Abstract

The failure to develop effective therapies for pediatric glioblastoma (pGBM) and diffuse intrinsic pontine glioma (DIPG) is in part due to their intrinsic heterogeneity. We aimed to quantitatively assess the extent to which this was present in these tumors through subclonal genomic analyses and to determine whether distinct tumor subpopulations may interact to promote tumorigenesis by generating subclonal patient-derived models in vitro and in vivo. Analysis of 142 sequenced tumors revealed multiple tumor subclones, spatially and temporally coexisting in a stable manner as observed by multiple sampling strategies. We isolated genotypically and phenotypically distinct subpopulations that we propose cooperate to enhance tumorigenicity and resistance to therapy. Inactivating mutations in the H4K20 histone methyltransferase KMT5B (SUV420H1), present in <1% of cells, abrogate DNA repair and confer increased invasion and migration on neighboring cells, in vitro and in vivo, through chemokine signaling and modulation of integrins. These data indicate that even rare tumor subpopulations may exert profound effects on tumorigenesis as a whole and may represent a new avenue for therapeutic development. Unraveling the mechanisms of subclonal diversity and communication in pGBM and DIPG will be an important step toward overcoming barriers to effective treatments.

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Acknowledgements

We would like to thank L. Howell for confocal microcopy expertise, M. Lambros for technical advice, and H. Vogel for neuropathology expertise and assistance with autopsies at Stanford University. We are indebted to the multidisciplinary teams at the Royal Marsden Hospital, St George’s Hospital and Kings College Hospital for their continued assistance with prospective sample collection. Finally we thank the many children and families who contributed to this study through the donation of tumor tissue. This study makes use of data generated by the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project, C. Hawkins and the Hospital for Sick Children, and the McGill University-DKFZ Pediatric Brain Tumour Consortium. This work was supported by Cancer Research UK (grants C13468/A13982 and C13468/A23536), Abbie’s Army and the DIPG Collaborative, and the INSTINCT network funded by The Brain Tumour Charity, Great Ormond Street Children’s Charity and Children with Cancer UK. We further acknowledge funding from the Brainchild Foundation (Australia), Children’s Hospital Foundation Queensland, the Xarxa de Bancs de Tumors de Catalunya (XBTC) sponsored by Pla Director d’Oncologia de Catalunya, ISCIII-FEDER (CP13/00189), McKenna Claire Foundation, and the US National Institutes of Health (grants K08NS070926 and R01NS092597). We acknowledge the support of the Queensland Children’s Tumour Bank (QCTB) for provision of samples and clinical data. The QCTB is supported by the Children’s Hospital Foundation (Queensland) and the Brainchild Foundation. The authors acknowledge NHS funding to the NIHR Biomedical Research Centre at The Royal Marsden and the ICR and Experimental Cancer Medicines Centre (ECMC) funding.

Author information

Author notes

    • Mara Vinci

    Present address: Bambino Gesù Children’s Hospital–IRCCS, Rome, Italy

    • Stergios Zacharoulis

    Present address: Department of Pediatric Hematology Oncology, Columbia University Medical Center, New York, NY, USA

Affiliations

  1. Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK

    • Mara Vinci
    • , Anna Burford
    • , Valeria Molinari
    • , Ketty Kessler
    • , Sergey Popov
    • , Matthew Clarke
    • , Kathryn R. Taylor
    • , Diana Carvalho
    • , Alan Mackay
    •  & Chris Jones
  2. Division of Molecular Pathology, The Institute of Cancer Research, London, UK

    • Mara Vinci
    • , Anna Burford
    • , Valeria Molinari
    • , Ketty Kessler
    • , Sergey Popov
    • , Matthew Clarke
    • , Kathryn R. Taylor
    • , Diana Carvalho
    • , Alan Mackay
    •  & Chris Jones
  3. Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK

    • Mara Vinci
    • , Anna Burford
    • , Valeria Molinari
    • , Ketty Kessler
    • , Sergey Popov
    • , Matthew Clarke
    • , Kathryn R. Taylor
    • , Diana Carvalho
    • , Alan Mackay
    •  & Chris Jones
  4. Department of Cellular Pathology, University Hospital of Wales, Cardiff, UK

    • Sergey Popov
  5. Stanford University School of Medicine, Stanford, CA, USA

    • Kathryn R. Taylor
    •  & Elizabeth Y. Qin
  6. CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK

    • Helen N. Pemberton
    •  & Christopher J. Lord
  7. UCL Cancer Institute, University College London, London, UK

    • Alice Gutteridge
    •  & Tim Forshew
  8. Paediatric Oncology Drug Development Team, Children and Young People’s Unit, Royal Marsden Hospital, Sutton, UK

    • Lynley V. Marshall
    • , Stergios Zacharoulis
    •  & Sucheta Vaidya
  9. UQ Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia

    • Wendy J. Ingram
    •  & Andrew S. Moore
  10. Oncology Services Group, Children’s Health Queensland Hospital and Health Service, Brisbane, Queensland, Australia

    • Wendy J. Ingram
    •  & Andrew S. Moore
  11. The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia

    • Andrew S. Moore
  12. Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China

    • Ho-Keung Ng
  13. Department of Cytogenetics and Reproductive Biology, Farhat HACHED Hospital, Sousse, Tunisia

    • Saoussen Trabelsi
    •  & Dorra H’mida-Ben Brahim
  14. Faculty of Medicine, Sousse, Tunisia

    • Dorra H’mida-Ben Brahim
  15. Centre Hospitalier Régional et Universitaire Hautepierre, Strasbourg, France

    • Natacha Entz-Werle
  16. Department of Radiotherapy, Royal Marsden Hospital, Sutton, UK

    • Henry C. Mandeville
  17. Department of Cellular Pathology, St George’s Hospital NHS Trust, London, UK

    • Leslie R. Bridges
  18. Department of Neurosurgery, St George’s Hospital NHS Trust, London, UK

    • Andrew J. Martin
  19. Department of Neuropathology, Kings College Hospital, London, UK

    • Safa Al-Sarraj
  20. Department of Neurosurgery, Kings College Hospital, London, UK

    • Christopher Chandler
  21. Hospital Sant Joan de Deu, Barcelona, Spain

    • Mariona Sunol
    • , Jaume Mora
    • , Carmen de Torres
    • , Ofelia Cruz
    •  & Angel M. Carcaboso
  22. Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA

    • Michelle Monje

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Contributions

M.V., A.B., A.M. and C.J. conceived the study and wrote the manuscript with contributions from all authors. M.V., A.B., V.M., K.K., S.P., M.C., K.R.T., H.N.P., C.J.L., A.G., T.F. and D.C. carried out experiments. M.V., A.B., A.M. and C.J. analyzed data. L.V.M., E.Y.Q., W.J.I., A.S.M., H.-K.N., S.T., D.H.-B.B., N.E.-W., S.Z., S.V., H.C.M., L.R.B., A.J.M., S.A.-S., C.C., J.M., C.d.T., O.C., M.S., A.M.C., M.M. and A.M. prepared samples and provided clinical annotations. All authors approved the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Chris Jones.

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DOI

https://doi.org/10.1038/s41591-018-0086-7

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