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Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations

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Abstract

The majority of patients with neuroblastoma have tumors that initially respond to chemotherapy, but a large proportion will experience therapy-resistant relapses. The molecular basis of this aggressive phenotype is unknown. Whole-genome sequencing of 23 paired diagnostic and relapse neuroblastomas showed clonal evolution from the diagnostic tumor, with a median of 29 somatic mutations unique to the relapse sample. Eighteen of the 23 relapse tumors (78%) showed mutations predicted to activate the RAS-MAPK pathway. Seven of these events were detected only in the relapse tumor, whereas the others showed clonal enrichment. In neuroblastoma cell lines, we also detected a high frequency of activating mutations in the RAS-MAPK pathway (11/18; 61%), and these lesions predicted sensitivity to MEK inhibition in vitro and in vivo. Our findings provide a rationale for genetic characterization of relapse neuroblastomas and show that RAS-MAPK pathway mutations may function as a biomarker for new therapeutic approaches to refractory disease.

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Figure 1: Mutational spectra of diagnostic and relapsed neuroblastomas.
Figure 2: RAS-MAPK pathway mutations reside within major relapsed neuroblastoma subclones.
Figure 3: Sensitivity of neuroblastoma cell line models to MEK inhibition therapy.

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  • 20 July 2015

    In the version of this article initially published online, affiliation 30 stating that "These authors jointly supervised this work" was incorrectly omitted for author Jan J. Molenaar. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

The authors would like to thank N. Ross for sample preparation and quality control. This study was supported in part by US National Institutes of Health grants RC1MD004418 to the TARGET consortium and CA98543 and CA98413 to the Children's Oncology Group and was supported in part by a grant throughout the University of Pennsylvania Genome Frontiers Institute. In addition, this project was funded in part with federal funds from the National Cancer Institute, US National Institutes of Health, under contract HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services nor does mention of trade names, commercial products or organizations imply endorsement by the US government. The binimetinib xenograft studies were supported through a research collaborative agreement between the Children's Hospital of Philadelphia and Novartis Pharmaceuticals. In France, this study was supported by the Annenberg Foundation and the Nelia and Amadeo Barletta Foundation. Funding was also obtained from SiRIC/INCa (grant INCa-DGOS-4654) and from the Comité d'Evaluation et Suivi des Projets de Recherche de Transfert (CEST) of Institut Curie. This study was also funded by the Associations Enfants et Santé, Association Hubert Gouin Enfance et Cancer, Les Bagouz à Manon and Les Amis de Claire. Deep sequencing experiments were conducted on the ICGex next-generation sequencing platform at the Institut Curie funded by the EQUIPEX Investissements d'Avenir program (ANR-10-EQPX-03) and ANR10-INBS-09-08 from the Agence Nationale de le Recherche and by the Canceropôle Ile-de-France. In the Netherlands, this study was supported by grants from the Villa Joep Foundation, the Kinderen Kankervrij Foundation and the Netherlands Cancer Foundation.

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Contributions

J.M.M., J.J.M. and G.S. co-coordinated the project. T.F.E., D.A.O., V.B., J. Koster, R.V., G.S., J.J.M. and J.M.M. prepared the manuscript. D.A.O., J. Koster, L.C.D., V.B., N.B.B., P.L.-N., S.J.D., T.J.P., E.F.A., J.S.W., S.Z., S.A., T.B.K.W., D.A.Z. and A.N. generated microarray and/or next-generation sequencing data and/or performed computational data analysis. T.F.E., L.S.H., J.R. and J.M.M. conceived drug testing and gene manipulation experiments and analyzed the data. P.v.S., M.E.E., E.L., V.C., A.B. and M.C. performed sample preparation. L.S.H., J.R., L.S., A.H., M.E.M.D. and T.F.E. contributed to in vitro drug testing and manipulation experiments. A.B., M.C., P.L.-N., D.A.O., T.J.P., E.v.W. and C.E.v.d.S. performed subclonal detection of mutational and structural variants. J.M.G.-F., M.D.H., E.M.W., J.H.S., G.A.T., H.N.C., J.M. and V.C. contributed patient tissue and/or other biological reagents. M.A.S., J.M.G.A., D.S.G., J. Khan and J.M.M. organized the US neuroblastoma TARGET consortium sequencing effort. J.J.M., R.V., J. Koster. and H.N.C. organized the Dutch consortium sequencing effort. G.S., J.M., I.J.-L. and O.D. organized the French consortium sequencing effort.

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Correspondence to Gudrun Schleiermacher or Jan J Molenaar or John M Maris.

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Competing interests

J.M.M. has commercial research grants from Novartis Pharmaceuticals and GlaxoSmithKline. H.N.C. is employed by Roche.

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Eleveld, T., Oldridge, D., Bernard, V. et al. Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations. Nat Genet 47, 864–871 (2015). https://doi.org/10.1038/ng.3333

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