Diffuse intrinsic pontine glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children, with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and to the selection of therapies on the basis of assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic makeup of this brain cancer, with nearly 80% found to harbor a p.Lys27Met histone H3.3 or p.Lys27Met histone H3.1 alteration. However, DIPGs are still thought of as one disease, with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs, we integrated whole-genome sequencing with methylation, expression and copy number profiling, discovering that DIPGs comprise three molecularly distinct subgroups (H3-K27M, silent and MYCN) and uncovering a new recurrent activating mutation affecting the activin receptor gene ACVR1 in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of the downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer.

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  1. 1.

    Population based survival rates for childhood cancer in Britain, 1980–1991. Br. Med. J. 309, 1612–1616 (1994).

  2. 2.

    & Chemotherapy for brain stem gliomas. Childs Nerv. Syst. 15, 545–553 (1999).

  3. 3.

    et al. Brainstem glioma: I. Pathology, clinical features, and therapy. J. Child Neurol. 8, 112–128 (1993).

  4. 4.

    , & Diffuse brainstem glioma in children: critical review of clinical trials. Lancet Oncol. 7, 241–248 (2006).

  5. 5.

    , & Advances toward an understanding of brainstem gliomas. J. Clin. Oncol. 24, 1266–1272 (2006).

  6. 6.

    et al. Aurora kinase B is a potential therapeutic target in pediatric diffuse intrinsic pontine glioma. Brain Pathol. 23, 244–253 (2013).

  7. 7.

    et al. Genome-wide analyses identify recurrent amplifications of receptor tyrosine kinases and cell-cycle regulatory genes in diffuse intrinsic pontine glioma. J. Clin. Oncol. 29, 3999–4006 (2011).

  8. 8.

    et al. Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease. J. Clin. Oncol. 28, 3061–3068 (2010).

  9. 9.

    et al. Whole-genome profiling of pediatric diffuse intrinsic pontine gliomas highlights platelet-derived growth factor receptor α and poly (ADP-ribose) polymerase as potential therapeutic targets. J. Clin. Oncol. 28, 1337–1344 (2010).

  10. 10.

    et al. K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol. 124, 439–447 (2012).

  11. 11.

    et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 482, 226–231 (2012).

  12. 12.

    et al. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat. Genet. 44, 251–253 (2012).

  13. 13.

    , & Analysis of telomeres and telomerase. Curr. Protoc. Cell Biol. Chapter 18, Unit 18.6 (2003).

  14. 14.

    et al. DNA C-circles are specific and quantifiable markers of alternative-lengthening-of-telomeres activity. Nat. Biotechnol. 27, 1181–1185 (2009).

  15. 15.

    et al. Molecular consequences of the ACVR1R206H mutation of fibrodysplasia ossificans progressiva. J. Biol. Chem. 285, 22542–22553 (2010).

  16. 16.

    et al. Classic and atypical fibrodysplasia ossificans progressiva (FOP) phenotypes are caused by mutations in the bone morphogenetic protein (BMP) type I receptor ACVR1. Hum. Mutat. 30, 379–390 (2009).

  17. 17.

    et al. Novel mutations in ACVR1 result in atypical features in two fibrodysplasia ossificans progressiva patients. PLoS ONE 4, e5005 (2009).

  18. 18.

    , , , & Id2 and Id3 define the potency of cell proliferation and differentiation responses to transforming growth factor β and bone morphogenetic protein. Mol. Cell. Biol. 24, 4241–4254 (2004).

  19. 19.

    , , , & BMP signaling is responsible for serum-induced Id2 expression. Biochem. Biophys. Res. Commun. 420, 281–287 (2012).

  20. 20.

    et al. Identification of a novel bone morphogenetic protein (BMP)-inducible transcript, BMP-inducible transcript-1, by utilizing the conserved BMP-responsive elements in the Id genes. J. Bone Miner. Metab. 31, 34–43 (2013).

  21. 21.

    , , & ID2: a negative transcription factor regulating oligodendroglia differentiation. J. Neurosci. Res. 90, 925–932 (2012).

  22. 22.

    et al. Overexpressed DNA-binding protein inhibitor 2 as an unfavorable prognosis factor promotes cell proliferation in nasopharyngeal carcinoma. Acta Biochim. Biophys. Sin. (Shanghai) 44, 503–512 (2012).

  23. 23.

    et al. The intracellular localization of ID2 expression has a predictive value in non small cell lung cancer. PLoS ONE 4, e4158 (2009).

  24. 24.

    , , , & The mRNA expression of inhibitors of DNA binding-1 and -2 is associated with advanced tumour stage and adverse clinical outcome in human breast cancer. Anticancer Res. 33, 2179–2183 (2013).

  25. 25.

    & Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).

  26. 26.

    , & PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics 28, 2576–2583 (2012).

  27. 27.

    et al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res. 21, 830–839 (2011).

  28. 28.

    et al. Savant Genome Browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res. 40, W615–W621 (2012).

  29. 29.

    , , , & Detecting copy number variation with mated short reads. Genome Res. 20, 1613–1622 (2010).

  30. 30.

    et al. O6-methylguanine-DNA methyltransferase is downregulated in transformed astrocyte cells: implications for anti-glioma therapies. Mol. Cancer 6, 36 (2007).

  31. 31.

    & Statistics notes. The odds ratio. Br. Med. J. 320, 1468 (2000).

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We would like to thank all of the patients and families for donating tissue for this research. This work was supported by the Canadian Institutes of Health Research (CIHR, MOP 115004) and was funded in part by a Genome Canada/CIHR grant (cofunding from Genome BC, Génome Québec, CIHR-ICR (Institute for Cancer Research) and C17, through the Genome Canada/CIHR joint ATID Competition (project title: The Canadian Paediatric Cancer Genome Consortium (CPCGC): Translating Next-Generation Sequencing Technologies into Improved Therapies for High-Risk Childhood Cancer)). P.B. is a recipient of a CIHR Doctoral Frederick Banting and Charles Best Canada Graduate Scholarships award. O.B. is a Damon Runyon Clinical Investigator and is supported by the US Department of Defense and the Pediatric Brain Tumor Foundation. C.J., A. Mackay and K.R.T. acknowledge National Health Service (NHS) funding to the Biomedical Research Centre and support from the Stavros Niarchos Foundation. Sample collection for M.A.K. and D.Z. was supported in part by grant UL1TR000038 from the National Center for Research Resources, US National Institutes of Health and by grant 5P30CA016087-32 from the National Cancer Institute.

Author information

Author notes

    • Pawel Buczkowicz
    •  & Christine Hoeman

    These authors contributed equally to this work.

    • Oren Becher
    •  & Cynthia Hawkins

    These authors jointly directed this work.


  1. Division of Pathology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

    • Pawel Buczkowicz
    •  & Cynthia Hawkins
  2. Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Pawel Buczkowicz
    • , Patricia Rakopoulos
    • , Sanja Pajovic
    • , Andrew Morrison
    • , Jennifer Zuccaro
    • , Sameer Agnihotri
    • , Scott Ryall
    • , Mark Barszczyk
    • , Yevgen Chornenkyy
    • , Pedro Castelo-Branco
    • , Joshua Mangerel
    • , Uri Tabori
    • , King Ching Ho
    • , Annie Huang
    •  & Cynthia Hawkins
  3. Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.

    • Pawel Buczkowicz
    • , Patricia Rakopoulos
    • , Mark Barszczyk
    • , Yevgen Chornenkyy
    •  & Cynthia Hawkins
  4. Division of Pediatric Hematology/Oncology, Duke University Medical Center, Durham, North Carolina, USA.

    • Christine Hoeman
    • , Francisco Cordero
    •  & Oren Becher
  5. Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada.

    • Louis Letourneau
    • , Mathieu Bourgey
    • , Guillaume Bourque
    •  & Alexandre Montpetit
  6. Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

    • Misko Dzamba
    •  & Michael Brudno
  7. Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York, USA.

    • Peter Lewis
    •  & C David Allis
  8. Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Eric Bouffet
    • , Ute Bartels
    • , Uri Tabori
    •  & Annie Huang
  9. Division of Cancer Therapeutics, Institute of Cancer Research, London, UK.

    • Kathryn R Taylor
    • , Alan Mackay
    •  & Chris Jones
  10. Department of Pediatric Hematology-Oncology, Children's Hospitals and Clinics of Minnesota, Minneapolis, Minnesota, USA.

    • Anne E Bendel
  11. Center for Genetic Medicine, Children's National Medical Center, Washington, DC, USA.

    • Javad Nazarian
  12. Department of Pediatrics-Hematology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.

    • Jason R Fangusaro
  13. Division of Pediatric Hematology/Oncology and Neuropathology, New York University Cancer Institute, New York University Langone Medical Center, New York, New York, USA.

    • Matthias A Karajannis
    •  & David Zagzag
  14. Department of Pediatrics, Children's Hospital Colorado, Denver, Colorado, USA.

    • Nicholas K Foreman
    •  & Andrew Donson
  15. Department of Pathology, Arnold Palmer Hospital for Children, Orlando, Florida, USA.

    • Julia V Hegert
    •  & Amy Smith
  16. Clark H. Smith Brain Tumour Centre, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.

    • Jennifer Chan
    •  & Lucy Lafay-Cousin
  17. Department of Pediatric Neurology and Neuro-Oncology, BC Children's Hospital, Vancouver, British Columbia, Canada.

    • Sandra Dunn
    • , Juliette Hukin
    •  & Chris Dunham
  18. Division of Hematology/Oncology, McMaster Children's Hospital, Hamilton, Ontario, Canada.

    • Katrin Scheinemann
  19. Department of Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

    • Jean Michaud
  20. Department of Hematology/Oncology, Children's Hospital London Health Sciences Centre, London, Ontario, Canada.

    • Shayna Zelcer
    •  & David Ramsay
  21. Monash Institute of Medical Research, Monash Medical Centre, Clayton, Victoria, Australia.

    • Jason Cain
  22. Department of Neurological Surgery, Weill Cornell Medical College and Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

    • Cameron Brennan
    •  & Mark M Souweidane
  23. The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Michael Brudno


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E.B., U.B., P.B., O.B. and C. Hawkins designed the study. P.B., C. Hoeman, F.C., P.R., S.P., A. Morrison, J.Z., S.A., S.R., M. Barszczyk, Y.C., P.C.-B., K.C.H. and J. Mangerel performed experiments. P.B., C. Hoeman, F.C., P.R., L.L., M.D., M. Bourgey, G.B. and A. Montpetit collected and analyzed data. O.B., C. Hawkins, C.J., K.R.T., A. Mackay, A.E.B., J.N., J.R.F., M.A.K., D.Z., N.K.F., A.D., J.V.H., A.S., J. Chan, L.L.-C., S.D., J.H., C.D., K.S., J. Michaud, S.Z., D.R., J. Cain, M.M.S., E.B., U.T. and U.B. provided reagents, tissue and mice. P.B., P.R., S.P., M.D., O.B. and C. Hawkins wrote the manuscript. P.L., C.B., C.D.A., M. Brudno, A.H. and U.T. gave technical support and conceptual advice. All authors approved the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Oren Becher or Cynthia Hawkins.

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