Abstract
We used high-resolution SNP genotyping to identify regions of genomic gain and loss in the genomes of 212 medulloblastomas, malignant pediatric brain tumors. We found focal amplifications of 15 known oncogenes and focal deletions of 20 known tumor suppressor genes (TSG), most not previously implicated in medulloblastoma. Notably, we identified previously unknown amplifications and homozygous deletions, including recurrent, mutually exclusive, highly focal genetic events in genes targeting histone lysine methylation, particularly that of histone 3, lysine 9 (H3K9). Post-translational modification of histone proteins is critical for regulation of gene expression, can participate in determination of stem cell fates and has been implicated in carcinogenesis. Consistent with our genetic data, restoration of expression of genes controlling H3K9 methylation greatly diminishes proliferation of medulloblastoma in vitro. Copy number aberrations of genes with critical roles in writing, reading, removing and blocking the state of histone lysine methylation, particularly at H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma.
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Acknowledgements
We thank the individuals and families who agreed to take part in these studies. We thank S. Egan, J. Ellis and R. Bremner for critical review of the manuscript. We thank R. Wechsler-Reya (Duke), A.M. Kenney (Memorial-Sloan Kettering) and D. Rowitch (University of California San Francisco) for reagents and helpful discussions. We are grateful to K. Helin (University of Copenhagen) for providing JMJD2C expression constructs. We thank P. Paroutis for artwork and S. Archer for editing. We are grateful to C. Marshall and J. Wei for assistance with copy number analysis. This work was supported by the Canadian Cancer Society and the Pediatric Brain Tumor Foundation. M.D.T. is supported by a Sontag Foundation Distinguished Scholar award. Additional research support was obtained from the Hospital for Sick Children Foundation, The Neurosurgery Research and Education Foundation, BRAINCHILD, the 407 Express Toll Route, and the Walker family. M.D.T. was supported by the Laurie Berman fund in Brain Tumor Research, the American Brain Tumor Association and a Clinician-Scientist award from the Canadian Institutes of Health Research. P.A.N. was supported by a Restracomp salary award from the Hospital for Sick Children.
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Contributions
P.A.N. coordinated and designed the study, wrote the manuscript, isolated nucleic acids from tumors, performed copy number and LOH analysis and identified regions of interest, validated copy number regions, performed qRT-PCR analyses, generated stable cell lines and retroviruses, and performed in vitro functional assays, immunoblotting, immunofluorescence, and ChIP assays. Y.N. isolated DNA from cell lines, performed copy number and LOH analysis, and validated copy number regions. X.W. built expression constructs and generated stable cell lines. L.F. identified and filtered known CNVs from the datasets. D.W.E. performed FISH and IHC on medulloblastoma TMA. S.C. performed IHC on P7 murine CB and scored medulloblastoma TMAs. S.M. performed GISTIC analysis and validated copy number regions. P.N.K. isolated DNA from tumors, performed copy number and LOH analysis, and validated copy number regions. J.P. built expression constructs, analyzed qRT-PCR data and validated copy number regions. A.D. built expression constructs. Y.S.R. performed mouse experiments. K.Z. validated copy number regions. J.M. performed animal husbandry and mouse experiments. S.W.S. provided technical advice/intellectual contribution. J.S.R. performed statistical analyses. C.G.E. performed IHC on medulloblastoma TMA. W.G., Y.G., B.L., R.G., I.F.P., R.L.H., T.V.M., C.G.C., F.B. and D.B. contributed clinical materials. R.J.G. and J.T.R. provided technical advice, intellectual contribution and helped write the manuscript. M.D.T. designed the study and experiments, interpreted the results, provided supervision, and wrote the manuscript and revisions.
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Supplementary Text and Figures
Supplementary Figures 1–4, Supplementary Methods and Supplementary Tables 4 and 5 (PDF 10194 kb)
Supplementary Note
Clinical and sample information for the medulloblastoma cohort analyzed by SNP array (XLS 38 kb)
Supplementary Table 1
Known copy number variants identified in the medulloblastoma genome (XLS 267 kb)
Supplementary Table 2
Regions of genomic gain and loss in the medulloblastoma genome (XLS 1799 kb)
Supplementary Table 3
GISTIC analysis of medulloblastoma copy number data (XLS 18 kb)
Supplementary Table 6
List of primers (XLS 11 kb)
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Northcott, P., Nakahara, Y., Wu, X. et al. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat Genet 41, 465–472 (2009). https://doi.org/10.1038/ng.336
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DOI: https://doi.org/10.1038/ng.336
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