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Yang SF, Nelson CB, Wells JK, Fernando M, Lu R, Allen JAM, Malloy L, Lamm N, Murphy VJ, Mackay JP, Deans AJ, Cesare AJ, Sobinoff AP, Pickett HA. ZNF827 is a single-stranded DNA binding protein that regulates the ATR-CHK1 DNA damage response pathway. Nat Commun 2024; 15:2210. [PMID: 38472229 PMCID: PMC10933417 DOI: 10.1038/s41467-024-46578-0] [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: 06/15/2022] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
The ATR-CHK1 DNA damage response pathway becomes activated by the exposure of RPA-coated single-stranded DNA (ssDNA) that forms as an intermediate during DNA damage and repair, and as a part of the replication stress response. Here, we identify ZNF827 as a component of the ATR-CHK1 kinase pathway. We demonstrate that ZNF827 is a ssDNA binding protein that associates with RPA through concurrent binding to ssDNA intermediates. These interactions are dependent on two clusters of C2H2 zinc finger motifs within ZNF827. We find that ZNF827 accumulates at stalled forks and DNA damage sites, where it activates ATR and promotes the engagement of homologous recombination-mediated DNA repair. Additionally, we demonstrate that ZNF827 depletion inhibits replication initiation and sensitizes cancer cells to the topoisomerase inhibitor topotecan, revealing ZNF827 as a therapeutic target within the DNA damage response pathway.
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Affiliation(s)
- Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Jadon K Wells
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Madushan Fernando
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Lisa Malloy
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Noa Lamm
- Nuclear Dynamics Group, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, 2145, Australia.
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2
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Nelson CB, Rogers S, Roychoudhury K, Tan YS, Atkinson CJ, Sobinoff AP, Tomlinson CG, Hsu A, Lu R, Dray E, Haber M, Fletcher JI, Cesare AJ, Hegde RS, Pickett HA. The Eyes Absent family members EYA4 and EYA1 promote PLK1 activation and successful mitosis through tyrosine dephosphorylation. Nat Commun 2024; 15:1385. [PMID: 38360978 PMCID: PMC10869800 DOI: 10.1038/s41467-024-45683-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
The Eyes Absent proteins (EYA1-4) are a biochemically unique group of tyrosine phosphatases known to be tumour-promoting across a range of cancer types. To date, the targets of EYA phosphatase activity remain largely uncharacterised. Here, we identify Polo-like kinase 1 (PLK1) as an interactor and phosphatase substrate of EYA4 and EYA1, with pY445 on PLK1 being the primary target site. Dephosphorylation of pY445 in the G2 phase of the cell cycle is required for centrosome maturation, PLK1 localization to centrosomes, and polo-box domain (PBD) dependent interactions between PLK1 and PLK1-activation complexes. Molecular dynamics simulations support the rationale that pY445 confers a structural impairment to PBD-substrate interactions that is relieved by EYA-mediated dephosphorylation. Depletion of EYA4 or EYA1, or chemical inhibition of EYA phosphatase activity, dramatically reduces PLK1 activation, causing mitotic defects and cell death. Overall, we have characterized a phosphotyrosine signalling network governing PLK1 and mitosis.
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Affiliation(s)
- Christopher B Nelson
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Samuel Rogers
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Kaushik Roychoudhury
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Caroline J Atkinson
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Alexander P Sobinoff
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Christopher G Tomlinson
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Anton Hsu
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Robert Lu
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Eloise Dray
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Research Centre, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Anthony J Cesare
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Rashmi S Hegde
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hilda A Pickett
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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3
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Taherian Fard A, Leeson HC, Aguado J, Pietrogrande G, Power D, Gómez-Inclán C, Zheng H, Nelson CB, Soheilmoghaddam F, Glass N, Dharmaratne M, Watson ER, Lu J, Martin S, Pickett HA, Cooper-White J, Wolvetang EJ, Mar JC. Deconstructing heterogeneity of replicative senescence in human mesenchymal stem cells at single cell resolution. GeroScience 2024; 46:999-1015. [PMID: 37314668 PMCID: PMC10828319 DOI: 10.1007/s11357-023-00829-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: 10/04/2022] [Accepted: 05/15/2023] [Indexed: 06/15/2023] Open
Abstract
Following prolonged cell division, mesenchymal stem cells enter replicative senescence, a state of permanent cell cycle arrest that constrains the use of this cell type in regenerative medicine applications and that in vivo substantially contributes to organismal ageing. Multiple cellular processes such as telomere dysfunction, DNA damage and oncogene activation are implicated in promoting replicative senescence, but whether mesenchymal stem cells enter different pre-senescent and senescent states has remained unclear. To address this knowledge gap, we subjected serially passaged human ESC-derived mesenchymal stem cells (esMSCs) to single cell profiling and single cell RNA-sequencing during their progressive entry into replicative senescence. We found that esMSC transitioned through newly identified pre-senescent cell states before entering into three different senescent cell states. By deconstructing this heterogeneity and temporally ordering these pre-senescent and senescent esMSC subpopulations into developmental trajectories, we identified markers and predicted drivers of these cell states. Regulatory networks that capture connections between genes at each timepoint demonstrated a loss of connectivity, and specific genes altered their gene expression distributions as cells entered senescence. Collectively, this data reconciles previous observations that identified different senescence programs within an individual cell type and should enable the design of novel senotherapeutic regimes that can overcome in vitro MSC expansion constraints or that can perhaps slow organismal ageing.
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Affiliation(s)
- Atefeh Taherian Fard
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Hannah C Leeson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Dominique Power
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Cecilia Gómez-Inclán
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Huiwen Zheng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Christopher B Nelson
- Children's Medical Research Institute, University of Sydney, Westmead, Sydney, NSW, Australia
| | - Farhad Soheilmoghaddam
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Chemical Engineering, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Australia
| | - Nick Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Malindrie Dharmaratne
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ebony R Watson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Jennifer Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St Lucia, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, Sydney, NSW, Australia
| | - Justin Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
- School of Chemical Engineering, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia.
| | - Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia.
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4
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Lu R, Nelson CB, Rogers S, Cesare AJ, Sobinoff AP, Pickett HA. Distinct modes of telomere synthesis and extension contribute to Alternative Lengthening of Telomeres. iScience 2024; 27:108655. [PMID: 38213617 PMCID: PMC10783591 DOI: 10.1016/j.isci.2023.108655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/13/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair mechanism that becomes activated in a subset of cancers to maintain telomere length. One of the defining features of ALT cells is the prevalence of extrachromosomal telomeric repeat (ECTR) DNA. Here, we identify that ALT cells engage in two modes of telomere synthesis. Non-productive telomere synthesis occurs during the G2 phase of the cell cycle and is characterized by newly synthesized internal telomeric regions that are not retained in the subsequent G1, coinciding with an induction of ECTR DNA. Productive telomere synthesis occurs specifically during the transition from G2 to mitosis and is defined as the extension of the telomere termini. While many proteins associated with break-induced telomere synthesis function in both non-productive and productive telomere synthesis, POLH specifically promotes productive telomere lengthening and suppresses non-productive telomere synthesis. These findings delineate the mechanism and cell cycle regulation of ALT-mediated telomere synthesis and extension.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Christopher B. Nelson
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Samuel Rogers
- Genome Integrity Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Anthony J. Cesare
- Genome Integrity Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Alexander P. Sobinoff
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children’s Medical Research Institute, University of Sydney, Westmead, NSW, Australia
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5
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Bruedigam C, Porter AH, Song A, Vroeg In de Wei G, Stoll T, Straube J, Cooper L, Cheng G, Kahl VFS, Sobinoff AP, Ling VY, Jebaraj BMC, Janardhanan Y, Haldar R, Bray LJ, Bullinger L, Heidel FH, Kennedy GA, Hill MM, Pickett HA, Abdel-Wahab O, Hartel G, Lane SW. Imetelstat-mediated alterations in fatty acid metabolism to induce ferroptosis as a therapeutic strategy for acute myeloid leukemia. Nat Cancer 2024; 5:47-65. [PMID: 37904045 PMCID: PMC10824665 DOI: 10.1038/s43018-023-00653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/14/2023] [Indexed: 11/01/2023]
Abstract
Telomerase enables replicative immortality in most cancers including acute myeloid leukemia (AML). Imetelstat is a first-in-class telomerase inhibitor with clinical efficacy in myelofibrosis and myelodysplastic syndromes. Here, we develop an AML patient-derived xenograft resource and perform integrated genomics, transcriptomics and lipidomics analyses combined with functional genetics to identify key mediators of imetelstat efficacy. In a randomized phase II-like preclinical trial in patient-derived xenografts, imetelstat effectively diminishes AML burden and preferentially targets subgroups containing mutant NRAS and oxidative stress-associated gene expression signatures. Unbiased, genome-wide CRISPR/Cas9 editing identifies ferroptosis regulators as key mediators of imetelstat efficacy. Imetelstat promotes the formation of polyunsaturated fatty acid-containing phospholipids, causing excessive levels of lipid peroxidation and oxidative stress. Pharmacological inhibition of ferroptosis diminishes imetelstat efficacy. We leverage these mechanistic insights to develop an optimized therapeutic strategy using oxidative stress-inducing chemotherapy to sensitize patient samples to imetelstat causing substantial disease control in AML.
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Affiliation(s)
- Claudia Bruedigam
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia.
| | - Amy H Porter
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Axia Song
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Thomas Stoll
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jasmin Straube
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Leanne Cooper
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Guidan Cheng
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Vivian F S Kahl
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Victoria Y Ling
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Yashaswini Janardhanan
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rohit Haldar
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Laura J Bray
- Faculty of Engineering, School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lars Bullinger
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine Berlin, Campus Virchow Klinikum, Berlin, Germany
| | - Florian H Heidel
- Hematology, Oncology, Stem Cell Transplantation and Palliative Care, University Medicine Greifswald, Greifswald, Germany
- Leibniz Institute on Aging, Jena, Germany
| | - Glen A Kennedy
- Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Michelle M Hill
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunter Hartel
- Statistics Unit, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Steven W Lane
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia.
- Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
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6
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Sobinoff AP, Di Maro S, Low RRJ, Benedetti R, Tomassi S, D'Aniello A, Russo R, Baglivo I, Chianese U, Pedone PV, Chambery A, Cesare AJ, Altucci L, Pickett HA, Cosconati S. Irreversible inhibition of TRF2 TRFH recruiting functions by a covalent cyclic peptide induces telomeric replication stress in cancer cells. Cell Chem Biol 2023; 30:1652-1665.e6. [PMID: 38065101 DOI: 10.1016/j.chembiol.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
The TRF2 shelterin component is an essential regulator of telomere homeostasis and genomic stability. Mutations in the TRF2TRFH domain physically impair t-loop formation and prevent the recruitment of several factors that promote efficient telomere replication, causing telomeric DNA damage. Here, we design, synthesize, and biologically test covalent cyclic peptides that irreversibly target the TRF2TRFH domain. We identify APOD53 as our most promising compound, as it consistently induces a telomeric DNA damage response in cancer cell lines. APOD53 forms a covalent adduct with a reactive cysteine residue present in the TRF2TRFH domain and induces phenotypes consistent with TRF2TRFH domain mutants. These include induction of a telomeric DNA damage response, increased telomeric replication stress, and impaired recruitment of RTEL1 and SLX4 to telomeres. We demonstrate that APOD53 impairs cancer cell growth and find that co-treatment with APOD53 can exacerbate telomere replication stress caused by the G4 stabilizer RHPS4 and low dose aphidicolin (APH).
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Affiliation(s)
- Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Salvatore Di Maro
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ronnie R J Low
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy; Azienda Ospedaliera Universitaria "Luigi Vanvitelli", Medical Epigenetics Program
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Antonia D'Aniello
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosita Russo
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Paolo V Pedone
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy; BIOGEM, 83031 Ariano Irpino, Italy; Azienda Ospedaliera Universitaria "Luigi Vanvitelli", Medical Epigenetics Program; IEOS CNR, Napoli, Italy
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia.
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy.
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7
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Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study. Genome Med 2023; 15:74. [PMID: 37723522 PMCID: PMC10507925 DOI: 10.1186/s13073-023-01223-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Uwe Dressel
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Norris
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia
| | - Daffodil M Canson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Dylan M Glubb
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Cristina Fortuno
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Miranda E Vidgen
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Mohammad K Al-Shinnag
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel L Austin
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Elisa J Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cassandra B Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Marion T Harris
- Monash Health Familial Cancer, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Megan J Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Emilia L Ip
- Cancer Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | | | - Chiyan Lau
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genomics, Pathology Queensland, Brisbane, QLD, Australia
| | - Julia L Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael W Millward
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Melissa J Monnik
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Abiramy Ragunathan
- Familial Cancer Services, The Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Rachel D Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Sharron L Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Simon L Troth
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Katherine M Tucker
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mathew J Wallis
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Maie Walsh
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Rachel A Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ingrid M Winship
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
- Genomic Medicine and Familial Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Helen G Mar Fan
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Robyn L Ward
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia.
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Rahman ST, Waterhouse M, Pham H, Duarte Romero B, Baxter C, McLeod DSA, English DR, Ebeling PR, Hartel G, Armstrong BK, O'Connell RL, van der Pols JC, Venn AJ, Webb PM, Wells JK, Whiteman DC, Pickett HA, Neale RE. Effects of Vitamin D Supplementation on Telomere Length: An Analysis of Data from the Randomised Controlled D-Health Trial. J Nutr Health Aging 2023; 27:609-616. [PMID: 37702332 DOI: 10.1007/s12603-023-1948-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/01/2023] [Indexed: 09/14/2023]
Abstract
OBJECTIVES Observational studies have suggested that a higher 25-hydroxyvitamin D concentration may be associated with longer telomere length; however, this has not been investigated in randomised controlled trials. We conducted an ancillary study within a randomised, double-blind, placebo-controlled trial of monthly vitamin D (the D-Health Trial) for the prevention of all-cause mortality, conducted from 2014 to 2020, to assess the effect of vitamin D supplementation on telomere length (measured as the telomere to single copy gene (T/S) ratio). DESIGN, SETTING, PARTICIPANTS, AND INTERVENTION Participants were Australians aged 60-84 years and we randomly selected 1,519 D-Health participants (vitamin D: n=744; placebo: n=775) for this analysis. We used quantitative polymerase chain reaction to measure the relative telomere length (T/S ratio) at 4 or 5 years after randomisation. We compared the mean T/S ratio between the vitamin D and placebo groups to assess the effect of vitamin D supplementation on relative telomere length, using a linear regression model with adjustment for age, sex, and state which were used to stratify the randomisation. RESULTS The mean T/S ratio was 0.70 for both groups (standard deviation 0.18 and 0.16 for the vitamin D and placebo groups respectively). The adjusted mean difference (vitamin D minus placebo) was -0.001 (95% CI -0.02 to 0.02). There was no effect modification by age, sex, body mass index, or predicted baseline 25-hydroxyvitamin D concentration. CONCLUSION In conclusion, routinely supplementing older adults, who are largely vitamin D replete, with monthly doses of vitamin D is unlikely to influence telomere length.
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Affiliation(s)
- S T Rahman
- Professor Rachel E. Neale, QIMR Berghofer Medical Research Institute, Locked Bag 2000, Royal Brisbane Hospital, QLD 4029, Australia, , +61 7 38453598
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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, 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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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Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, 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Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV. Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, 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Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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11
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Abstract
Cancer cells establish replicative immortality by activating a telomere-maintenance mechanism (TMM), be it telomerase or the alternative lengthening of telomeres (ALT) pathway. Targeting telomere maintenance represents an intriguing opportunity to treat the vast majority of all cancer types. Whilst telomerase inhibitors have historically been heralded as promising anticancer agents, the reality has been more challenging, and there are currently no therapeutic options for cancer types that use ALT despite their aggressive nature and poor prognosis. In this Review, we discuss the mechanistic differences between telomere maintenance by telomerase and ALT, the current methods used to detect each mechanism, the utility of these tests for clinical diagnosis, and recent developments in the therapeutic strategies being employed to target both telomerase and ALT. We present notable developments in repurposing established therapeutic agents and new avenues that are emerging to target cancer types according to which TMM they employ. These opportunities extend beyond inhibition of telomere maintenance, by finding and exploiting inherent weaknesses in the telomeres themselves to trigger rapid cellular effects that lead to cell death.
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Affiliation(s)
- Jixuan Gao
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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12
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de Nonneville A, Salas S, Bertucci F, Sobinoff AP, Adélaïde J, Guille A, Finetti P, Noble JR, Churikov D, Chaffanet M, Lavit E, Pickett HA, Bouvier C, Birnbaum D, Reddel RR, Géli V. TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT. EMBO Mol Med 2022; 14:e15859. [PMID: 35920001 PMCID: PMC9549729 DOI: 10.15252/emmm.202215859] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high-grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild-type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT-positive ATRX-wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX-mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX-wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.
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Affiliation(s)
- Alexandre de Nonneville
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance,Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia,Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Sébastien Salas
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - François Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Pascal Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Jane R Noble
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Dimitri Churikov
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
| | - Max Chaffanet
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Elise Lavit
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Corinne Bouvier
- Department of PathologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Roger R Reddel
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
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13
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Lu R, Allen JA, Galaviz P, Pickett HA. A DNA-fiber protocol for single molecule analysis of telomere (SMAT) length and extension events in cancer cells. STAR Protoc 2022; 3:101212. [PMID: 35265860 PMCID: PMC8899046 DOI: 10.1016/j.xpro.2022.101212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a homologous recombination-based telomere maintenance mechanism. It is active in approximately 10–15% of cancers. We present a DNA-fiber protocol, combining YOYO-1 staining of genomic DNA, telomere fluorescence in situ hybridization (FISH), and EdU labeling of nascent DNA, to measure telomere extension events in ALT cancer cells. The protocol can be used to delineate ALT-mediated telomere extension. For complete details on the use and execution of this protocol, please refer to Barroso-Gonzalez et al. (2021). DNA fiber microscopy for measuring telomere extension events in ALT cancer cells DNA fibers are stretched uniformly using a constant stretching factor Delineates terminal from nonterminal EdU tracts at telomeres on DNA fibers
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14
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Abstract
Telomeres are nucleoprotein structures that cap the ends of linear chromosomes. Telomeric DNA comprises terminal tracts of G-rich tandem repeats, which are inherently difficult for the replication machinery to navigate. Structural aberrations that promote activation of the alternative lengthening of telomeres (ALT) pathway of telomere maintenance exacerbate replication stress at ALT telomeres, driving fork stalling and fork collapse. This form of telomeric DNA damage perpetuates recombination-mediated repair pathways and break-induced telomere synthesis. The relationship between replication stress and DNA repair is tightly coordinated for the purpose of regulating telomere length in ALT cells, but has been shown to be experimentally manipulatable. This raises the intriguing possibility that induction of replication stress can be used as a means to cause toxic levels of DNA damage at ALT telomeres, thereby selectively disrupting the viability of ALT cancers.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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15
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Holmes O, Nones K, Tang YH, Loffler KA, Lee M, Patch AM, Dagg RA, Lau LMS, Leonard C, Wood S, Xu Q, Pickett HA, Reddel RR, Barbour AP, Grimmond SM, Waddell N, Pearson JV. qmotif: determination of telomere content from whole-genome sequence data. Bioinform Adv 2022; 2:vbac005. [PMID: 36699384 PMCID: PMC9710677 DOI: 10.1093/bioadv/vbac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/15/2021] [Indexed: 01/28/2023]
Abstract
Motivation Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA samples. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing. Results qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time-usually under a minute. Availability and implementation qmotif is implemented in Java and source code is available at https://github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from https://adamajava.readthedocs.io/en/latest/. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Oliver Holmes
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Yue Hang Tang
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia
| | - Kelly A Loffler
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia,Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Michael Lee
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Rebecca A Dagg
- Children’s Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Loretta M S Lau
- Children’s Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Hilda A Pickett
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Andrew P Barbour
- Surgical Oncology Group, Diamantina Institute, The University of Queensland, Translational Research Institute at the Princess Alexandra Hospital, Woolloongabba, Brisbane 4102, QLD, Australia
| | - Sean M Grimmond
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,University of Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,To whom correspondence should be addressed. or
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston, Brisbane 4006, QLD, Australia,Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane 4072, QLD, Australia,To whom correspondence should be addressed. or
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16
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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17
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Mackintosh JA, Pietsch M, Lutzky V, Enever D, Bancroft S, Apte SH, Tan M, Yerkovich ST, Dickinson JL, Pickett HA, Selvadurai H, Grainge C, Goh NS, Hopkins P, Glaspole I, Reynolds PN, Wrobel J, Jaffe A, Corte TJ, Chambers DC. TELO-SCOPE study: a randomised, double-blind, placebo-controlled, phase 2 trial of danazol for short telomere related pulmonary fibrosis. BMJ Open Respir Res 2021; 8:8/1/e001127. [PMID: 34857525 PMCID: PMC8640666 DOI: 10.1136/bmjresp-2021-001127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
Introduction Recent discoveries have identified shortened telomeres and related mutations in people with pulmonary fibrosis (PF). There is evidence to suggest that androgens, including danazol, may be effective in lengthening telomeres in peripheral blood cells. This study aims to assess the safety and efficacy of danazol in adults and children with PF associated with telomere shortening. Methods and analysis A multi-centre, double-blind, placebo-controlled, randomised trial of danazol will be conducted in subjects aged >5 years with PF associated with age-adjusted telomere length ≤10th centile measured by flow fluorescence in situ hybridisation; or in children, a diagnosis of dyskeratosis congenita. Adult participants will receive danazol 800 mg daily in two divided doses or identical placebo capsules orally for 12 months, in addition to standard of care (including pirfenidone or nintedanib). Paediatric participants will receive danazol 2 mg/kg/day orally in two divided doses or identical placebo for 6 months. If no side effects are encountered, the dose will be escalated to 4 mg/kg/day (maximum 800 mg daily) orally in two divided doses for a further 6 months. The primary outcome is change in absolute telomere length in base pairs, measured using the telomere shortest length assay (TeSLA), at 12 months in the intention to treat population. Ethics and dissemination Ethics approval has been granted in Australia by the Metro South Human Research Ethics Committee (HREC/2020/QMS/66385). The study will be conducted and reported according to Standard Protocol Items: Recommendations for Interventional Trials guidelines. Results will be published in peer-reviewed journals and presented at international and national conferences. Trial registration numbers NCT04638517; Australian New Zealand Clinical Trials Registry (ACTRN12620001363976p).
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Affiliation(s)
- John A Mackintosh
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Maria Pietsch
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Viviana Lutzky
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Debra Enever
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Sandra Bancroft
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Simon H Apte
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Maxine Tan
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| | - Stephanie T Yerkovich
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Hiran Selvadurai
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.,Discipline of Paediatrics and Child Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher Grainge
- Department of Respiratory Medicine, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Nicole S Goh
- Respiratory and Sleep Medicine Department, Austin Health, Heidelberg, Victoria, Australia.,Institute for Breathing and Sleep, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter Hopkins
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Ian Glaspole
- Department of Allergy and Respiratory Medicine, Alfred Hospital, Melbourne, Victoria, Australia
| | - Paul N Reynolds
- Department of Respiratory Medicine, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Jeremy Wrobel
- Advanced Lung Disease Unit, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.,Department of Medicine, University of Notre Dame, Perth, Western Australia, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Tamera J Corte
- Respiratory Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Daniel C Chambers
- Queensland Lung Transplant Service, Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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18
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Kychygina A, Dall'Osto M, Allen JAM, Cadoret JC, Piras V, Pickett HA, Crabbe L. Progerin impairs 3D genome organization and induces fragile telomeres by limiting the dNTP pools. Sci Rep 2021; 11:13195. [PMID: 34162976 PMCID: PMC8222272 DOI: 10.1038/s41598-021-92631-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 01/26/2021] [Accepted: 06/11/2021] [Indexed: 11/09/2022] Open
Abstract
Chromatin organization within the nuclear volume is essential to regulate many aspects of its function and to safeguard its integrity. A key player in this spatial scattering of chromosomes is the nuclear envelope (NE). The NE tethers large chromatin domains through interaction with the nuclear lamina and other associated proteins. This organization is perturbed in cells from Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder characterized by premature aging features. Here, we show that HGPS-related lamina defects trigger an altered 3D telomere organization with increased contact sites between telomeres and the nuclear lamina, and an altered telomeric chromatin state. The genome-wide replication timing signature of these cells is perturbed, with a shift to earlier replication for regions that normally replicate late. As a consequence, we detected a higher density of replication forks traveling simultaneously on DNA fibers, which relies on limiting cellular dNTP pools to support processive DNA synthesis. Remarkably, increasing dNTP levels in HGPS cells rescued fragile telomeres, and improved the replicative capacity of the cells. Our work highlights a functional connection between NE dysfunction and telomere homeostasis in the context of premature aging.
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Affiliation(s)
- Anna Kychygina
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.,INSERM UMR1291, CNRS UMR5051, UT3, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), 31059, Toulouse, France
| | - Marina Dall'Osto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | | | - Vincent Piras
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Integrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France.
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19
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Arthur JW, Pickett HA, Barbaro PM, Kilo T, Vasireddy RS, Beilharz TH, Powell DR, Hackett EL, Bennetts B, Curtin JA, Jones K, Christodoulou J, Reddel RR, Teo J, Bryan TM. A novel cause of DKC1-related bone marrow failure: Partial deletion of the 3' untranslated region. EJHaem 2021; 2:157-166. [PMID: 35845273 PMCID: PMC9175968 DOI: 10.1002/jha2.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Telomere biology disorders (TBDs), including dyskeratosis congenita (DC), are a group of rare inherited diseases characterized by very short telomeres. Mutations in the components of the enzyme telomerase can lead to insufficient telomere maintenance in hematopoietic stem cells, resulting in the bone marrow failure that is characteristic of these disorders. While an increasing number of genes are being linked to TBDs, the causative mutation remains unidentified in 30‐40% of patients with DC. There is therefore a need for whole genome sequencing (WGS) in these families to identify novel genes, or mutations in regulatory regions of known disease‐causing genes. Here we describe a family in which a partial deletion of the 3′ untranslated region (3′ UTR) of DKC1, encoding the protein dyskerin, was identified by WGS, despite being missed by whole exome sequencing. The deletion segregated with disease across the family and resulted in reduced levels of DKC1 mRNA in the proband. We demonstrate that the DKC1 3′ UTR contains two polyadenylation signals, both of which were removed by this deletion, likely causing mRNA instability. Consistent with the major function of dyskerin in stabilization of the RNA subunit of telomerase, hTR, the level of hTR was also reduced in the proband, providing a molecular basis for his very short telomeres. This study demonstrates that the terminal region of the 3′ UTR of the DKC1 gene is essential for gene function and illustrates the importance of analyzing regulatory regions of the genome for molecular diagnosis of inherited disease.
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Affiliation(s)
- Jonathan W Arthur
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Hilda A Pickett
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Pasquale M Barbaro
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Tatjana Kilo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Raja S Vasireddy
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Traude H Beilharz
- Monash Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria Australia
| | - David R Powell
- Monash Bioinformatics Platform Monash University Clayton Victoria Australia
| | - Emma L Hackett
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - Bruce Bennetts
- Department of Molecular Genetics Children's Hospital Westmead Westmead New South Wales Australia.,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia
| | - Julie A Curtin
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Kristi Jones
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Department of Clinical Genetics Children's Hospital Westmead Westmead New South Wales Australia
| | - John Christodoulou
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health University of Sydney Westmead New South Wales Australia.,Murdoch Children's Research Institute and Department of Paediatrics Melbourne Medical School Parkville Victoria Australia
| | - Roger R Reddel
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
| | - Juliana Teo
- Haematology Department Children's Hospital at Westmead Westmead New South Wales Australia
| | - Tracy M Bryan
- Children's Medical Research Institute Faculty of Medicine and Health, University of Sydney Westmead New South Wales Australia
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20
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Chen J, Nelson C, Wong M, Tee AE, Liu PY, La T, Fletcher JI, Kamili A, Mayoh C, Bartenhagen C, Trahair TN, Xu N, Jayatilleke N, Wong M, Peng H, Atmadibrata B, Cheung BB, Lan Q, Bryan TM, Mestdagh P, Vandesompele J, Combaret V, Boeva V, Wang JY, Janoueix-Lerosey I, Cowley MJ, MacKenzie KL, Dolnikov A, Li J, Polly P, Marshall GM, Reddel RR, Norris MD, Haber M, Fischer M, Zhang XD, Pickett HA, Liu T. Targeted Therapy of TERT-Rearranged Neuroblastoma with BET Bromodomain Inhibitor and Proteasome Inhibitor Combination Therapy. Clin Cancer Res 2020; 27:1438-1451. [PMID: 33310889 DOI: 10.1158/1078-0432.ccr-20-3044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 08/03/2020] [Revised: 10/23/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE TERT gene rearrangement with transcriptional superenhancers leads to TERT overexpression and neuroblastoma. No targeted therapy is available for clinical trials in patients with TERT-rearranged neuroblastoma. EXPERIMENTAL DESIGN Anticancer agents exerting the best synergistic anticancer effects with BET bromodomain inhibitors were identified by screening an FDA-approved oncology drug library. The synergistic effects of the BET bromodomain inhibitor OTX015 and the proteasome inhibitor carfilzomib were examined by immunoblot and flow cytometry analysis. The anticancer efficacy of OTX015 and carfilzomib combination therapy was investigated in mice xenografted with TERT-rearranged neuroblastoma cell lines or patient-derived xenograft (PDX) tumor cells, and the role of TERT reduction in the anticancer efficacy was examined through rescue experiments in mice. RESULTS The BET bromodomain protein BRD4 promoted TERT-rearranged neuroblastoma cell proliferation through upregulating TERT expression. Screening of an approved oncology drug library identified the proteasome inhibitor carfilzomib as the agent exerting the best synergistic anticancer effects with BET bromodomain inhibitors including OTX015. OTX015 and carfilzomib synergistically reduced TERT protein expression, induced endoplasmic reticulum stress, and induced TERT-rearranged neuroblastoma cell apoptosis which was blocked by TERT overexpression and endoplasmic reticulum stress antagonists. In mice xenografted with TERT-rearranged neuroblastoma cell lines or PDX tumor cells, OTX015 and carfilzomib synergistically blocked TERT expression, induced tumor cell apoptosis, suppressed tumor progression, and improved mouse survival, which was largely reversed by forced TERT overexpression. CONCLUSIONS OTX015 and carfilzomib combination therapy is likely to be translated into the first clinical trial of a targeted therapy in patients with TERT-rearranged neuroblastoma.
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Affiliation(s)
- Jingwei Chen
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Christopher Nelson
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Matthew Wong
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Andrew E Tee
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Pei Y Liu
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Ting La
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Alvin Kamili
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, Medical Faculty, University Hospital, University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Toby N Trahair
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Ning Xu
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Marie Wong
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Hui Peng
- Advanced Analytics Institute, University of Technology Sydney, Ultimo, Australia
| | | | - Belamy B Cheung
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Pieter Mestdagh
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Valerie Combaret
- Centre Léon-Bérard, Laboratoire de Recherche Translationnelle, Lyon, France
| | - Valentina Boeva
- ETH Zürich, Department of Computer Science, Institute for Machine Learning, Swiss Institute of Bioinformaticsics (SIB), Zurich, Switzerland
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, Paris, France
| | - Jenny Y Wang
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Isabelle Janoueix-Lerosey
- Institut Curie, Paris Sciences et Lettres Research University, INSERM, U830, Equipe Labellisée Ligue contre le Cancer, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Mark J Cowley
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Karen L MacKenzie
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Alla Dolnikov
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Jinyan Li
- Advanced Analytics Institute, University of Technology Sydney, Ultimo, Australia
| | - Patsie Polly
- Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Roger R Reddel
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Murray D Norris
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Michelle Haber
- Children's Cancer Institute, Randwick, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Medical Faculty, University Hospital, University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Xu D Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, Australia
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Hilda A Pickett
- Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute, Randwick, Sydney, Australia.
- School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
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21
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Nathan V, Palmer JM, Johansson PA, Hamilton HR, Warrier SK, Glasson W, McGrath LA, Kahl VFS, Vasireddy RS, Pickett HA, Brooks KM, Pritchard AL, Hayward NK. Loss-of-function variants in POT1 predispose to uveal melanoma. J Med Genet 2020; 58:234-236. [PMID: 32907878 DOI: 10.1136/jmedgenet-2020-107098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 11/04/2022]
Affiliation(s)
- Vaishnavi Nathan
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Jane M Palmer
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter A Johansson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hayley R Hamilton
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sunil K Warrier
- Queensland Ocular Oncology Services, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - William Glasson
- Queensland Ocular Oncology Services, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Lindsay A McGrath
- Queensland Ocular Oncology Services, The Terrace Eye Centre, Brisbane, Queensland, Australia
| | - Vivian F S Kahl
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Raja S Vasireddy
- Children's Hospital at Westmead, Sydney Children's Hospitals Network, Westmead, New South Wales, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Kelly M Brooks
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Antonia L Pritchard
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Division of Biomedical Sciences, University of the Highlands and Islands, Inverness, Scotland, UK
| | - Nicholas K Hayward
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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22
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Kahl VFS, Allen JAM, Nelson CB, Sobinoff AP, Lee M, Kilo T, Vasireddy RS, Pickett HA. Telomere Length Measurement by Molecular Combing. Front Cell Dev Biol 2020; 8:493. [PMID: 32612998 PMCID: PMC7308456 DOI: 10.3389/fcell.2020.00493] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Telomeres are repetitive regions of DNA bound by specialized proteins at the termini of linear chromosomes that prevent the natural chromosome ends from being recognized as DNA double strand breaks. Telomeric DNA is gradually eroded with each round of cell division, resulting in the accumulation of critically short or dysfunctional telomeres that eventually trigger cellular senescence. Consequently, telomere length is indicative of the proliferative capacity of a cell. Multiple methods exist to measure telomere length and telomere content, but a simple and reliable technique to accurately measure individual telomere lengths is currently lacking. We have developed the Telomere length Combing Assay (TCA) to measure telomere length on stretched DNA fibers. We used TCA to measure telomere erosion in primary human fibroblasts, and to detect telomere lengthening in response to activation of telomere maintenance pathways. TCA was also used to accurately measure telomere length in healthy individuals, and to identify critically short telomeres in patients with telomere biology disorders. TCA is performed on isolated DNA, negating the need for cycling cells. TCA is amenable to semi-automated image analysis, and can be fully automated using the Genomic Vision molecular combing platform. This not only precludes sampling bias, but also provides the potential for high-throughput applications and clinical development. TCA is a simple and versatile technique to measure the distribution of individual telomere lengths in a cell population, offering improved accuracy, and more detailed biological insight for telomere length measurement applications.
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Affiliation(s)
- Vivian F S Kahl
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tatjana Kilo
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Raja S Vasireddy
- Department of Hematology, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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23
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Ginn SL, Amaya AK, Liao SHY, Zhu E, Cunningham SC, Lee M, Hallwirth CV, Logan GJ, Tay SS, Cesare AJ, Pickett HA, Grompe M, Dilworth K, Lisowski L, Alexander IE. Efficient in vivo editing of OTC-deficient patient-derived primary human hepatocytes. JHEP Rep 2020; 2:100065. [PMID: 32039406 PMCID: PMC7005564 DOI: 10.1016/j.jhepr.2019.100065] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022] Open
Abstract
Background & Aims Genome editing technology has immense therapeutic potential and is likely to rapidly supplant contemporary gene addition approaches. Key advantages include the capacity to directly repair mutant loci with resultant recovery of physiological gene expression and maintenance of durable therapeutic effects in replicating cells. In this study, we aimed to repair a disease-causing point mutation in the ornithine transcarbamylase (OTC) locus in patient-derived primary human hepatocytes in vivo at therapeutically relevant levels. Methods Editing reagents for precise CRISPR/SaCas9-mediated cleavage and homology-directed repair (HDR) of the human OTC locus were first evaluated against an OTC minigene cassette transposed into the mouse liver. The editing efficacy of these reagents was then tested on the native OTC locus in patient-derived primary human hepatocytes xenografted into the FRG (Fah-/-Rag2-/-Il2rg-/-) mouse liver. A highly human hepatotropic capsid (NP59) was used for adeno-associated virus (AAV)-mediated gene transfer. Editing events were characterised using next-generation sequencing and restoration of OTC expression was evaluated using immunofluorescence. Results Following AAV-mediated delivery of editing reagents to patient-derived primary human hepatocytes in vivo, OTC locus-specific cleavage was achieved at efficiencies of up to 72%. Importantly, successful editing was observed in up to 29% of OTC alleles at clinically relevant vector doses. No off-target editing events were observed at the top 10 in silico-predicted sites in the genome. Conclusions We report efficient single-nucleotide correction of a disease-causing mutation in the OTC locus in patient-derived primary human hepatocytes in vivo at levels that, if recapitulated in the clinic, would provide benefit for even the most therapeutically challenging liver disorders. Key challenges for clinical translation include the cell cycle dependence of classical HDR and mitigation of unintended on- and off-target editing events. Lay summary The ability to efficiently and safely correct disease-causing mutations remains the holy grail of gene therapy. Herein, we demonstrate, for the first time, efficient in vivo correction of a patient-specific disease-causing mutation in the OTC gene in primary human hepatocytes, using therapeutically relevant vector doses. We also highlight the challenges that need to be overcome for this technology to be translated into clinical practice. Therapeutically relevant levels of single-nucleotide repair of the human OTC locus were achieved in vivo. Single-nucleotide editing of primary human hepatocytes was facilitated by a highly hepatotropic bioengineered AAV capsid. A novel human minigene platform proved highly effective for evaluation of human liver-specific genome editing reagents.
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Key Words
- 7 NGS, next-generation sequencing
- AAV, adeno-associated virus
- BrdU, bromodeoxyuridine
- CRISPR-Cas9
- FRG, Fah-/-Rag2-/-Il2rg-/-
- HDR, homology-directed repair
- ITR, inverted terminal repeats
- InDels, insertions and deletions
- LSP1, liver-specific promoter
- NHEJ, non-homologous end joining
- NP59 capsid
- OTC deficiency
- PAM, protospacer adjacent motif
- PRE, mutant form of the Woodchuck hepatitis virus posttranscriptional regulatory element
- RTA, Real Time Analysis
- SV40 pA, SV40 polyadenylation signal sequence
- SaCas9, Staphylococcus aureus Cas9 nuclease
- TBG, human thyroxine binding globulin promoter
- U6, RNA polymerase III promoter for human U6 snRNA
- WT, wild-type
- genome editing
- homology-directed repair
- humanised FRG mice
- pA, bovine growth hormone polyadenylation signal sequence
- primary human hepatocytes
- rAAV, recombinant adeno-associated virus
- recombinant AAV
- sgRNA, single guide RNA
- synthetic capsid
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Affiliation(s)
- Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Sharon C Cunningham
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Szun S Tay
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Markus Grompe
- School of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Kimberley Dilworth
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Group and Vector & Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, Pulway, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
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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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25
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Pinese M, Lacaze P, Rath EM, Stone A, Brion MJ, Ameur A, Nagpal S, Puttick C, Husson S, Degrave D, Cristina TN, Kahl VFS, Statham AL, Woods RL, McNeil JJ, Riaz M, Barr M, Nelson MR, Reid CM, Murray AM, Shah RC, Wolfe R, Atkins JR, Fitzsimmons C, Cairns HM, Green MJ, Carr VJ, Cowley MJ, Pickett HA, James PA, Powell JE, Kaplan W, Gibson G, Gyllensten U, Cairns MJ, McNamara M, Dinger ME, Thomas DM. The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly. Nat Commun 2020; 11:435. [PMID: 31974348 PMCID: PMC6978518 DOI: 10.1038/s41467-019-14079-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/13/2019] [Indexed: 01/24/2023] Open
Abstract
Population health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing. Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.
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Affiliation(s)
- Mark Pinese
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Emma M Rath
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Andrew Stone
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Marie-Jo Brion
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Adam Ameur
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sini Nagpal
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Clare Puttick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Shane Husson
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dmitry Degrave
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Vivian F S Kahl
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Aaron L Statham
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Robyn L Woods
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - John J McNeil
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Moeen Riaz
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Margo Barr
- Centre for Primary Health Care and Equity, University of New South Wales, Sydney, NSW, Australia
| | - Mark R Nelson
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Christopher M Reid
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia.,School of Public Health, Curtin University, Perth, WA, Australia
| | - Anne M Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Minneapolis, MN, USA.,Division of Geriatrics, Department of Medicine, Hennepin County Medical Center and University of Minnesota, Minneapolis, MN, USA
| | - Raj C Shah
- Department of Family Medicine and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Rory Wolfe
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Chantel Fitzsimmons
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Heath M Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Melissa J Green
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuroscience Research Australia, Sydney, NSW, Australia
| | - Vaughan J Carr
- School of Psychiatry, University of New South Wales, Sydney, NSW, Australia.,Neuroscience Research Australia, Sydney, NSW, Australia.,Department of Psychiatry, School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark J Cowley
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, NSW, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Joseph E Powell
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.,Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ulf Gyllensten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia.,Centre for Brain and Mental Health Research, Hunter Medical Research Institute, Newcastle, NSW, Australia
| | | | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - David M Thomas
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
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26
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Perera ON, Sobinoff AP, Teber ET, Harman A, Maritz MF, Yang SF, Pickett HA, Cesare AJ, Arthur JW, MacKenzie KL, Bryan TM. Telomerase promotes formation of a telomere protective complex in cancer cells. Sci Adv 2019; 5:eaav4409. [PMID: 31616780 PMCID: PMC6774720 DOI: 10.1126/sciadv.aav4409] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 09/09/2019] [Indexed: 05/04/2023]
Abstract
Telomerase is a ribonucleoprotein complex that catalyzes addition of telomeric DNA repeats to maintain telomeres in replicating cells. Here, we demonstrate that the telomerase protein hTERT performs an additional role at telomeres that is independent of telomerase catalytic activity yet essential for telomere integrity and cell proliferation. Short-term depletion of endogenous hTERT reduced the levels of heat shock protein 70 (Hsp70-1) and the telomere protective protein Apollo at telomeres, and induced telomere deprotection and cell cycle arrest, in the absence of telomere shortening. Short-term expression of hTERT promoted colocalization of Hsp70-1 with telomeres and Apollo and reduced numbers of deprotected telomeres, in a manner independent of telomerase catalytic activity. These data reveal a previously unidentified noncanonical function of hTERT that promotes formation of a telomere protective complex containing Hsp70-1 and Apollo and is essential for sustained proliferation of telomerase-positive cancer cells, likely contributing to the known cancer-promoting effects of both hTERT and Hsp70-1.
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Affiliation(s)
- Omesha N. Perera
- Cell Biology Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Alexander P. Sobinoff
- Telomere Length Regulation Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Erdahl T. Teber
- Bioinformatics Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Ashley Harman
- Cell Biology Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle F. Maritz
- Children’s Cancer Institute, School of Women’s and Children’s Health, University of NSW, NSW 2052, Australia
| | - Sile F. Yang
- Telomere Length Regulation Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Anthony J. Cesare
- Genome Integrity Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan W. Arthur
- Bioinformatics Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Karen L. MacKenzie
- Children’s Cancer Institute, School of Women’s and Children’s Health, University of NSW, NSW 2052, Australia
| | - Tracy M. Bryan
- Cell Biology Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
- Corresponding author.
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27
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Richards LA, Kumari A, Knezevic K, Thoms JA, von Jonquieres G, Napier CE, Ali Z, O'Brien R, Marks-Bluth J, Maritz MF, Pickett HA, Morris J, Pimanda JE, MacKenzie KL. DKC1 is a transcriptional target of GATA1 and drives upregulation of telomerase activity in normal human erythroblasts. Haematologica 2019; 105:1517-1526. [PMID: 31413099 PMCID: PMC7271591 DOI: 10.3324/haematol.2018.215699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 08/13/2019] [Indexed: 12/15/2022] Open
Abstract
Telomerase is a ribonucleoprotein complex that maintains the length and integrity of telomeres, and thereby enables cellular proliferation. Understanding the regulation of telomerase in hematopoietic cells is relevant to the pathogenesis of leukemia, in which telomerase is constitutively activated, as well as bone marrow failure syndromes that feature telomerase insufficiency. Past studies showing high levels of telomerase in human erythroblasts and a prevalence of anemia in disorders of telomerase insufficiency provide the rationale for investigating telomerase regulation in erythroid cells. Here it is shown for the first time that the telomerase RNA-binding protein dyskerin (encoded by DKC1) is dramatically upregulated as human hematopoietic stem and progenitor cells commit to the erythroid lineage, driving an increase in telomerase activity in the presence of limiting amounts of TERT mRNA. It is also shown that upregulation of DKC1 was necessary for expansion of glycophorin A+ erythroblasts and sufficient to extend telomeres in erythroleukemia cells. Chromatin immunoprecipitation and reporter assays implicated GATA1-mediated transcriptional regulation of DKC1 in the modulation of telomerase in erythroid lineage cells. Together these results describe a novel mechanism of telomerase regulation in erythroid cells which contrasts with mechanisms centered on transcriptional regulation of TERT that are known to operate in other cell types. This is the first study to reveal a biological context in which telomerase is upregulated by DKC1 and to implicate GATA1 in telomerase regulation. The results from this study are relevant to hematopoietic disorders involving DKC1 mutations, GATA1 deregulation and/or telomerase insufficiency.
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Affiliation(s)
| | - Ashu Kumari
- Children's Cancer Institute Australia, Randwick
| | - Kathy Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney
| | - Julie Ai Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney.,School of Medical Sciences, UNSW, Sydney
| | | | | | - Zara Ali
- Cancer Research Unit, Children's Medical Research Institute, Westmead
| | | | - Jonathon Marks-Bluth
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney
| | | | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Westmead
| | - Jonathan Morris
- The University of Sydney School of Medicine, Kolling Institute of Medical Research, St Leonards
| | - John E Pimanda
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney.,School of Medical Sciences, UNSW, Sydney
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Randwick .,Cancer Research Unit, Children's Medical Research Institute, Westmead.,School of Women's and Children's Health, UNSW, Sydney.,Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
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28
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Lee M, Teber ET, Holmes O, Nones K, Patch AM, Dagg RA, Lau LMS, Lee JH, Napier CE, Arthur JW, Grimmond SM, Hayward NK, Johansson PA, Mann GJ, Scolyer RA, Wilmott JS, Reddel RR, Pearson JV, Waddell N, Pickett HA. Telomere sequence content can be used to determine ALT activity in tumours. Nucleic Acids Res 2019; 46:4903-4918. [PMID: 29718321 PMCID: PMC6007693 DOI: 10.1093/nar/gky297] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 01/16/2023] Open
Abstract
The replicative immortality of human cancer cells is achieved by activation of a telomere maintenance mechanism (TMM). To achieve this, cancer cells utilise either the enzyme telomerase, or the Alternative Lengthening of Telomeres (ALT) pathway. These distinct molecular pathways are incompletely understood with respect to activation and propagation, as well as their associations with clinical outcomes. We have identified significant differences in the telomere repeat composition of tumours that use ALT compared to tumours that do not. We then employed a machine learning approach to stratify tumours according to telomere repeat content with an accuracy of 91.6%. Importantly, this classification approach is applicable across all tumour types. Analysis of pathway mutations that were under-represented in ALT tumours, across 1,075 tumour samples, revealed that the autophagy, cell cycle control of chromosomal replication, and transcriptional regulatory network in embryonic stem cells pathways are involved in the survival of ALT tumours. Overall, our approach demonstrates that telomere sequence content can be used to stratify ALT activity in cancers, and begin to define the molecular pathways involved in ALT activation.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Erdahl T Teber
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Oliver Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Katia Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ann-Marie Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Rebecca A Dagg
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Loretta M S Lau
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Joyce H Lee
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas K Hayward
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Oncogenomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Peter A Johansson
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Graham J Mann
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, University of Sydney, Westmead, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, University of Sydney, North Sydney, New South Wales, Australia.,Discipline of Pathology, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - John V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nicola Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
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29
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Lu R, O'Rourke JJ, Sobinoff AP, Allen JAM, Nelson CB, Tomlinson CG, Lee M, Reddel RR, Deans AJ, Pickett HA. The FANCM-BLM-TOP3A-RMI complex suppresses alternative lengthening of telomeres (ALT). Nat Commun 2019; 10:2252. [PMID: 31138797 PMCID: PMC6538672 DOI: 10.1038/s41467-019-10180-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [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: 10/23/2018] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
The collapse of stalled replication forks is a major driver of genomic instability. Several committed mechanisms exist to resolve replication stress. These pathways are particularly pertinent at telomeres. Cancer cells that use Alternative Lengthening of Telomeres (ALT) display heightened levels of telomere-specific replication stress, and co-opt stalled replication forks as substrates for break-induced telomere synthesis. FANCM is a DNA translocase that can form independent functional interactions with the BLM-TOP3A-RMI (BTR) complex and the Fanconi anemia (FA) core complex. Here, we demonstrate that FANCM depletion provokes ALT activity, evident by increased break-induced telomere synthesis, and the induction of ALT biomarkers. FANCM-mediated attenuation of ALT requires its inherent DNA translocase activity and interaction with the BTR complex, but does not require the FA core complex, indicative of FANCM functioning to restrain excessive ALT activity by ameliorating replication stress at telomeres. Synthetic inhibition of FANCM-BTR complex formation is selectively toxic to ALT cancer cells.
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Affiliation(s)
- Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute, 9 Princes St, Fitzroy, 3065, VIC, Australia
- Department of Medicine (St. Vincent's), University of Melbourne, Parkville, 3052, VIC, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Christopher B Nelson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Christopher G Tomlinson
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Michael Lee
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute, 9 Princes St, Fitzroy, 3065, VIC, Australia.
- Department of Medicine (St. Vincent's), University of Melbourne, Parkville, 3052, VIC, Australia.
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, 2145, NSW, Australia.
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30
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Van Ly D, Low RRJ, Frölich S, Bartolec TK, Kafer GR, Pickett HA, Gaus K, Cesare AJ. Telomere Loop Dynamics in Chromosome End Protection. Mol Cell 2018; 71:510-525.e6. [PMID: 30033372 DOI: 10.1016/j.molcel.2018.06.025] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/28/2018] [Accepted: 06/15/2018] [Indexed: 01/07/2023]
Abstract
Telomeres regulate DNA damage response (DDR) and DNA repair activity at chromosome ends. How telomere macromolecular structure contributes to ATM regulation and its potential dissociation from control over non-homologous end joining (NHEJ)-dependent telomere fusion is of central importance to telomere-dependent cell aging and tumor suppression. Using super-resolution microscopy, we identify that ATM activation at mammalian telomeres with reduced TRF2 or at human telomeres during mitotic arrest occurs specifically with a structural change from telomere loops (t-loops) to linearized telomeres. Additionally, we find the TRFH domain of TRF2 regulates t-loop formation while suppressing ATM activity. Notably, we demonstrate that ATM activation and telomere linearity occur separately from telomere fusion via NHEJ and that linear DDR-positive telomeres can remain resistant to fusion, even during an extended G1 arrest, when NHEJ is most active. Collectively, these results suggest t-loops act as conformational switches that specifically regulate ATM activation independent of telomere mechanisms to inhibit NHEJ.
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Affiliation(s)
- David Van Ly
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medicine, The University of Notre Dame Australia, Sydney, NSW 2010, Australia
| | - Ronnie Ren Jie Low
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Sonja Frölich
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Tara K Bartolec
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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31
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Dagg RA, Pickett HA, Neumann AA, Napier CE, Henson JD, Teber ET, Arthur JW, Reynolds CP, Murray J, Haber M, Sobinoff AP, Lau LMS, Reddel RR. Extensive Proliferation of Human Cancer Cells with Ever-Shorter Telomeres. Cell Rep 2018. [PMID: 28636942 DOI: 10.1016/j.celrep.2017.05.087] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Acquisition of replicative immortality is currently regarded as essential for malignant transformation. This is achieved by activating a telomere lengthening mechanism (TLM), either telomerase or alternative lengthening of telomeres, to counter normal telomere attrition. However, a substantial proportion of some cancer types, including glioblastomas, liposarcomas, retinoblastomas, and osteosarcomas, are reportedly TLM-negative. As serial samples of human tumors cannot usually be obtained to monitor telomere length changes, it has previously been impossible to determine whether tumors are truly TLM-deficient, there is a previously unrecognized TLM, or the assay results are false-negative. Here, we show that a subset of high-risk neuroblastomas (with ∼50% 5-year mortality) lacked significant TLM activity. Cancer cells derived from these highly aggressive tumors initially had long telomeres and proliferated for >200 population doublings with ever-shorter telomeres. This indicates that prevention of telomere shortening is not always required for oncogenesis, which has implications for inhibiting TLMs for cancer therapy.
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Affiliation(s)
- Rebecca A Dagg
- Children's Cancer Research Unit, The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jeremy D Henson
- Cancer Cell Immortality Group, Adult Cancer Program, Prince of Wales Clinical School, University of New South Wales, Randwick, NSW 2052, Australia
| | - Erdahl T Teber
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - C Patrick Reynolds
- Cancer Center, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Cell Biology and Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pediatrics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jayne Murray
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Australia, Randwick, NSW 2031, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Australia, Randwick, NSW 2031, Australia
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Loretta M S Lau
- Children's Cancer Research Unit, The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia; Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.
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32
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Chan FL, Vinod B, Novy K, Schittenhelm RB, Huang C, Udugama M, Nunez-Iglesias J, Lin JI, Hii L, Chan J, Pickett HA, Daly RJ, Wong LH. Aurora Kinase B, a novel regulator of TERF1 binding and telomeric integrity. Nucleic Acids Res 2017; 45:12340-12353. [PMID: 29040668 PMCID: PMC5716096 DOI: 10.1093/nar/gkx904] [Citation(s) in RCA: 13] [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: 02/05/2017] [Accepted: 09/26/2017] [Indexed: 01/24/2023] Open
Abstract
AURKB (Aurora Kinase B) is a serine/threonine kinase better known for its role at the mitotic kinetochore during chromosome segregation. Here, we demonstrate that AURKB localizes to the telomeres in mouse embryonic stem cells, where it interacts with the essential telomere protein TERF1. Loss of AURKB function affects TERF1 telomere binding and results in aberrant telomere structure. In vitro kinase experiments successfully identified Serine 404 on TERF1 as a putative AURKB target site. Importantly, in vivo overexpression of S404-TERF1 mutants results in fragile telomere formation. These findings demonstrate that AURKB is an important regulator of telomere structural integrity.
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Affiliation(s)
- Foong Lyn Chan
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Benjamin Vinod
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Karel Novy
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Cheng Huang
- Monash Biomedical Proteomics Facility & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Maheshi Udugama
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Juan Nunez-Iglesias
- Life Sciences Computation Centre, University of Melbourne, Carlton, VIC 3010, Australia
| | - Jane I Lin
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linda Hii
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Julie Chan
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Roger J Daly
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Lee H Wong
- Department of Biochemistry and Molecular Biology, Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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33
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Sobinoff AP, Pickett HA. Alternative Lengthening of Telomeres: DNA Repair Pathways Converge. Trends Genet 2017; 33:921-932. [DOI: 10.1016/j.tig.2017.09.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 08/30/2017] [Accepted: 09/08/2017] [Indexed: 02/08/2023]
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34
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Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MCJ, Bruxner TJC, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Hiriyur Nagaraj S, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Vittoria Davì M, Landoni L, Malpaga A, Miotto M, Whitehall VLJ, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras MC, Fisher WE, Dagg RA, Lau LMS, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours. Nature 2017; 550:548. [PMID: 28953865 DOI: 10.1038/nature24026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This corrects the article DOI: 10.1038/nature21063.
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35
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Sobinoff AP, Allen JA, Neumann AA, Yang SF, Walsh ME, Henson JD, Reddel RR, Pickett HA. BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres. EMBO J 2017; 36:2907-2919. [PMID: 28877996 DOI: 10.15252/embj.201796889] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [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: 03/06/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere lengthening pathway that predominates in aggressive tumors of mesenchymal origin; however, the underlying mechanism of telomere synthesis is not fully understood. Here, we show that the BLM-TOP3A-RMI (BTR) dissolvase complex is required for ALT-mediated telomere synthesis. We propose that recombination intermediates formed during strand invasion are processed by the BTR complex, initiating rapid and extensive POLD3-dependent telomere synthesis followed by dissolution, with no overall exchange of telomeric DNA. This process is counteracted by the SLX4-SLX1-ERCC4 complex, which promotes resolution of the recombination intermediate, resulting in telomere exchange in the absence of telomere extension. Our data are consistent with ALT being a conservative DNA replication process, analogous to break-induced replication, which is dependent on BTR and counteracted by SLX4 complex-mediated resolution events.
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Affiliation(s)
- Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Joshua Am Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Sile F Yang
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Monica E Walsh
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Jeremy D Henson
- Cancer Cell Immortality Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
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36
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Hayward NK, Wilmott JS, Waddell N, Johansson PA, Field MA, Nones K, Patch AM, Kakavand H, Alexandrov LB, Burke H, Jakrot V, Kazakoff S, Holmes O, Leonard C, Sabarinathan R, Mularoni L, Wood S, Xu Q, Waddell N, Tembe V, Pupo GM, De Paoli-Iseppi R, Vilain RE, Shang P, Lau LMS, Dagg RA, Schramm SJ, Pritchard A, Dutton-Regester K, Newell F, Fitzgerald A, Shang CA, Grimmond SM, Pickett HA, Yang JY, Stretch JR, Behren A, Kefford RF, Hersey P, Long GV, Cebon J, Shackleton M, Spillane AJ, Saw RPM, López-Bigas N, Pearson JV, Thompson JF, Scolyer RA, Mann GJ. Whole-genome landscapes of major melanoma subtypes. Nature 2017; 545:175-180. [PMID: 28467829 DOI: 10.1038/nature22071] [Citation(s) in RCA: 871] [Impact Index Per Article: 124.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/15/2017] [Indexed: 12/16/2022]
Abstract
Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.
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Affiliation(s)
- Nicholas K Hayward
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peter A Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Matthew A Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland 4878, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hojabr Kakavand
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | | | - Hazel Burke
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Radhakrishnan Sabarinathan
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Loris Mularoni
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Varsha Tembe
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Gulietta M Pupo
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Ricardo De Paoli-Iseppi
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ricardo E Vilain
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ping Shang
- Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Loretta M S Lau
- Children's Medical Research Institute, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Rebecca A Dagg
- Children's Hospital at Westmead, The University of Sydney, Westmead, New South Wales Sydney, 2145, Australia
| | - Sarah-Jane Schramm
- Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Antonia Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Ken Dutton-Regester
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Anna Fitzgerald
- Bioplatforms Australia, North Ryde, Sydney, New South Wales 2109, Australia
| | - Catherine A Shang
- Bioplatforms Australia, North Ryde, Sydney, New South Wales 2109, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Parkville, Melbourne, Victoria 3052, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
| | - Jean Y Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University, Austin Health, Heidelberg, Melbourne, Victoria 3084, Australia
| | - Richard F Kefford
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Macquarie University, North Ryde, Sydney, New South Wales 2109, Australia
| | - Peter Hersey
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Department of Medical Oncology, Royal North Shore Hospital, St Leonards, Sydney, New South Wales 2065, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University, Austin Health, Heidelberg, Melbourne, Victoria 3084, Australia
| | - Mark Shackleton
- Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Andrew J Spillane
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Núria López-Bigas
- Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia.,Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Discipline of Pathology, Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, Sydney, New South Wales 2050, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, North Sydney, Sydney, New South Wales 2065, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, New South Wales 2145, Australia
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37
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Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MCJ, Bruxner TJC, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SH, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Davì MV, Landoni L, Malpaga A, Miotto M, Whitehall VLJ, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras MC, Fisher WE, Dagg RA, Lau LMS, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Whole-genome landscape of pancreatic neuroendocrine tumours. Nature 2017; 543:65-71. [PMID: 28199314 DOI: 10.1038/nature21063] [Citation(s) in RCA: 578] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 12/15/2016] [Indexed: 12/20/2022]
Abstract
The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.
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Affiliation(s)
- Aldo Scarpa
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Vincenzo Corbo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Rita T Lawlor
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Amber L Johns
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - David K Miller
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Andrea Mafficini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Borislav Rusev
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Maria Scardoni
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Davide Antonello
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Stefano Barbi
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Katarzyna O Sikora
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Sara Cingarlini
- Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Caterina Vicentini
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Skye McKay
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Michael C J Quinn
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Timothy J C Bruxner
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Angelika N Christ
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Senel Idrisoglu
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Suzanne McLean
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Craig Nourse
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Ehsan Nourbakhsh
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Peter J Wilson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Matthew J Anderson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - J Lynn Fink
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Stephen H Kazakoff
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Shivashankar Hiriyur Nagaraj
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Eliana Amato
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Irene Dalai
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Samantha Bersani
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Ivana Cataldo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Angelo P Dei Tos
- Department of Pathology, General Hospital of Treviso, Department of Medicine, University of Padua, Italy
| | - Paola Capelli
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Maria Vittoria Davì
- Department of Medicine, Section of Endocrinology, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Anna Malpaga
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Marco Miotto
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Vicki L J Whitehall
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- The University of Queensland, School of Medicine, Brisbane 4006, Australia
- Pathology Queensland, Brisbane 4006, Australia
| | - Barbara A Leggett
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- The University of Queensland, School of Medicine, Brisbane 4006, Australia
- Royal Brisbane and Women's Hospital, Department of Gastroenterology and Hepatology, Brisbane 4006, Australia
| | - Janelle L Harris
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
| | - Jonathan Harris
- Institute of Health Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Marc D Jones
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Jeremy Humphris
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Lorraine A Chantrill
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Venessa Chin
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Adnan M Nagrial
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Christopher J Scarlett
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- School of Environmental &Life Sciences, University of Newcastle, Ourimbah, New South Wales 2258, Australia
| | - Andreia Pinho
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Ilse Rooman
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Christopher Toon
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Jianmin Wu
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Centre for Cancer Bioinformatics, Peking University Cancer Hospital &Institute, Beijing 100142, China
| | - Mark Pinese
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Mark Cowley
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Andrew Barbour
- Department of Surgery, Princess Alexandra Hospital, Ipswich Rd, Woollongabba, Queensland 4102, Australia
| | - Amanda Mawson
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Emily S Humphrey
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Emily K Colvin
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Angela Chou
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Anatomical Pathology. St Vincent's Hospital, Sydney, New South Wales 2010, Australia
| | - Jessica A Lovell
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G4 OSF, UK
| | - Fraser Duthie
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- Department of Pathology, Queen Elizabeth University Hospital, Greater Glasgow &Clyde NHS, Glasgow G51 4TF, UK
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas 77030-3411, USA
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411, USA
| | - William E Fisher
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411, USA
| | - Rebecca A Dagg
- Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Loretta M S Lau
- Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Michael Lee
- Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Roger R Reddel
- Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Jaswinder S Samra
- Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, New South Wales 2065, Australia
- University of Sydney. Sydney, New South Wales 2006, Australia
| | - James G Kench
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- University of Sydney. Sydney, New South Wales 2006, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
| | - Neil D Merrett
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- School of Medicine, Western Sydney University, Penrith, New South Wales 2175, Australia
| | - Krishna Epari
- Department of Surgery, Fremantle Hospital, Alma Street, Fremantle, Western Australia 6160, Australia
| | - Nam Q Nguyen
- Department of Gastroenterology, Royal Adelaide Hospital, North Terrace, Adelaide, South Australia 5000, Australia
| | - Nikolajs Zeps
- School of Surgery M507, University of Western Australia, 35 Stirling Highway, Nedlands, Western Australia 6009, Australia
- St John of God Pathology, 12 Salvado Rd, Subiaco, Western Australia 6008, Australia
- Bendat Family Comprehensive Cancer Centre, St John of God Subiaco Hospital, Subiaco, Western Australia 6008, Australia
| | - Massimo Falconi
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Michele Simbolo
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Giovanni Butturini
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - George Van Buren
- Michael E. DeBakey Department of Surgery and The Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030-3411, USA
| | - Stefano Partelli
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Matteo Fassan
- ARC-Net Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
| | - Anthony J Gill
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- University of Sydney. Sydney, New South Wales 2006, Australia
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas 77030-3411, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas 77030-3411, USA
| | - Elizabeth A Musgrove
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Claudio Bassi
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Giampaolo Tortora
- Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Paolo Pederzoli
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Herston Road, Brisbane 4006, Australia
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
- The Kinghorn Cancer Centre, Cancer Division, Garvan Institute of Medical Research, University of New South Wales, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, 3010, Victoria, Australia
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Lee M, Napier CE, Yang SF, Arthur JW, Reddel RR, Pickett HA. Comparative analysis of whole genome sequencing-based telomere length measurement techniques. Methods 2016; 114:4-15. [PMID: 27565742 DOI: 10.1016/j.ymeth.2016.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 06/06/2016] [Revised: 08/17/2016] [Accepted: 08/20/2016] [Indexed: 12/30/2022] Open
Abstract
Telomeres are regions of repetitive DNA at the ends of human chromosomes that function to maintain the integrity of the genome. Telomere attrition is associated with cellular ageing, whilst telomere maintenance is a prerequisite for malignant transformation. Whole genome sequencing (WGS) captures sequence information from the entire genome, including the telomeres, and is increasingly being applied in research and in the clinic. Several bioinformatics tools have been designed to determine telomere content and length from WGS data, and include Motif_counter, TelSeq, Computel, qMotif, and Telomerecat. These tools utilise different approaches to identify, quantify and normalise telomeric reads; however, it is not known how they compare to one another. Here we describe the details and utility of each tool, and directly compare WGS telomere length output with laboratory-based telomere length measurements. In addition, we evaluate the accessibility, practicality, speed, and additional features of each tool. Each tool was tested using a range of telomere read extraction criteria, to determine the optimal parameters for the specific WGS read length. The aim of this article is to improve the accessibility of WGS telomere length measurement tools, which have the potential to be applied to WGS cohorts for clinical as well as research benefit.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Sile F Yang
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Jonathan W Arthur
- Bioinformatics Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.
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O'Brien R, Tran SL, Maritz MF, Liu B, Kong CF, Purgato S, Yang C, Murray J, Russell AJ, Flemming CL, von Jonquieres G, Pickett HA, London WB, Haber M, Gunaratne PH, Norris MD, Perini G, Fletcher JI, MacKenzie KL. MYC-Driven Neuroblastomas Are Addicted to a Telomerase-Independent Function of Dyskerin. Cancer Res 2016; 76:3604-17. [PMID: 27197171 DOI: 10.1158/0008-5472.can-15-0879] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 04/01/2015] [Accepted: 03/14/2016] [Indexed: 11/16/2022]
Abstract
The RNA-binding protein dyskerin, encoded by the DKC1 gene, functions as a core component of the telomerase holoenzyme as well as ribonuclear protein complexes involved in RNA processing and ribosome biogenesis. The diverse roles of dyskerin across many facets of RNA biology implicate its potential contribution to malignancy. In this study, we examined the expression and function of dyskerin in neuroblastoma. We show that DKC1 mRNA levels were elevated relative to normal cells across a panel of 15 neuroblastoma cell lines, where both N-Myc and c-Myc directly targeted the DKC1 promoter. Upregulation of MYCN was shown to dramatically increase DKC1 expression. In two independent neuroblastoma patient cohorts, high DKC1 expression correlated strongly with poor event-free and overall survival (P < 0.0001), independently of established prognostic factors. RNAi-mediated depletion of dyskerin inhibited neuroblastoma cell proliferation, including cells immortalized via the telomerase-independent ALT mechanism. Furthermore, dyskerin attenuation impaired anchorage-independent proliferation and tumor growth. Overexpression of the telomerase RNA component, hTR, demonstrated that this proliferative impairment was not a consequence of telomerase suppression. Instead, ribosomal stress, evidenced by depletion of small nucleolar RNAs and nuclear dispersal of ribosomal proteins, was the likely cause of the proliferative impairment in dyskerin-depleted cells. Accordingly, dyskerin suppression caused p53-dependent G1 cell-cycle arrest in p53 wild-type cells, and a p53-independent pathway impaired proliferation in cells with p53 dysfunction. Together, our findings highlight dyskerin as a new therapeutic target in neuroblastoma with crucial telomerase-independent functions and broader implications for the spectrum of malignancies driven by MYC family oncogenes. Cancer Res; 76(12); 3604-17. ©2016 AACR.
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Affiliation(s)
- Rosemary O'Brien
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Sieu L Tran
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Michelle F Maritz
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Bing Liu
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Cheng Fei Kong
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Stefania Purgato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Chen Yang
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Jayne Murray
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Amanda J Russell
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Claudia L Flemming
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Georg von Jonquieres
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Laboratory, Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Wendy B London
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Michelle Haber
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Preethi H Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Murray D Norris
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jamie I Fletcher
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Randwick, Sydney, New South Wales, Australia.
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Pickett HA, Reddel RR. Molecular mechanisms of activity and derepression of alternative lengthening of telomeres. Nat Struct Mol Biol 2015; 22:875-80. [PMID: 26581522 DOI: 10.1038/nsmb.3106] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/01/2015] [Indexed: 02/08/2023]
Abstract
Alternative lengthening of telomeres (ALT) involves homology-directed telomere synthesis. This multistep process is facilitated by loss of the ATRX or DAXX chromatin-remodeling factors and by abnormalities of the telomere nucleoprotein architecture, including altered DNA sequence and decreased TRF2 saturation. Induction of telomere-specific DNA damage triggers homology-directed searches, and NuRD-ZNF827 protein-protein interactions provide a platform for the telomeric recruitment of homologous recombination (HR) proteins. Telomere lengthening proceeds by strand exchange and template-driven DNA synthesis, which culminates in dissolution of HR intermediates.
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Affiliation(s)
- Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
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Udugama M, M Chang FT, Chan FL, Tang MC, Pickett HA, R McGhie JD, Mayne L, Collas P, Mann JR, Wong LH. Histone variant H3.3 provides the heterochromatic H3 lysine 9 tri-methylation mark at telomeres. Nucleic Acids Res 2015; 43:10227-37. [PMID: 26304540 PMCID: PMC4666390 DOI: 10.1093/nar/gkv847] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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: 03/28/2015] [Accepted: 08/11/2015] [Indexed: 11/15/2022] Open
Abstract
In addition to being a hallmark at active genes, histone variant H3.3 is deposited by ATRX at repressive chromatin regions, including the telomeres. It is unclear how H3.3 promotes heterochromatin assembly. We show that H3.3 is targeted for K9 trimethylation to establish a heterochromatic state enriched in trimethylated H3.3K9 at telomeres. In H3f3a−/− and H3f3b−/− mouse embryonic stem cells (ESCs), H3.3 deficiency results in reduced levels of H3K9me3, H4K20me3 and ATRX at telomeres. The H3f3b−/− cells show increased levels of telomeric damage and sister chromatid exchange (t-SCE) activity when telomeres are compromised by treatment with a G-quadruplex (G4) DNA binding ligand or by ASF1 depletion. Overexpression of wild-type H3.3 (but not a H3.3K9 mutant) in H3f3b−/− cells increases H3K9 trimethylation level at telomeres and represses t-SCE activity induced by a G4 ligand. This study demonstrates the importance of H3.3K9 trimethylation in heterochromatin formation at telomeres. It provides insights into H3.3 function in maintaining integrity of mammalian constitutive heterochromatin, adding to its role in mediating transcription memory in the genome.
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Affiliation(s)
- Maheshi Udugama
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Fiona T M Chang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - F Lyn Chan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle C Tang
- Department of Zoology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Hilda A Pickett
- Telomere Length Regulation Group, Children's Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - James D R McGhie
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Lynne Mayne
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, and Norwegian Center for Stem Cell Research, University of Oslo, 0317 Oslo, Norway
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Lee H Wong
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Killedar A, Stutz MD, Sobinoff AP, Tomlinson CG, Bryan TM, Beesley J, Chenevix-Trench G, Reddel RR, Pickett HA. A Common Cancer Risk-Associated Allele in the hTERT Locus Encodes a Dominant Negative Inhibitor of Telomerase. PLoS Genet 2015; 11:e1005286. [PMID: 26053551 PMCID: PMC4459975 DOI: 10.1371/journal.pgen.1005286] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/14/2015] [Indexed: 12/21/2022] Open
Abstract
The TERT-CLPTM1L region of chromosome 5p15.33 is a multi-cancer susceptibility locus that encodes the reverse transcriptase subunit, hTERT, of the telomerase enzyme. Numerous cancer-associated single-nucleotide polymorphisms (SNPs), including rs10069690, have been identified within the hTERT gene. The minor allele (A) at rs10069690 creates an additional splice donor site in intron 4 of hTERT, and is associated with an elevated risk of multiple cancers including breast and ovarian carcinomas. We previously demonstrated that the presence of this allele resulted in co-production of full length (FL)-hTERT and an alternatively spliced, INS1b, transcript. INS1b does not encode the reverse transcriptase domain required for telomerase enzyme activity, but we show here that INS1b protein retains its ability to bind to the telomerase RNA subunit, hTR. We also show that INS1b expression results in decreased telomerase activity, telomere shortening, and an increased telomere-specific DNA damage response (DDR). We employed antisense oligonucleotides to manipulate endogenous transcript expression in favor of INS1b, which resulted in a decrease in telomerase activity. These data provide the first detailed mechanistic insights into a cancer risk-associated SNP in the hTERT locus, which causes cell type-specific expression of INS1b transcript from the presence of an additional alternative splice site created in intron 4 by the risk allele. We predict that INS1b expression levels cause subtle inadequacies in telomerase-mediated telomere maintenance, resulting in an increased risk of genetic instability and therefore of tumorigenesis. Multiple cancer-associated single nucleotide polymorphisms (SNPs) associated with risk of a wide variety of cancers have been identified in the TERT-CLPTM1L region of 5p15.33, identifying this as a multi-cancer susceptibility locus. hTERT encodes the catalytic subunit of the enzyme telomerase, which is responsible for telomere length maintenance in the germline and in most immortalised cancer cells. To date, very little is known regarding the mechanisms by which specific hTERT SNPs predispose to cancer. In this study, we carried out detailed functional analyses on the intron 4 SNP rs10069690, which is associated with a small, but highly significant risk for many types of cancer. We show that the risk-associated minor allele of this SNP results in an hTERT mRNA splice variant, encoding a catalytically inactive protein which acts as a dominant negative inhibitor of telomerase activity and therefore decreases total telomerase activity. We propose that individuals who carry the rs10069690 minor allele have less telomerase activity in some cell types due to cell type-specific alternative splicing, which may result in slightly shorter telomeres, and hence an increased risk of genetic instability and tumorigenesis.
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Affiliation(s)
- Anagha Killedar
- Telomere Length Regulation Group, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Michael D. Stutz
- Telomere Length Regulation Group, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Alexander P. Sobinoff
- Telomere Length Regulation Group, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Christopher G. Tomlinson
- Cell Biology Unit, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Tracy M. Bryan
- Cell Biology Unit, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Jonathan Beesley
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Georgia Chenevix-Trench
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Roger R. Reddel
- Cancer Research Unit, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Hilda A. Pickett
- Telomere Length Regulation Group, Children’s Medical Research Institute, University of Sydney, Westmead, New South Wales, Australia
- * E-mail:
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Conomos D, Reddel RR, Pickett HA. NuRD-ZNF827 recruitment to telomeres creates a molecular scaffold for homologous recombination. Nat Struct Mol Biol 2014; 21:760-70. [PMID: 25150861 DOI: 10.1038/nsmb.2877] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/22/2014] [Indexed: 12/13/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homologous recombination (HR)-dependent mechanism for de novo synthesis of telomeric DNA in mammalian cells. Nuclear receptors are bound to the telomeres of cells that use ALT. Here we demonstrate that nuclear receptors recruit ZNF827, a zinc-finger protein of unknown function, which recruits the nucleosome remodeling and histone deacetylation (NuRD) complex via binding to an N-terminal RRK motif within ZNF827. This results in decreased shelterin binding, hypoacetylation of telomeric chromatin, enhanced telomere-telomere interactions and recruitment of HR proteins, and it is critically important for cell viability and proliferation. We propose that NuRD-ZNF827 recruitment to human telomeres causes remodeling of telomeric chromatin and creates an environment that promotes telomere-telomere recombination and integrates and controls multiple mechanistic elements of ALT activity.
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Affiliation(s)
- Dimitri Conomos
- 1] Telomere Length Regulation Group, Children's Medical Research Institute, Westmead, New South Wales, Australia. [2] Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Roger R Reddel
- 1] Sydney Medical School, University of Sydney, New South Wales, Australia. [2] Cancer Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Hilda A Pickett
- 1] Telomere Length Regulation Group, Children's Medical Research Institute, Westmead, New South Wales, Australia. [2] Sydney Medical School, University of Sydney, New South Wales, Australia
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Bull CF, Mayrhofer G, O'Callaghan NJ, Au AY, Pickett HA, Low GKM, Zeegers D, Hande MP, Fenech MF. Folate deficiency induces dysfunctional long and short telomeres; both states are associated with hypomethylation and DNA damage in human WIL2-NS cells. Cancer Prev Res (Phila) 2013; 7:128-38. [PMID: 24253316 DOI: 10.1158/1940-6207.capr-13-0264] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The essential role of dietary micronutrients for genome stability is well documented, yet the effect of folate deficiency or excess on telomeres is not known. Accordingly, human WIL2-NS cells were maintained in medium containing 30, 300, or 3,000 nmol/L folic acid (FA) for 42 days to test the hypothesis that chronic folate deficiency would cause telomere shortening and dysfunction. After 14 days, telomere length (TL) in FA-deficient (30 nmol/L) cultures was 26% longer than that of 3,000 nmol/L FA cultures; however, this was followed by rapid telomere attrition over the subsequent 28 days (P trend, P < 0.0001); both long and short telomere status was positively correlated with biomarkers of chromosome instability (P ≤ 0.003) and mitotic dysfunction (P = 0.01), measured by the cytokinesis-block micronucleus cytome (CBMN-cyt) assay. The early increase in TL was associated with FA-deficiency-induced global DNA hypomethylation (P = 0.05), with an effect size similar to that induced by the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine. Quantitative PCR analysis indicated a negative association between FA concentration and uracil incorporation into telomeric DNA (r = -0.47, P = 0.1), suggesting a possible plausible mechanism for uracil as a cause of folate deficiency-induced telomere dysfunction or deletion. Peptide nucleic acid-FISH (PNA-FISH) analysis showed that FA deficiency resulted in 60% of micronuclei containing acentric terminal fragments, an observation consistent with the 3-fold increase in terminal deletions (P = 0.0001). Together, these results demonstrate the impact of folate deficiency on biomarkers of telomere maintenance and integrity, and provide evidence that dysfunctional long telomeres may be as important as critically short telomeres as a cause of chromosomal instability.
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Affiliation(s)
- Caroline F Bull
- CSIRO Animal, Food and Health Sciences, P.O. Box 10041, Adelaide BC, South Australia 5000, Australia. ; and Michael F. Fenech,
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Lee M, Hills M, Conomos D, Stutz MD, Dagg RA, Lau LMS, Reddel RR, Pickett HA. Telomere extension by telomerase and ALT generates variant repeats by mechanistically distinct processes. Nucleic Acids Res 2013; 42:1733-46. [PMID: 24225324 PMCID: PMC3919612 DOI: 10.1093/nar/gkt1117] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Telomeres are terminal repetitive DNA sequences on chromosomes, and are considered to comprise almost exclusively hexameric TTAGGG repeats. We have evaluated telomere sequence content in human cells using whole-genome sequencing followed by telomere read extraction in a panel of mortal cell strains and immortal cell lines. We identified a wide range of telomere variant repeats in human cells, and found evidence that variant repeats are generated by mechanistically distinct processes during telomerase- and ALT-mediated telomere lengthening. Telomerase-mediated telomere extension resulted in biased repeat synthesis of variant repeats that differed from the canonical sequence at positions 1 and 3, but not at positions 2, 4, 5 or 6. This indicates that telomerase is most likely an error-prone reverse transcriptase that misincorporates nucleotides at specific positions on the telomerase RNA template. In contrast, cell lines that use the ALT pathway contained a large range of variant repeats that varied greatly between lines. This is consistent with variant repeats spreading from proximal telomeric regions throughout telomeres in a stochastic manner by recombination-mediated templating of DNA synthesis. The presence of unexpectedly large numbers of variant repeats in cells utilizing either telomere maintenance mechanism suggests a conserved role for variant sequences at human telomeres.
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Affiliation(s)
- Michael Lee
- Telomere Length Regulation Group, Children's Medical Research Institute, Westmead NSW 2145, Australia, Cancer Research Unit, Children's Medical Research Institute, Westmead NSW 2145, Australia, Terry Fox Laboratory, BC Cancer Agency, Vancouver V5Z 1L3, Canada, Sydney Medical School, University of Sydney, Sydney NSW 2006, Australia and Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead NSW 2145, Australia
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46
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Bojesen SE, Pooley KA, Johnatty SE, Beesley J, Michailidou K, Tyrer JP, Edwards SL, Pickett HA, Shen HC, Smart CE, Hillman KM, Mai PL, Lawrenson K, Stutz MD, Lu Y, Karevan R, Woods N, Johnston RL, French JD, Chen X, Weischer M, Nielsen SF, Maranian MJ, Ghoussaini M, Ahmed S, Baynes C, Bolla MK, Wang Q, Dennis J, McGuffog L, Barrowdale D, Lee A, Healey S, Lush M, Tessier DC, Vincent D, Bacot F, Vergote I, Lambrechts S, Despierre E, Risch HA, González-Neira A, Rossing MA, Pita G, Doherty JA, Álvarez N, Larson MC, Fridley BL, Schoof N, Chang-Claude J, Cicek MS, Peto J, Kalli KR, Broeks A, Armasu SM, Schmidt MK, Braaf LM, Winterhoff B, Nevanlinna H, Konecny GE, Lambrechts D, Rogmann L, Guénel P, Teoman A, Milne RL, Garcia JJ, Cox A, Shridhar V, Burwinkel B, Marme F, Hein R, Sawyer EJ, Haiman CA, Wang-Gohrke S, Andrulis IL, Moysich KB, Hopper JL, Odunsi K, Lindblom A, Giles GG, Brenner H, Simard J, Lurie G, Fasching PA, Carney ME, Radice P, Wilkens LR, Swerdlow A, Goodman MT, Brauch H, García-Closas M, Hillemanns P, Winqvist R, Dürst M, Devilee P, Runnebaum I, Jakubowska A, Lubinski J, Mannermaa A, Butzow R, Bogdanova NV, Dörk T, Pelttari LM, Zheng W, Leminen A, Anton-Culver H, Bunker CH, Kristensen V, Ness RB, Muir K, Edwards R, Meindl A, Heitz F, Matsuo K, du Bois A, Wu AH, Harter P, Teo SH, Schwaab I, Shu XO, Blot W, Hosono S, Kang D, Nakanishi T, Hartman M, Yatabe Y, Hamann U, Karlan BY, Sangrajrang S, Kjaer SK, Gaborieau V, Jensen A, Eccles D, Høgdall E, Shen CY, Brown J, Woo YL, Shah M, Azmi MAN, Luben R, Omar SZ, Czene K, Vierkant RA, Nordestgaard BG, Flyger H, Vachon C, Olson JE, Wang X, Levine DA, Rudolph A, Weber RP, Flesch-Janys D, Iversen E, Nickels S, Schildkraut JM, Silva IDS, Cramer DW, Gibson L, Terry KL, Fletcher O, Vitonis AF, van der Schoot CE, Poole EM, Hogervorst FBL, Tworoger SS, Liu J, Bandera EV, Li J, Olson SH, Humphreys K, Orlow I, Blomqvist C, Rodriguez-Rodriguez L, Aittomäki K, Salvesen HB, Muranen TA, Wik E, Brouwers B, Krakstad C, Wauters E, Halle MK, Wildiers H, Kiemeney LA, Mulot C, Aben KK, Laurent-Puig P, van Altena AM, Truong T, Massuger LFAG, Benitez J, Pejovic T, Perez JIA, Hoatlin M, Zamora MP, Cook LS, Balasubramanian SP, Kelemen LE, Schneeweiss A, Le ND, Sohn C, Brooks-Wilson A, Tomlinson I, Kerin MJ, Miller N, Cybulski C, Henderson BE, Menkiszak J, Schumacher F, Wentzensen N, Marchand LL, Yang HP, Mulligan AM, Glendon G, Engelholm SA, Knight JA, Høgdall CK, Apicella C, Gore M, Tsimiklis H, Song H, Southey MC, Jager A, van den Ouweland AMW, Brown R, Martens JWM, Flanagan JM, Kriege M, Paul J, Margolin S, Siddiqui N, Severi G, Whittemore AS, Baglietto L, McGuire V, Stegmaier C, Sieh W, Müller H, Arndt V, Labrèche F, Gao YT, Goldberg MS, Yang G, Dumont M, McLaughlin JR, Hartmann A, Ekici AB, Beckmann MW, Phelan CM, Lux MP, Permuth-Wey J, Peissel B, Sellers TA, Ficarazzi F, Barile M, Ziogas A, Ashworth A, Gentry-Maharaj A, Jones M, Ramus SJ, Orr N, Menon U, Pearce CL, Brüning T, Pike MC, Ko YD, Lissowska J, Figueroa J, Kupryjanczyk J, Chanock SJ, Dansonka-Mieszkowska A, Jukkola-Vuorinen A, Rzepecka IK, Pylkäs K, Bidzinski M, Kauppila S, Hollestelle A, Seynaeve C, Tollenaar RAEM, Durda K, Jaworska K, Hartikainen JM, Kosma VM, Kataja V, Antonenkova NN, Long J, Shrubsole M, Deming-Halverson S, Lophatananon A, Siriwanarangsan P, Stewart-Brown S, Ditsch N, Lichtner P, Schmutzler RK, Ito H, Iwata H, Tajima K, Tseng CC, Stram DO, van den Berg D, Yip CH, Ikram MK, Teh YC, Cai H, Lu W, Signorello LB, Cai Q, Noh DY, Yoo KY, Miao H, Iau PTC, Teo YY, McKay J, Shapiro C, Ademuyiwa F, Fountzilas G, Hsiung CN, Yu JC, Hou MF, Healey CS, Luccarini C, Peock S, Stoppa-Lyonnet D, Peterlongo P, Rebbeck TR, Piedmonte M, Singer CF, Friedman E, Thomassen M, Offit K, Hansen TVO, Neuhausen SL, Szabo CI, Blanco I, Garber J, Narod SA, Weitzel JN, Montagna M, Olah E, Godwin AK, Yannoukakos D, Goldgar DE, Caldes T, Imyanitov EN, Tihomirova L, Arun BK, Campbell I, Mensenkamp AR, van Asperen CJ, van Roozendaal KEP, Meijers-Heijboer H, Collée JM, Oosterwijk JC, Hooning MJ, Rookus MA, van der Luijt RB, van Os TAM, Evans DG, Frost D, Fineberg E, Barwell J, Walker L, Kennedy MJ, Platte R, Davidson R, Ellis SD, Cole T, Paillerets BBD, Buecher B, Damiola F, Faivre L, Frenay M, Sinilnikova OM, Caron O, Giraud S, Mazoyer S, Bonadona V, Caux-Moncoutier V, Toloczko-Grabarek A, Gronwald J, Byrski T, Spurdle AB, Bonanni B, Zaffaroni D, Giannini G, Bernard L, Dolcetti R, Manoukian S, Arnold N, Engel C, Deissler H, Rhiem K, Niederacher D, Plendl H, Sutter C, Wappenschmidt B, Borg Å, Melin B, Rantala J, Soller M, Nathanson KL, Domchek SM, Rodriguez GC, Salani R, Kaulich DG, Tea MK, Paluch SS, Laitman Y, Skytte AB, Kruse TA, Jensen UB, Robson M, Gerdes AM, Ejlertsen B, Foretova L, Savage SA, Lester J, Soucy P, Kuchenbaecker KB, Olswold C, Cunningham JM, Slager S, Pankratz VS, Dicks E, Lakhani SR, Couch FJ, Hall P, Monteiro ANA, Gayther SA, Pharoah PDP, Reddel RR, Goode EL, Greene MH, Easton DF, Berchuck A, Antoniou AC, Chenevix-Trench G, Dunning AM. Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat Genet 2013; 45:371-84, 384e1-2. [PMID: 23535731 PMCID: PMC3670748 DOI: 10.1038/ng.2566] [Citation(s) in RCA: 435] [Impact Index Per Article: 39.5] [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: 07/06/2012] [Accepted: 01/31/2013] [Indexed: 12/13/2022]
Abstract
TERT-locus SNPs and leukocyte telomere measures are reportedly associated with risks of multiple cancers. Using the Illumina custom genotyping array iCOGs, we analyzed ∼480 SNPs at the TERT locus in breast (n = 103,991), ovarian (n = 39,774) and BRCA1 mutation carrier (n = 11,705) cancer cases and controls. Leukocyte telomere measurements were also available for 53,724 participants. Most associations cluster into three independent peaks. The minor allele at the peak 1 SNP rs2736108 associates with longer telomeres (P = 5.8 × 10(-7)), lower risks for estrogen receptor (ER)-negative (P = 1.0 × 10(-8)) and BRCA1 mutation carrier (P = 1.1 × 10(-5)) breast cancers and altered promoter assay signal. The minor allele at the peak 2 SNP rs7705526 associates with longer telomeres (P = 2.3 × 10(-14)), higher risk of low-malignant-potential ovarian cancer (P = 1.3 × 10(-15)) and greater promoter activity. The minor alleles at the peak 3 SNPs rs10069690 and rs2242652 increase ER-negative (P = 1.2 × 10(-12)) and BRCA1 mutation carrier (P = 1.6 × 10(-14)) breast and invasive ovarian (P = 1.3 × 10(-11)) cancer risks but not via altered telomere length. The cancer risk alleles of rs2242652 and rs10069690, respectively, increase silencing and generate a truncated TERT splice variant.
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Affiliation(s)
- Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Karen A Pooley
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Sharon E Johnatty
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Jonathan Beesley
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stacey L Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Hilda A Pickett
- Cancer Research Unit, Children's Medical Research Institute, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Howard C Shen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chanel E Smart
- University of Queensland, UQ Centre for Clinical Research (UQCCR) Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Kristine M Hillman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Phuong L Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael D Stutz
- Cancer Research Unit, Children's Medical Research Institute, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Yi Lu
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Rod Karevan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Woods
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rebecca L Johnston
- University of Queensland, UQ Centre for Clinical Research (UQCCR) Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Juliet D French
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Xiaoqing Chen
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Maren Weischer
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sune F Nielsen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Melanie J Maranian
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Shahana Ahmed
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Sue Healey
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Daniel C Tessier
- McGill University, Montréal, QC, Canada
- Génome Québec Innovation Centre, Montréal, QC, Canada
| | - Daniel Vincent
- McGill University, Montréal, QC, Canada
- Génome Québec Innovation Centre, Montréal, QC, Canada
| | - Françis Bacot
- McGill University, Montréal, QC, Canada
- Génome Québec Innovation Centre, Montréal, QC, Canada
| | - Study Group members
- Australian Cancer Study, Australian Ovarian Cancer Study Group, kConFab, GENICA, SWE-BRCA, HEBON, EMBRACE, GEMO Study Collaborators. Full membership lists are provided in the Supplementary Note
| | - Ignace Vergote
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
- Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
- Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Evelyn Despierre
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
- Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Harvey A Risch
- Department of Epidemiology and Public Health, Yale University School of Public Health and School of Medicine, New Haven, CT, USA
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mary Anne Rossing
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Guillermo Pita
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jennifer A Doherty
- Section of Biostatistics and Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Nuria Álvarez
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Melissa C Larson
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Nils Schoof
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mine S Cicek
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Annegien Broeks
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sebastian M Armasu
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Linde M Braaf
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Boris Winterhoff
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Gottfried E Konecny
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Belgium
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Lisa Rogmann
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Pascal Guénel
- INSERM U1018, CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Attila Teoman
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
| | - Roger L Milne
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Joaquin J Garcia
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, UK
| | - Vijayalakshmi Shridhar
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- PMV Research Group at the Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Elinor J Sawyer
- Division of Cancer Studies, NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust in partnership with King's College London, London, UK
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Ontario Cancer Genetics Network, Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, VIC, Australia
| | - Kunle Odunsi
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec, Canada
| | - Galina Lurie
- Cancer Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Michael E Carney
- Cancer Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Germany
| | - Montserrat García-Closas
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, University of Oulu, Oulu University Hospital, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital, Jena, Germany
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingo Runnebaum
- Department of Gynecology, Jena University Hospital, Jena, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
- Department of Pathology, Helsinki University Central Hospital, Helsinki, Finland
| | - Natalia V Bogdanova
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Clareann H Bunker
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), UiO, Norway
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Kenneth Muir
- Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | | | - Alfons Meindl
- Department of Gynecology and Obstetrics, Division of Tumor Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Klinik Wiesbaden, Wiesbaden, Germany
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Klinik Wiesbaden, Wiesbaden, Germany
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Klinik Wiesbaden, Wiesbaden, Germany
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, Wiesbaden, Germany
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Daehee Kang
- Seoul National University College of Medicine, Seoul, Korea
| | - Toru Nakanishi
- Department of Gynecologic Oncology, Aichi Cancer Center Central Hospital, Nagoya, Aichi, Japan
| | - Mikael Hartman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore
- Saw Swee Hock School of Public Health, National University of Singapore
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostic, Aichi Cancer Center Central Hospital, Nagoya, Aichi, Japan
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beth Y Karlan
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Susanne Krüger Kjaer
- Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- The Juliane Marie Centre, Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | | | - Allan Jensen
- Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Estrid Høgdall
- Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Chen-Yang Shen
- Colleague of Public Health, China Medical University, Taichong, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Judith Brown
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Yin Ling Woo
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mat Adenan Noor Azmi
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Robert Luben
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siti Zawiah Omar
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Robert A Vierkant
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Edwin Iversen
- Department of Statistical Science, Duke University, Durham, NC, USA
- Cancer Prevention, Detection and Control Research Program, Duke Cancer Institute, Durham, NC, USA
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
- Cancer Prevention, Detection and Control Research Program, Duke Cancer Institute, Durham, NC, USA
| | - Isabel Dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Lorna Gibson
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Allison F Vitonis
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Elizabeth M Poole
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Frans B L Hogervorst
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Elisa V Bandera
- The Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Taru A Muranen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Elisabeth Wik
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Barbara Brouwers
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Els Wauters
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Belgium
- Vesalius Research Center (VRC), VIB, Leuven, Belgium
| | - Mari K Halle
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospitals Leuven, Belgium
| | - Lambertus A Kiemeney
- Comprehensive Cancer Center The Netherlands, Utrecht, The Netherlands
- Department of Epidemiology, Biostatistics and HTA, Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Urology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Claire Mulot
- Université Paris Sorbonne Cité, UMR-S775 Inserm, Paris, France
| | - Katja K Aben
- Comprehensive Cancer Center The Netherlands, Utrecht, The Netherlands
- Department of Epidemiology, Biostatistics and HTA, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | - Anne M van Altena
- Department of Gynecology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Thérèse Truong
- INSERM U1018, CESP (Center for Research in Epidemiology and Population Health), Environmental Epidemiology of Cancer, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Leon F A G Massuger
- Department of Gynecology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Javier Benitez
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Maureen Hoatlin
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR, USA
| | - M Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, NM, USA
| | | | - Linda E Kelemen
- Department of Population Health Research, Alberta Health Services-Cancer Care, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Department of Oncology, University of Calgary, Calgary, Alberta, Canada
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Christof Sohn
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Ian Tomlinson
- Welcome Trust Centre for Human Genetics, University of Oxford, UK
- Oxford Biomedical Research Centre, University of Oxford, UK
| | - Michael J Kerin
- School of medicine, National University of Ireland Galway, Ireland
| | - Nicola Miller
- School of medicine, National University of Ireland Galway, Ireland
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical Academy, Szczecin, Poland
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Janusz Menkiszak
- Department of Surgical Gynecology and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University, Szczecin, Poland
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI, USA
| | - Hannah P Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Gord Glendon
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Svend Aage Engelholm
- Department of Radiation Oncology, Rigshospitalet, University of Copenhagen, Denmark
| | - Julia A Knight
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Claus K Høgdall
- The Juliane Marie Centre, Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, VIC, Australia
| | - Martin Gore
- Gynecological Oncology Unit, The Royal Marsden Hospital, London, UK
| | - Helen Tsimiklis
- Genetic Epidemiology Department, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Honglin Song
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Melissa C Southey
- Genetic Epidemiology Department, Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Agnes Jager
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Robert Brown
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - John W M Martens
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James M Flanagan
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Mieke Kriege
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James Paul
- The Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - Sara Margolin
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nadeem Siddiqui
- Department of Gynecological Oncology, Glasgow Royal Infirmary, Glasgow, UK
| | - Gianluca Severi
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Baglietto
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Weiva Sieh
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Heiko Müller
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - France Labrèche
- Département de médecine sociale et préventive, Département de santé environnementale et santé au travail, Université de Montréal, Montreal, Quebec, Canada
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, Quebec, Canada
| | - Gong Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec, Canada
| | - John R McLaughlin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, Faculty of Medicine, University of Toronto, Canada
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Michael P Lux
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Jenny Permuth-Wey
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Filomena Ficarazzi
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy
| | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Argyrios Ziogas
- Department of Epidemiology, Center for Cancer Genetics Research and Prevention, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | | | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Usha Menon
- Gynaecological Cancer Research Centre, UCL EGA Institute for Women's Health, London, UK
| | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-Universität Bochum, Bochum, Germany
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn GmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, Warsaw, Poland
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jolanta Kupryjanczyk
- Department of Molecular Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Molecular Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | | | - Iwona K Rzepecka
- Department of Molecular Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics, University of Oulu, Oulu University Hospital, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mariusz Bidzinski
- Department of Gynecologic Oncology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Antoinette Hollestelle
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC, Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC, Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Rob A E M Tollenaar
- Department of Surgical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Jaana M Hartikainen
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Martha Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sandra Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Artitaya Lophatananon
- Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | | | | | - Nina Ditsch
- Department of Gynecology and Obstetrics, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter Lichtner
- Insitute of Human Genetics, Technische Universität, Munich, Germany
| | - Rita K Schmutzler
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Kazuo Tajima
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David van den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Cheng Har Yip
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - M Kamran Ikram
- Singapore Eye Research Institute, National University of Singapore, Singapore
| | - Yew-Ching Teh
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Lisa B Signorello
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dong-Young Noh
- Seoul National University College of Medicine, Seoul, Korea
| | - Keun-Young Yoo
- Seoul National University College of Medicine, Seoul, Korea
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore
| | - Philip Tsau-Choong Iau
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Charles Shapiro
- Division of Oncology, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | | | - George Fountzilas
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Macedonia, Greece
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, Taipei, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan
- Department of Surgery, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan
| | - Catherine S Healey
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Department of Tumour Biology, Paris, France
- Institut Curie, INSERM U830, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, France
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Timothy R Rebbeck
- Basser Research Centre, Abramson Cancer Center, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Center for Clinical Epidemiology and Biostatistics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marion Piedmonte
- Gynecologic Oncology Group Statistical and Data Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christian F Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
- Institute of Oncology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Csilla I Szabo
- Center for Translational Cancer Research, Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Ignacio Blanco
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | - Judy Garber
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | | | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research Demokritos, Aghia Paraskevi Attikis, Athens, Greece
| | - David E Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC, Madrid, Spain
| | | | | | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ian Campbell
- VBCRC Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Canter, Maastricht, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, The Netherlands
| | - J Margriet Collée
- Department of Clinical Genetics, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan C Oosterwijk
- University of Groningen, University Medical Center, Department of Genetics, Groningen, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Matti A Rookus
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Theo A M van Os
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - D Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Elena Fineberg
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Julian Barwell
- Leicestershire Clinical Genetics Service, University Hospitals of Leicester NHS Trust, UK
| | - Lisa Walker
- Oxford Regional Genetics Service, Churchill Hospital, Oxford, UK
| | - M John Kennedy
- Academic Unit of Clinical and Molecular Oncology, Trinity College Dublin and St James's Hospital, Dublin, Eire
| | - Radka Platte
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Steve D Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's Hospital Healthcare NHS Trust, Edgbaston, Birmingham, UK
| | - Brigitte Bressac-de Paillerets
- INSERM U946, Fondation Jean Dausset, Paris, France
- Service de Génétique, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Bruno Buecher
- Institut Curie, Department of Tumour Biology, Paris, France
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Laurence Faivre
- Centre de Génétique, CHU Dijon, Université de Bourgogne, Dijon, France, and Centre Georges François Leclerc, Dijon, France
| | | | - Olga M Sinilnikova
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, Centre Léon Bérard, Lyon, France
| | - Olivier Caron
- Consultation de Génétique, Département de Médecine, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Sophie Giraud
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, Centre Léon Bérard, Lyon, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Valérie Bonadona
- Unité de Prévention et d'Epidémiologie Génétique, Centre Léon Bérard, Lyon, France
- Université Lyon 1, CNRS UMR5558, Lyon, France
| | | | | | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Byrski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Amanda B Spurdle
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Australia
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Daniela Zaffaroni
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | | | - Loris Bernard
- Cogentech Cancer Genetic Test Laboratory, Milan, Italy
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
| | - Riccardo Dolcetti
- Cancer Bioimmunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Norbert Arnold
- Department of Gynecology and Obstetrics, University Hospital of Schleswig-Holstein/University Kiel, Kiel, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | - Kerstin Rhiem
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Dieter Niederacher
- Department of Obstetrics and Gynecology, University Medical Center, Heinrich-Heine University, Düsseldorf, Germany
| | - Hansjoerg Plendl
- Institute of Human Genetics, University Hospital of Schleswig-Holstein, University Kiel, Kiel, Germany
| | - Christian Sutter
- Department of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Centre for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Åke Borg
- Department of Oncology, Lund University, Lund, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Johanna Rantala
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Soller
- Department of Clinical Genetics, University and Regional Laboratories, Lund University Hospital, Lund, Sweden
| | - Katherine L Nathanson
- Basser Research Centre, Abramson Cancer Center, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Susan M Domchek
- Basser Research Centre, Abramson Cancer Center, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Gustavo C Rodriguez
- Division of Gynecologic Oncology, North Shore University Health System, University of Chicago, Evanston, IL, USA
| | - Ritu Salani
- Department of Obstetrics and Gynecology, Ohio State University College of Medicine, Columbus, OH, USA
| | - Daphne Gschwantler Kaulich
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Muy-Kheng Tea
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Shani Shimon Paluch
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
- Institute of Oncology, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
- Institute of Oncology, Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mark Robson
- Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jenny Lester
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Quebec, Canada
| | - Karoline B Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Vernon S Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ed Dicks
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Sunil R Lakhani
- University of Queensland, UQ Centre for Clinical Research (UQCCR) Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- The UQ Centre for Clinical Research, The University of Queensland, The Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo Clinic, Rochester, MN, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alvaro N A Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, Westmead, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Andrew Berchuck
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
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Abstract
Some cancers use alternative lengthening of telomeres (ALT), a mechanism whereby new telomeric DNA is synthesized from a DNA template. To determine whether normal mammalian tissues have ALT activity, we generated a mouse strain containing a DNA tag in a single telomere. We found that the tagged telomere was copied by other telomeres in somatic tissues but not the germline. The tagged telomere was also copied by other telomeres when introgressed into CAST/EiJ mice, which have telomeres more similar in length to those of humans. We conclude that ALT activity occurs in normal mouse somatic tissues.
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Affiliation(s)
- Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia
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48
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Abstract
To escape from the normal limits on proliferative potential, cancer cells must employ a means to counteract the gradual telomere attrition that accompanies semi-conservative DNA replication. While the majority of human cancers do this by up-regulating telomerase enzyme activity, most of the remainder use a homologous recombination-mediated mechanism of telomere elongation known as alternative lengthening of telomeres (ALT). Many molecular details of the ALT pathway are unknown, and even less is known regarding the mechanisms by which this pathway is activated. Here, we review current findings about telomere structure in ALT cells, including DNA sequence, shelterin content, and heterochromatic state. We speculate that remodeling of the telomere architecture may contribute to the emergence and maintenance of the ALT phenotype.
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Affiliation(s)
- Dimitri Conomos
- Cancer Research Unit, Children's Medical Research Institute Westmead, NSW, Australia ; Sydney Medical School, University of Sydney NSW, Australia
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49
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Conomos D, Stutz MD, Hills M, Neumann AA, Bryan TM, Reddel RR, Pickett HA. Variant repeats are interspersed throughout the telomeres and recruit nuclear receptors in ALT cells. ACTA ACUST UNITED AC 2013; 199:893-906. [PMID: 23229897 PMCID: PMC3518223 DOI: 10.1083/jcb.201207189] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [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: 11/26/2022]
Abstract
Variant repeats interspersed throughout ALT telomeres recruit nuclear receptors, leading to the destabilized telomere architecture and enhanced telomeric recombination. Telomeres in cells that use the recombination-mediated alternative lengthening of telomeres (ALT) pathway elicit a DNA damage response that is partly independent of telomere length. We therefore investigated whether ALT telomeres contain structural abnormalities that contribute to ALT activity. Here we used next generation sequencing to analyze the DNA content of ALT telomeres. We discovered that variant repeats were interspersed throughout the telomeres of ALT cells. We found that the C-type (TCAGGG) variant repeat predominated and created a high-affinity binding site for the nuclear receptors COUP-TF2 and TR4. Nuclear receptors were directly recruited to telomeres and ALT-associated characteristics were induced after incorporation of the C-type variant repeat by a mutant telomerase. We propose that the presence of variant repeats throughout ALT telomeres results from recombination-mediated telomere replication and spreading of variant repeats from the proximal regions of the telomeres and that the consequent binding of nuclear receptors alters the architecture of telomeres to facilitate further recombination.
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Affiliation(s)
- Dimitri Conomos
- Cancer Research Unit, Children's Medical Research Institute, Westmead NSW 2145, Australia
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50
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Abstract
Some cancers use alternative lengthening of telomeres (ALT), a mechanism whereby new telomeric DNA is synthesized from a DNA template. To determine whether normal mammalian tissues have ALT activity, we generated a mouse strain containing a DNA tag in a single telomere. We found that the tagged telomere was copied by other telomeres in somatic tissues but not the germline. The tagged telomere was also copied by other telomeres when introgressed into CAST/EiJ mice, which have telomeres more similar in length to those of humans. We conclude that ALT activity occurs in normal mouse somatic tissues.
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Affiliation(s)
- Axel A Neumann
- Cancer Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia
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