1
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Pusch FF, Dorado García H, Xu R, Gürgen D, Bei Y, Brückner L, Röefzaad C, von Stebut J, Bardinet V, Chamorro Gonzalez R, Eggert A, Schulte JH, Hundsdörfer P, Seifert G, Haase K, Schäfer BW, Wachtel M, Kühl AA, Ortiz MV, Wengner AM, Scheer M, Henssen AG. Elimusertib has Antitumor Activity in Preclinical Patient-Derived Pediatric Solid Tumor Models. Mol Cancer Ther 2024; 23:507-519. [PMID: 38159110 PMCID: PMC10985474 DOI: 10.1158/1535-7163.mct-23-0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 09/12/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The small-molecule inhibitor of ataxia telangiectasia and Rad3-related protein (ATR), elimusertib, is currently being tested clinically in various cancer entities in adults and children. Its preclinical antitumor activity in pediatric malignancies, however, is largely unknown. We here assessed the preclinical activity of elimusertib in 38 cell lines and 32 patient-derived xenograft (PDX) models derived from common pediatric solid tumor entities. Detailed in vitro and in vivo molecular characterization of the treated models enabled the evaluation of response biomarkers. Pronounced objective response rates were observed for elimusertib monotherapy in PDX, when treated with a regimen currently used in clinical trials. Strikingly, elimusertib showed stronger antitumor effects than some standard-of-care chemotherapies, particularly in alveolar rhabdomysarcoma PDX. Thus, elimusertib has strong preclinical antitumor activity in pediatric solid tumor models, which may translate to clinically meaningful responses in patients.
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Affiliation(s)
- Fabian F Pusch
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heathcliff Dorado García
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology (EPO), Berlin, Germany
| | - Yi Bei
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Claudia Röefzaad
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jennifer von Stebut
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor Bardinet
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Rocío Chamorro Gonzalez
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Tübingen, Tübingen, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Georg Seifert
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | | | | | - Anja A Kühl
- iPATH.Berlin-Core Unit Immunopathology for Experimental Models, Charité Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York City, New York
| | | | - Monika Scheer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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2
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Bei Y, Bramé L, Kirchner M, Fritsche-Guenther R, Kunz S, Bhattacharya A, Rusu MC, Gürgen D, Dubios FP, Köppke JK, Proba J, Wittstruck N, Sidorova OA, Chamorro González R, Dorado Garcia H, Brückner L, Xu R, Giurgiu M, Rodriguez-Fos E, Yu Q, Spanjaard B, Koche RP, Schmitt CA, Schulte JH, Eggert A, Haase K, Kirwan J, Hagemann AI, Mertins P, Dörr JR, Henssen AG. Passenger Gene Coamplifications Create Collateral Therapeutic Vulnerabilities in Cancer. Cancer Discov 2024; 14:492-507. [PMID: 38197697 PMCID: PMC10911929 DOI: 10.1158/2159-8290.cd-23-1189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024]
Abstract
DNA amplifications in cancer do not only harbor oncogenes. We sought to determine whether passenger coamplifications could create collateral therapeutic vulnerabilities. Through an analysis of >3,000 cancer genomes followed by the interrogation of CRISPR-Cas9 loss-of-function screens across >700 cancer cell lines, we determined that passenger coamplifications are accompanied by distinct dependency profiles. In a proof-of-principle study, we demonstrate that the coamplification of the bona fide passenger gene DEAD-Box Helicase 1 (DDX1) creates an increased dependency on the mTOR pathway. Interaction proteomics identified tricarboxylic acid (TCA) cycle components as previously unrecognized DDX1 interaction partners. Live-cell metabolomics highlighted that this interaction could impair TCA activity, which in turn resulted in enhanced mTORC1 activity. Consequently, genetic and pharmacologic disruption of mTORC1 resulted in pronounced cell death in vitro and in vivo. Thus, structurally linked coamplification of a passenger gene and an oncogene can result in collateral vulnerabilities. SIGNIFICANCE We demonstrate that coamplification of passenger genes, which were largely neglected in cancer biology in the past, can create distinct cancer dependencies. Because passenger coamplifications are frequent in cancer, this principle has the potential to expand target discovery in oncology. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Luca Bramé
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marieluise Kirchner
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Severine Kunz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Animesh Bhattacharya
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mara-Camelia Rusu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Dennis Gürgen
- Experimental Pharmacology and Oncology (EPO), Berlin, Germany
| | - Frank P.B. Dubios
- Institute of pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Julia K.C. Köppke
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jutta Proba
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Nadine Wittstruck
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Alexandra Sidorova
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rocío Chamorro González
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lotte Brückner
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Qinghao Yu
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bastiaan Spanjaard
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clemens A. Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Kirwan
- Core Unit Metabolomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja I.H. Hagemann
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Mertins
- Core Unit Proteomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jan R. Dörr
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Technology Platform Electron Microscopy, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
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3
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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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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. Cell Genom 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [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] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 2023; 19:e1011379. [PMID: 37871126 PMCID: PMC10621967 DOI: 10.1371/journal.pcbi.1011379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 11/02/2023] [Accepted: 07/22/2023] [Indexed: 10/25/2023] Open
Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
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Affiliation(s)
- Thomas B. K. Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Matthew R. Huska
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Tom L. Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Emilia L. Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cody B. Duncan
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Haase
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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6
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Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat Genet 2023; 55:880-890. [PMID: 37142849 PMCID: PMC10181933 DOI: 10.1038/s41588-023-01386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.
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Affiliation(s)
- Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Thomas Conrad
- Genomics Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maja C Stöber
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Life Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Katharina Kasack
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Potsdam, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Eric van Leen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Maria E Stefanova
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Yi Bei
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco Lodrini
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hedwig E Deubzer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Sascha Sauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany.
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7
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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, 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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, 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Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, 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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, 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Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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9
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Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles‐Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton‐Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 2023; 259:56-68. [PMID: 36219477 PMCID: PMC10098817 DOI: 10.1002/path.6019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/02/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Melanoma is a heterogenous malignancy with an unpredictable clinical course. Most patients who present in the clinic are diagnosed with primary melanoma, yet large-scale sequencing efforts have focused primarily on metastatic disease. In this study we sequence-profiled 524 American Joint Committee on Cancer Stage I-III primary tumours. Our analysis of these data reveals recurrent driver mutations, mutually exclusive genetic interactions, where two genes were never or rarely co-mutated, and an absence of co-occurring genetic events. Further, we intersected copy number calls from our primary melanoma data with whole-genome CRISPR screening data to identify the transcription factor interferon regulatory factor 4 (IRF4) as a melanoma-associated dependency. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sofia Birkeälv
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Mark Harland
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Larissa Satiko Alcantara Sekimoto Matsuyama
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - Mamun Rashid
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Ishan Mehta
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Jonathan P Laye
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | | | - Tracey Mell
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Vivek Iyer
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | - Carla Daniela Robles‐Espinoza
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
- Laboratorio Internacional de Investigación sobre el Genoma HumanoUniversidad Nacional Autónoma de México, Campus JuriquillaSantiago de QuerétaroMexico
| | - Ultan McDermott
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
| | | | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of MedicineUniversity of OsloOsloNorway
- Department of Pathology and Leiden Center for Computational OncologyLeiden University Medical CenterLeidenthe Netherlands
| | - Patricia A Possik
- Division of Experimental and Translational ResearchBrazilian National Cancer InstituteRio de JaneiroBrazil
| | - Silvya Stuchi Maria Engler
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical SciencesUniversity of Sao PauloSao PauloBrazil
| | - D Timothy Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - Julia Newton‐Bishop
- Division of Haematology and ImmunologyUniversity of Leeds School of MedicineLeedsUK
| | - David J Adams
- Wellcome Sanger InstituteWellcome Trust Genome CampusCambridgeUK
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10
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Kaufmann TL, Petkovic M, Watkins TBK, Colliver EC, Laskina S, Thapa N, Minussi DC, Navin N, Swanton C, Van Loo P, Haase K, Tarabichi M, Schwarz RF. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol 2022; 23:241. [PMID: 36376909 PMCID: PMC9661799 DOI: 10.1186/s13059-022-02794-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states.
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Affiliation(s)
- Tom L Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Marchstr. 23, 10587, Berlin, Germany.
- BIFOLD, Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
| | - Marina Petkovic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University of Berlin, Unter den Linden 6, 10099, Berlin, Germany
- Division of Oncology and Hematology, Department of Pediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | | | | | - Sofya Laskina
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - Nisha Thapa
- UCL Medical School, University College London, London, UK
| | - Darlan C Minussi
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, 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
| | - Kerstin Haase
- Division of Oncology and Hematology, Department of Pediatrics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- BIFOLD, Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
- Institute for Computational Cancer Biology, Center for Integrated Oncology (CIO) and Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
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11
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Pilleron S, Sun V, Hannan M, Haase K, Kenis C, Arthur E, Krok-Schoen J, Monginot S, Navarrete E, Nikita N, Roggendorf S, Schmidt H, Trevino K, Ayala A, Puts M. Loneliness in older adults with cancer: A scoping review. J Geriatr Oncol 2022. [DOI: 10.1016/s1879-4068(22)00388-5] [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: 11/07/2022]
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12
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Drews RM, Hernando B, Tarabichi M, Haase K, Lesluyes T, Smith PS, Morrill Gavarró L, Couturier DL, Liu L, Schneider M, Brenton JD, Van Loo P, Macintyre G, Markowetz F. A pan-cancer compendium of chromosomal instability. Nature 2022; 606:976-983. [PMID: 35705807 DOI: 10.1038/s41586-022-04789-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Chromosomal instability (CIN) results in the accumulation of large-scale losses, gains and rearrangements of DNA1. The broad genomic complexity caused by CIN is a hallmark of cancer2; however, there is no systematic framework to measure different types of CIN and their effect on clinical phenotypes pan-cancer. Here we evaluate the extent, diversity and origin of CIN across 7,880 tumours representing 33 cancer types. We present a compendium of 17 copy number signatures that characterize specific types of CIN, with putative aetiologies supported by multiple independent data sources. The signatures predict drug response and identify new drug targets. Our framework refines the understanding of impaired homologous recombination, which is one of the most therapeutically targetable types of CIN. Our results illuminate a fundamental structure underlying genomic complexity in human cancers and provide a resource to guide future CIN research.
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Affiliation(s)
- Ruben M Drews
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | | | - Maxime Tarabichi
- The Francis Crick Institute, London, UK.,Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Kerstin Haase
- The Francis Crick Institute, London, UK.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | | | | | | | - Dominique-Laurent Couturier
- Cancer Research UK Cambridge Institute, Cambridge, UK.,Medical Research Council Biostatistics Unit, Cambridge, UK
| | - Lydia Liu
- The Francis Crick Institute, London, UK.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - James D Brenton
- Cancer Research UK Cambridge Institute, Cambridge, UK.,Addenbrooke's Hospital, Cambridge, UK.,Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, Cambridge, UK. .,Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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13
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Steele CD, Abbasi A, Islam SMA, Bowes AL, Khandekar A, Haase K, Hames-Fathi S, Ajayi D, Verfaillie A, Dhami P, McLatchie A, Lechner M, Light N, Shlien A, Malkin D, Feber A, Proszek P, Lesluyes T, Mertens F, Flanagan AM, Tarabichi M, Van Loo P, Alexandrov LB, Pillay N. Signatures of copy number alterations in human cancer. Nature 2022; 606:984-991. [PMID: 35705804 PMCID: PMC9242861 DOI: 10.1038/s41586-022-04738-6] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/07/2022] [Indexed: 12/15/2022]
Abstract
Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.
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Affiliation(s)
- Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Amy L Bowes
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Shadi Hames-Fathi
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Dolapo Ajayi
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | | | - Pawan Dhami
- CRUK-UCL Cancer Institute Translational Technology Platform (Genomics), London, UK
| | - Alex McLatchie
- CRUK-UCL Cancer Institute Translational Technology Platform (Genomics), London, UK
| | - Matt Lechner
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Nicholas Light
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Malkin
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Feber
- Translational Epigenetics, Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Clinical Genomics, Translational Research Laboratory, Royal Marsden NHS Trust, London, UK
| | - Paula Proszek
- Translational Epigenetics, Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Clinical Genomics, Translational Research Laboratory, Royal Marsden NHS Trust, London, UK
| | - Tom Lesluyes
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA.
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK.
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK.
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14
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Thorwarth A, Haase K, Röefzaad C, Pajtler KW, Schramm K, Hauptmann K, Behnke A, Vokuhl C, Elgeti T, Gratopp A, Schulte JH, Scheer M, Hernáiz Driever P, Nysom K, Eggert A, Henssen AG, Deubzer HE. Genomic Evolution and Personalized Therapy of an Infantile Fibrosarcoma Harboring an NTRK Oncogenic Fusion. JCO Precis Oncol 2022; 6:e2100283. [PMID: 35613412 PMCID: PMC9200398 DOI: 10.1200/po.21.00283] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Precision medicine for infantile fibrosarcoma by monitoring of spatial and temporal clonal evolution (requested from authors: Would you be so kind to let us know when the article is announced via Twitter?).![]()
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Affiliation(s)
- Anne Thorwarth
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Kerstin Haase
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany
| | - Claudia Röefzaad
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Kristian W Pajtler
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Kathrin Schramm
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Kathrin Hauptmann
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Anke Behnke
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Christian Vokuhl
- Section of Pediatric Pathology, Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Thomas Elgeti
- Department of Radiology (including Pediatric Radiology), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Alexander Gratopp
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité-Universitäts-Medizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany
| | - Monika Scheer
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Pablo Hernáiz Driever
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany
| | - Karsten Nysom
- Department of Pediatrics and Adolescent Medicine, Juliane Marie Centre, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angelika Eggert
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
| | - Anton G Henssen
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany
| | - Hedwig E Deubzer
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC) of the Charité and the Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Sites Berlin and Heidelberg, Germany.,Berliner Institut für Gesundheitsforschung (BIH), Berlin, Germany
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15
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Haase K, Sattar S, Pilleron S, Lambrechts Y, Hannan M, Navarrete E, Kantilal K, Newton L, Kantilal K, Jin R, van der Wal-Huisman H, Strohschein F, Pergolotti M, Read K, Kenis C, Puts M. Ageism in cancer care: A scoping review by the International Society of Geriatric Oncology (SIOG) Nursing and Allied Health Interest Group. J Geriatr Oncol 2021. [DOI: 10.1016/s1879-4068(21)00371-4] [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: 10/19/2022]
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16
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Sattar S, Haase K, Kaur A, Ahmed S. Impact of the COVID-19 pandemic on physical activities in older adults with cancer in a Canadian central province. J Geriatr Oncol 2021. [PMCID: PMC8675175 DOI: 10.1016/s1879-4068(21)00376-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Sattar S, Alibhai S, Haase K, Effa C, Nedeljak J, Amir E, Campbell D, McNeely M. Feasibility of a virtual hybrid exercise program for older adults with cancer and its effects on lower body strength and balance. J Geriatr Oncol 2021. [DOI: 10.1016/s1879-4068(21)00373-8] [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: 11/29/2022]
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18
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Schmelz K, Toedling J, Huska M, Cwikla MC, Kruetzfeldt LM, Proba J, Ambros PF, Ambros IM, Boral S, Lodrini M, Chen CY, Burkert M, Guergen D, Szymansky A, Astrahantseff K, Kuenkele A, Haase K, Fischer M, Deubzer HE, Hertwig F, Hundsdoerfer P, Henssen AG, Schwarz RF, Schulte JH, Eggert A. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions. Nat Commun 2021; 12:6804. [PMID: 34815394 PMCID: PMC8611017 DOI: 10.1038/s41467-021-26870-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/23/2020] [Accepted: 10/18/2021] [Indexed: 01/12/2023] Open
Abstract
Intratumour heterogeneity is a major cause of treatment failure in cancer. We present in-depth analyses combining transcriptomic and genomic profiling with ultra-deep targeted sequencing of multiregional biopsies in 10 patients with neuroblastoma, a devastating childhood tumour. We observe high spatial and temporal heterogeneity in somatic mutations and somatic copy-number alterations which are reflected on the transcriptomic level. Mutations in some druggable target genes including ALK and FGFR1 are heterogeneous at diagnosis and/or relapse, raising the issue whether current target prioritization and molecular risk stratification procedures in single biopsies are sufficiently reliable for therapy decisions. The genetic heterogeneity in gene mutations and chromosome aberrations observed in deep analyses from patient courses suggest clonal evolution before treatment and under treatment pressure, and support early emergence of metastatic clones and ongoing chromosomal instability during disease evolution. We report continuous clonal evolution on mutational and copy number levels in neuroblastoma, and detail its implications for therapy selection, risk stratification and therapy resistance.
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Affiliation(s)
- Karin Schmelz
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joern Toedling
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matt Huska
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Maja C Cwikla
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Jutta Proba
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter F Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Inge M Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Sengül Boral
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Lodrini
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Celine Y Chen
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dennis Guergen
- Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO), Berlin, Germany
| | | | | | - Annette Kuenkele
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Kerstin Haase
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Medical Faculty, University Children's Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hedwig E Deubzer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Falk Hertwig
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdoerfer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Anton G Henssen
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
| | - Johannes H Schulte
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Angelika Eggert
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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19
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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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20
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Ross EM, Haase K, Van Loo P, Markowetz F. Allele-specific multi-sample copy number segmentation in ASCAT. Bioinformatics 2021; 37:1909-1911. [PMID: 32449758 PMCID: PMC8317109 DOI: 10.1093/bioinformatics/btaa538] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/08/2020] [Accepted: 05/19/2020] [Indexed: 11/17/2022] Open
Abstract
MOTIVATION Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other. RESULTS Here, we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT. AVAILABILITY AND IMPLEMENTATION asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.
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Affiliation(s)
- Edith M. Ross
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | | | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
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21
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Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, Sengupta S, Anur P, Jolly C, Cmero M, Rosebrock D, Schumacher SE, Fan Y, Fittall M, Drews RM, Yao X, Watkins TBK, Lee J, Schlesner M, Zhu H, Adams DJ, McGranahan N, Swanton C, Getz G, Boutros PC, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Martincorena I, Markowetz F, Mustonen V, Yuan K, Gerstung M, Spellman PT, Wang W, Morris QD, Wedge DC, Van Loo P. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 2021; 184:2239-2254.e39. [PMID: 33831375 PMCID: PMC8054914 DOI: 10.1016/j.cell.2021.03.009] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 09/21/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.
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Affiliation(s)
- Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
| | | | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Jeff Wintersinger
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Amit G Deshwar
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Kaixian Yu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulia Rubanova
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Ignacio Vázquez-García
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; University of Cambridge, Cambridge CB2 0QQ, UK; Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Kortine Kleinheinz
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Heidelberg University, 69120 Heidelberg, Germany
| | | | - Salem Malikic
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nilgun Donmez
- Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | | | - Pavana Anur
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Clemency Jolly
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Marek Cmero
- University of Melbourne, Melbourne, VIC 3010, Australia; Walter + Eliza Hall Institute, Melbourne, VIC 3000, Australia
| | | | | | - Yu Fan
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Fittall
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ruben M Drews
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaotong Yao
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Juhee Lee
- University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Hongtu Zhu
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Cancer Genome Evolution Research Group, University College London Cancer Institute, London WC1E 6DD, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6BT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Massachusetts General Hospital, Department of Pathology, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02215, USA
| | - Paul C Boutros
- University of Toronto, Toronto, ON M5S 3E1, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marcin Imielinski
- Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY 10013, USA
| | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - S Cenk Sahinalp
- Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yuan Ji
- NorthShore University HealthSystem, Evanston, IL 60201, USA; The University of Chicago, Chicago, IL 60637, USA
| | - Martin Peifer
- Department of Translational Genomics, Center for Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | | | - Florian Markowetz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Ke Yuan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; School of Computing Science, University of Glasgow, Glasgow G12 8RZ, UK
| | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK; European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Paul T Spellman
- Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97231, USA
| | - Wenyi Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Quaid D Morris
- University of Toronto, Toronto, ON M5S 3E1, Canada; Vector Institute, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK; Oxford NIHR Biomedical Research Centre, Oxford OX4 2PG, UK; Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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22
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Watkins TBK, Lim EL, Petkovic M, Elizalde S, Birkbak NJ, Wilson GA, Moore DA, Grönroos E, Rowan A, Dewhurst SM, Demeulemeester J, Dentro SC, Horswell S, Au L, Haase K, Escudero M, Rosenthal R, Bakir MA, Xu H, Litchfield K, Lu WT, Mourikis TP, Dietzen M, Spain L, Cresswell GD, Biswas D, Lamy P, Nordentoft I, Harbst K, Castro-Giner F, Yates LR, Caramia F, Jaulin F, Vicier C, Tomlinson IPM, Brastianos PK, Cho RJ, Bastian BC, Dyrskjøt L, Jönsson GB, Savas P, Loi S, Campbell PJ, Andre F, Luscombe NM, Steeghs N, Tjan-Heijnen VCG, Szallasi Z, Turajlic S, Jamal-Hanjani M, Van Loo P, Bakhoum SF, Schwarz RF, McGranahan N, Swanton C. Pervasive chromosomal instability and karyotype order in tumour evolution. Nature 2020; 587:126-132. [PMID: 32879494 PMCID: PMC7611706 DOI: 10.1038/s41586-020-2698-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 04/01/2019] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal instability in cancer consists of dynamic changes to the number and structure of chromosomes1,2. The resulting diversity in somatic copy number alterations (SCNAs) may provide the variation necessary for tumour evolution1,3,4. Here we use multi-sample phasing and SCNA analysis of 1,421 samples from 394 tumours across 22 tumour types to show that continuous chromosomal instability results in pervasive SCNA heterogeneity. Parallel evolutionary events, which cause disruption in the same genes (such as BCL9, MCL1, ARNT (also known as HIF1B), TERT and MYC) within separate subclones, were present in 37% of tumours. Most recurrent losses probably occurred before whole-genome doubling, that was found as a clonal event in 49% of tumours. However, loss of heterozygosity at the human leukocyte antigen (HLA) locus and loss of chromosome 8p to a single haploid copy recurred at substantial subclonal frequencies, even in tumours with whole-genome doubling, indicating ongoing karyotype remodelling. Focal amplifications that affected chromosomes 1q21 (which encompasses BCL9, MCL1 and ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal yet appeared to be clonal within single samples. Analysis of an independent series of 1,024 metastatic samples revealed that 13 focal SCNAs were enriched in metastatic samples, including gains in chromosome 8q24.1 (encompassing MYC) in clear cell renal cell carcinoma and chromosome 11q13.3 (encompassing CCND1) in HER2+ breast cancer. Chromosomal instability may enable the continuous selection of SCNAs, which are established as ordered events that often occur in parallel, throughout tumour evolution.
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Affiliation(s)
- Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Marina Petkovic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sergi Elizalde
- Department of Mathematics, Dartmouth College, Hanover, NH, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Stefan C Dentro
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Lewis Au
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Mickael Escudero
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hang Xu
- Stanford Cancer Institute, Stanford, CA, USA
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Wei Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thanos P Mourikis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK
| | - Lavinia Spain
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - George D Cresswell
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Philippe Lamy
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Francesc Castro-Giner
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Lucy R Yates
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Clinical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Franco Caramia
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Cécile Vicier
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, Marseille, France
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Priscilla K Brastianos
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Boris C Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Peter Savas
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sherene Loi
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Fabrice Andre
- INSERM U981, PRISM Institute, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Medical School, Université Paris Saclay, Kremlin Bicetre, France
| | - Nicholas M Luscombe
- Bioinformatics and Computational Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute of Science & Technology, Okinawa, Japan
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vivianne C G Tjan-Heijnen
- Department of Medical Oncology, School of GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- 2nd Department of Pathology, SE-NAP Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, University College London Cancer Institute, University College London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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23
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Sattar S, Haase K, Kuster S, Puts M, Spoelstra S, Bradley C, Wildes TM, Alibhai S. Falls in older adults with cancer: an updated systematic review of prevalence, injurious falls, and impact on cancer treatment. Support Care Cancer 2020; 29:21-33. [PMID: 32671565 DOI: 10.1007/s00520-020-05619-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE This update of our 2016 systematic review answers the following questions: (1) How often do older adults with cancer fall? (2) What are the predictors for falls? (3) What are the rates and predictors of injurious falls? (4) What are the circumstances and outcomes of falls? (5) How do falls in older patients affect subsequent cancer treatment? and a new research question, (6) Which fall reduction interventions are efficacious in this population? METHODS MEDLINE, PubMed, CINAHL, and Embase were searched (September 2015-January 25, 2019). Eligible studies included clinical trials and cohort, case-control, and cross-sectional studies published in English in which the sample (or subgroup) included adults aged ≥ 60, with cancer, in whom falls were examined as an outcome. RESULTS A total of 2521 titles were reviewed, 67 full-text articles were screened for eligibility, and 30 new studies were identified. The majority involved the outpatient setting (n = 19) utilizing cross-sectional method (n = 18). Sample size ranged from 21 to 17,958. Fall rates ranged from 1.52 to 3.41% per 1000 patient days (inpatient setting) and from 39%/24 months to 64%/12 months (outpatient setting). One out of the 6 research questions contributed to a new finding: one study reported that 1 in 20 older patients experienced impact on cancer treatment due to falls. No consistent predictors for falls/fall injuries and no studies on fall reduction interventions in the geriatric oncology setting were identified. CONCLUSION This updated review highlights a new gap in knowledge pertaining to interventions to prevent falls. Additionally, new knowledge also emerged in terms of impact of falls on cancer treatment; however, further research may increase generalizability. Falls and fall-related injuries are common in older adults with cancer and may affect subsequent cancer treatment. Further studies on predictors of falls, subsequent impacts, and fall reduction in the oncology setting are warranted.
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Affiliation(s)
- S Sattar
- College of Nursing, University of Saskatchewan, 4400 4th Avenue, Room 108, Regina, Saskatchewan, S4T 0H8, Canada.
| | - K Haase
- College of Nursing, University of Saskatchewan, Saskatoon, Canada
| | - S Kuster
- Faculty of Kinesiology & Health Studies, University of Regina, Regina, Canada
| | - M Puts
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, Canada
| | - S Spoelstra
- Kirkhof College of Nursing, Grand Valley State University, Grand Rapids, MI, USA
| | - C Bradley
- Library, University of Regina, Regina, Canada
| | - T M Wildes
- Division of Medical Oncology, Washington University School of Medicine, St Louis, MO, USA
| | - S Alibhai
- Department of Medicine, Institute of Health Policy, Management, and Evaluations, University of Toronto, Toronto, Canada.,University Health Network, Toronto, Canada
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24
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Rath B, Swenshon S, Haase K, Szeles T, Jung C, Jacobi F, Myles P. Using a mobile application to detect health needs among children and adolescents who are newly arrived migrants in Europe. J Public Health (Oxf) 2020; 41:840-849. [PMID: 30423143 DOI: 10.1093/pubmed/fdy191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 08/15/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Unprecedented numbers of migrants have arrived in Europe, including children and adolescents. Little is known about their unique health needs. Prospective data collection has been sparse. Mobile applications may help to facilitate global health surveillance. METHODS A pre-validated survey instrument was converted into a mobile application covering self-reported exposures and disruptions of healthcare before/during migration, communicable and non-communicable diseases. Participation was voluntary, anonymous and confidential. RESULTS Data were obtained from 405 migrant children and adolescents in Berlin, Germany, between 7 October 2015 and 15 March 2016 (median age 19 years, range: 1-24; 80.7% males) with the majority from Syria (62.5%), Afghanistan (9.1%) and Iraq (8.2%). In total, 55% were without family, 64% registered asylum-seekers with access to healthcare; 54% had seen a doctor since arrival, with colds or respiratory complaints (37.5 and 13.6%), followed by pain (26.7%) gastrointestinal (12.4%) and skin problems (11.1%). Underlying conditions were reported in 15.6%, predominantly asthma. Overall, 73% reported being up-to date on immunizations, but only 22% held a vaccination record with 46.4% having lost it during migration. CONCLUSIONS The lack of medical and immunization records among newly arrived migrants provides a challenge to healthcare systems. Mobile applications offer rapid screening tools in times of crisis, helping stakeholders with timely information.
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Affiliation(s)
- B Rath
- Department of Public Health, Vienna Vaccine Safety Initiative, Berlin, Germany.,Division of Epidemiology and Public Health, The University of Nottingham, Nottingham, UK
| | - S Swenshon
- Department of Clinical Psychology, Psychologische Hochschule Berlin, Berlin, Germany
| | - K Haase
- Department of Clinical Psychology, Psychologische Hochschule Berlin, Berlin, Germany
| | - T Szeles
- Department of Clinical Psychology, Psychologische Hochschule Berlin, Berlin, Germany
| | - C Jung
- Department of Clinical Psychology, Psychologische Hochschule Berlin, Berlin, Germany
| | - F Jacobi
- Department of Clinical Psychology, Psychologische Hochschule Berlin, Berlin, Germany
| | - P Myles
- Division of Epidemiology and Public Health, The University of Nottingham, Nottingham, UK
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25
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López S, Lim EL, Horswell S, Haase K, Huebner A, Dietzen M, Mourikis TP, Watkins TBK, Rowan A, Dewhurst SM, Birkbak NJ, Wilson GA, Van Loo P, Jamal-Hanjani M, Swanton C, McGranahan N. Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution. Nat Genet 2020; 52:283-293. [PMID: 32139907 PMCID: PMC7116784 DOI: 10.1038/s41588-020-0584-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/28/2020] [Indexed: 01/24/2023]
Abstract
Whole-genome doubling (WGD) is a prevalent event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and prognostic relevance, the evolutionary selection pressures for WGD in cancer have not been investigated. Here, we combine evolutionary simulations with an analysis of cancer sequencing data to explore WGD during cancer evolution. Simulations suggest that WGD can be selected to mitigate the irreversible, ratchet-like, accumulation of deleterious somatic alterations, provided that they occur at a sufficiently high rate. Consistent with this, we observe an enrichment for WGD in tumor types with extensive loss of heterozygosity, including lung squamous cell carcinoma and triple-negative breast cancers, and we find evidence for negative selection against homozygous loss of essential genes before, but not after, WGD. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify novel tumor suppressor genes and to obtain a deeper characterization of known cancer genes.
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Affiliation(s)
- Saioa López
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics Group, Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Thanos P Mourikis
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK.
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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26
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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, 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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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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. The evolutionary history of 2,658 cancers. Nature 2020; 578:122-128. [PMID: 32025013 PMCID: PMC7054212 DOI: 10.1038/s41586-019-1907-7] [Citation(s) in RCA: 518] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/18/2019] [Indexed: 01/28/2023]
Abstract
Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.
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Affiliation(s)
- Moritz Gerstung
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.10306.340000 0004 0606 5382Wellcome 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
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
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28
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Sattar S, Puts M, Spoelstra S, Yokom D, Haase K, Kuster S, Bradley C, Fazalzad R, Wildes T, Alibhai S. FALLS IN OLDER ADULTS WITH CANCER: PRELIMINARY ANALYSIS OF AN UPDATED SYSTEMATIC REVIEW OF PREVALENCE, INJURIOUS FALLS, AND IMPACT ON CANCER TREATMENT. J Geriatr Oncol 2019. [DOI: 10.1016/s1879-4068(19)31283-4] [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: 10/25/2022]
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29
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Haase K, Putts M, Sattar S, Gray M, Kenis C, Donison V, Mclean B, Willis A, Howell D. A SYSTEMATIC REVIEW OF SELF-MANAGEMENT INTERVENTIONS FOR OLDER ADULTS WITH CANCER. J Geriatr Oncol 2019. [DOI: 10.1016/s1879-4068(19)31256-1] [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: 10/25/2022]
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30
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Sattar S, Haase K, Bradley C, Papadopoulos E, Kuster S, Mina D, Joshua A, Souied O, Rediger C, Alibhai S. PERCEPTION OF STRUCTURED EXERCISE PROGRAMS AND FACTORS ASSOCIATED WITH PARTICIPATION AND ADHERENCE AMONG MEN WITH PROSTATE CANCER: A SCOPING REVIEW. J Geriatr Oncol 2019. [DOI: 10.1016/s1879-4068(19)31282-2] [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: 11/29/2022]
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31
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Steele CD, Tarabichi M, Oukrif D, Webster AP, Ye H, Fittall M, Lombard P, Martincorena I, Tarpey PS, Collord G, Haase K, Strauss SJ, Berisha F, Vaikkinen H, Dhami P, Jansen M, Behjati S, Amary MF, Tirabosco R, Feber A, Campbell PJ, Alexandrov LB, Van Loo P, Flanagan AM, Pillay N. Undifferentiated Sarcomas Develop through Distinct Evolutionary Pathways. Cancer Cell 2019; 35:441-456.e8. [PMID: 30889380 PMCID: PMC6428691 DOI: 10.1016/j.ccell.2019.02.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 02/06/2019] [Indexed: 01/01/2023]
Abstract
Undifferentiated sarcomas (USARCs) of adults are diverse, rare, and aggressive soft tissue cancers. Recent sequencing efforts have confirmed that USARCs exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the molecular basis of the structural complexity in USARCs by integrating DNA sequencing, ploidy analysis, gene expression, and methylation profiling. We identified whole genome duplication as a prevalent and pernicious force in USARC tumorigenesis. Using mathematical deconvolution strategies to unravel the complex copy-number profiles and mutational timing models we infer distinct evolutionary pathways of these rare cancers. In addition, 15% of tumors exhibited raised mutational burdens that correlated with gene expression signatures of immune infiltration, and good prognosis.
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Affiliation(s)
- Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Dahmane Oukrif
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Amy P Webster
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Hongtao Ye
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Matthew Fittall
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Patrick Lombard
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Iñigo Martincorena
- 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
| | - Grace Collord
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK
| | - Sandra J Strauss
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Oncology, University College London Hospital NHS Foundation Trust, London, NW1 2PG, UK
| | - Fitim Berisha
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Heli Vaikkinen
- Genomics and Genome Engineering Core Facility, CRUK-UCL Centre, Cancer Institute, University College London, London WC1E 6BT, UK; Research Department of Oncology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Pawan Dhami
- Genomics and Genome Engineering Core Facility, CRUK-UCL Centre, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Marnix Jansen
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular Pathology, University College London Hospital NHS Foundation Trust, London NW1 2BU, UK
| | - 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
| | - M Fernanda Amary
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Roberto Tirabosco
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Andrew Feber
- Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London WC1E 6BT, 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
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1BF, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK; Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK.
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32
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Author Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2019; 10:288. [PMID: 30643118 PMCID: PMC6331546 DOI: 10.1038/s41467-018-07886-4] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc. Chicago, IL, USA was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Tempus Labs, Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), 17007, Girona 17007, Spain.
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33
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Pitt JJ, Riester M, Zheng Y, Yoshimatsu TF, Sanni A, Oluwasola O, Veloso A, Labrot E, Wang S, Odetunde A, Ademola A, Okedere B, Mahan S, Leary R, Macomber M, Ajani M, Johnson RS, Fitzgerald D, Grundstad AJ, Tuteja JH, Khramtsova G, Zhang J, Sveen E, Hwang B, Clayton W, Nkwodimmah C, Famooto B, Obasi E, Aderoju V, Oludara M, Omodele F, Akinyele O, Adeoye A, Ogundiran T, Babalola C, MacIsaac K, Popoola A, Morrissey MP, Chen LS, Wang J, Olopade CO, Falusi AG, Winckler W, Haase K, Van Loo P, Obafunwa J, Papoutsakis D, Ojengbede O, Weber B, Ibrahim N, White KP, Huo D, Olopade OI, Barretina J. Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features. Nat Commun 2018; 9:4181. [PMID: 30327465 PMCID: PMC6191428 DOI: 10.1038/s41467-018-06616-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [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: 10/08/2017] [Accepted: 09/13/2018] [Indexed: 02/08/2023] Open
Abstract
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the molecular features of breast cancers using 194 patients from Nigeria and 1037 patients from The Cancer Genome Atlas (TCGA). Relative to Black and White cohorts in TCGA, Nigerian HR + /HER2 - tumors are characterized by increased homologous recombination deficiency signature, pervasive TP53 mutations, and greater structural variation-indicating aggressive biology. GATA3 mutations are also more frequent in Nigerians regardless of subtype. Higher proportions of APOBEC-mediated substitutions strongly associate with PIK3CA and CDH1 mutations, which are underrepresented in Nigerians and Blacks. PLK2, KDM6A, and B2M are also identified as previously unreported significantly mutated genes in breast cancer. This dataset provides novel insights into potential molecular mechanisms underlying outcome disparities and lay a foundation for deployment of precision therapeutics in underserved populations.
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Affiliation(s)
- Jason J Pitt
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA.,Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Yonglan Zheng
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Toshio F Yoshimatsu
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Ayodele Sanni
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Artur Veloso
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Emma Labrot
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Shengfeng Wang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Abayomi Odetunde
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Adeyinka Ademola
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Babajide Okedere
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Scott Mahan
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Rebecca Leary
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Maura Macomber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Mustapha Ajani
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Ryan S Johnson
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Dominic Fitzgerald
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - A Jason Grundstad
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jigyasa H Tuteja
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Galina Khramtsova
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jing Zhang
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Elisabeth Sveen
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bryce Hwang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wendy Clayton
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | - Bisola Famooto
- Department of Surgery, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Esther Obasi
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Victor Aderoju
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Mobolaji Oludara
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Folusho Omodele
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Odunayo Akinyele
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adewunmi Adeoye
- Department of Pathology, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Chinedum Babalola
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria.,Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Kenzie MacIsaac
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Abiodun Popoola
- Oncology Unit, Department of Radiology, Lagos State University, Ikeja, Lagos, Nigeria
| | | | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Jiebiao Wang
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Christopher O Olopade
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Wendy Winckler
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Human Genetics, University of Leuven, Oude Markt 13, Leuven, 3000, Belgium
| | - John Obafunwa
- Department of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | | | - Oladosu Ojengbede
- Centre for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Barbara Weber
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Nasiru Ibrahim
- Department of Surgery, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Tempus Labs Inc., Chicago, IL, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA. .,Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA.
| | - Olufunmilayo I Olopade
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA. .,Center for Clinical Cancer Genetics & Global Health, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Jordi Barretina
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA. .,Girona Biomedical Research Institute (IDIBGI), Girona, 17007, Spain.
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Jolly C, Gerstung M, Leshchiner I, Dentro SC, Gonzalez S, Mitchell TJ, Rubanova Y, Anur P, Rosebrock D, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vásquez-García I, Haase K, 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, Juan K, Wang W, Morris QD, Spellman PT, Wedge DC, Loo PV. Abstract 218: The evolutionary history of 2,658 cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-218] [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
Cancer develops through a continuous process of somatic evolution. Whole genome sequencing provides a snapshot of the tumor genome at the point of sampling, however, the data can contain information that permits the reconstruction of a tumor's evolutionary past.
Here, we apply such life history analyses on an unprecedented scale, to a set of 2,658 tumors spanning 39 cancer types. We estimated the timing of large chromosomal gains during tumor evolution, by comparing the rates of doubled to non-doubled point mutations within gained regions. Although we find that such events typically occur in the second half of clonal evolution, we also observe distinctive and early chromosomal gains in some cancer types, such as gains of chromosomes 7, 19 and 20 in glioblastoma, and isochromosome 17q in medulloblastoma. By integrating these results with the qualitative timing of individual driver mutations, we obtained an overall ranking, from early to late, of frequent somatic events per cancer type, which both identified novel patterns of tumor evolution, and incorporated additional detail into known models, such as the progression of APC-KRAS-TP53 in colorectal cancer proposed by Vogelstein and Fearon.
To estimate how mutational processes acting on the tumor genome change over time, we classified mutations in each sample according to three broad time periods (early clonal, late clonal, and subclonal), and quantified the activity of mutational signatures in each period. Most mutational processes appear to remain remarkably constant, however, certain signatures show clear and consistent changes during clonal evolution. Particularly, mutational signatures associated with exposure to carcinogens, such as smoking and UV light, tend to decrease over time. In contrast, signatures associated with defective endogenous processes, such as APOBEC mutagenesis and defective double strand break repair, show an increase between early and late phases of tumor evolution.
Making use of clock-like mutational signatures, we converted mutational time estimates for large events, such as whole genome duplication (WGD), and the emergence of the most recent common ancestor (MRCA), into real time estimates, which allowed us to combine our analyses into overall timelines of cancer evolution, per tumor type. For example, the typical timeline of ovarian adenocarcinoma development shows that early tumor evolution is characterized by mutations in TP53, and widespread genome instability, with WGD events taking place on average 8 years prior to diagnosis. In later stages of evolution, signatures of defective repair processes increase, and the MRCA emerges on average 1 year before diagnosis.
Taken together, these data reveal the common and divergent evolutionary trajectories available to a cancer, which might be crucial in understanding specific tumor biology, and in providing new opportunities for early detection and cancer prevention.
Citation Format: Clemency Jolly, Moritz Gerstung, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Daniel Rosebrock, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vásquez-García, Kerstin Haase, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Mark Cmero, Jonas Demeulemeester, Steve Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Juan, Wenyi Wang, Quaid D. Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo, PCAWG Evolution and Heterogeneity Working Group. The evolutionary history of 2,658 cancers [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 218.
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Affiliation(s)
| | - Moritz Gerstung
- 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | | | | | - Santiago Gonzalez
- 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | | | | | - Pavana Anur
- 6Oregon Health and Science University, Portland, OR
| | | | - Kaixian Yu
- 7The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Amit Deshwar
- 5University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Kerstin Haase
- 1The Francis Crick Institute, London, United Kingdom
| | | | - Geoff Macintyre
- 10Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Salem Malikic
- 11Simon Fraser University, Vancouver, British Columbia, Canada
| | - Nilgun Donmez
- 11Simon Fraser University, Vancouver, British Columbia, Canada
| | | | - Mark Cmero
- 12University of Melbourne, Melbourne, Australia
| | | | | | - Yu Fan
- 7The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Juhee Lee
- 14University of California Santa Cruz, Santa Cruz, CA
| | | | | | | | - Hongtu Zhu
- 7The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gad Getz
- 3Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | - Yuan Ji
- 9NorthShore University HealthSystem, Evanston, IL
| | | | - Florian Markowetz
- 10Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Ke Juan
- 10Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Wenyi Wang
- 7The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Peter Van Loo
- 1The Francis Crick Institute, London, United Kingdom
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Haase K, Dentro S, Leshchiner I, Wintersinger J, Deshwar A, Tarabichi M, Morris Q, Wedge D, Loo PV. 33 PAN-cancer whole genome sequencing reveals patterns of subclonal mutations, signature changes and selection. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.33] [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: 11/04/2022] Open
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36
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Jülicher K, Wähner A, Haase K, Barbour KW, Berger FG, Wiehlmann L, Davenport C, Schuster-Gossler K, Stitz J, Cantz T, Eggenschwiler R. Functional characterization of the mouse Serpina1 paralog DOM-7. Biol Chem 2018; 399:577-582. [PMID: 29498931 DOI: 10.1515/hsz-2018-0154] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/25/2018] [Indexed: 11/15/2022]
Abstract
The generation of authentic mouse-models for human α1-antitrypsin (A1AT)-deficiency is difficult due to the high complexity of the mouse Serpina1 gene locus. Depending on the exact mouse strain, three to five paralogs are expressed, with different proteinase inhibitory properties. Nowadays with CRISPR-technology, genome editing of complex genomic loci is feasible and could be employed for the generation of A1AT-deficiency mouse models. In preparation of a CRISPR/Cas9-based genome-engineering approach we identified cDNA clones with a functional CDS for the Serpina1-paralog DOM-7. Here, we show that DOM-7 functionally inhibits neutrophil elastase (ELANE) and chymotrypsin, and therefore needs to be considered when aiming at the generation of A1AT-deficient models.
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Affiliation(s)
- Karen Jülicher
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, D-30625 Hannover, Germany.,University of Applied Sciences, Cologne Faculty of Applied Natural Sciences and Pharmaceutical Biotechnology, Campus Leverkusen, D-51368 Leverkusen, Germany
| | - Annabell Wähner
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, D-30625 Hannover, Germany.,Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | | | - Karen W Barbour
- Department of Biological Sciences, and Center for Colon Cancer Research, University of South Carolina, Columbia, SC 29208, USA
| | - Franklin G Berger
- Department of Biological Sciences, and Center for Colon Cancer Research, University of South Carolina, Columbia, SC 29208, USA
| | - Lutz Wiehlmann
- Core Unit 'Next Generation Sequencing', Hannover Medical School, D-30625 Hannover, Germany
| | - Colin Davenport
- Core Unit 'Next Generation Sequencing', Hannover Medical School, D-30625 Hannover, Germany
| | | | - Jörn Stitz
- University of Applied Sciences, Cologne Faculty of Applied Natural Sciences and Pharmaceutical Biotechnology, Campus Leverkusen, D-51368 Leverkusen, Germany
| | - Tobias Cantz
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, D-30625 Hannover, Germany.,Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
| | - Reto Eggenschwiler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, D-30625 Hannover, Germany.,Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Hannover Medical School, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany
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37
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Myles P, Swenshon S, Haase K, Szeles T, Jung C, Jacobi F, Rath B. A comparative analysis of psychological trauma experienced by children and young adults in two scenarios: evacuation after a natural disaster vs forced migration to escape armed conflict. Public Health 2018; 158:163-175. [PMID: 29628203 DOI: 10.1016/j.puhe.2018.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
Abstract
OBJECTIVES Little is known about the psychological trauma experienced by children and young adults (CYAs) following displacement after natural disasters vs migration from conflict zones. In both instances, the decision to leave is usually cast by the family, and the life of CYAs is suddenly disrupted by external circumstances. STUDY DESIGN An anonymous survey. METHODS The same survey instrument, provided by the National Child Traumatic Stress Network (NCTSN), was used to survey self-reported health needs among CYAs during the aftermath of Hurricane Katrina (Health Survey for Children and Adolescents After Katrina) in October 2005-February 2006 and again during the peak of refugee arrivals in Berlin between October 2015 and March 2016. A weighted index to measure cumulative exposure to traumatic stresses during migration was developed along with an unweighted psychological impact score based on the 22-item NCTS psychological impact questionnaire. Spearman's correlation coefficient (rho) was used to assess the correlation between age and the two psychological impact indices. The two-tailed t-test was used to investigate differences in trauma experienced and psychological impact by gender. Logistic regression was used to investigate differences in types of traumatic stress experienced and psychological impact among CYAs displaced because of Hurricane Katrina and those seeking asylum in Berlin. RESULTS The Katrina cohort included a total of 1133 CYAs, the Berlin cohort, a total of 405 CYAs. The median age in the Katrina cohort was 6.73 years (standard deviation [SD] 5.67, range 0-24; 50.13% males) compared with 17.64 years (SD, range 0-24; 83% males) in the Berlin cohort. Comparative analyses were adjusted to age and gender and revealed significant differences between the two cohorts, both with regards to the amount of trauma experienced and the psychological impact. A statistically significant and moderate positive correlation was observed between trauma experienced and psychological impact of migration in the refugee population (rho = 0.4955, P < 0.001); the correlation was less pronounced but still significant in the Katrina cohort (rho = 0.0942, P = 0.0015). Free-text responses revealed that in addition to common concerns about health, housing and safety, refugees were also pre-occupied with language acquisition and the adaptation to a new culture. CONCLUSIONS The observed differences in the experience and the consequences of trauma in displaced CYAs warrant additional investigation. It was replicated that human-made disaster seems to show more traumatising potential than natural disaster. Stakeholders need to be aware of the potential medium and long-term consequences of migration/evacuation and allocate resources accordingly.
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Affiliation(s)
- P Myles
- Department of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - S Swenshon
- Psychologische Hochschule, Berlin, Germany
| | - K Haase
- Psychologische Hochschule, Berlin, Germany
| | - T Szeles
- Psychologische Hochschule, Berlin, Germany
| | - C Jung
- Psychologische Hochschule, Berlin, Germany
| | - F Jacobi
- Psychologische Hochschule, Berlin, Germany
| | - B Rath
- Department of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; Vienna Vaccine Safety Initiative, Berlin, Germany; Tulane Hospital for Children, New Orleans, LA, USA.
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Haase K, Kröger-Lui N, Pucci A, Schönhals A, Petrich W. Advancements in quantum cascade laser-based infrared microscopy of aqueous media. Faraday Discuss 2018; 187:119-34. [PMID: 27032367 DOI: 10.1039/c5fd00177c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The large mid-infrared absorption coefficient of water frequently hampers the rapid, label-free infrared microscopy of biological objects in their natural aqueous environment. However, the high spectral power density of quantum cascade lasers is shifting this limitation such that mid-infrared absorbance images can be acquired in situ within signal-to-noise ratios of up to 100. Even at sample thicknesses well above 50 μm, signal-to-noise ratios above 10 are readily achieved. The quantum cascade laser-based microspectroscopy of aqueous media is exemplified by imaging an aqueous yeast solution and quantifying glucose consumption, ethanol generation as well as the production of carbon dioxide gas during fermentation.
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Affiliation(s)
- K Haase
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - N Kröger-Lui
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - A Pucci
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - A Schönhals
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - W Petrich
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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39
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Boussommier-Calleja A, Atiyas Y, Haase K, Headley M, Lewis C, Kamm RD. The effects of monocytes on tumor cell extravasation in a 3D vascularized microfluidic model. Biomaterials 2018; 198:180-193. [PMID: 29548546 DOI: 10.1016/j.biomaterials.2018.03.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 02/17/2018] [Accepted: 03/02/2018] [Indexed: 02/07/2023]
Abstract
Metastasis is the leading cause of cancer-related deaths. Recent developments in cancer immunotherapy have shown exciting therapeutic promise for metastatic patients. While most therapies target T cells, other immune cells, such as monocytes, hold great promise for therapeutic intervention. In our study, we provide primary evidence of direct engagement between human monocytes and tumor cells in a 3D vascularized microfluidic model. We first characterize the novel application of our model to investigate and visualize at high resolution the evolution of monocytes as they migrate from the intravascular to the extravascular micro-environment. We also demonstrate their differentiation into macrophages in our all-human model. Our model replicates physiological differences between different monocyte subsets. In particular, we report that inflammatory, but not patrolling, monocytes rely on actomyosin based motility. Finally, we exploit this platform to study the effect of monocytes, at different stages of their life cycle, on cancer cell extravasation. Our data demonstrates that monocytes can directly reduce cancer cell extravasation in a non-contact dependent manner. In contrast, we see little effect of monocytes on cancer cell extravasation once monocytes transmigrate through the vasculature and are macrophage-like. Taken together, our study brings novel insight into the role of monocytes in cancer cell extravasation, which is an important step in the metastatic cascade. These findings establish our microfluidic platform as a powerful tool to investigate the characteristics and function of monocytes and monocyte-derived macrophages in normal and diseased states. We propose that monocyte-cancer cell interactions could be targeted to potentiate the anti-metastatic effect we observe in vitro, possibly expanding the milieu of immunotherapies available to tame metastasis.
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Affiliation(s)
| | - Y Atiyas
- Biological Engineering, Massachussetts Institute of Technology, USA
| | - K Haase
- Mechanical Engineering, Massachussetts Institute of Technology, USA
| | - M Headley
- Department of Pathology, University of California, San Francisco, CA, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - C Lewis
- Department of Oncology & Metabolism, University of Sheffield, UK
| | - R D Kamm
- Mechanical Engineering, Massachussetts Institute of Technology, USA; Biological Engineering, Massachussetts Institute of Technology, USA.
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40
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Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, Davies H, Stratton MR, Campbell PJ. Universal Patterns of Selection in Cancer and Somatic Tissues. Cell 2017; 171:1029-1041.e21. [PMID: 29056346 PMCID: PMC5720395 DOI: 10.1016/j.cell.2017.09.042] [Citation(s) in RCA: 755] [Impact Index Per Article: 107.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 08/09/2017] [Accepted: 09/22/2017] [Indexed: 01/17/2023]
Abstract
Cancer develops as a result of somatic mutation and clonal selection, but quantitative measures of selection in cancer evolution are lacking. We adapted methods from molecular evolution and applied them to 7,664 tumors across 29 cancer types. Unlike species evolution, positive selection outweighs negative selection during cancer development. On average, <1 coding base substitution/tumor is lost through negative selection, with purifying selection almost absent outside homozygous loss of essential genes. This allows exome-wide enumeration of all driver coding mutations, including outside known cancer genes. On average, tumors carry ∼4 coding substitutions under positive selection, ranging from <1/tumor in thyroid and testicular cancers to >10/tumor in endometrial and colorectal cancers. Half of driver substitutions occur in yet-to-be-discovered cancer genes. With increasing mutation burden, numbers of driver mutations increase, but not linearly. We systematically catalog cancer genes and show that genes vary extensively in what proportion of mutations are drivers versus passengers.
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Affiliation(s)
| | - Keiran M Raine
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK
| | - Kevin J Dawson
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | | | - Peter Van Loo
- The Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, Leuven 3000, Belgium
| | - Helen Davies
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | | | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK; Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK.
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41
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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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Behjati S, Tarpey PS, Haase K, Ye H, Young MD, Alexandrov LB, Farndon SJ, Collord G, Wedge DC, Martincorena I, Cooke SL, Davies H, Mifsud W, Lidgren M, Martin S, Latimer C, Maddison M, Butler AP, Teague JW, Pillay N, Shlien A, McDermott U, Futreal PA, Baumhoer D, Zaikova O, Bjerkehagen B, Myklebost O, Amary MF, Tirabosco R, Van Loo P, Stratton MR, Flanagan AM, Campbell PJ. Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma. Nat Commun 2017; 8:15936. [PMID: 28643781 PMCID: PMC5490007 DOI: 10.1038/ncomms15936] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [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: 10/12/2016] [Accepted: 05/15/2017] [Indexed: 02/08/2023] Open
Abstract
Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. It may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike.
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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
- Corpus Christi College, Cambridge CB2 1RH, UK
| | - Patrick S. Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Hongtao Ye
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Matthew D. Young
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ludmil B. Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Sarah J. Farndon
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Grace Collord
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - David C. Wedge
- Oxford Big Data Institute and Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Inigo Martincorena
- 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
| | - Helen Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - William Mifsud
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Mathias Lidgren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sancha Martin
- 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
| | - Mark Maddison
- 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
| | - Nischalan Pillay
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
- University College London Cancer Institute, Huntley Street, London WC1E 6BT, UK
| | - Adam Shlien
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - 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
| | - Daniel Baumhoer
- Bone Tumour Reference Centre, Institute of Pathology, University Hospital Basel, University of Basel, Basel 4031, Switzerland
| | | | | | - Ola Myklebost
- Oslo University Hospital, Oslo 0379, Norway
- University of Bergen, Bergen 5020, Norway
| | - M. Fernanda Amary
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Roberto Tirabosco
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Peter Van Loo
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, Leuven B-3000, Belgium
| | - Michael R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Adrienne M. Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
- University College London Cancer Institute, Huntley Street, London WC1E 6BT, 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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43
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Cozzarelli IM, Skalak KJ, Kent DB, Engle MA, Benthem A, Mumford AC, Haase K, Farag A, Harper D, Nagel SC, Iwanowicz LR, Orem WH, Akob DM, Jaeschke JB, Galloway J, Kohler M, Stoliker DL, Jolly GD. Environmental signatures and effects of an oil and gas wastewater spill in the Williston Basin, North Dakota. Sci Total Environ 2017; 579:1781-1793. [PMID: 27939081 DOI: 10.1016/j.scitotenv.2016.11.157] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Wastewaters from oil and gas development pose largely unknown risks to environmental resources. In January 2015, 11.4ML (million liters) of wastewater (300g/L TDS) from oil production in the Williston Basin was reported to have leaked from a pipeline, spilling into Blacktail Creek, North Dakota. Geochemical and biological samples were collected in February and June 2015 to identify geochemical signatures of spilled wastewaters as well as biological responses along a 44-km river reach. February water samples had elevated chloride (1030mg/L) and bromide (7.8mg/L) downstream from the spill, compared to upstream levels (11mg/L and <0.4mg/L, respectively). Lithium (0.25mg/L), boron (1.75mg/L) and strontium (7.1mg/L) were present downstream at 5-10 times upstream concentrations. Light hydrocarbon measurements indicated a persistent thermogenic source of methane in the stream. Semi-volatile hydrocarbons indicative of oil were not detected in filtered samples but low levels, including tetramethylbenzenes and di-methylnaphthalenes, were detected in unfiltered water samples downstream from the spill. Labile sediment-bound barium and strontium concentrations (June 2015) were higher downstream from the Spill Site. Radium activities in sediment downstream from the Spill Site were up to 15 times the upstream activities and, combined with Sr isotope ratios, suggest contributions from the pipeline fluid and support the conclusion that elevated concentrations in Blacktail Creek water are from the leaking pipeline. Results from June 2015 demonstrate the persistence of wastewater effects in Blacktail Creek several months after remediation efforts started. Aquatic health effects were observed in June 2015; fish bioassays showed only 2.5% survival at 7.1km downstream from the spill compared to 89% at the upstream reference site. Additional potential biological impacts were indicated by estrogenic inhibition in downstream waters. Our findings demonstrate that environmental signatures from wastewater spills are persistent and create the potential for long-term environmental health effects.
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Affiliation(s)
- I M Cozzarelli
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA.
| | - K J Skalak
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - D B Kent
- U.S. Geological Survey, National Research Program, Menlo Park, CA 94025, USA
| | - M A Engle
- U.S. Geological Survey, Eastern Energy Resources Science Center, Reston, VA 20192, USA
| | - A Benthem
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - A C Mumford
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - K Haase
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - A Farag
- U.S. Geological Survey, Columbia Environmental Research Center, Jackson Field Research Station, Jackson, WY 83001, USA
| | - D Harper
- U.S. Geological Survey, Columbia Environmental Research Center, Jackson Field Research Station, Jackson, WY 83001, USA
| | - S C Nagel
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO 65211, USA
| | - L R Iwanowicz
- U.S. Geological Survey, Leetown Science Center, Kearneysville, WV 25430, USA
| | - W H Orem
- U.S. Geological Survey, Eastern Energy Resources Science Center, Reston, VA 20192, USA
| | - D M Akob
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - J B Jaeschke
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
| | - J Galloway
- U.S. Geological Survey, North Dakota Water Science Center, Bismarck, ND 58503, USA
| | - M Kohler
- U.S. Geological Survey, National Research Program, Menlo Park, CA 94025, USA
| | - D L Stoliker
- U.S. Geological Survey, National Research Program, Menlo Park, CA 94025, USA
| | - G D Jolly
- U.S. Geological Survey, National Research Program, Reston, VA 20192, USA
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44
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Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR. Mutational signatures associated with tobacco smoking in human cancer. Science 2016; 354:618-622. [PMID: 27811275 PMCID: PMC6141049 DOI: 10.1126/science.aag0299] [Citation(s) in RCA: 654] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Tobacco smoking increases the risk of at least 17 classes of human cancer. We analyzed somatic mutations and DNA methylation in 5243 cancers of types for which tobacco smoking confers an elevated risk. Smoking is associated with increased mutation burdens of multiple distinct mutational signatures, which contribute to different extents in different cancers. One of these signatures, mainly found in cancers derived from tissues directly exposed to tobacco smoke, is attributable to misreplication of DNA damage caused by tobacco carcinogens. Others likely reflect indirect activation of DNA editing by APOBEC cytidine deaminases and of an endogenous clocklike mutational process. Smoking is associated with limited differences in methylation. The results are consistent with the proposition that smoking increases cancer risk by increasing the somatic mutation load, although direct evidence for this mechanism is lacking in some smoking-related cancer types.
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Affiliation(s)
- Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87102, USA
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Kerstin Haase
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Van Loo
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Iñigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Medical Genetics, Addenbrooke's Hospital National Health Service Trust, Cambridge, UK
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Paolo Vineis
- Human Genetics Foundation, 10126 Torino, Italy
- Department of Epidemiology and Biostatistics, Medical Research Council (MRC)-Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - David H Phillips
- King's College London, MRC-PHE Centre for Environment and Health, Analytical and Environmental Sciences Division, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK.
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45
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Haase K, Mösch A, Frishman D. Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data. BMC Med Genomics 2015; 8:71. [PMID: 26530187 PMCID: PMC4632268 DOI: 10.1186/s12920-015-0146-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 12/11/2014] [Accepted: 10/28/2015] [Indexed: 11/24/2022] Open
Abstract
Background Human endogenous retroviruses (HERVs) are flanked by long terminal repeats (LTRs), which possess promoter activity and can therefore influence the expression of neighboring genes. HERV involvement in different types of cancer has already been thoroughly documented. However, so far there has been no systematic study of HERV expression patterns in a multitude of cell types in health and disease. In particular, the publication of the comprehensive ENCODE dataset has already facilitated many gene expression studies, but none so far focusing exclusively on HERVs. Results We present a comprehensive differential analysis of HERV expression based on ENCODE Tier 1 and Tier 2 RNA-seq data produced by Cold Spring Harbor Laboratories and the California Institute of Technology. This analysis was conducted for individual HERV loci and for entire HERV families in twelve different cell lines, of which six correspond to the normal condition and the other six represent cancer cell types. Although the principal component analysis revealed that the two groups of cells show distinguishable expression patterns, we were not able to link these differences to one or multiple particular HERV families. Two samples exhibit expression patterns, which are not similar to the corresponding cell lines of the other producing lab. Instead they show signs of cancer formation and expression of the pluripotency marker HERVH, despite being classified as a normal cell line and a differentiated cell, respectively. Conclusions Our study demonstrates that ENCODE data are generally comparable between the different contributing labs and that the analysis of HERV elements can provide novel insights into differentiation and disease state of a cell that are easily overlooked when focusing on protein-coding genes. Our findings hint at a change in HERV expression during cancerogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0146-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kerstin Haase
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising, 85354, Germany.
| | - Anja Mösch
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising, 85354, Germany.
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising, 85354, Germany. .,Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany. .,St Petersburg State Polytechnical University, St. Petersburg, 195251, Russia.
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46
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Kröger-Lui N, Gretz N, Haase K, Kränzlin B, Neudecker S, Pucci A, Regenscheit A, Schönhals A, Petrich W. Rapid identification of goblet cells in unstained colon thin sections by means of quantum cascade laser-based infrared microspectroscopy. Analyst 2015; 140:2086-92. [PMID: 25649324 DOI: 10.1039/c4an02001d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Changes in the volume covered by mucin-secreting goblet cell regions within colon thin sections may serve as a means to differentiate between ulcerative colitis and infectious colitis. Here we show that rapid, quantum cascade laser-based mid-infrared microspectroscopy might be able to contribute to the differential diagnosis of colitis ulcerosa, an inflammatory bowel disease. Infrared hyperspectral images of mouse colon thin sections were obtained within 7.5 minutes per section with a pixel size of 3.65 × 3.65 μm(2) and a field of view of 2.8 × 3.1 mm(2). The spectra were processed by training a random decision forest classifier on the basis of k-means clustering on one thin section. The trained algorithm was then applied to 5 further thin sections for a blinded validation and it was able to identify goblet cells in all sections. The rapid identification of goblet cells within these unstained, paraffinized thin sections of colon tissue was enabled by the high content of glycopeptides within the goblet cells as revealed by the pronounced spectral signatures in the 7.6 μm-8.6 μm and the 9.2 μm-9.7 μm wavelength ranges of the electromagnetic spectrum. More so, the simple calculation of the ratio between the absorbance values at 9.29 μm and 8.47 μm provides the potential to further shorten the time for measurement and analysis of a thin section down to well below 1 minute.
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Affiliation(s)
- N Kröger-Lui
- Heidelberg University, Kirchhoff Institute for Physics, Im Neuenheimer Feld 227, Heidelberg, 69120 Germany.
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47
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Haase K, Raffegerst S, Schendel DJ, Frishman D. Expitope: a web server for epitope expression. Bioinformatics 2015; 31:1854-6. [PMID: 25644270 DOI: 10.1093/bioinformatics/btv068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/27/2015] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy. AVAILABILITY AND IMPLEMENTATION The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope.
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Affiliation(s)
- Kerstin Haase
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia
| | - Silke Raffegerst
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia
| | - Dolores J Schendel
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany, Immune Monitoring Group, Helmholtz Zentrum Munich, Institute of Molecular Immunology, 81377 München, Germany, Medigene Immunotherapies GmbH a Subsidiary of Medigene AG, 82152 Planegg, Germany, Helmholtz Zentrum Munich, Institute of Bioinformatics and Systems Biology, 85764 Neuherberg, Germany and St Petersburg State Polytechnical University, St Petersburg, 195251, Russia
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Habermehl D, Lindel K, Rieken S, Haase K, Goeppert B, Büchler MW, Schirmacher P, Welzel T, Debus J, Combs SE. Chemoradiation in patients with unresectable extrahepatic and hilar cholangiocarcinoma or at high risk for disease recurrence after resection : Analysis of treatment efficacy and failure in patients receiving postoperative or primary chemoradiation. Strahlenther Onkol 2012; 188:795-801. [PMID: 22526232 DOI: 10.1007/s00066-012-0099-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 02/22/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND The purpose of this work was to determine efficacy, toxicity, and patterns of recurrence after concurrent chemoradiation (CRT) in patients with extrahepatic bile duct cancer (EHBDC) and hilar cholangiocarcinoma (Klatskin tumours) in case of incomplete resection or unresectable disease. PATIENTS AND METHODS From 2003-2010, 25 patients with nonmetastasized EHBDC and hilar cholangiocarcinoma were treated with radiotherapy and CRT at our institution in an postoperative setting (10 patients, 9 patients with R1 resections) or in case of unresectable disease (15 patients). Median age was 63 years (range 38-80 years) and there were 20 men and 5 women. Median applied dose was 45 Gy in both patient groups. RESULTS Patients at high risk (9 times R1 resection, 1 pathologically confirmed lymphangiosis) for tumour recurrence after curative surgery had a median time to disease progression of 8.7 months and an estimated mean overall survival of 23.2 months (6 of 10 patients are still under observation). Patients undergoing combined chemoradiation in case of unresectable primary tumours are still having a poor prognosis with a progression-free survival of 7.1 months and a median overall survival of 12.0 months. The main site of progression was systemic (liver, peritoneum) in both patient groups. CONCLUSION Chemoradiation with gemcitabine is safe and can be applied safely in either patients with EHBDC or Klatskin tumours at high risk for tumour recurrence after resection and patients with unresectable tumours. Escalation of systemic and local treatment should be investigated in future clinical trials.
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Affiliation(s)
- D Habermehl
- Department of Radiation Oncology, University Hospital of Heidelberg, Germany.
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Abstract
In case of the co-occurrence of facial palsy and inflammation-like symptoms of the same ear, the differential diagnosis is focused on viral (herpes zoster) or bacterial diseases. We report a patient for whom the surgical exploration of the middle ear revealed a benign tumor: a myxoma. These neoplasias are rare tumors in the head and neck region. The typical tumor site is the atrium of heart. In the ear, the tumor grows slowly and remains asymptomatic unless it irritates structures such as the facial nerve or the vestibular organ. Histologically, the tumor presents a "myxoid" matrix that is rich in acid mucopolysaccarides. The treatment of choice is complete surgical resection. Using the case presented, we discuss the causality between the tumor and the facial palsy, although during the operation the bony canal of the nerve was found to be intact. In any cases with clinically and radiologically unclear findings of the ear in connection with facial palsy, surgical exposure should be considered.
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Affiliation(s)
- T Zehlicke
- Universitätsklinik und Poliklinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie Otto Körner, Doberaner Strasse 137-139, 18057 Rostock.
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White ML, Russo RS, Zhou Y, Mao H, Varner RK, Ambrose J, Veres P, Wingenter OW, Haase K, Stutz J, Talbot R, Sive BC. Volatile organic compounds in northern New England marine and continental environments during the ICARTT 2004 campaign. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jd009161] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [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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