Abstract

Medulloblastomas are the most common malignant brain tumours in children1. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles2,3,4,5. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, β-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medulloblastoma.

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Data deposits

Sequence data used for this analysis are available in dbGaP under accession phs000504.v1.p1.

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Acknowledgements

This work was supported by NIH grants NHGRI U54HG003067 to E. S. Lander (E.S., D.A., S.B.G., G.G., M.M.); R01CA109467 (S.L.P., J.P.M.); R01CA105607 (H.G., T.M.R., M.M., S.L.P.); P30 HD18655 (S.L.P.); R01 CA030002 and CA050661 (T.M.R.); R01 NS046789 (G.R.C.); R01 CA154480 (P.T.); R25NS070682 (S.S.) and R01CA148699 (M.D.T.); St. Baldrick’s Foundation Scholar Award and the Beirne Faculty Scholar endowment and Center for Children’s Brain Tumors at Stanford University (Y.-J.C.); German Cancer Aid (109252) and the BMBF ICGC-PedBrain project (N.J., D.T.W.J., P.L., S.M.P.); HHMI (G.R.C.); the Pediatric Brain Tumor Foundation (M.D.T.); Canadian Institutes of Health Research Fellowship (T.J.P.); Restracomp funding from the Hospital for Sick Children (P.A.N.); and the Mullarkey Research Fund (S.L.P.). We thank Children’s Oncology Group and the Cooperative Human Tissue Network for providing tumour samples, the staff of the Broad Institute Biological Samples, Genome Sequencing and Genetic Analysis Platforms for their assistance in genomic processing of samples and generating the sequencing data used in this analysis, K. Keho and M. Brown at Pacific Biosciences for technical support with sample barcoding methods, and L. Gaffney of Broad Institute Communications for assistance with figure layout and design.

Author information

Affiliations

  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Trevor J. Pugh
    • , Daniel Auclair
    • , James Bochicchio
    • , Mauricio O. Carneiro
    • , Scott L. Carter
    • , Kristian Cibulskis
    • , Rachel L. Erlich
    • , Heidi Greulich
    • , Michael S. Lawrence
    • , Niall J. Lennon
    • , Aaron McKenna
    • , James Meldrim
    • , Alex H. Ramos
    • , Michael G. Ross
    • , Carsten Russ
    • , Erica Shefler
    • , Andrey Sivachenko
    • , Brian Sogoloff
    • , Petar Stojanov
    • , Pablo Tamayo
    • , Jill P. Mesirov
    • , Stacey B. Gabriel
    • , Gad Getz
    • , Matthew Meyerson
    • , Scott L. Pomeroy
    •  & Yoon-Jae Cho
  2. Center for Cancer Genome Discovery, Departments of Medical Oncology and of Biological Chemistry and Molecular Pharmacology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Trevor J. Pugh
    • , Heidi Greulich
    • , Alex H. Ramos
    • , Thomas M. Roberts
    •  & Matthew Meyerson
  3. Harvard Medical School, Boston, Massachusetts 02115, USA

    • Trevor J. Pugh
    • , Shyamal Dilhan Weeraratne
    • , Tenley C. Archer
    • , Heidi Greulich
    • , Alex H. Ramos
    • , Vladimir Amani
    • , Natalia Teider
    • , Soma Sengupta
    • , Jessica Pierre Francois
    • , Thomas M. Roberts
    • , Matthew Meyerson
    • , Scott L. Pomeroy
    •  & Yoon-Jae Cho
  4. Department of Neurology, Children’s Hospital Boston, Boston, Massachusetts 02115, USA

    • Shyamal Dilhan Weeraratne
    • , Tenley C. Archer
    • , Vladimir Amani
    • , Natalia Teider
    • , Soma Sengupta
    • , Jessica Pierre Francois
    • , Scott L. Pomeroy
    •  & Yoon-Jae Cho
  5. Brandeis University, Waltham, Massachusetts 02453, USA

    • Daniel A. Pomeranz Krummel
  6. The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada

    • Paul A. Northcott
    •  & Michael D. Taylor
  7. Departments of Neurology and Neurosurgery, Stanford University School of Medicine, Stanford, California 94305, USA

    • Furong Yu
    • , Gerald R. Crabtree
    • , Amanda G. Kautzman
    •  & Yoon-Jae Cho
  8. Howard Hughes Medical Institute at Stanford University, Stanford, California 94305, USA

    • Gerald R. Crabtree
  9. German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany

    • Natalie Jäger
    • , David T. W. Jones
    • , Peter Lichter
    •  & Stefan M. Pfister
  10. Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA

    • Matthew Meyerson

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Contributions

Y.-J.C., M.M. and S.L.P. conceived the project. Y.-J.C., T.J.P., M.M. and S.L.P. wrote the manuscript with input from co-authors. S.D.W., T.C.A., J.P.F., S.S., N.T., Y.-J.C., A.G.K. and F.Y. performed functional characterization studies. D.A.P.K. generated in silico structural modelling of DDX3X mutations. T.J.P. conducted the bioinformatic analysis, supported by S.L.C., P.S., K.C., M.S.L., A.M., A.H.R., A.S., H.G., P.T., J.P.M., N.J. and D.T.W.J.; D.A., E.S., S.B.G., and G.G. facilitated transfer, sequencing and analysis of samples. P.A.N. and M.D.T. provided tissues for analysis. Y.-J.C., J.P.F. and V.A. processed tumour and blood samples for study. G.R.C. generated reagents used in functional characterization studies. P.L., S.M.P. and T.M.R. assisted with interpretation of results. J.B., M.O.C., R.L.E., N.J.L., J.M., M.G.R., C.R. and B.S. performed microfluidic PCR and single-molecule real-time sequencing for validation analysis.

Competing interests

M.M. is a paid consultant for and equity holder in Foundation Medicine, a genomics-based oncology diagnostics company, and is a paid consultant for Novartis. Y.-J.C. has served on an advisory board for Novartis.

Corresponding authors

Correspondence to Matthew Meyerson or Scott L. Pomeroy or Yoon-Jae Cho.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Text and additional references, Supplementary Figures 1-3 and Supplementary Table 5.

Zip files

  1. 1.

    Supplementary Data 1

    This zipped file contains Supplementary Table 1, showing the clinical, copy number and mutation data matrix.

  2. 2.

    Supplementary Data 2

    This zipped file contains Supplementary Table 2 showing the list of candidate somatic mutations, Supplementary Table 4 showing the somatic mutations in histone methyltransferases and Supplementary Table 6, which shows the somatic mutations in RNA helicases.

  3. 3.

    Supplementary Data 3

    This zipped file contains Supplementary Table 3, which shows MutSig hits for each medulloblastoma subtype considered independently.

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DOI

https://doi.org/10.1038/nature11329

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