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


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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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.

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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.

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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.

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Correspondence to Annie Huang or Jacek Majewski or Nada Jabado.

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The authors declare no competing financial interests.

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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)

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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

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