1
|
Yu Y, Wang X, Fox J, Yu R, Thakre P, McCauley B, Nikoloutsos N, Yu Y, Li Q, Hastings PJ, Dang W, Chen K, Ira G. Yeast EndoG prevents genome instability by degrading extranuclear DNA species. Nat Commun 2024; 15:7653. [PMID: 39227600 PMCID: PMC11372161 DOI: 10.1038/s41467-024-52147-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/28/2024] [Indexed: 09/05/2024] Open
Abstract
In metazoans mitochondrial DNA (mtDNA) or retrotransposon cDNA released to cytoplasm are degraded by nucleases to prevent sterile inflammation. It remains unknown whether degradation of these DNA also prevents nuclear genome instability. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. In non-dividing stationary phase cells, Pol4-mediated non-homologous end-joining increases, resulting in frequent insertions of 1-3 nucleotides, and insertions of mtDNA (NUMTs) or retrotransposon cDNA. Yeast EndoG (Nuc1) nuclease limits insertion of cDNA and transfer of very long mtDNA ( >10 kb) to the nucleus, where it forms unstable circles, while promoting the formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of extranuclear DNA to nucleus in aging or meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating extranuclear DNA preserve genome stability.
Collapse
Affiliation(s)
- Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Xin Wang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA
| | - Jordan Fox
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Pilendra Thakre
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Brenna McCauley
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Nicolas Nikoloutsos
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX, USA
| | - Yang Yu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA
| | - Qian Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, USA.
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| |
Collapse
|
2
|
Yu Y, Wang X, Fox J, Yu R, Thakre P, McCauley B, Nikoloutsos N, Li Q, Hastings PJ, Dang W, Chen K, Ira G. Yeast EndoG prevents genome instability by degrading cytoplasmic DNA. RESEARCH SQUARE 2024:rs.3.rs-3641411. [PMID: 38260641 PMCID: PMC10802722 DOI: 10.21203/rs.3.rs-3641411/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease 1. Cytoplasmic nucleases degrade these DNA species to limit inflammation 2,3. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nuclear mtDNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
Collapse
Affiliation(s)
- Yang Yu
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| | - Xin Wang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Jordan Fox
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| | - Ruofan Yu
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Pilendra Thakre
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| | - Brenna McCauley
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Nicolas Nikoloutsos
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qian Li
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| | - P. J. Hastings
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| | - Weiwei Dang
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Grzegorz Ira
- Baylor College of Medicine, Department of Molecular and Human Genetics, One Baylor Plaza, Houston, TX 77030, USA
| |
Collapse
|
3
|
Yu Y, Wang X, Fox J, Yu R, Thakre P, McCauley B, Nikoloutsos N, Li Q, Hastings PJ, Dang W, Chen K, Ira G. Yeast EndoG prevents genome instability by degrading cytoplasmic DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571550. [PMID: 38168242 PMCID: PMC10760121 DOI: 10.1101/2023.12.13.571550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease. Cytoplasmic nucleases degrade these DNA species to limit inflammation. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nu clear mt DNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (∼45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
Collapse
|
4
|
Alikhani M, Touati E, Karimipoor M, Vosough M, Mohammadi M. Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players. J Gastrointest Cancer 2021; 53:770-781. [PMID: 34486088 DOI: 10.1007/s12029-021-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Alterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents.
Collapse
Affiliation(s)
- Mehdi Alikhani
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS UMR2001, Institut Pasteur, 25-28 Rue du Dr Roux cedex 15, 75724, Paris, France
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Mohammadi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
5
|
Puertas MJ, González-Sánchez M. Insertions of mitochondrial DNA into the nucleus—effects and role in cell evolution. Genome 2020; 63:365-374. [DOI: 10.1139/gen-2019-0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria. The fragments are inserted into the nucleus during the double-strand breaks repair via the non-homologous end-joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations, or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis, and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution, representing a major source of genomic variation.
Collapse
Affiliation(s)
- María J. Puertas
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
| | - Mónica González-Sánchez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
| |
Collapse
|
6
|
Eldarov CM, Vangely IM, Vays VB, Sheval EV, Holtze S, Hildebrandt TB, Kolosova NG, Popkov VA, Plotnikov EY, Zorov DB, Bakeeva LE, Skulachev VP. Mitochondria in the Nuclei of Rat Myocardial Cells. Cells 2020; 9:E712. [PMID: 32183238 PMCID: PMC7140638 DOI: 10.3390/cells9030712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/01/2023] Open
Abstract
Electron microscopic study of cardiomyocytes taken from healthy Wistar and OXYS rats and naked mole rats (Heterocephalus glaber) revealed mitochondria in nuclei that lacked part of the nuclear envelope. The direct interaction of mitochondria with nucleoplasm is shown. The statistical analysis of the occurrence of mitochondria in cardiomyocyte nuclei showed that the percentage of nuclei with mitochondria was roughly around 1%, and did not show age and species dependency. Confocal microscopy of normal rat cardiac myocytes revealed a branched mitochondrial network in the vicinity of nuclei with an organization different than that of interfibrillar mitochondria. This mitochondrial network was energetically functional because it carried the membrane potential that responded by oscillatory mode after photodynamic challenge. We suggest that the presence of functional mitochondria in the nucleus is not only a consequence of certain pathologies but rather represents a normal biological phenomenon involved in mitochondrial/nuclear interactions.
Collapse
Affiliation(s)
- Chupalav M Eldarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Vangely
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Valeriya B Vays
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Thomas B Hildebrandt
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Natalia G Kolosova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vasily A Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Egor Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry B Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Lora E Bakeeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir P Skulachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| |
Collapse
|
7
|
Singh B, Modica-Napolitano JS, Singh KK. Defining the momiome: Promiscuous information transfer by mobile mitochondria and the mitochondrial genome. Semin Cancer Biol 2017; 47:1-17. [PMID: 28502611 PMCID: PMC5681893 DOI: 10.1016/j.semcancer.2017.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/20/2017] [Accepted: 05/07/2017] [Indexed: 12/30/2022]
Abstract
Mitochondria are complex intracellular organelles that have long been identified as the powerhouses of eukaryotic cells because of the central role they play in oxidative metabolism. A resurgence of interest in the study of mitochondria during the past decade has revealed that mitochondria also play key roles in cell signaling, proliferation, cell metabolism and cell death, and that genetic and/or metabolic alterations in mitochondria contribute to a number of diseases, including cancer. Mitochondria have been identified as signaling organelles, capable of mediating bidirectional intracellular information transfer: anterograde (from nucleus to mitochondria) and retrograde (from mitochondria to nucleus). More recently, evidence is now building that the role of mitochondria extends to intercellular communication as well, and that the mitochondrial genome (mtDNA) and even whole mitochondria are indeed mobile and can mediate information transfer between cells. We define this promiscuous information transfer function of mitochondria and mtDNA as "momiome" to include all mobile functions of mitochondria and the mitochondrial genome. Herein, we review the "momiome" and explore its role in cancer development, progression, and treatment.
Collapse
Affiliation(s)
- Bhupendra Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Keshav K Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Environmental Health, Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Aging, University of Alabama at Birmingham, Birmingham, AL, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA; Birmingham Veterans Affairs Medical Center, Birmingham, AL, USA.
| |
Collapse
|
8
|
Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MTM, van't Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res 2015; 25:814-24. [PMID: 25963125 PMCID: PMC4448678 DOI: 10.1101/gr.190470.115] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
Abstract
Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.
Collapse
Affiliation(s)
- Young Seok Ju
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - William Mifsud
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Beiyuan Fu
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Helen R Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Manasa Ramakrishna
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Lucy Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Patrick S Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sam Behjati
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sancha Martin
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Anthony Fullam
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Moritz Gerstung
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jyoti Nangalia
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Anthony R Green
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Carlos Caldas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; Cancer Research UK (CRUK) Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Åke Borg
- BioCare, Strategic Cancer Research Program, SE-223 81 Lund, Sweden; CREATE Health, Strategic Centre for Translational Cancer Research, SE-221 00 Lund, Sweden; Department of Oncology and Pathology, Lund University Cancer Center, SE-221 85 Lund, Sweden
| | - Andrew Tutt
- Breakthrough Breast Cancer Research Unit, Research Oncology, King's College London, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Ming Ta Michael Lee
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, 230-0045 Yokohama, Japan; National Center for Genome Medicine, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Laura J van't Veer
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA; Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Benita K T Tan
- Department of General Surgery, Singapore General Hospital, Singapore 169608
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver V5Z 1L3, Canada
| | - Paul N Span
- Department of Radiation Oncology and Department of Laboratory Medicine, Radboud University Medical Center, 6525 HP Nijmegen, Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Anne Vincent-Salomon
- Institut Curie, INSERM U934 and Department of Tumor Biology, 75248 Paris cédex 05, France
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | | | | | - Adrienne M Flanagan
- Royal National Orthopaedic Hospital, Middlesex HA7 4LP, United Kingdom; UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
| | - Christopher Foster
- University of Liverpool and HCA Pathology Laboratories, London WC1E 6JA, United Kingdom
| | - David E Neal
- Urological Research Laboratory, Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, United Kingdom; Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Colin Cooper
- Institute of Cancer Research, Sutton, London SM2 5NG, United Kingdom; Department of Biological Sciences and School of Medicine, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton SM2 5NG, United Kingdom; Royal Marsden NHS Foundation Trust, London SW3 6JJ and Sutton SM2 5PT, United Kingdom
| | | | - Sunil R Lakhani
- University of Queensland, School of Medicine, Brisbane, QLD 4006, Australia; Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD 4029, Australia; University of Queensland, UQ Centre for Clinical Research, Brisbane, QLD 4029, Australia
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, 1000 Brussels, Belgium
| | - Gilles Thomas
- Université Lyon 1, Institut National du Cancer (INCa)-Synergie, 69008 Lyon, France
| | - Andrea L Richardson
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Colin A Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Alastair M Thompson
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| |
Collapse
|