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Abstract

Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system1. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive2,3,4. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type1,2,5. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours.

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Change history

  • 28 October 2015

    Spelling of author C.G. was corrected.

Accessions

Data deposits

All high-throughput data have been deposited at the European Genome-phenome Archive (https://www.ebi.ac.uk/ega/) under accession number EGAS00001001308.

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Acknowledgements

We are indebted to the patients and their parents for making available the tumour specimens analysed in this study. We thank the German Neuroblastoma Biobank for providing samples from patients. The Institutional Review Board approved collection and use of all specimens in this study. We also thank our colleagues N. Hemstedt, H. Düren, E. Hess, J. Kreth, and J. Gopalakrishnan; and our collaboration partners I. Amit and F. Paul at the Weizmann Institute of Science for technical assistance. We further acknowledge the Center for Molecular Medicine Cologne light microscope facility for helping us to obtain high-quality data of FISH analyses, and S. Wolf and the Next Generation Sequencing Unit at the German Cancer Research Center (DKFZ) for sequencing. This work was supported by the German Cancer Aid (grant 110122) to M.F., F.W., J.H.S., A.S., and S.A.; the German Ministry of Science and Education (BMBF) as part of the e:Med initiative (grant 01ZX1303A to M.P., M.F., J.H.S., R.B., U.L., and R.K.T., grant 01ZX1406 to M.P., and grant 01ZX1307D to M.F. and F.W.); the BMBF (grant 0316076A to F.W.); the European Union (grant 259348 to F.W.); the Fördergesellschaft Kinderkrebs-Neuroblastom-Forschung e.V. (to M.F.); the German-Israeli Helmholtz Research School in Cancer Biology (to M.G. and F.W.); the Volkswagenstiftung (Lichtenberg Program) (to M.R.S.); and the Center for Molecular Medicine Cologne.

Author information

Author notes

    • Martin Peifer
    • , Falk Hertwig
    • , Frederik Roels
    • , Daniel Dreidax
    • , Moritz Gartlgruber
    • , Frank Westermann
    • , Roman K. Thomas
    •  & Matthias Fischer

    These authors contributed equally to this work.

Affiliations

  1. Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany

    • Martin Peifer
    • , Graziella Bosco
    •  & Roman K. Thomas
  2. Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany

    • Martin Peifer
    • , Falk Hertwig
    • , Frederik Roels
    • , Andrea Krämer
    • , Frederik Sand
    • , Fakhera Ikram
    • , Sandra Ackermann
    • , Peter Nürnberg
    • , Aruljothi Mariappan
    •  & Matthias Fischer
  3. Department of Pediatric Oncology and Hematology, University Children’s Hospital of Cologne, Medical Faculty, University of Cologne, 50937 Cologne, Germany

    • Falk Hertwig
    • , Frederik Roels
    • , Andrea Krämer
    • , Fakhera Ikram
    • , Sandra Ackermann
    • , Anne Engesser
    • , Yvonne Kahlert
    • , Jessica Theissen
    • , Ruth Volland
    • , Frank Berthold
    • , Barbara Hero
    •  & Matthias Fischer
  4. Division Neuroblastoma Genomics (B087), German Cancer Research Center, 69120 Heidelberg, Germany

    • Daniel Dreidax
    • , Moritz Gartlgruber
    • , Kai-Oliver Henrich
    • , Larissa Savelyeva
    • , Emma Bell
    •  & Frank Westermann
  5. Department of Prostate Cancer Research, Institute of Pathology, Center for Integrated Oncology Cologne-Bonn, University Hospital of Bonn, 53127 Bonn, Germany

    • Roopika Menon
    • , Wenzel Vogel
    •  & Sven Perner
  6. NEO New Oncology AG, 51105 Cologne, Germany

    • Roopika Menon
    • , Johannes M. Heuckmann
    • , Stefanie Heynck
    • , Erika Mariotti
    •  & Christian Gloeckner
  7. Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute (UPCI), Hillman Cancer Center, Pittsburgh, Pennsylvania 15213, USA

    • Justin L. Roncaioli
    •  & Roderick J. O’Sullivan
  8. Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany

    • Fakhera Ikram
    • , Janine Altmüller
    •  & Peter Nürnberg
  9. Institute of Biostatistics and Clinical Research, University of Münster, 48149 Münster, Germany

    • Rene Schmidt
  10. Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany

    • Peter Nürnberg
  11. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA

    • Jean Thierry-Mieg
    •  & Danielle Thierry-Mieg
  12. Department of Pathology, University of Kiel, 24118 Kiel, Germany

    • Ivo Leuschner
  13. Functional Epigenomics, University of Cologne, 50931 Cologne, Germany

    • Michal R. Schweiger
  14. Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA

    • Simon C. Watkins
  15. Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Chunxuan Shao
    •  & Thomas Höfer
  16. Computing Center, University of Cologne, 50931 Cologne, Germany

    • Viktor Achter
    •  & Ulrich Lang
  17. Department of Informatics, University of Cologne, 50931 Cologne, Germany

    • Ulrich Lang
  18. Division of Biostatistics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Maral Saadati
  19. Department of Pediatric Oncology and Hematology, Charité University Medical Center Berlin, 10117 Berlin, Germany

    • Angelika Eggert
    •  & Johannes H. Schulte
  20. Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium

    • Bram de Wilde
  21. BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083 China

    • Zhiyu Peng
  22. Center for Pharmacogenomics and Fudan-Zhangjiang Center for Clinical Genomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology School of Pharmacy and School of Life Sciences, Fudan University, Shanghai 201203, China

    • Chen Zhao
    •  & Leming Shi
  23. Department of Pathology, University of Cologne, 50937 Cologne, Germany

    • Monika Ortmann
    • , Reinhard Büttner
    •  & Roman K. Thomas
  24. Department of Pediatric Oncology and Hematology, University Children’s Hospital, 45147 Essen, Germany

    • Alexander Schramm
  25. German Cancer Consortium (DKTK), 10117 Berlin, Germany

    • Johannes H. Schulte
  26. German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Johannes H. Schulte
  27. Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany

    • Carl Herrmann
  28. Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany

    • Carl Herrmann
  29. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Carl Herrmann
  30. Max Planck Institute for Metabolism Research, 50931 Cologne, Germany

    • Matthias Fischer

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Contributions

Conception and design: M.P., F.H., F.R., D.D., M.G., F.W., R.K.T., and M.F. Administrative support, provision of study materials and patients: M.P., J.H., I.L., T.H., P.N., V.A., U.L., A.Eg., F.B., Z.P., C.Z., L.Sh., R.B., S.P., B.H., A.S., J.H.S., F.W., R.J.O., R.K.T., and M.F. Conduct of the experiments, data analysis, and interpretation: M.P., F.H., F.R., D.D., M.G., R.M., A.K., J.L.R., F.S., J.H., F.I., R.S., S.A., A.En., Y.K., W.V., J.A., J.T.-M., D.T.-M., A.M., S.H., E.M., K.-O.H., C.G., G.B., M.-R.S., L.Sa., S.C.W., C.S., E.B., J.T., R.V., M.S., B.D., M.O., B.H., C.H., R.J.O., F.W., R.K.T., and M.F. Manuscript writing: M.P., F.H., F.R., F.W., R.K.T., and M.F. All authors read and approved the final manuscript.

Competing interests

M.P. is a co-founder and shareholder of NEO New Oncology, and received consulting fees from NEO New Oncology. R.K.T. is a founder and shareholder of NEO New Oncology, and received consulting and lecture fees from NEO New Oncology, Sanofi-Aventis, Merck, Roche, Lilly, Boehringer Ingelheim, AstraZeneca, Atlas Biolabs, Daiichi Sankyo, Johnson & Johnson, Puma and Clovis, as well as research support from Merck, EOS and AstraZeneca.

Corresponding authors

Correspondence to Martin Peifer or Frank Westermann or Roman K. Thomas or Matthias Fischer.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    This table contains WGS samples overview.

  2. 2.

    Supplementary Table 2

    This table contains the detected somatic mutations.

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DOI

https://doi.org/10.1038/nature14980

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