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Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

Author

Listed:
  • Volker Hovestadt

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • David T. W. Jones

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Simone Picelli

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Wei Wang

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Marcel Kool

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Paul A. Northcott

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Marc Sultan

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany)

  • Katharina Stachurski

    (Hematology and Clinical Immunology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, Düsseldorf 40225, Germany)

  • Marina Ryzhova

    (NN Burdenko Neurosurgical Institute, 4th Tverskaya-Yamskaya 16, Moscow 125047, Russia)

  • Hans-Jörg Warnatz

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany)

  • Meryem Ralser

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany)

  • Sonja Brun

    (Tumor Initiation and Maintenance Program, National Cancer Institute (NCI)–Designated Cancer Center, Sanford-Burnham Medical Research Institute, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037, USA)

  • Jens Bunt

    (Queensland Brain Institute, University of Queensland, QBI Building, St Lucia, Queensland 4072, Australia
    AMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands)

  • Natalie Jäger

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Kortine Kleinheinz

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Serap Erkek

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany)

  • Ursula D. Weber

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Cynthia C. Bartholomae

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg 69120, Germany)

  • Christof von Kalle

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg 69120, Germany)

  • Chris Lawerenz

    (Data Management Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Jürgen Eils

    (Data Management Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Jan Koster

    (AMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands)

  • Rogier Versteeg

    (AMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, the Netherlands)

  • Till Milde

    (Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany
    Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Olaf Witt

    (Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany
    Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Sabine Schmidt

    (Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Stephan Wolf

    (Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Torsten Pietsch

    (University of Bonn Medical Center, Sigmund-Freud-Strasse 25, Bonn 53105, Germany)

  • Stefan Rutkowski

    (University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg 20246, Germany)

  • Wolfram Scheurlen

    (Cnopf’sche Kinderklinik, Nürnberg Children’s Hospital, St.-Johannis-Mühlgasse 19, Nürnberg 90419, Germany)

  • Michael D. Taylor

    (Program in Developmental and Stem Cell Biology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    University of Toronto, Toronto, Ontario M5S 1A8, Canada)

  • Benedikt Brors

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Jörg Felsberg

    (Heinrich Heine University Düsseldorf, Moorenstrasse 5, Düsseldorf 40225, Germany
    German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Guido Reifenberger

    (Heinrich Heine University Düsseldorf, Moorenstrasse 5, Düsseldorf 40225, Germany
    German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Arndt Borkhardt

    (Hematology and Clinical Immunology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, Düsseldorf 40225, Germany)

  • Hans Lehrach

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany)

  • Robert J. Wechsler-Reya

    (Tumor Initiation and Maintenance Program, National Cancer Institute (NCI)–Designated Cancer Center, Sanford-Burnham Medical Research Institute, 2880 Torrey Pines Scenic Drive, La Jolla, California 92037, USA)

  • Roland Eils

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Heidelberg 69120, Germany
    Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg 69120, Germany
    Heidelberg Center for Personalised Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Marie-Laure Yaspo

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, Berlin 14195, Germany)

  • Pablo Landgraf

    (Hematology and Clinical Immunology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, Düsseldorf 40225, Germany)

  • Andrey Korshunov

    (University of Heidelberg, Im Neuenheimer Feld 220, Heidelberg 69120, Germany
    Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 220-221, Heidelberg, 69120 Germany)

  • Marc Zapatka

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Bernhard Radlwimmer

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

  • Stefan M. Pfister

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Hematology & Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, Heidelberg 69120, Germany)

  • Peter Lichter

    (German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
    Heidelberg Center for Personalised Oncology (DKFZ-HIPO), Im Neuenheimer Feld 280, Heidelberg 69120, Germany)

Abstract

Medulloblastoma is a malignant childhood brain tumour presenting major clinical challenges; here, a comprehensive genome-wide DNA methylation data set from human and mouse tumours, coupled with analysis of histone modifications, RNA transcripts and genome sequencing, uncovers a wealth of alterations that provide insights into the epigenetic regulation of transcription and genome organization in medulloblastoma pathogenesis.

Suggested Citation

  • Volker Hovestadt & David T. W. Jones & Simone Picelli & Wei Wang & Marcel Kool & Paul A. Northcott & Marc Sultan & Katharina Stachurski & Marina Ryzhova & Hans-Jörg Warnatz & Meryem Ralser & Sonja Bru, 2014. "Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing," Nature, Nature, vol. 510(7506), pages 537-541, June.
    • Handle: RePEc:nat:nature:v:510:y:2014:i:7506:d:10.1038_nature13268
    DOI: 10.1038/nature13268
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    Citations

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    Cited by:

    1. Yuanyuan Chen & Reka Toth & Sara Chocarro & Dieter Weichenhan & Joschka Hey & Pavlo Lutsik & Stefan Sawall & Georgios T. Stathopoulos & Christoph Plass & Rocio Sotillo, 2022. "Club cells employ regeneration mechanisms during lung tumorigenesis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Konstantin Okonechnikov & Aylin Camgöz & Owen Chapman & Sameena Wani & Donglim Esther Park & Jens-Martin Hübner & Abhijit Chakraborty & Meghana Pagadala & Rosalind Bump & Sahaana Chandran & Katerina K, 2023. "3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Jamie L. Endicott & Paula A. Nolte & Hui Shen & Peter W. Laird, 2022. "Cell division drives DNA methylation loss in late-replicating domains in primary human cells," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    4. Sibo Zhao & Jia Li & Huiyuan Zhang & Lin Qi & Yuchen Du & Mari Kogiso & Frank K. Braun & Sophie Xiao & Yulun Huang & Jianfang Li & Wan-Yee Teo & Holly Lindsay & Patricia Baxter & Jack M. F. Su & Adeku, 2022. "Epigenetic Alterations of Repeated Relapses in Patient-matched Childhood Ependymomas," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Shweta Godbole & Hannah Voß & Antonia Gocke & Simon Schlumbohm & Yannis Schumann & Bojia Peng & Martin Mynarek & Stefan Rutkowski & Matthias Dottermusch & Mario M. Dorostkar & Andrey Korshunov & Thoma, 2024. "Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level," Nature Communications, Nature, vol. 15(1), pages 1-24, December.

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