Abstract

Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC1,2. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter3 that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B4,5. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.

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Acknowledgements

This work was supported by the Cancer Research Society and was funded in part by Hungarian Scientific Research Fund (OTKA) contract T-04639, by National Research and Development Fund (NKFP) contracts 1A/002/2004 (P.H., M. Garami and L.B.) and TÁMOP-4.2.2A-11/1/KONV-2012-0025 (A.K. and L.B.), and by Canadian Institutes of Health Research grant 102684 (A.H.). N.J. is a member of the Penny Cole laboratory and is the recipient of a Chercheur Clinicien Senior Award. S.B. is supported by an RMGA (Reseau Médical de Génétique Apliquée; Network of Applied Genetic Medicine) fellowship. T.P. and J.M. hold Canada Research Chairs (tier 2). C.L.K. is the recipient of a fellowship award from the Fonds de Recherche du Québec-Santé, N.G. is the recipient of a studentship award from Cedars, and A.M.F. is the recipient of a studentship from the Canadian Institutes of Health Research and the McGill–Canadian Institutes of Health Research Training Program in Systems Biology. R.S. is supported by the Canadian Institutes of Health Research.

Author information

Author notes

    • Claudia L Kleinman
    •  & Noha Gerges

    These authors contributed equally to this work.

    • Annie Huang
    • , Jacek Majewski
    •  & Nada Jabado

    These authors jointly directed this work.

Affiliations

  1. McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada.

    • Claudia L Kleinman
    • , Simon Papillon-Cavanagh
    • , Albena Pramatarova
    • , Véronique Adoue
    • , Stephan Busche
    • , Maxime Caron
    • , Haig Djambazian
    • , Amandine Bemmo
    • , Jeremy Schwartzentruber
    • , Alfredo Staffa
    • , Alexandre Montpetit
    • , Pierre Berube
    • , Robert Sladek
    • , Tomi Pastinen
    •  & Jacek Majewski
  2. Department of Human Genetics, McGill University, Montreal, Quebec, Canada.

    • Claudia L Kleinman
    • , Noha Gerges
    • , Dong-Anh Khuong Quang
    • , Robert Sladek
    • , Jacek Majewski
    •  & Nada Jabado
  3. Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Patrick Sin-Chan
    • , Tara Spence
    •  & Annie Huang
  4. Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.

    • Adam M Fontebasso
    •  & Nada Jabado
  5. Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada.

    • Steffen Albrecht
  6. Second Department of Paediatrics, Semmelweis University, Budapest, Hungary.

    • Peter Hauser
    •  & Miklos Garami
  7. Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary.

    • Almos Klekner
    •  & Laszlo Bognar
  8. Division of Neurosurgery, Department of Surgery, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada.

    • Jose-Luis Montes
  9. Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland.

    • Magdalena Zakrzewska
    •  & Pawel P Liberski
  10. Department of Neurosurgery, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland.

    • Krzysztof Zakrzewski
  11. Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.

    • Zhifeng Dong
    •  & Peter M Siegel
  12. Department of Biochemistry, McGill University, Montreal, Quebec, Canada.

    • Thomas Duchaine
  13. Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.

    • Christian Perotti
    •  & Jennifer A Chan
  14. Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada.

    • Adam Fleming
    •  & Damien Faury
  15. Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Marc Remke
    • , Marco Gallo
    • , Peter Dirks
    •  & Michael D Taylor
  16. Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.

    • Annie Huang

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Contributions

N.G., D.-A.K.Q., A.P., P.S.-C., V.A., S.B., A.M.F., Z.D., C.P., T.S., D.F. and P.M.S. performed experimental work. C.L.K., M.C., H.D., S.B., S.P.-C., A.B., A.M. and J.S. performed bioinformatic analyses. C.L.K., N.G., Z.D., A.H., P.S.-C., T.D., S.P.-C., T.P., S.B., V.A., A.S., P.B., R.S., J.M. and N.J. performed data analyses and generated the text and figures. C.L.K., S.P.-C., P.H., A.K., M. Garami, M.Z., M.R., M. Gallo, P.D., M.D.T., P.P.L., L.B., J.-L.M., J.A.C., K.Z., S.A., A.F. and N.J. collected data and provided patient materials. J.M. and N.J. provided leadership for the project. All authors contributed to the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Annie Huang or Jacek Majewski or Nada Jabado.

Supplementary information

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    Supplementary Figures 1–16 and Supplementary Tables 1–7

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    Supplementary Table 8

    Differential expression analysis for all UCSC genes expressed above a minimum cutoff level

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DOI

https://doi.org/10.1038/ng.2849

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