Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

Trevor J. Pugh, Shyamal Dilhan Weeraratne, Tenley C. Archer, Daniel A. Pomeranz Krummel, Daniel Auclair, James Bochicchio, Mauricio O. Carneiro, Scott L. Carter, Kristian Cibulskis, Rachel L. Erlich, Heidi Greulich, Michael S. Lawrence, Niall J. Lennon, Aaron Mc Kenna, James Meldrim, Alex H. Ramos, Michael G. Ross, Carsten Russ, Erica Shefler, Andrey SivachenkoBrian Sogoloff, Petar Stojanov, Pablo Tamayo, Jill P. Mesirov, Vladimir Amani, Natalia Teider, Soma Sengupta, Jessica Pierre Francois, Paul A. Northcott, Michael D. Taylor, Furong Yu, Gerald R. Crabtree, Amanda G. Kautzman, Stacey B. Gabriel, Gad Getz, Natalie Jäger, David T.W. Jones, Peter Lichter, Stefan M. Pfister, Thomas M. Roberts, Matthew Meyerson, Scott L. Pomeroy, Yoon Jae Cho

Research output: Contribution to journalLetter

490 Scopus citations

Abstract

Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, β-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medulloblastoma.

Original languageEnglish (US)
Pages (from-to)106-110
Number of pages5
JournalNature
Volume488
Issue number7409
DOIs
StatePublished - Aug 2 2012

ASJC Scopus subject areas

  • General

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    Pugh, T. J., Weeraratne, S. D., Archer, T. C., Pomeranz Krummel, D. A., Auclair, D., Bochicchio, J., Carneiro, M. O., Carter, S. L., Cibulskis, K., Erlich, R. L., Greulich, H., Lawrence, M. S., Lennon, N. J., Mc Kenna, A., Meldrim, J., Ramos, A. H., Ross, M. G., Russ, C., Shefler, E., ... Cho, Y. J. (2012). Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature, 488(7409), 106-110. https://doi.org/10.1038/nature11329