Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR

Nature Genetics volume 46, pages 39–44 (2014)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genomic regions involved in the rearrangement leading to ETMR.
Figure 2: Analysis of methylation and DNMT3B expression in cancer samples and normal brain.
Figure 3: Expression analysis of RBL2 and DNMT3B in patient samples, an ETMR-derived xenograft and neural stem cells transfected with C19MC miRNAs.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Sequence Read Archive

References

  1. Li, M. et al. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell 16, 533–546 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Pfister, S. et al. Novel genomic amplification targeting the microRNA cluster at 19q13.42 in a pediatric embryonal tumor with abundant neuropil and true rosettes. Acta Neuropathol. 117, 457–464 (2009).

    Article  CAS  PubMed  Google Scholar 

  3. Yanagisawa, Y., Ito, E., Yuasa, Y. & Maruyama, K. The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents. Biochim. Biophys. Acta 1577, 457–465 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Benetti, R. et al. A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat. Struct. Mol. Biol. 15, 268–279 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Sinkkonen, L. et al. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 15, 259–267 (2008).

    Article  CAS  PubMed  Google Scholar 

  6. Korshunov, A. et al. Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes. Acta Neuropathol. 120, 253–260 (2010).

    Article  PubMed  Google Scholar 

  7. Gessi, M. et al. Embryonal tumors with abundant neuropil and true rosettes: a distinctive CNS primitive neuroectodermal tumor. Am. J. Surg. Pathol. 33, 211–217 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Korshunov, A. et al. LIN28A immunoreactivity is a potent diagnostic marker of embryonal tumor with multilayered rosettes (ETMR). Acta Neuropathol. 124, 875–881 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Picard, D. et al. Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis. Lancet Oncol. 13, 838–848 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Bentwich, I. et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37, 766–770 (2005).

    Article  CAS  PubMed  Google Scholar 

  11. Suzuki, M. & Mizuno, A. A novel human Cl− channel family related to Drosophila flightless locus. J. Biol. Chem. 279, 22461–22468 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Rosenbloom, K.R. et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 41, D56–D63 (2013).

    Article  CAS  PubMed  Google Scholar 

  13. Meacham, F. et al. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12, 451 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  14. Bernstein, B.E. et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045–1048 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Jin, B. et al. DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development, neurogenesis and immune function. Hum. Mol. Genet. 17, 690–709 (2008).

    Article  CAS  PubMed  Google Scholar 

  16. Watanabe, D., Uchiyama, K. & Hanaoka, K. Transition of mouse de novo methyltransferases expression from Dnmt3b to Dnmt3a during neural progenitor cell development. Neuroscience 142, 727–737 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Hayette, S. et al. High DNA methyltransferase DNMT3B levels: a poor prognostic marker in acute myeloid leukemia. PLoS ONE 7, e51527 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Okano, M., Bell, D.W., Haber, D.A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

    Article  CAS  PubMed  Google Scholar 

  19. Tan, M.H. et al. An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo. Mol. Syst. Biol. 9, 632 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  20. Morales-Prieto, D.M., Ospina-Prieto, S., Chaiwangyen, W., Schoenleben, M. & Markert, U.R. Pregnancy-associated miRNA-clusters. J. Reprod. Immunol. 97, 51–61 (2013).

    Article  CAS  PubMed  Google Scholar 

  21. Vaira, V. et al. The microRNA cluster C19MC is deregulated in parathyroid tumours. J. Mol. Endocrinol. 49, 115–124 (2012).

    Article  CAS  PubMed  Google Scholar 

  22. Flor, I. & Bullerdiek, J. The dark side of a success story: microRNAs of the C19MC cluster in human tumours. J. Pathol. 227, 270–274 (2012).

    Article  CAS  PubMed  Google Scholar 

  23. Fornari, F. et al. In hepatocellular carcinoma miR-519d is up-regulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2. J. Pathol. 227, 275–285 (2012).

    Article  CAS  PubMed  Google Scholar 

  24. Rhee, I. et al. DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552–556 (2002).

    Article  CAS  PubMed  Google Scholar 

  25. Oka, M. et al. De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2′-deoxycytidine. Oncogene 24, 3091–3099 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Ostler, K.R. et al. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene 26, 5553–5563 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. You, J.S. & Jones, P.A. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22, 9–20 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Martins-Taylor, K., Schroeder, D.I., LaSalle, J.M., Lalande, M. & Xu, R.H. Role of DNMT3B in the regulation of early neural and neural crest specifiers. Epigenetics 7, 71–82 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  30. Shi, Y. & Majewski, J. FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data. Bioinformatics 29, 1461–1462 (2013).

    Article  CAS  PubMed  Google Scholar 

  31. Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).

    Article  PubMed  Google Scholar 

  32. Lohse, M. et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622–W627 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Thorvaldsdóttir, H., Robinson, J.T. & Mesirov, J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

    Article  PubMed  Google Scholar 

  36. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  37. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article  CAS  PubMed  Google Scholar 

  39. Kent, W.J. BLAT—the BLAST-Like Alignment Tool. Genome Res. 12, 656–664 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Untergasser, A. et al. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 35, W71–W74 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  41. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).

  42. Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).

    Article  CAS  Google Scholar 

  43. Maksimovic, J., Gordon, L. & Oshlack, A. SWAN: subset-quantile within array normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome Biol. 13, R44 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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

  1. Claudia L Kleinman and Noha Gerges: These authors contributed equally to this work.

  2. Annie Huang, Jacek Majewski and Nada Jabado: These authors jointly directed this work.

Authors and 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. Department of Pediatrics, Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada

    Annie Huang

Authors
  1. Claudia L Kleinman
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Noha Gerges
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Simon Papillon-Cavanagh
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Patrick Sin-Chan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Albena Pramatarova
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dong-Anh Khuong Quang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Véronique Adoue
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Stephan Busche
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Maxime Caron
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Haig Djambazian
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Amandine Bemmo
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Adam M Fontebasso
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Tara Spence
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Jeremy Schwartzentruber
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Steffen Albrecht
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Peter Hauser
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Miklos Garami
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Almos Klekner
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Laszlo Bognar
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Jose-Luis Montes
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Alfredo Staffa
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Alexandre Montpetit
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Pierre Berube
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Magdalena Zakrzewska
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Krzysztof Zakrzewski
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Pawel P Liberski
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. Zhifeng Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Peter M Siegel
    View author publications

    You can also search for this author in PubMed Google Scholar

  29. Thomas Duchaine
    View author publications

    You can also search for this author in PubMed Google Scholar

  30. Christian Perotti
    View author publications

    You can also search for this author in PubMed Google Scholar

  31. Adam Fleming
    View author publications

    You can also search for this author in PubMed Google Scholar

  32. Damien Faury
    View author publications

    You can also search for this author in PubMed Google Scholar

  33. Marc Remke
    View author publications

    You can also search for this author in PubMed Google Scholar

  34. Marco Gallo
    View author publications

    You can also search for this author in PubMed Google Scholar

  35. Peter Dirks
    View author publications

    You can also search for this author in PubMed Google Scholar

  36. Michael D Taylor
    View author publications

    You can also search for this author in PubMed Google Scholar

  37. Robert Sladek
    View author publications

    You can also search for this author in PubMed Google Scholar

  38. Tomi Pastinen
    View author publications

    You can also search for this author in PubMed Google Scholar

  39. Jennifer A Chan
    View author publications

    You can also search for this author in PubMed Google Scholar

  40. Annie Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  41. Jacek Majewski
    View author publications

    You can also search for this author in PubMed Google Scholar

  42. Nada Jabado
    View author publications

    You can also search for this author in PubMed Google Scholar

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.

Corresponding authors

Correspondence to Annie Huang, Jacek Majewski or Nada Jabado.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–16 and Supplementary Tables 1–7 (PDF 3736 kb)

Supplementary Table 8

Differential expression analysis for all UCSC genes expressed above a minimum cutoff level (XLSX 4406 kb)

Source data

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kleinman, C., Gerges, N., Papillon-Cavanagh, S. et al. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet 46, 39–44 (2014). https://doi.org/10.1038/ng.2849

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Cancer

Sign up for the Nature Briefing: Cancer newsletter — what matters in cancer research, free to your inbox weekly.

Get what matters in cancer research, free to your inbox weekly. Sign up for Nature Briefing: Cancer