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An in vivo screen identifies ependymoma oncogenes and tumor-suppressor genes

Nature Genetics volume 47, pages 878–887 (2015)Cite this article

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Abstract

Cancers are characterized by non-random chromosome copy number alterations that presumably contain oncogenes and tumor-suppressor genes (TSGs). The affected loci are often large, making it difficult to pinpoint which genes are driving the cancer. Here we report a cross-species in vivo screen of 84 candidate oncogenes and 39 candidate TSGs, located within 28 recurrent chromosomal alterations in ependymoma. Through a series of mouse models, we validate eight new ependymoma oncogenes and ten new ependymoma TSGs that converge on a small number of cell functions, including vesicle trafficking, DNA modification and cholesterol biosynthesis, identifying these as potential new therapeutic targets.

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Figure 1: Candidate ependymoma oncogenes and TSGs.
Figure 2: In vivo screen of candidate ependymoma oncogenes.
Figure 3: Enrichment of candidate oncogenes in NSC pool-derived tumors.
Figure 4: Validation of ependymoma oncogenes.
Figure 5: In vivo ependymoma TSG screen.
Figure 6: Ependymoma oncogene and TSG trafficking of growth factor receptors.
Figure 7: Suppression of cholesterol biosynthesis in cerebral ependymomas.

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Acknowledgements

We are grateful to F.B. Gertler (Massachusetts Institute of Technology) and S. Gupton (University of North Carolina) for the generous gift of the VAMP7-phlorin construct and the staffs of the Hartwell Center for Bioinformatics and Biotechnology, the Small Animal Imaging Center, the Animal Resources Center, the Cell and Tissue Imaging Center, and the Flow Cytometry and Cell Sorting Shared Resource at St. Jude Children's Research Hospital for technical assistance. This work was supported by grants from the US National Institutes of Health (R01CA129541, P01CA96832 and P30CA021765, R.J.G.), by the Collaborative Ependymoma Research Network (CERN) and by the American Lebanese Syrian Associated Charities (ALSAC).

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Author notes

  1. Kumarasamypet M Mohankumar and David S Currle: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Kumarasamypet M Mohankumar, David S Currle, Elsie White, Nidal Boulos, Jason Dapper, Christopher Eden, Birgit Nimmervoll, Radhika Thiruvenkatam & Richard J Gilbertson

  2. Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Michele Connelly & Tanya A Kranenburg

  3. Hartwell Center for Biotechnology and Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Geoffrey Neale & Scott Olsen

  4. Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Yong-Dong Wang & David Finkelstein

  5. Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Karen Wright & Richard J Gilbertson

  6. Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Kirti Gupta & David W Ellison

  7. Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA

    Arzu Onar Thomas

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  1. Kumarasamypet M Mohankumar
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Contributions

K.M.M. and D.S.C. conducted the great majority of the experiments and contributed to their design. E.W., N.B., J.D., C.E., B.N., R.T., M.C. and T.A.K. conducted mouse experimental work. G.N., S.O., Y.-D.W. and D.F. conducted microarray and deep sequencing studies. K.W. assisted with human genomic analyses. K.G. and D.W.E. conducted all neuropathological reviews. A.O.T. conducted all statistical analyses. R.J.G. conceived, designed and oversaw the study. All authors contributed to writing of the manuscript.

Corresponding author

Correspondence to Richard J Gilbertson.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Relative gain and loss of loci harboring ependymoma candidate oncogenes and TSGs in human cancers.

Heat maps report the relative gain and loss of loci harboring candidate ependymoma oncogenes and TSGs, respectively, across 3,116 samples of 9 different human tumors reported on the COSMIC database.

Supplementary Figure 2 Relative gain and loss of validated oncogenes and TSGs and non-validated candidates in human cancer.

Relative gain and loss of validated oncogenes and TSGs and non-validated candidates across 3,116 samples of 9 different human tumors reported on the COSMIC database (boxes extend from the 25th to 75th percentiles and contain a horizontal line marking the median value; whiskers extend to the maximum and minimum values).

Supplementary Figure 3 AGDEX analysis of human and mouse ependymomas.

AGDEX analysis comparing the transcriptomic similarities of human cerebral ependymoma positive or negative for C11orf95-RELA fusion with our three new mouse models of cerebral ependymoma driven by BCL7C, RAB3A or ZNF668.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Note. (PDF 318 kb)

Supplementary Table 1

Candidate ependymoma oncogenes detected by integrated gene expression and copy number analysis of human ependymoma. (XLS 41 kb)

Supplementary Table 2

Candidate ependymoma tumor-suppressor genes detected by integrated gene expression and copy number analysis of human ependymoma. (XLS 54 kb)

Supplementary Table 3

Diploid control genes that are not amplified or overexpressed in human ependymoma. (XLS 33 kb)

Supplementary Table 4

Details of individual mice harboring pools 1–11 of NSCs carrying candidate oncogenes. (XLS 67 kb)

Supplementary Table 5

Details of individual mice harboring NSCs carrying diploid control genes. (XLS 36 kb)

Supplementary Table 6

Details of individual mice harboring NSCs carrying singlecandidate oncogenes. (XLS 96 kb)

Supplementary Table 7

The top most positively and negatively enriched gene sets common to mouse ependymomas driven by RAB3A, BCL7C and ZNF668 relative to cNSCs, detected by GSEA. (XLS 95 kb)

Supplementary Table 8

Details of individual mice harboring pools 1–4 of EPHB2-transduced cNSCs carrying shRNAs targeting candidate TSGs. (XLS 43 kb)

Supplementary Table 9

Validated ependymoma oncogenes and tumor-suppressor genes identified in in vivo screens. (XLS 33 kb)

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Mohankumar, K., Currle, D., White, E. et al. An in vivo screen identifies ependymoma oncogenes and tumor-suppressor genes. Nat Genet 47, 878–887 (2015). https://doi.org/10.1038/ng.3323

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