | - Anssi Auvinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Thomas J. Smith
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pirkko-Liisa Kellokumpu-Lehtinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - William B. Isaacs
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
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Valkonen M, Hognas G, Bova GS, Ruusuvuori P. Generalized Fixation Invariant Nuclei Detection Through Domain Adaptation Based Deep Learning. IEEE J Biomed Health Inform 2021; 25:1747-1757. [PMID: 33211668 DOI: 10.1109/jbhi.2020.3039414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Nucleus detection is a fundamental task in histological image analysis and an important tool for many follow up analyses. It is known that sample preparation and scanning procedure of histological slides introduce a great amount of variability to the histological images and poses challenges for automated nucleus detection. Here, we studied the effect of histopathological sample fixation on the accuracy of a deep learning based nuclei detection model trained with hematoxylin and eosin stained images. We experimented with training data that includes three methods of fixation; PAXgene, formalin and frozen, and studied the detection accuracy results of various convolutional neural networks. Our results indicate that the variability introduced during sample preparation affects the generalization of a model and should be considered when building accurate and robust nuclei detection algorithms. Our dataset includes over 67 000 annotated nuclei locations from 16 patients and three different sample fixation types. The dataset provides excellent basis for building an accurate and robust nuclei detection model, and combined with unsupervised domain adaptation, the workflow allows generalization to images from unseen domains, including different tissues and images from different labs.
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Hägnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature 2020; 584:E18. [PMID: 32728210 DOI: 10.1038/s41586-020-2581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000, Leuven, Belgium.,Cancer Research UK London Research Institute, London, WC2A3LY, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Daniel S Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,The Genome Analysis Centre, Norwich, NR4 7UH, UK
| | - Heini M L Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Gunilla Hägnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Sarah O'Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kevin J Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, 21287, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Maryland, 20892, USA.,Avoneaux Medical Institute, Oxford, Maryland, 21654, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Christopher Foster
- University of Liverpool andHCA Pathology Laboratories, London, WC1E6JA, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB18RN, UK
| | - Hayley C Whitaker
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK
| | | | - David E Neal
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK.,Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Colin S Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK.,Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; and, Sutton, SM2 5PT, UK
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - G Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
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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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15
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Kallio HML, Hieta R, Latonen L, Brofeldt A, Annala M, Kivinummi K, Tammela TL, Nykter M, Isaacs WB, Lilja HG, Bova GS, Visakorpi T. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Br J Cancer 2018; 119:347-356. [PMID: 29988112 PMCID: PMC6070921 DOI: 10.1038/s41416-018-0172-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [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: 02/14/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A significant subset of prostate cancer (PC) patients with a castration-resistant form of the disease (CRPC) show primary resistance to androgen receptor (AR)-targeting drugs developed against CRPC. As one explanation could be the expression of constitutively active androgen receptor splice variants (AR-Vs), our current objectives were to study AR-Vs and other AR aberrations to better understand the emergence of CRPC. METHODS We analysed specimens from different stages of prostate cancer by next-generation sequencing and immunohistochemistry. RESULTS AR mutations and copy number variations were detected only in CRPC specimens. Genomic structural rearrangements of AR were observed in 5/30 metastatic CRPC patients, but they were not associated with expression of previously known AR-Vs. The predominant AR-Vs detected were AR-V3, AR-V7 and AR-V9, with the expression levels being significantly higher in CRPC cases compared to prostatectomy samples. Out of 25 CRPC metastases that expressed any AR variant, 17 cases harboured expression of all three of these AR-Vs. AR-V7 protein expression was highly heterogeneous and higher in CRPC compared to hormone-naïve tumours. CONCLUSIONS AR-V3, AR-V7 and AR-V9 are co-expressed in CRPC metastases highlighting the fact that inhibiting AR function via regions common to all AR-Vs is likely to provide additional benefit to patients with CRPC.
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Affiliation(s)
- Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland.
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Leena Latonen
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Anniina Brofeldt
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Teuvo L Tammela
- Department of Urology, University of Tampere, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans G Lilja
- Departments of Surgery (Urology), Laboratory Medicine and Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Department of Translational Medicine, Lund University, Malmö, Sweden.,Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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16
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Kallio HM, Hieta R, Brofeldt A, Annala M, Kivinummi K, Tammela TL, Nykter M, Isaacs WB, Lilja HG, Bova GS, Visakorpi T. Abstract 1802: Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Prostate cancer (PC) is the most commonly diagnosed male cancer both in the United States and in Europe. Approximately 20-25% of cases will develop metastatic disease, which eventually progresses to lethal castration-resistant form of the disease (CRPC). Even though the exact mechanism by which CRPC develops remains to be fully understood, several mechanisms of castration resistance have been identified. Importantly, androgen signaling remains active even in the CRPC stage. This has led to the clinical development of second-generation AR-targeting drugs enzalutamide and abiraterone that target the ligand-binding domain of AR directly and indirectly, respectively. Unfortunately, a significant subset of patients show primary resistance to these agents. One potential explanation for this is the presence of AR splice variants (AR-Vs). AR-Vs are alternatively spliced isoforms of the AR mRNA usually resulting in truncated AR protein product. Even though AR-Vs lack variable portions of the AR COOH-terminal domain including the ligand-binding domain (LBD), they are constitutively active as transcription factors. The aim of this work was to study AR-Vs and also AR rearrangements, mutations and copy number variations (CNVs) to better understand the emergence of CRPC. This was done by analyzing specimens from different stages of prostate cancer by next-generation sequencing methods. Our sample cohorts included hormone-naïve PCs and lymph node metastases as well as locally recurrent and metastatic CRPCs. AR mutations and CNVs were detected only in CRPC specimens. Genomic structural rearrangements of AR (AR-GSRs) were observed in 5/30 metastatic CRPC patients but they were not associated with the expression of previously known AR-Vs, and their variant allele fractions were low. The main AR-Vs detected were AR-V3, AR-V7 and AR-V9, whose expression levels were higher in CRPC cases in comparison to prostatectomy samples. The differences were statistically significant for either variant alone or when their expression fractions were combined (p=0.0006). In addition, metastatic CRPC cases expressed significantly more AR-V3, AR-V7 and AR-V9 when compared to non-androgen deprived pelvic lymph node metastases (p=0.0282). The expression of these AR-Vs was strongly associated with the levels of full-length AR. Out of 25 CRPC metastases that expressed any AR variant, 17 cases harbored expression of all three of these AR-Vs. In conclusion, AR-V3, AR-V7 and AR-V9 tend to be co-expressed in metastatic CRPC highlighting the fact that targeting of the AR ligand-binding domain might not be sufficient to achieve a treatment response in certain patients. Consequently, targeting of AR via regions common to all AR-Vs is likely to provide additional benefit to patients suffering from CRPC.
Citation Format: Heini M. Kallio, Reija Hieta, Anniina Brofeldt, Matti Annala, Kati Kivinummi, Teuvo L. Tammela, Matti Nykter, William B. Isaacs, Hans G. Lilja, G Steven Bova, Tapio Visakorpi. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1802.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hans G. Lilja
- 4Memorial Sloan-Kettering Cancer Center, New York, NY
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17
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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18
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Sainio M, Visakorpi T, Tolonen T, Ilvesaro J, Bova GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract 2018; 214:848-856. [PMID: 29728311 DOI: 10.1016/j.prp.2018.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/09/2018] [Accepted: 04/20/2018] [Indexed: 12/31/2022]
Abstract
Neuroendocrine differentiation (NED) is a common phenomenon in prostate cancer, and it has been associated with poor prognosis in some studies of primary prostate cancer. Incidence and patterns of NED in metastatic prostate cancer sites have not been examined widely. In this study, we studied expression of three commonly used markers of NED (chromogranin A, neuron specific enolase and synaptophysin) in 89 metastases from 31 men that died of castration-resistant prostate cancer and underwent rapid autopsy, and in 89 hormone-naïve primary tumors removed by radical prostatectomy. In addition, we examined NED association with androgen receptor, ERG and Ki-67 expression in metastatic tumor sites. Morphologically, 1 of 31 cases was classified as small cell carcinoma, and the remaining 30 were classified as usual prostate adenocarcinoma using a recently proposed classification of prostate cancers with NED. Metastases showed more expression of neuron specific enolase and synaptophysin compared to prostatectomies (6.3% of cells vs. 1.0%, p < 0.001 and 4.0% vs. 0.4%, p < 0.001, respectively). At least focal expression of one of the markers was seen in 78% of metastases. Strong expression was relatively uncommon, seen in 3/89 (chromogranin A), 8/89 (neuron specific enolase), and 5/89 (synaptophysin) metastases. Expression of chromogranin A and synaptophysin correlated with each other (r = 0.64, p < 0.001), but expression of neuron specific enolase did not correlate with the two other markers. Extent of NED varied significantly between different metastatic sites in individual patients. Absent androgen receptor expression was associated with strong expression of chromogranin A (p = .02) and neuron specific enolase (p = .02), but not with focal expression of any marker. No clear association was found between expression of NE markers and ERG or Ki-67. In conclusion, NED is a common and heterogeneous phenomenon in metastatic, castration-resistant prostate cancer. NED is more often present in castration-resistant prostate cancer compared to hormone-naïve disease, and it is associated with androgen receptor negativity. More research is needed to understand significance of NED in the progression of prostate cancer.
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Affiliation(s)
- Miika Sainio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
| | - Teemu Tolonen
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland; Department of Pathology, Tampere University Hospital, Fimlab Laboratories, Tampere, Finland.
| | - Joanna Ilvesaro
- Department of Pathology, Tampere University Hospital, Fimlab Laboratories, Tampere, Finland.
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
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19
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Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol 2017; 42:103-115. [PMID: 28984675 DOI: 10.1097/pas.0000000000000961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied. Our results suggest that it is feasible to use PFPE tissue for routine robot-assisted laparoscopic prostatectomy surgical pathology diagnostics and immunohistochemistry, with the benefit of significantly improvedDNA and RNA quality and RNA picogram yield per nucleus as compared with FFPE tissue. For fresh frozen, FFPE, and PFPE tissues, respectively, the average Genomic Quality Numbers were 7.9, 3.2, and 6.2, average RNA Quality Numbers were 8.7, 2.6, and 6.3, average DNA picogram yields per nucleus were 0.41, 0.69, and 0.78, and average RNA picogram yields per nucleus were 1.40, 0.94, and 2.24. These findings suggest that where DNA and/or RNA analysis of tissue is required, and when tissue size is small, PFPE may provide important advantages over FFPE. The results also suggest several interesting nuances including potential avenues to improve RNA quality in FFPE tissues and confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided.
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Affiliation(s)
- Gunilla Högnäs
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Signal Processing Laboratory, Tampere University of Technology, Pori
| | - Antti Koskenalho
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Department of Urology, University of Tampere
| | | | - Joanna Ilvesaro
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Saara Kares
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | | | - Marita Laurila
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tuomas Mirtti
- Institute for Molecular Medicine Finland, University of Helsinki.,Department of Pathology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Paula M Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
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20
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Kivinummi K, Urbanucci A, Leinonen K, Tammela TLJ, Annala M, Isaacs WB, Bova GS, Nykter M, Visakorpi T. The expression of AURKA is androgen regulated in castration-resistant prostate cancer. Sci Rep 2017; 7:17978. [PMID: 29269934 PMCID: PMC5740165 DOI: 10.1038/s41598-017-18210-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 06/12/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Abstract
Although second generation endocrine therapies have significantly improved survival, castration-resistant prostate cancer (CRPC) cells are eventually able to escape available hormonal treatments due to reactivation of androgen receptor (AR) signaling. Identification of novel, non-classical and druggable AR-target genes may provide new approaches to treat CRPC. Our previous analyses suggested that Aurora kinase A (AURKA) is regulated by androgens in prostate cancer cells that express high levels of AR. Here, we provide further evidence that AURKA is significantly overexpressed in AR-positive CRPC samples carrying amplification of AR gene and/or expressing AR in high levels. We also demonstrate androgen-induced AR binding in the intronic region of AURKA. The expression of AURKA is increased upon androgen stimulation in LNCaP-ARhi cells that express high levels of AR. The growth of the cells was also significantly inhibited by an AURKA specific inhibitor, alisertib (MLN8237). Together, these findings suggest that the expression of AURKA is regulated by androgen in prostate cancer cells that highly express AR, emphasizing its potential as a therapeutic target in patients with CRPC.
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Affiliation(s)
- Kati Kivinummi
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland.
| | - Alfonso Urbanucci
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland.,Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forksningsparken, University of Oslo, Oslo, Norway.,Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Katri Leinonen
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Matti Annala
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21287, USA
| | - G Steven Bova
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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21
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Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet 2017; 13:e1007001. [PMID: 28945760 PMCID: PMC5628936 DOI: 10.1371/journal.pgen.1007001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/05/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.
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Affiliation(s)
- Niedzica Camacho
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Sandra Edwards
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Jonathan D. Kay
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Lucy Matthews
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Nening Dennis
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sarah Thomas
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Barbara Kremeyer
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jorge Zamora
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Gunes Gundem
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Hayley Luxton
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Mohammed Ghori
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Luke Marsden
- Department of Physiology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Adam Lambert
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
| | - Katalin Karaszi
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Gill Pelvender
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Charlie E. Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- CRUK Cambridge Centre, Early Detection Programme, Urological Malignancies Programme, Hutchison-MRC Research Centre, Cambridge, Cambridgeshire, United Kingdom
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - William J. Howat
- Histopathology and in situ hybridization Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Steven Hazell
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Naomi Livni
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Cyril Fisher
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher Ogden
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Pardeep Kumar
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alan Thompson
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Nicol
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erik Mayer
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Tim Dudderidge
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Yongwei Yu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Nimish C. Shah
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - Vincent J. Gnanapragasam
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | | | - William Isaacs
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tapio Visakorpi
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Freddie Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Dan Berney
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology and Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, Oxfordshire, United Kingdom
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - David C. Wedge
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Oxford Big Data Institute & Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, United Kingdom
| | - Andrew G. Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, Fife, Scotland
| | | | - Yong Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - G. Steven Bova
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Hayley C. Whitaker
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David E. Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Colin S. Cooper
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
- Organisms and Ecosystems, The Earlham Institute, Norwich, Norfolk, United Kingdom
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22
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Affiliation(s)
- G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences, and at the BioMediTech Institute, University of Tampere, 33014 Tampere, Finland
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23
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Behjati S, Gundem G, Wedge DC, Roberts ND, Tarpey PS, Cooke SL, Van Loo P, Alexandrov LB, Ramakrishna M, Davies H, Nik-Zainal S, Hardy C, Latimer C, Raine KM, Stebbings L, Menzies A, Jones D, Shepherd R, Butler AP, Teague JW, Jorgensen M, Khatri B, Pillay N, Shlien A, Futreal PA, Badie C, McDermott U, Bova GS, Richardson AL, Flanagan AM, Stratton MR, Campbell PJ. Mutational signatures of ionizing radiation in second malignancies. Nat Commun 2016; 7:12605. [PMID: 27615322 PMCID: PMC5027243 DOI: 10.1038/ncomms12605] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Ionizing radiation is a potent carcinogen, inducing cancer through DNA damage. The signatures of mutations arising in human tissues following in vivo exposure to ionizing radiation have not been documented. Here, we searched for signatures of ionizing radiation in 12 radiation-associated second malignancies of different tumour types. Two signatures of somatic mutation characterize ionizing radiation exposure irrespective of tumour type. Compared with 319 radiation-naive tumours, radiation-associated tumours carry a median extra 201 deletions genome-wide, sized 1-100 base pairs often with microhomology at the junction. Unlike deletions of radiation-naive tumours, these show no variation in density across the genome or correlation with sequence context, replication timing or chromatin structure. Furthermore, we observe a significant increase in balanced inversions in radiation-associated tumours. Both small deletions and inversions generate driver mutations. Thus, ionizing radiation generates distinctive mutational signatures that explain its carcinogenic potential.
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Affiliation(s)
- Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Oxford Big Data Institute and Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Nicola D. Roberts
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Patrick S. Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Susanna L. Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Peter Van Loo
- The Francis Crick Institute, London WC2A 3LY, UK
- Department of Human Genetics, University of Leuven, Leuven B-3000, Belgium
| | - Ludmil B. Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Helen Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Claire Hardy
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Keiran M. Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Andy Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Rebecca Shepherd
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Adam P. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Jon W. Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Mette Jorgensen
- University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
| | - Bhavisha Khatri
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Nischalan Pillay
- University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Adam Shlien
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - P. Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Genomic Medicine, MD Anderson Cancer Center, University of Texas, Houston, Texas 77030, USA
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation Chemical and Environmental Hazards, Public Health England, Chilton, Didcot OX11 0RQ, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - G. Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere FI-33520, Finland
| | - Andrea L. Richardson
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115 USA
| | - Adrienne M. Flanagan
- University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
| | - Peter J. Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA UK
- Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK
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24
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Bova GS, Kallio HML, Annala M, Kivinummi K, Högnäs G, Häyrynen S, Rantapero T, Kivinen V, Isaacs WB, Tolonen T, Nykter M, Visakorpi T. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud 2016; 2:a000752. [PMID: 27148588 PMCID: PMC4853517 DOI: 10.1101/mcs.a000752] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We report the first combined analysis of whole-genome sequence, detailed clinical history, and transcriptome sequence of multiple prostate cancer metastases in a single patient (A21). Whole-genome and transcriptome sequence was obtained from nine anatomically separate metastases, and targeted DNA sequencing was performed in cancerous and noncancerous foci within the primary tumor specimen removed 5 yr before death. Transcriptome analysis revealed increased expression of androgen receptor (AR)-regulated genes in liver metastases that harbored an AR p.L702H mutation, suggesting a dominant effect by the mutation despite being present in only one of an estimated 16 copies per cell. The metastases harbored several alterations to the PI3K/AKT pathway, including a clonal truncal mutation in PIK3CG and present in all metastatic sites studied. The list of truncal genomic alterations shared by all metastases included homozygous deletion of TP53, hemizygous deletion of RB1 and CHD1, and amplification of FGFR1. If the patient were treated today, given this knowledge, the use of second-generation androgen-directed therapies, cessation of glucocorticoid administration, and therapeutic inhibition of the PI3K/AKT pathway or FGFR1 receptor could provide personalized benefit. Three previously unreported truncal clonal missense mutations (ABCC4 p.R891L, ALDH9A1 p.W89R, and ASNA1 p.P75R) were expressed at the RNA level and assessed as druggable. The truncal status of mutations may be critical for effective actionability and merit further study. Our findings suggest that a large set of deeply analyzed cases could serve as a powerful guide to more effective prostate cancer basic science and personalized cancer medicine clinical trials.
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Affiliation(s)
- G Steven Bova
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Heini M L Kallio
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Kati Kivinummi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Gunilla Högnäs
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Sergei Häyrynen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Tommi Rantapero
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Virpi Kivinen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Teemu Tolonen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, FI-33014 Tampere, Finland
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25
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Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MTM, Van't Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova GS, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR. Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res 2016; 26:717.2. [PMID: 27197245 PMCID: PMC4864453 DOI: 10.1101/gr.206557.116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Myneni S, Patel VL, Bova GS, Wang J, Ackerman CF, Berlinicke CA, Chen SH, Lindvall M, Zack DJ. Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration. Comput Methods Programs Biomed 2016; 126:160-70. [PMID: 26652980 PMCID: PMC4778387 DOI: 10.1016/j.cmpb.2015.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/21/2015] [Accepted: 11/03/2015] [Indexed: 06/05/2023]
Abstract
This paper describes a distributed collaborative effort between industry and academia to systematize data management in an academic biomedical laboratory. Heterogeneous and voluminous nature of research data created in biomedical laboratories make information management difficult and research unproductive. One such collaborative effort was evaluated over a period of four years using data collection methods including ethnographic observations, semi-structured interviews, web-based surveys, progress reports, conference call summaries, and face-to-face group discussions. Data were analyzed using qualitative methods of data analysis to (1) characterize specific problems faced by biomedical researchers with traditional information management practices, (2) identify intervention areas to introduce a new research information management system called Labmatrix, and finally to (3) evaluate and delineate important general collaboration (intervention) characteristics that can optimize outcomes of an implementation process in biomedical laboratories. Results emphasize the importance of end user perseverance, human-centric interoperability evaluation, and demonstration of return on investment of effort and time of laboratory members and industry personnel for success of implementation process. In addition, there is an intrinsic learning component associated with the implementation process of an information management system. Technology transfer experience in a complex environment such as the biomedical laboratory can be eased with use of information systems that support human and cognitive interoperability. Such informatics features can also contribute to successful collaboration and hopefully to scientific productivity.
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Affiliation(s)
- Sahiti Myneni
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, United States.
| | - Vimla L Patel
- New York Academy of Medicine, New York, NY, United States; Department of Biomedical Informatics, Arizona State University, United States
| | - G Steven Bova
- Departments of Pathology, Genetic Medicine, Health Sciences Informatics, Oncology, and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jian Wang
- BioFortis Inc., Columbia, MD, United States
| | - Christopher F Ackerman
- Fraunhofer Institute for Experimental Software Engineering, College Park, MD, United States
| | | | | | - Mikael Lindvall
- Fraunhofer Institute for Experimental Software Engineering, College Park, MD, United States
| | - Donald J Zack
- Departments of Pathology, Genetic Medicine, Health Sciences Informatics, Oncology, and Urology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Wilmer Eye Institute, United States; Institute of Genetic Medicine Johns Hopkins University School of Medicine, Baltimore, MD, United States
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27
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Sjöblom L, Saramäki O, Annala M, Leinonen K, Nättinen J, Tolonen T, Wahlfors T, Nykter M, Bova GS, Schleutker J, Tammela TLJ, Lilja H, Visakorpi T. Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer. PLoS One 2016; 11:e0150241. [PMID: 26939004 PMCID: PMC4777373 DOI: 10.1371/journal.pone.0150241] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/02/2016] [Indexed: 11/18/2022] Open
Abstract
Microseminoprotein-beta (MSMB, MSMB) is an abundant secretory protein contributed by the prostate, and is implicated as a prostate cancer (PC) biomarker based on observations of its lower expression in cancerous cells compared with benign prostate epithelium. However, as the current literature on MSMB is inconsistent, we assessed the expression of MSMB at the protein and mRNA levels in a comprehensive set of different clinical stages of PC. Immunohistochemistry using monoclonal and polyclonal antibodies against MSMB was used to study protein expression in tissue specimens representing prostatectomies (n = 261) and in diagnostic needle biopsies from patients treated with androgen deprivation therapy (ADT) (n = 100), and in locally recurrent castration-resistant PC (CRPC) (n = 105) and CRPC metastases (n = 113). The transcript levels of MSMB, nuclear receptor co-activator 4 (NCOA4) and MSMB-NCOA4 fusion were examined by qRT-PCR in prostatectomy samples and by RNA-sequencing in benign prostatic hyperplasia, PC, and CRPC samples. We also measured serum MSMB levels and genotyped the single nucleotide polymorphism rs10993994 using DNA from the blood of 369 PC patients and 903 controls. MSMB expression in PC (29% of prostatectomies and 21% of needle biopsies) was more frequent than in CRPC (9% of locally recurrent CRPCs and 9% of CRPC metastases) (p<0.0001). Detection of MSMB protein was inversely correlated with the Gleason score in prostatectomy specimens (p = 0.024). The read-through MSMB-NCOA4 transcript was detected at very low levels in PC. MSMB levels in serum were similar in cases of PC and controls but were significantly associated with PC risk when adjusted for age at diagnosis and levels of free or total PSA (p<0.001). Serum levels of MSMB in both PC patients and controls were significantly associated with the rs10993994 genotype (p<0.0001). In conclusion, decreased expression of MSMB parallels the clinical progression of PC and adjusted serum MSMB levels are associated with PC risk.
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Affiliation(s)
- Liisa Sjöblom
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Outi Saramäki
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - Katri Leinonen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Janika Nättinen
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - Teemu Tolonen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Tiina Wahlfors
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - G Steven Bova
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - Johanna Schleutker
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, School of Medicine, University of Tampere, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Hans Lilja
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland.,Departments of Laboratory Medicine, Surgery, and Medicine, Memorial Sloan Kettering Cancer Center, New York, United States of America.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom.,Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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28
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Kallio HM, Annala M, Kivinummi K, Högnäs G, Gundem G, Wedge DC, Van Loo P, Heyn H, Emmert-Buck MR, Isaacs WB, Esteller M, McDermott U, Nykter M, Visakorpi T, Bova GS. Abstract 3883: Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3883] [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
Prostate cancer (PC) is prevalent in both indolent and lethal forms. Although many PC patients diagnosed today have organ-confined disease curable by prostatectomy or radiation therapy, 20-30% of PCs will relapse to lethal disease within 5-years of treatment. Relatively little attention has been paid to distinguishing the molecular characteristics of proven lethal metastatic PC from non-lethal cancers. A better understanding of the origins and evolution of lethal cancers should allow screening and treatment to be better tailored to the needs of each patient. To this end, we performed an integrative molecular profiling of a lethal PC from one patient (A21). High-coverage whole genome sequence, transcriptome sequence, and methylation analysis was performed on 9 anatomically separate metastases obtained by autopsy, and targeted sequencing was performed in multiple cancerous and noncancerous foci within the radical prostatectomy specimen removed 5 years prior to death. Molecular results were analyzed in relation to detailed clinical data. Integrated whole genome sequence analysis revealed convergent evolution of AR gene amplification events, and inception of p.L702H mutation in the AR present only in liver metastases. In addition, the analysis showed parallel increases in AR regulated transcripts in the liver metastases, suggesting a dominant effect by the mutation. Mutation of PI3/PI4 kinase member PIK3CG was found in all metastases but in no primary tumor foci studied. The study demonstrated the power of an integrated approach to interrogate clonal evolution of cancer suggesting that such studies are valuable on the individual level and could lead the way towards personalized treatment. In the individual studied, cessation of corticosteroid treatment and/or therapeutic manipulation of PI3K/AKT/mTOR activity theoretically could have provided a personalized benefit. These findings suggest that similar integrated analysis in large cohorts of patients with metastatic cancer could accelerate progress in establishing effective personalized cancer medicine.
Citation Format: Heini M.L. Kallio, Matti Annala, Kati Kivinummi, Gunilla Högnäs, Gunes Gundem, David C. Wedge, Peter Van Loo, Holger Heyn, Michael R. Emmert-Buck, William B. Isaacs, Manel Esteller, Ultan McDermott, Matti Nykter, Tapio Visakorpi, G. Steven Bova. Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3883. doi:10.1158/1538-7445.AM2015-3883
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Affiliation(s)
- Heini M.L. Kallio
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Gunilla Högnäs
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Gunes Gundem
- 2Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - David C. Wedge
- 2Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Peter Van Loo
- 2Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Holger Heyn
- 3Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran i Reynals, Barcelona, Spain
| | - Michael R. Emmert-Buck
- 4Laboratory of Pathology, National Cancer Institute, National Institutes of Health, MD, USA. Present Address: Avoneaux Medical Institute, Oxford, MD
| | | | - Manel Esteller
- 3Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Hospital Duran i Reynals, Barcelona, Spain
| | - Ultan McDermott
- 2Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Matti Nykter
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - G. Steven Bova
- 1Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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29
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JM, Papaemmanuil E, Brewer DS, Kallio HM, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O’Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. The evolutionary history of lethal metastatic prostate cancer. Nature 2015; 520:353-357. [PMID: 25830880 PMCID: PMC4413032 DOI: 10.1038/nature14347] [Citation(s) in RCA: 954] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/23/2015] [Indexed: 02/07/2023]
Abstract
Cancers emerge from an ongoing Darwinian evolutionary process, often leading to multiple competing subclones within a single primary tumour. This evolutionary process culminates in the formation of metastases, which is the cause of 90% of cancer-related deaths. However, despite its clinical importance, little is known about the principles governing the dissemination of cancer cells to distant organs. Although the hypothesis that each metastasis originates from a single tumour cell is generally supported, recent studies using mouse models of cancer demonstrated the existence of polyclonal seeding from and interclonal cooperation between multiple subclones. Here we sought definitive evidence for the existence of polyclonal seeding in human malignancy and to establish the clonal relationship among different metastases in the context of androgen-deprived metastatic prostate cancer. Using whole-genome sequencing, we characterized multiple metastases arising from prostate tumours in ten patients. Integrated analyses of subclonal architecture revealed the patterns of metastatic spread in unprecedented detail. Metastasis-to-metastasis spread was found to be common, either through de novo monoclonal seeding of daughter metastases or, in five cases, through the transfer of multiple tumour clones between metastatic sites. Lesions affecting tumour suppressor genes usually occur as single events, whereas mutations in genes involved in androgen receptor signalling commonly involve multiple, convergent events in different metastases. Our results elucidate in detail the complex patterns of metastatic spread and further our understanding of the development of resistance to androgen-deprivation therapy in prostate cancer.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000 Leuven, Belgium
- Cancer Research UK London Research Institute, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Jose M.C. Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Daniel S. Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, UK
| | - Heini M.L. Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Gunilla Högnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Sarah O’Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kevin J. Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, MD, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Christopher Foster
- University of Liverpool and HCA Pathology Laboratories, London, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Hayley C. Whitaker
- Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, UK
| | | | - David E. Neal
- Uro-oncology Research Group, Cancer Research UK Cambridge Research Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Colin S. Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, UK
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Rosalind A. Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
| | - David C. Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - G. Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
- Senior Principal Investigators of the Cancer Research UK funded ICGC Prostate Cancer Project
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30
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Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A, Bolli N, Behjati S, Tarpey PS, Nangalia J, Massie CE, Butler AP, Teague JW, Vassiliou GS, Green AR, Du MQ, Unnikrishnan A, Pimanda JE, Teh BT, Munshi N, Greaves M, Vyas P, El-Naggar AK, Santarius T, Collins VP, Grundy R, Taylor JA, Hayes DN, Malkin D, Foster CS, Warren AY, Whitaker HC, Brewer D, Eeles R, Cooper C, Neal D, Visakorpi T, Isaacs WB, Bova GS, Flanagan AM, Futreal PA, Lynch AG, Chinnery PF, McDermott U, Stratton MR, Campbell PJ. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 2014; 3:e02935. [PMID: 25271376 PMCID: PMC4371858 DOI: 10.7554/elife.02935] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [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: 03/28/2014] [Accepted: 09/26/2014] [Indexed: 01/04/2023] Open
Abstract
Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are unclear. In this study, we analyzed somatic alterations in mtDNA from 1675 tumors. We identified 1907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C > T and A > G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. A number of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria and is fundamentally linked to mtDNA replication.
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Affiliation(s)
- Young Seok Ju
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Ludmil B Alexandrov
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Moritz Gerstung
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Inigo Martincorena
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Serena Nik-Zainal
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Manasa Ramakrishna
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Helen R Davies
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Gunes Gundem
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Adam Shlien
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Niccolo Bolli
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Sam Behjati
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Patrick S Tarpey
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Jyoti Nangalia
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Charles E Massie
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Adam P Butler
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Jon W Teague
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - George S Vassiliou
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Anthony R Green
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Ming-Qing Du
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Ashwin Unnikrishnan
- Lowy Cancer Research
Centre, University of New South Wales,
Sydney, Australia
| | - John E Pimanda
- Lowy Cancer Research
Centre, University of New South Wales,
Sydney, Australia
| | - Bin Tean Teh
- Laboratory of Cancer
Epigenome, National Cancer Centre,
Singapore, Singapore
- Duke-NUS Graduate Medical School,
Singapore, Singapore
| | - Nikhil Munshi
- Department of Hematologic
Oncology, Dana-Farber Cancer Institute,
Boston, United States
| | - Mel Greaves
- Institute of Cancer Research, Sutton,
London, United Kingdom
| | - Paresh Vyas
- Weatherall Institute for Molecular
Medicine, University of Oxford,
Oxford, United Kingdom
| | - Adel K El-Naggar
- Department of Pathology,
MD Anderson Cancer Center, Houston, United
States
| | - Tom Santarius
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - V Peter Collins
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Richard Grundy
- Children's Brain Tumour Research
Centre, University of Nottingham,
Nottingham, United Kingdom
| | - Jack A Taylor
- National Institute of Environmental
Health Sciences, National Institute of
Health, Triangle,
North Carolina, United
States
| | - D Neil Hayes
- Department of Internal
Medicine, University of North Carolina,
Chapel
Hill, United States
| | - David Malkin
- Hospital for Sick
Children, University of Toronto,
Toronto, Canada
| | - Christopher S Foster
- Department of Molecular and Clinical
Cancer Medicine, University of Liverpool,
London, United Kingdom
- HCA Pathology Laboratories,
London, United Kingdom
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Hayley C Whitaker
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Daniel Brewer
- Institute of Cancer Research, Sutton,
London, United Kingdom
- School of Biological
Sciences, University of East Anglia,
Norwich, United Kingdom
| | - Rosalind Eeles
- Institute of Cancer Research, Sutton,
London, United Kingdom
| | - Colin Cooper
- Institute of Cancer Research, Sutton,
London, United Kingdom
- School of Biological
Sciences, University of East Anglia,
Norwich, United Kingdom
| | - David Neal
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Tapio Visakorpi
- Institute of Biosciences and Medical
Technology - BioMediTech and Fimlab Laboratories,
University of Tampere and Tampere University Hospital,
Tampere, Finland
| | - William B Isaacs
- Department of Oncology,
Johns Hopkins University, Baltimore, United
States
| | - G Steven Bova
- Institute of Biosciences and Medical
Technology - BioMediTech and Fimlab Laboratories,
University of Tampere and Tampere University Hospital,
Tampere, Finland
| | - Adrienne M Flanagan
- Department of
Histopathology, Royal National Orthopaedic
Hospital, Middlesex, United Kingdom
- University College London Cancer
Institute, University College London,
London, United Kingdom
| | - P Andrew Futreal
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Department of Genomic
Medicine, The University of Texas, MD Anderson Cancer
Center, Houston, Texas, United States
| | - Andy G Lynch
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Patrick F Chinnery
- Wellcome Trust Centre for Mitochondrial
Research, Institute of Genetic Medicine, Newcastle
University, Newcastle-upon-tyne, United
Kingdom
| | - Ultan McDermott
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Peter J Campbell
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
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31
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Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, Veer LV, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 2014; 345:1251343. [PMID: 25082706 PMCID: PMC4380235 DOI: 10.1126/science.1251343] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [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] [Indexed: 12/12/2022]
Abstract
Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.
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Affiliation(s)
| | - Yilong Li
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Young Seok Ju
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | | | - Marta Tojo
- Department of Physiology, School of Medicine–Center for Resesarch in Molecular Medicine and Chronic Diseases, Instituto de Investigaciones Sanitarias, University of Santiago de Compostela, Spain
| | - Gunes Gundem
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Jorge Zamora
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Andrew Menzies
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Anthony Fullam
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Adam Shlien
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | | | - Stian Knappskog
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Peter Van Loo
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Human Genome Laboratory, Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium
| | | | - Helen R. Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - John Marshall
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - David C. Wedge
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Jon W. Teague
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Adam P. Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | | | - Sam Behjati
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Lucy R. Yates
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Niccolo Bolli
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Laura Mudie
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Claire Hardy
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stuart McLaren
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Sarah O'Meara
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Mark Maddison
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen Gamble
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Anne Y. Warren
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | - Hayley Whitaker
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Daniel Brewer
- Institute of Cancer Research, Sutton, London, UK
- University of East Anglia, Norwich, UK
| | | | - Colin Cooper
- Institute of Cancer Research, Sutton, London, UK
- University of East Anglia, Norwich, UK
| | - David Neal
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Andy G. Lynch
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology–BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | | | | | - Carlos Caldas
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Sam Aparicio
- British Columbia Cancer Agency, Vancouver, Canada
| | - John A. Foekens
- Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Sunil R. Lakhani
- School of Medicine, University of Queensland, Brisbane, Australia
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Brisbane, Australia
- UQ Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Gilles Thomas
- Université Lyon 1, Institut National du Cancer (INCa)–Synergie, Lyon, France
| | - Ola Myklebost
- Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Paul N. Span
- Department of Radiation Oncology and Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Marc Van de Vijver
- Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, Netherlands
| | - Anne Vincent-Salomon
- Institut Bergonié, 229 cours de l’Argone, 33076 Bordeaux, France
- Institut Curie, Department of Tumor Biology, 26 rue d’Ulm, 75248 Paris cédex 05, France
| | - Gert G. Van den Eynden
- Translational Cancer Research Unit and Department of Pathology, GZA Hospitals, Antwerp, Belgium
| | - Adrienne M. Flanagan
- Royal National Orthopaedic Hospital, Middlesex, UK
- UCL Cancer Institute, University College London, London, UK
| | - P. Andrew Futreal
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- MD Anderson Cancer Center, Houston, TX, USA
| | - Sam M. Janes
- Lungs for Living Research Centre, Rayne Institute, University College London (UCL), London, UK
| | - G. Steven Bova
- Institute of Biosciences and Medical Technology–BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland
| | | | - Ultan McDermott
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Peter J. Campbell
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - ICGC Prostate Cancer Group
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Institute of Cancer Research, Sutton, London, UK
- Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge, UK
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32
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Leinonen KA, Saramäki OR, Furusato B, Kimura T, Takahashi H, Egawa S, Suzuki H, Keiger K, Ho Hahm S, Isaacs WB, Tolonen TT, Stenman UH, Tammela TLJ, Nykter M, Bova GS, Visakorpi T. Loss of PTEN is associated with aggressive behavior in ERG-positive prostate cancer. Cancer Epidemiol Biomarkers Prev 2013; 22:2333-44. [PMID: 24083995 DOI: 10.1158/1055-9965.epi-13-0333-t] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [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] Open
Abstract
BACKGROUND The associations of ERG overexpression with clinical behavior and molecular pathways of prostate cancer are incompletely known. We assessed the association of ERG expression with AR, PTEN, SPINK1, Ki-67, and EZH2 expression levels, deletion, and mutations of chromosomal region 3p14 and TP53, and clinicopathologic variables. METHODS The material consisted of 326 prostatectomies, 166 needle biopsies from men treated primarily with endocrine therapy, 177 transurethral resections of castration-resistant prostate cancers (CRPC), and 114 CRPC metastases obtained from 32 men. Immunohistochemistry, FISH, and sequencing was used for the measurements. RESULTS ERG expression was found in about 45% of all patient cohorts. In a multivariate analysis, ERG expression showed independent value of favorable prognosis (P = 0.019). ERG positivity was significantly associated with loss of PTEN expression in prostatectomy (P = 0.0348), and locally recurrent CRPCs (P = 0.0042). Loss of PTEN expression was associated (P = 0.0085) with shorter progression-free survival in ERG-positive, but not in negative cases. When metastases in each subject were compared, consistent ERG, PTEN, and AR expression as well as TP53 mutations were found in a majority of subjects. CONCLUSIONS A similar frequency of ERG positivity from early to late stage of the disease suggests lack of selection of ERG expression during disease progression. The prognostic significance of PTEN loss solely in ERG-positive cases indicates interaction of these pathways. The finding of consistent genetic alterations in different metastases suggests that the major genetic alterations take place in the primary tumor. IMPACT Interaction of PTEN and ERG pathways warrants further studies.
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Affiliation(s)
- Katri A Leinonen
- Authors' Affiliations: Institute of Biomedical Technology and Institute of Signal Processing, Prostate Cancer Research Center, BioMediTech, Department of Urology, School of Medicine, University of Tampere and Tampere University Hospital, Tampere, Finland; Departments of Pathology and Urology, Jikei University School of Medicine, Minato-ku, Tokyo; Department of Urology, Toho University Sakura Medical Center, Sakura, Chiba, Japan; Departments of Pathology and Urology, Johns Hopkins University, Baltimore, Maryland; and Department of Clinical Chemistry, Helsinki University Central Hospital, Helsinki, Finland
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Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med 2013; 5:169ra10. [PMID: 23345608 DOI: 10.1126/scitranslmed.3005211] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cancers almost ubiquitously harbor epigenetic alterations. Although such alterations in epigenetic marks, including DNA methylation, are potentially heritable, they can also be dynamically altered. Given this potential for plasticity, the degree to which epigenetic changes can be subject to selection and act as drivers of neoplasia has been questioned. We carried out genome-scale analyses of DNA methylation alterations in lethal metastatic prostate cancer and created DNA methylation "cityscape" plots to visualize these complex data. We show that somatic DNA methylation alterations, despite showing marked interindividual heterogeneity among men with lethal metastatic prostate cancer, were maintained across all metastases within the same individual. The overall extent of maintenance in DNA methylation changes was comparable to that of genetic copy number alterations. Regions that were frequently hypermethylated across individuals were markedly enriched for cancer- and development/differentiation-related genes. Additionally, regions exhibiting high consistency of hypermethylation across metastases within individuals, even if variably hypermethylated across individuals, showed enrichment for cancer-related genes. Whereas some regions showed intraindividual metastatic tumor heterogeneity in promoter methylation, such methylation alterations were generally not correlated with gene expression. This was despite a general tendency for promoter methylation patterns to be strongly correlated with gene expression, particularly at regions that were variably methylated across individuals. These findings suggest that DNA methylation alterations have the potential for producing selectable driver events in carcinogenesis and disease progression and highlight the possibility of targeting such epigenome alterations for development of longitudinal markers and therapeutic strategies.
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Affiliation(s)
- Martin J Aryee
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231, USA
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Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HC, Fredrikson KM, Harkins TT, Milos P, Zbar B, Linehan WM, Yeager M, Andresson T, Dean M, Bova GS. Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Hum Mutat 2013; 34:1231-41. [PMID: 23636849 DOI: 10.1002/humu.22346] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/23/2013] [Accepted: 04/23/2013] [Indexed: 11/10/2022]
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease, and molecular markers that differentiate indolent from aggressive subtypes are needed. We sequenced the exomes of five metastatic tumors and healthy kidney tissue from an index case with mCRPC to identify lesions associated with disease progression and metastasis. An Ashkenazi Jewish (AJ) germline founder mutation, del185AG in BRCA1, was observed and AJ ancestry was confirmed. Sixty-two somatic variants altered proteins in tumors, including cancer-associated genes, TMPRSS2-ERG, PBRM1, and TET2. The majority (n = 53) of somatic variants were present in all metastases and only a subset (n = 31) was observed in the primary tumor. Integrating tumor next-generation sequencing and DNA copy number showed somatic loss of BRCA1 and TMPRSS2-ERG. We sequenced 19 genes with deleterious mutations in the index case in additional mCRPC samples and detected a frameshift, two somatic missense alterations, tumor loss of heterozygosity, and combinations of germline missense SNPs in TET2. In summary, genetic analysis of metastases from an index case permitted us to infer a chronology for the clonal spread of disease based on sequential accrual of somatic lesions. The role of TET2 in mCRPC deserves additional analysis and may define a subset of metastatic disease.
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Affiliation(s)
- Michael L Nickerson
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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35
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Liu W, Xie CC, Thomas CY, Kim ST, Lindberg J, Egevad L, Wang Z, Zhang Z, Sun J, Sun J, Koty PP, Kader AK, Cramer SD, Bova GS, Zheng SL, Grönberg H, Isaacs WB, Xu J. Genetic markers associated with early cancer-specific mortality following prostatectomy. Cancer 2013; 119:2405-12. [PMID: 23609948 DOI: 10.1002/cncr.27954] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 12/13/2022]
Abstract
BACKGROUND This study sought to identify novel effectors and markers of localized but potentially life-threatening prostate cancer (PCa), by evaluating chromosomal copy number alterations (CNAs) in tumors from patients who underwent prostatectomy and correlating these with clinicopathologic features and outcome. METHODS CNAs in tumor DNA samples from 125 patients in the discovery cohort who underwent prostatectomy were assayed with high-resolution Affymetrix 6.0 single-nucleotide polymorphism microarrays and then analyzed using the Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm. RESULTS The assays revealed 20 significant regions of CNAs, 4 of them novel, and identified the target genes of 4 of the alterations. By univariate analysis, 7 CNAs were significantly associated with early PCa-specific mortality. These included gains of chromosomal regions that contain the genes MYC, ADAR, or TPD52 and losses of sequences that incorporate SERPINB5, USP10, PTEN, or TP53. On multivariate analysis, only the CNAs of PTEN (phosphatase and tensin homolog) and MYC (v-myc myelocytomatosis viral oncogene homolog) contributed additional prognostic information independent of that provided by pathologic stage, Gleason score, and initial prostate-specific antigen level. Patients whose tumors had alterations of both genes had a markedly elevated risk of PCa-specific mortality (odds ratio = 53; 95% CI = 6.92-405, P = 1 × 10(-4)). Analyses of 333 tumors from 3 additional distinct patient cohorts confirmed the relationship between CNAs of PTEN and MYC and lethal PCa. CONCLUSIONS This study identified new CNAs and genes that likely contribute to the pathogenesis of localized PCa and suggests that patients whose tumors have acquired CNAs of PTEN, MYC, or both have an increased risk of early PCa-specific mortality.
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Affiliation(s)
- Wennuan Liu
- Center for Cancer Genomics, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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Rodriguez-Canales J, Hanson JC, Hipp JD, Balis UJ, Tangrea MA, Emmert-Buck MR, Bova GS. Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications. Methods Mol Biol 2013; 980:61-120. [PMID: 23359150 DOI: 10.1007/978-1-62703-287-2_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high-quality, appropriately anatomically tagged scientific results. Improvement in this area will significantly increase life science quality and productivity. The chapter is divided into introduction, materials, protocols, and notes subheadings. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this chapter, readers are advised to read through the entire chapter first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.
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Affiliation(s)
- Jaime Rodriguez-Canales
- Laser Capture Microdissection (LCM) Core, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Berlinicke CA, Ackermann CF, Chen SH, Schulze C, Shafranovich Y, Myneni S, Patel VL, Wang J, Zack DJ, Lindvall M, Bova GS. High-content screening data management for drug discovery in a small- to medium-size laboratory: results of a collaborative pilot study focused on user expectations as indicators of effectiveness. J Lab Autom 2012; 17:255-65. [PMID: 22357564 DOI: 10.1177/2211068211431207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-content screening (HCS) technology provides a powerful vantage point to approach biological problems; it allows analysis of cell parameters, including changes in cell or protein movement, shape, or texture. As part of a collaborative pilot research project to improve bioscience research data integration, we identified HCS data management as an area ripe for advancement. A primary goal was to develop an integrated data management and analysis system suitable for small- to medium-size HCS programs that would improve research productivity and increase work satisfaction. A system was developed that uses Labmatrix, a Web-based research data management platform, to integrate and query data derived from a Cellomics STORE database. Focusing on user expectations, several barriers to HCS productivity were identified and reduced or eliminated. The impact of the project on HCS research productivity was tested through a series of 18 lab-requested integrated data queries, 7 of which were fully enabled, 7 partially enabled, and 4 enabled through data export to standalone data analysis tools. The results are limited to one laboratory, but this pilot suggests that through an "implementation research" approach, a network of small- to medium-size laboratories involved in HCS projects could achieve greater productivity and satisfaction in drug discovery research.
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Li Y, Tao SC, Bova GS, Liu AY, Chan DW, Zhu H, Zhang H. Detection and verification of glycosylation patterns of glycoproteins from clinical specimens using lectin microarrays and lectin-based immunosorbent assays. Anal Chem 2011; 83:8509-16. [PMID: 21975078 DOI: 10.1021/ac201452f] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Aberrant glycosylation is a fundamental characteristic of progression of diseases such as cancer. Therefore, characterization of glycosylation patterns of proteins from disease tissues may identify changes specific to the disease development and improve diagnostic performance. Thus, analysis strategies with sufficient sensitivity for evaluation of glycosylation patterns in clinical specimens are needed. Here, we describe an analytical strategy for detection and verification of glycosylation patterns. It is based on a two-phase platform including a pattern discovery phase to identify the glycosylation changes using high-density lectin microarrays and a verification phase by developing lectin-based immunosorbent assays using the identified lectins. We evaluated the analytical performance of the platform using the glycoprotein standard and found that the lectin microarray could detect specific bindings of glycoprotein to lectins at the nanogram level and the lectin-based immunosorbent assay could be used for verification of protein glycosylation. We then applied the approach to the analysis of glycosylation patterns of two glycoproteins, which are highly expressed in prostate cancer in our prior studies, prostate specific antigen (PSA) and membrane metallo-endopeptidase (MME), from aggressive (AC) and nonaggressive prostate cancer (NAC) tissues. The observed differences in glycosylation patterns of PSA and MME may represent a significant clinical importance and could be used to develop multiplex assays for diagnosis of aggressive prostate cancer.
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Affiliation(s)
- Yan Li
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
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39
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Schwartzman J, Mongoue-Tchokote S, Gibbs A, Gao L, Corless CL, Jin J, Zarour L, Higano C, True LD, Vessella RL, Wilmot B, Bottomly D, McWeeney SK, Bova GS, Partin AW, Mori M, Alumkal J. A DNA methylation microarray-based study identifies ERG as a gene commonly methylated in prostate cancer. Epigenetics 2011; 6:1248-56. [PMID: 21946329 DOI: 10.4161/epi.6.10.17727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation of promoter regions is a common event in prostate cancer, one of the most common cancers in men worldwide. Because prior reports demonstrating that DNA methylation is important in prostate cancer studied a limited number of genes, we systematically quantified the DNA methylation status of 1505 CpG dinucleotides for 807 genes in 78 paraffin-embedded prostate cancer samples and three normal prostate samples. The ERG gene, commonly repressed in prostate cells in the absence of an oncogenic fusion to the TMPRSS2 gene, was one of the most commonly methylated genes, occurring in 74% of prostate cancer specimens. In an independent group of patient samples, we confirmed that ERG DNA methylation was common, occurring in 57% of specimens, and cancer-specific. The ERG promoter is marked by repressive chromatin marks mediated by polycomb proteins in both normal prostate cells and prostate cancer cells, which may explain ERG's predisposition to DNA methylation and the fact that tumors with ERG DNA methylation were more methylated, in general. These results demonstrate that bead arrays offer a high-throughput method to discover novel genes with promoter DNA methylation such as ERG, whose measurement may improve our ability to more accurately detect prostate cancer.
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Affiliation(s)
- Jacob Schwartzman
- Division of Hematology/Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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Tian Y, Bova GS, Zhang H. Quantitative glycoproteomic analysis of optimal cutting temperature-embedded frozen tissues identifying glycoproteins associated with aggressive prostate cancer. Anal Chem 2011; 83:7013-9. [PMID: 21780747 DOI: 10.1021/ac200815q] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Prostate cancer is the most common malignancy in men in the United States, and one in seven men with prostate cancer dies of the disease. A major issue of prostate diagnosis is that there is no good method to reliably distinguish aggressive prostate cancer from nonaggressive prostate cancer. This leads to significant unnecessary suffering among prostate cancer patients and massive unnecessary health care expenditures. In this study, we aim to identify glycoproteins associated with aggressive prostate cancer using optimal cutting temperature (OCT)-embedded frozen tissues obtained from patients with known clinical outcome. To eliminate the interference of mass spectrometric analysis by the compounds in OCT and identify extracellular proteins that are likely to serve as biomarkers in body fluids, we employed glycoproteomic analysis using solid-phase extraction of glycopeptides, which allowed the immobilization of glycopeptides to solid support and removal of OCT from sample proteins before releasing the glycopeptides from the solid support for mass spectrometry analysis. Tumor tissues were cryostat microdissected from four cases of aggressive and four cases of nonaggressive prostate tumors, and glycopeptides were isolated and labeled with iTRAQ reagents before the samples were analyzed with LTQ Orbitrap Velos. From the aggressive prostate cancer tissues, we identified the overexpression of three glycoproteins involved in an extracellular matrix remodeling and further examined two glycoproteins, cathepsin L and periostin, using Western blot and immunohistochemistry analyses. This is the first proteomic study to identify proteins potentially associated with aggressive prostate cancer using OCT-embedded frozen tissues. Further study of these proteins will be needed to understand the roles of extracellular matrix proteins in cancer progression and their potential clinical utility in improving diagnosis of aggressive prostate cancer.
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Affiliation(s)
- Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland 21231, United States
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Yu G, Zhang B, Bova GS, Xu J, Shih IM, Wang Y. BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data. ACTA ACUST UNITED AC 2011; 27:1473-80. [PMID: 21498400 DOI: 10.1093/bioinformatics/btr183] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
MOTIVATION Identification of somatic DNA copy number alterations (CNAs) and significant consensus events (SCEs) in cancer genomes is a main task in discovering potential cancer-driving genes such as oncogenes and tumor suppressors. The recent development of SNP array technology has facilitated studies on copy number changes at a genome-wide scale with high resolution. However, existing copy number analysis methods are oblivious to normal cell contamination and cannot distinguish between contributions of cancerous and normal cells to the measured copy number signals. This contamination could significantly confound downstream analysis of CNAs and affect the power to detect SCEs in clinical samples. RESULTS We report here a statistically principled in silico approach, Bayesian Analysis of COpy number Mixtures (BACOM), to accurately estimate genomic deletion type and normal tissue contamination, and accordingly recover the true copy number profile in cancer cells. We tested the proposed method on two simulated datasets, two prostate cancer datasets and The Cancer Genome Atlas high-grade ovarian dataset, and obtained very promising results supported by the ground truth and biological plausibility. Moreover, based on a large number of comparative simulation studies, the proposed method gives significantly improved power to detect SCEs after in silico correction of normal tissue contamination. We develop a cross-platform open-source Java application that implements the whole pipeline of copy number analysis of heterogeneous cancer tissues including relevant processing steps. We also provide an R interface, bacomR, for running BACOM within the R environment, making it straightforward to include in existing data pipelines. AVAILABILITY The cross-platform, stand-alone Java application, BACOM, the R interface, bacomR, all source code and the simulation data used in this article are freely available at authors' web site: http://www.cbil.ece.vt.edu/software.htm.
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Affiliation(s)
- Guoqiang Yu
- Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA
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Li Y, Alsagabi M, Fan D, Bova GS, Tewfik AH, Dehm SM. Intragenic rearrangement and altered RNA splicing of the androgen receptor in a cell-based model of prostate cancer progression. Cancer Res 2011; 71:2108-17. [PMID: 21248069 DOI: 10.1158/0008-5472.can-10-1998] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [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
Androgen depletion for advanced prostate cancer (PCa) targets activity of the androgen receptor (AR), a steroid receptor transcription factor required for PCa growth. The emergence of lethal castration-resistant PCa (CRPCa) is marked by aberrant reactivation of the AR despite ongoing androgen depletion. Recently, alternative splicing has been described as a mechanism giving rise to COOH-terminally truncated, constitutively active AR isoforms that can support the CRPCa phenotype. However, the pathologic origin of these truncated AR isoforms is unknown. The goal of this study was to investigate alterations in AR expression arising in a cell-based model of PCa progression driven by truncated AR isoform activity. We show that stable, high-level expression of truncated AR isoforms in 22Rv1 CRPCa cells is associated with intragenic rearrangement of an approximately 35-kb AR genomic segment harboring a cluster of previously described alternative AR exons. Analysis of genomic data from clinical specimens indicated that related AR intragenic copy number alterations occurred in CRPCa in the context of AR amplification. Cloning of the break fusion junction in 22Rv1 cells revealed long interspersed nuclear elements (LINE-1) flanking the rearranged segment and a DNA repair signature consistent with microhomology-mediated, break-induced replication. This rearrangement served as a marker for the emergence of a rare subpopulation of CRPCa cells expressing high levels of truncated AR isoforms during PCa progression in vitro. Together, these data provide the first report of AR intragenic rearrangements in CRPCa and an association with pathologic expression of truncated AR isoforms in a cell-based model of PCa progression.
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Affiliation(s)
- Yingming Li
- Department of Electrical and Computer Engineering, Masonic Cancer Center, University of Minnesota, Twin Cities, Minnesota 55455, USA
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Nelson WG, Haffner MC, Aryee MJ, Esopi DM, Isaacs WB, Bova GS, Meeker AK, Netto G, Marzo AMD, Yegnasubramanian S. Abstract CN05-04: Early molecular changes in prostate carcinogenesis. Cancer Prev Res (Phila) 2010. [DOI: 10.1158/1940-6207.prev-10-cn05-04] [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
After castration was shown by Charles Huggins in 1941 to be an effective treatment for advanced prostate cancer, androgenic hormones were assumed to be responsible in some way for disease development.
Nonetheless, the manner in which androgens might contribute to prostatic carcinogenesis has remained elusive over the subsequent seven decades. Androgen levels decline steadily throughout adulthood in men, just as prostate cancers begin to appear (Rohrmann S et al. J Clin Endocrinol Metabol 92:2519-25, 2007). In addition, the action of testosterone, and its metabolite dihydrotestosterone, on prostate epithelial cells in adult men tends to be the promotion of terminal differentiation by activating transcription of target genes, such as PSA and TMPRSS2, which form the secretion elaborated by the prostate for the ejaculate. By driving terminal differentiation of normal prostate cells, androgens seem unlikely to cause neoplastic transformation. However, new insights into the generation of somatic genome rearrangements that create fusion oncogenes in prostate cells have revealed a new mechanism of androgen receptor-associated cancer pathogenesis. The fusion oncogene TMPRSS2-ERG, present in at least half of all prostate cancer cases, may be the most common somatic gene fusion event in all of human cancer (Tomlins SA et al. Science 310:644-8, 2005). We have found that androgen receptor-triggered transcription in prostate cells leads to the recruitment of topoisomerase II-beta (TOP2B) by the receptor to sites of TMPRSS2-ERG genomic breakpoints, promoting TOP2B-mediated DNA double strand breaks and de novo TMPRSS2-ERG fusion transcripts. The results implicate androgens in the creation of TMPRSS2-ERG rearrangements, via a mechanism involving the androgen receptor and TOP2B, and provide new hints as to how prostate cancers might be better prevented.
Citation Information: Cancer Prev Res 2010;3(12 Suppl):CN05-04.
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Affiliation(s)
| | | | - Martin J. Aryee
- 1Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - David M. Esopi
- 1Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD
| | | | - G. Steven Bova
- 1Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Alan K. Meeker
- 1Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - George Netto
- 1Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD
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Nickerson ML, Im KM, Dean M, Bova GS. Exome sequencing of multiple metastases from a lethal prostate cancer reveals BRCA1 deficiency and additional somatic alterations which suggest alternate therapeutic options. Clin Cancer Res 2010. [DOI: 10.1158/diag-10-pr8] [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
Exome libraries were prepared from five metastatic tumors and healthy tissue from an Ashkenazi Jewish man who died from metastatic prostate cancer. A total of 6.77 × 109 bases were sequenced using a 454 FLX. Germline alteration and somatic loss of heterozygosity of the BRCA1 tumor suppressor gene were observed. Novel, somatic variants in the catalytic domain of two kinases and alteration of two oncogenes were also potential drivers of this cancer. We identified an insertion in the TMPRSS2 gene in addition to fusion with ERG. Alteration of several signaling pathways was predicted as a result of a surprising combination of germline and somatic alterations. Clonal as well as subclonal variants were identified that allow a ‘natural history’ of this individual's cancer to be described. Several alterations, including BRCA1 loss, suggest therapeutic options that may have been effective in this patient.
This talk is also presented as Poster B17.
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Haffner MC, Aryee MJ, Toubaji A, Esopi DM, Albadine R, Gurel B, Isaacs WB, Bova GS, Liu W, Xu J, Meeker AK, Netto G, De Marzo AM, Nelson WG, Yegnasubramanian S. Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nat Genet 2010; 42:668-75. [PMID: 20601956 PMCID: PMC3157086 DOI: 10.1038/ng.613] [Citation(s) in RCA: 463] [Impact Index Per Article: 33.1] [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: 01/25/2010] [Accepted: 06/02/2010] [Indexed: 12/21/2022]
Abstract
DNA double strand breaks (DSB) can lead to development of genomic rearrangements, which are hallmarks of cancer. TMPRSS2-ERG gene fusions in prostate cancer (PCa) are among the most common genomic rearrangements observed in human cancer. We show that androgen signaling promotes co-recruitment of androgen receptor (AR) and topoisomerase II beta (TOP2B) to sites of TMPRSS2-ERG genomic breakpoints, triggering recombinogenic TOP2B-mediated DSB. Furthermore, androgen stimulation resulted in de novo production of TMPRSS2-ERG fusion transcripts in a process requiring TOP2B and components of DSB repair machinery. Finally, unlike normal prostate epithelium, prostatic intraepithelial neoplasia (PIN) cells showed strong co-expression of AR and TOP2B. These findings implicate androgen-induced TOP2B-mediated DSB in generating TMPRSS2-ERG rearrangements.
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Affiliation(s)
- Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
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Schwartzman J, Mongoue-Tchokote S, Zarour L, DeMarzo A, Bova GS, Mori M, Alumkal JJ. Abstract 144: A microarray-based study of DNA methylation changes in prostate cancer. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-144] [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
Background: Prostate cancer is the most common cancer in men in the United States. Prior work, based on analyses of selected genes, has shown that epigenetic changes are important in disease progression and pathogenesis. We hypothesized that a global comparative analysis of DNA methylation changes in neoplastic prostate cells would provide an opportunity to discover novel genes involved in prostate carcinogenesis. We designed such a study using DNA from paraffin embedded normal and cancer specimens and from commonly used prostate cancer cell lines.
Methods: DNA from LNCaP, VCaP, DU145, DUPRO, PC3, LAPC4, and 22RV cells, paraffin-embedded clinical samples including 78 cancer samples and 3 normal prostate samples from radical prostatectomies, positive control in vitro methylated DNA, and negative control DKO cells, in which the DNMT1 and DNMT3b enzymes were genetically disrupted, were modified with sodium bisulfite. Along with these samples, non bisulfite-modified genomic DNA, which served as an additional negative control, was also hybridized to Illumina Golden Gate BeadArrays after labeling and amplification, which allowed for the assessment of 1505 CpG sites in 807 genes. A Beta methylation value from the BeadStudio Software is assigned to each CpG site. Probes with Beta>0.25 were considered methylated (Beta>0.5 represented a strong methylation level). In order to enrich for cancer-specific methylation, we excluded probes with methylation in normal prostate samples, genomic DNA samples, or DKO negative control samples. Probes unmethylated in the positive control in vitro methylated DNA samples were also excluded.
Results: 101 genes were methylated in at least one prostate cancer cell line and clinical sample and in the positive control samples but not in the negative control samples or normal prostate samples. Pathways whose members were silenced by DNA methylation included: growth factor signaling, cell-cell adhesion, differentiation, and apoptosis. The methylation status of single genes or combinations of 2 or more methylated genes resulted in 78%-90% sensitivity and 100% specificity for prostate cancer tissues versus normal tissues.
Conclusions: Our results demonstrate that high density 96-well BeadArrays are an efficient and cost-effective method to ascertain the DNA methylation status of many genes simultaneously in cell lines and in paraffin-embedded clinical samples. Of equal importance, our study demonstrates the importance of including positive and negative controls both for DNA methylation and for bisulfite conversion in such studies to more specifically identify cancer-specific DNA methylation changes that will most likely result in cancer- specific gene silencing. Our results have implications not only for improving prostate cancer detection but also for understanding the genes, whose silencing by DNA methylation, may be critical for prostate cancer development and progression.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 144.
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Affiliation(s)
| | | | - Luai Zarour
- 1Oregon Health & Science Univ., Portland, OR
| | | | | | - Motomi Mori
- 1Oregon Health & Science Univ., Portland, OR
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Abstract
Disseminated intravascular coagulation (DIC) as a complication of surgery for ventriculoperitoneal (VP) shunts is extremely rare, and only one case has been documented in the literature. The authors present the case of a 9-year-old girl with shunted hydrocephalus who presented with a 3-day history of headaches and vomiting. A head CT showed enlarged ventricles compared with baseline. An emergent VP shunt revision was performed, during which an obstructed proximal catheter was found. Immediately after extubation, the patient became apneic and progressed to cardiopulmonary arrest. A breathing tube was reinserted followed by resuscitation attempts that led to extracorporeal membrane oxygenation. Soon after reintubation, bloody drainage was noted in the endotracheal tube, and subsequent laboratory studies were consistent with DIC. The patient died on postoperative Day 1, and autopsy findings confirmed DIC. Note that DIC is a recognized complication of trauma, particularly with brain injury, but it is rare with neurosurgical procedures. Disseminated intravascular coagulation should be considered if excessive bleeding occurs after any brain insult.
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Affiliation(s)
- James L Frazier
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS. Erratum: Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med 2009. [DOI: 10.1038/nm0709-819a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med 2009; 15:559-65. [PMID: 19363497 PMCID: PMC2839160 DOI: 10.1038/nm.1944] [Citation(s) in RCA: 473] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 02/24/2009] [Indexed: 01/02/2023]
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Parsons JK, Saria EA, Nakayama M, Vessella RL, Sawyers CL, Isaacs WB, Faith DA, Bova GS, Mitchell R, De Marzo AM. Comprehensive mutational analysis and mRNA isoform quantification of TP63 in normal and neoplastic human prostate cells. Prostate 2009; 69:559-69. [PMID: 19142959 PMCID: PMC2875878 DOI: 10.1002/pros.20904] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND The role of TP63 in cancer remains controversial since both oncogenic and tumor suppressive actions have been reported. p63 protein is found in the nuclei of basal cells of the normal prostate, yet it is absent in the vast majority of prostate cancer nuclei. Since a complex array of TP63 mRNA transcripts encode polypeptides with distinct functional properties, it is important to determine which forms are expressed in normal and prostate cancer tissue. METHODS We used real-time RT-PCR to distinguish TP63 mRNA isoforms in prostate cancer cell lines (n = 7), and samples from prostate cancer patients. We sequenced all TP63 exons from 20 primary tumors, 20 metastases, 28 tumor xenografts, and 7 prostate cancer cell lines. RESULTS TP63 mRNA isoforms were present in all tumors, albeit at levels lower than in normal prostate. The most abundant N-terminal variant was DeltaN; the most abundant C-terminal variant was the alpha form. The prostate tumor cell line CWR22Rv1 contained a single G to T substitution in exon 8 that is identical to a dominant-negative DNA binding inactivation mutation occurring in patients with a congenital TP63 deficiency syndrome. One patient tumor contained a somatic mutation in exon 11. CONCLUSIONS The pattern of TP63 mRNA expression in normal prostate tissue is retained in reduced amounts in prostate cancer, and a potentially functional TP63 mutation was identified in one prostate tumor. Thus, if TP63 is a prostate cancer gene it likely functions as a tumor suppressor. Further study of the role of TP63 isoforms in regulating stem cell functions of normal and neoplastic prostate epithelial cells is needed. Prostate 69:559-569, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- J. Kellogg Parsons
- Division of Urology, University of California, San Diego Medical Center, San Diego, CA
- Moores UCSD Cancer Center, La Jolla, CA
- Veterans Affairs Medical Center, San Diego, CA
| | - Elizabeth A. Saria
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Masashi Nakayama
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Robert L. Vessella
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Charles L. Sawyers
- Department of Medicine, University of California, Los Angeles School of Medicine, Los Angeles, CA
| | - William B. Isaacs
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Dennis A. Faith
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
| | - G. Steven Bova
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Rebecca Mitchell
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Angelo M. De Marzo
- The Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
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