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.
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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.
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Supplementary Figures and Text
Supplementary Figures 1–12 & Supplementary Tables 1–3 (PDF 3464 kb)
Supplementary Data 1
2,620 CpGs most divergent between primary and metatatic tumor cell lines. (XLSX 322 kb)
Supplementary Data 2
CpGs located outside CpG islands most divergent between primary and metastatic tumor cell lines. (XLSX 12 kb)
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. (XLSX 14 kb)
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Vizoso, M., Ferreira, H., Lopez-Serra, P. et al. Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR. Nat Med 21, 741–750 (2015). https://doi.org/10.1038/nm.3863
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DOI: https://doi.org/10.1038/nm.3863
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