Abstract

Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Here, using H3K27ac and BRD4 chromatin immunoprecipitation followed by sequencing (ChIP-seq) coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-seq, that is responsible for subgroup divergence, and implicates candidate cells of origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.

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Data deposits

Short-read sequencing data have been deposited at the European Genome-Phenome Archive (EGA, http://www.ebi.ac.uk/ega/) hosted by the EBI, under accession number EGAS00001000215. The data generated in this study are also available at the St Jude PeCan Data Portal (https://pecan.stjude.org/dataset/northcott).

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Acknowledgements

S.E. is a recipient of Human Frontiers Science Program long-term postdoctoral fellowship (LT000432/2014). S.M.W. received funding through a SNSF Early Postdoc Mobility Fellowship (P2ELP3_155365) and an EMBO Long-Term Fellowship (ALTF 755-2014). C.Y.L. is supported by a US Department of Defense CDMRP CA120184 postdoctoral fellowship. P.A.N. is a V Foundation V Scholar in Childhood Cancer Research. We thank Creative Science Studios (http://www.creativesciencestudios.com/) for assistance with artwork. We acknowledge J. Zhang and X. Zhou for their assistance in making this data accessible via the St. Jude PeCan Data Portal (https://pecan.stjude.org/dataset/northcott).

Author information

Author notes

    • Charles Y. Lin

    Present address: Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, Texas 77030, USA.

    • Charles Y. Lin
    •  & Serap Erkek

    These authors contributed equally to this work.

    • Stefan M. Pfister
    • , James E. Bradner
    •  & Paul A. Northcott

    These authors jointly supervised this work.

Affiliations

  1. Medical Oncology, Dana Farber Cancer Institute (DFCI), Boston, Massachusetts 02215, USA

    • Charles Y. Lin
    • , Alexander J. Federation
    • , Rhamy Zeid
    • , Donald R. Polaski
    •  & James E. Bradner
  2. Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany

    • Serap Erkek
    • , Maia Segura-Wang
    • , Sebastian M. Waszak
    •  & Jan O. Korbel
  3. Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Serap Erkek
    • , Daisuke Kawauchi
    • , Barbara C. Worst
    • , David T. W. Jones
    • , Marcel Kool
    • , Laura Sieber
    • , Pascal Johann
    • , Lukas Chavez
    • , Stefan M. Pfister
    •  & Paul A. Northcott
  4. Developmental Neurobiology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Yiai Tong
    •  & Paul A. Northcott
  5. Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA

    • Linlin Yin
    •  & Wenbiao Chen
  6. Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Marc Zapatka
    • , Volker Hovestadt
    •  & Peter Lichter
  7. Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington 98105, USA

    • Parthiv Haldipur
    •  & Kathleen J. Millen
  8. Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany

    • Thomas Risch
    • , Hans-Jörg Warnatz
    • , Vyacheslav Amstislavskiy
    • , Hans Lehrach
    •  & Marie-Laure Yaspo
  9. Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Bensheng Ju
  10. Department of Pathology, St Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA

    • Brent A. Orr
  11. German Cancer Consortium (DKTK), 69120 Heidelberg, Germany

    • David T. W. Jones
    • , Marcel Kool
    • , Andrey Korshunov
    • , Peter Lichter
    •  & Stefan M. Pfister
  12. Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Ivo Buchhalter
    •  & Roland Eils
  13. Department of Translational Oncology, NCT Heidelberg, 69120 Heidelberg, Germany

    • Stefan Gröschel
  14. Department of Neuropathology, NN Burdenko Neurosurgical Institute, 125047 Moscow, Russia

    • Marina Ryzhova
  15. Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and Department of Neuropathology University Hospital, 69120 Heidelberg, Germany

    • Andrey Korshunov
  16. Department of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, Tennessee 38163, USA

    • Victor V. Chizhikov
  17. Department of Pediatrics, Genetics Division, University of Washington, Seattle, Washington 98195, USA

    • Kathleen J. Millen
  18. Institute of Pharmacy and Molecular Biotechnology and BioQuant, University of Heidelberg, 69117 Heidelberg, Germany

    • Roland Eils
  19. Department of Pediatrics, University of Heidelberg, 69117 Heidelberg, Germany

    • Stefan M. Pfister

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Contributions

P.A.N., J.E.B., and S.M.P. conceived and co-led the study. C.Y.L. and S.E. performed all bioinformatics related to the analysis of medulloblastoma enhancers and super-enhancers. Y.T., L.Y., D.K., B.C.W., B.J., and W.C. validated subgroup-specific enhancers in vivo. C.Y.L. and A.J.F. constructed medulloblastoma regulatory circuitry networks. M.Z., S.M.W., R.Z., D.R.P., M.S.-W., D.T.W.J., M.K., V.H., I.B., and L.C. provided informatics and general scientific support. P.H., V.V.C., and K.J.M. performed the developmental studies with dreher and WT mouse embryonic cerebella. T.R., H.-J.W., V.A., H.L., and M.-L.Y. conducted RNA-seq data generation and enhancer RNA analysis. B.A.O. performed ALK staining on medulloblastoma TMAs. L.S., P.J., and S.G. performed 4C-seq experiments. M.R. and A.K. provided medulloblastoma tissue samples. R.E., P.L., J.O.K., S.M.P., J.E.B., and P.A.N. provided institutional support and project supervision. C.Y.L., S.E., S.M.P., J.E.B., and P.A.N. prepared the figures and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Stefan M. Pfister or James E. Bradner or Paul A. Northcott.

Extended data

Supplementary information

Excel files

  1. 1.

    Supplementary Table 1

    List of primary medulloblastoma samples included in the study, including their subgroup affiliation, patient demographic and clinical information, and availability of supporting NGS data.

  2. 2.

    Supplementary Table 2

    Genomic coordinates of common and differentially-regulated enhancers identified in medulloblastoma.

  3. 3.

    Supplementary Table 3

    Target gene assignments of differentially-regulated enhancers and their overlap with SEs, cancer gene and drug target databases, and published medulloblastoma signature genes.

  4. 4.

    Supplementary Table 4

    Genomic coordinates of medulloblastoma SEs.

  5. 5.

    Supplementary Table 5

    SE-associated target genes and their overlap with multiple databases.

  6. 6.

    Supplementary Table 6

    Genomic coordinates of all medulloblastoma SEs and their subgroup-specificity.

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DOI

https://doi.org/10.1038/nature16546

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