The integrated landscape of driver genomic alterations in glioblastoma

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Abstract

Glioblastoma is one of the most challenging forms of cancer to treat. Here we describe a computational platform that integrates the analysis of copy number variations and somatic mutations and unravels the landscape of in-frame gene fusions in glioblastoma. We found mutations with loss of heterozygosity in LZTR1, encoding an adaptor of CUL3-containing E3 ligase complexes. Mutations and deletions disrupt LZTR1 function, which restrains the self renewal and growth of glioma spheres that retain stem cell features. Loss-of-function mutations in CTNND2 target a neural-specific gene and are associated with the transformation of glioma cells along the very aggressive mesenchymal phenotype. We also report recurrent translocations that fuse the coding sequence of EGFR to several partners, with EGFR-SEPT14 being the most frequent functional gene fusion in human glioblastoma. EGFR-SEPT14 fusions activate STAT3 signaling and confer mitogen independence and sensitivity to EGFR inhibition. These results provide insights into the pathogenesis of glioblastoma and highlight new targets for therapeutic intervention.

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Figure 1: Chromosome view of validated GBM genes scoring at the top of each of the three categories by MutComFocal.
Figure 2: Interaction with CUL3 and protein stability of wild-type and mutant LZTR1.
Figure 3: Functional analysis of wild-type LZTR1 and GBM-associated mutants in GBM-derived cells.
Figure 4: Expression of δ-catenin in neurons and δ-catenin–driven loss of mesenchymal markers in GBM.
Figure 5: Functional analysis of δ-catenin in mesenchymal GBM.
Figure 6: The EGFR-SEPT14 gene fusion identified by whole-transcriptome sequencing.
Figure 7: Functional analysis of the EGFR-SEPT14 fusion and the effect of inhibition of EGFR kinase on glioma growth.

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Acknowledgements

This work was supported by National Cancer Institute grants R01CA101644 and R01CA131126 (A.L.) and R01CA085628 and R01CA127643 (A.I.), the Stewart Foundation (R.R.), the Partnership for Cure (R.R.), US National Institutes of Health (NIH) grant NIH 1 P50 MH094267-01 (R.R.), the Lymphoma Research Foundation (R.R.), NIH 1 U54 CA121852-05 (R.R.), NIH 1R01CA164152-01 (R.R.), the Leukemia and Lymphoma Society (R.R.), the Canadian Cancer Society (G.G.P.), the Cancer Research Society (G.G.P.), the National Institute of Neurological Disorders and Stroke R01NS061776 (A.I.) and a grant from The Chemotherapy Foundation (A.I.). G.F. was supported by grants from the Associazione Italiana per la Ricerca sul Cancro and from the Italian Ministry of Health. V.F., P.Z., C.D. and F.N. are supported by fellowships from the Italian Ministry of Welfare/Provincia di Benevento and the Federazione Italiana Associazioni Genitori Oncoematologia Pedriatica (FIAGOP) (C.D.). We thank J. Parkinson for helpful discussions on the phylogeny of LZTR1 genes, L. Bertin for help with protein blots, J. Kroll (Tumor Biology Center, Freiburg) for the LZTR1 plasmids and M. Pagano (New York University) for CUL3 expression plasmids.

Author information

A.L., R.R. and A.I. conceived the ideas for this study. R.R. designed and supervised the computational approach, and A.L. and A.I. designed and supervised the experimental platform. A.L. performed or assisted in each step of the experimental platform. V.F., A.C., M.L., F.N. and C.D. conducted biological experiments. V.T. performed the MutComFocal analysis. J.M.C. and F.A. performed the gene fusion analysis, allele-specific expression and most of the bioinformatics analyses. P.Z. performed bioinformatics and statistical analyses. S.T.K., H.Y., R.E.M. and D.D.B. performed the human glioma xenograft analyses to evaluate the effects of EGFR inhibitors and provided human GBM specimens. A.X.J. and G.G.P. performed the modeling analysis of LZTR1. I.D. and A.H. conducted the targeted sequencing analysis. P.P., S.P., D.J.P., P.C., J.N.B., K.A., G.G., G.F. and T.M. provided tissue materials from study subjects. A.L., R.R. and A.I. wrote the manuscript with contributions from all other authors.

Correspondence to Anna Lasorella or Raul Rabadan or Antonio Iavarone.

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Frattini, V., Trifonov, V., Chan, J. et al. The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet 45, 1141–1149 (2013) doi:10.1038/ng.2734

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