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Abstract

Metastasis is responsible for most cancer-related deaths, and, among common tumor types, melanoma is one with great potential to metastasize. Here we study the contribution of epigenetic changes to the dissemination process by analyzing the changes that occur at the DNA methylation level between primary cancer cells and metastases. We found a hypomethylation event that reactivates a cryptic transcript of the Rab GTPase activating protein TBC1D16 (TBC1D16-47 kDa; referred to hereafter as TBC1D16-47KD) to be a characteristic feature of the metastatic cascade. This short isoform of TBC1D16 exacerbates melanoma growth and metastasis both in vitro and in vivo. By combining immunoprecipitation and mass spectrometry, we identified RAB5C as a new TBC1D16 target and showed that it regulates EGFR in melanoma cells. We also found that epigenetic reactivation of TBC1D16-47KD is associated with poor clinical outcome in melanoma, while conferring greater sensitivity to BRAF and MEK inhibitors.

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Acknowledgements

We thank the patients and their families. The research leading to these results has received funding from the European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement no. PIAPP-GA-2009-230614–Target-Melanoma project (F.P., J.O., W.M.G., M.E.), the Worldwide Cancer Research grant reference no. 15-0354 (M.E.), the European Research Council Advanced grant no. 268626–EPINORC project (M.E.), the Ministerio de Ciencia e Innovacion grant numbers SAF2011-22803 (M.E.) and FIS PI13-01339 (A. Villanueva), the CRUK Manchester Institute (C5759/A12328 to R.M.), the Wellcome Trust (100282/Z/12/Z to R.M.), the Cellex Foundation (M.E.) and the Health and Science Departments of the Catalan Government Generalitat de Catalunya 2005-SGR00727 (A. Villanueva) and 2014-SGR 633 (M.E.). M.V. was supported by a Formacion de Profesorado Universitario fellowship from the Spanish Ministry of Education. We thank the staff of the Animal Core Facility of Bellvitge Biomedical Research Institute for mouse care and maintenance. M.E. is an Institucio Catalana de Recerca i Estudis Avançats Research Professor.

Author information

Affiliations

  1. Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain.

    • Miguel Vizoso
    • , Humberto J Ferreira
    • , Paula Lopez-Serra
    • , F Javier Carmona
    • , Anna Martínez-Cardús
    • , Sonia Guil
    • , Catia Moutinho
    • , Julia Liz
    • , Anna Portela
    • , Holger Heyn
    • , Sebastian Moran
    •  & Manel Esteller
  2. Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester, UK.

    • Maria Romina Girotti
    •  & Richard Marais
  3. Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain.

    • Alberto Villanueva
    •  & Maria Martinez-Iniesta
  4. Department of Pathological Anatomy, Bellvitge University Hospital, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain.

    • August Vidal
  5. Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain.

    • Jose L Manzano
  6. Pathology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain.

    • Maria Teresa Fernandez-Figueras
  7. Medical Oncology Service, Vall d'Hebron University Hospital, Barcelona, Catalonia, Spain.

    • Elena Elez
    •  & Eva Muñoz-Couselo
  8. Dermatology Service, Hospital La Fe, Universidad de Valencia, Valencia, Spain.

    • Rafael Botella-Estrada
  9. Medical Oncology Service, Hospital General, Valencia, Spain.

    • Alfonso Berrocal
  10. Department of Pathology, University Hospital of Uppsala, Uppsala, Sweden.

    • Fredrik Pontén
  11. Translational Cell & Tissue Pathology, Katholieke Universiteit Leuven, Leuven, Belgium.

    • Joost van den Oord
  12. University College Dublin School of Biomolecular and Biomedical Science, University College Dublin Conway Institute, University College Dublin, Belfield, Dublin, Ireland.

    • William M Gallagher
  13. Center for Melanoma, Massachusetts General Hospital Cancer Center, Boston, Massachusetts.

    • Dennie T Frederick
    •  & Keith T Flaherty
  14. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Ultan McDermott
  15. University of Manchester, Christie National Health Service Foundation Trust, Manchester, UK.

    • Paul Lorigan
  16. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.

    • Manel Esteller
  17. Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.

    • Manel Esteller

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Contributions

M.V. and M.E. conceived the study and wrote the manuscript. M.V. performed most experiments with the help of H.J.F., P.L.-S., F.J.C., S.G., C.M., J.L., A.P., H.H. and S.M. A.Vidal and A. Villanueva, together with M.M.-I., performed the mouse studies. A.M.-C., M.R.G., J.L.M., M.T.F.-F., E.E., E.M.-C., R.B.-E., A.B., F.P., J.v.d.O., W.M.G., D.T.F., K.T.F., U.M., P.L. and R.M. analyzed the clinical outcome and drug response data and provided conceptual input. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Manel Esteller.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures and Text

    Supplementary Figures 1–12 & Supplementary Tables 1–3

Excel files

  1. 1.

    Supplementary Data 1

    2,620 CpGs most divergent between primary and metatatic tumor cell lines.

  2. 2.

    Supplementary Data 2

    CpGs located outside CpG islands most divergent between primary and metastatic tumor cell lines.

  3. 3.

    Supplementary Data 3

    DNA methylation profile of the TBC1D16-45/47KD promoter CpG island according to the DNA methylation microarray values in 36 melanoma cell lines.

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DOI

https://doi.org/10.1038/nm.3863

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