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Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A, Rabadan R, Iavarone A. The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet 2013; 45:1141-9. [PMID: 23917401 PMCID: PMC3799953 DOI: 10.1038/ng.2734] [Citation(s) in RCA: 412] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 07/29/2013] [Indexed: 12/12/2022]
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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Affiliation(s)
- Veronique Frattini
- 1] Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA. [2]
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Chen CP, Huang MC, Chen YY, Chern SR, Wu PS, Su JW, Town DD, Wang W. Cri-du-chat (5p-) syndrome presenting with cerebellar hypoplasia and hypospadias: prenatal diagnosis and aCGH characterization using uncultured amniocytes. Gene 2013; 524:407-11. [PMID: 23500598 DOI: 10.1016/j.gene.2013.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 02/20/2013] [Accepted: 03/02/2013] [Indexed: 11/28/2022]
Abstract
We present prenatal diagnosis of a de novo distal deletion involving 5p(5p15.1→pter) using uncultured amniocytes in a pregnancy with cerebellar hypoplasia, hypospadias and facial dysmorphisms in the fetus. We discuss the genotype-phenotype correlation and the consequence of haploinsufficiency of CTNND2, SEMA5A, TERT, SRD5A1 and TPPP. We speculate that haploinsufficiency of SRD5A1 and TPPP may be responsible for hypospadias and cerebellar hypoplasia, respectively, in this case.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan.
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Figueroa-Romero C, Hur J, Bender DE, Delaney CE, Cataldo MD, Smith AL, Yung R, Ruden DM, Callaghan BC, Feldman EL. Identification of epigenetically altered genes in sporadic amyotrophic lateral sclerosis. PLoS One 2012; 7:e52672. [PMID: 23300739 PMCID: PMC3530456 DOI: 10.1371/journal.pone.0052672] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 11/19/2012] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a terminal disease involving the progressive degeneration of motor neurons within the motor cortex, brainstem and spinal cord. Most cases are sporadic (sALS) with unknown causes suggesting that the etiology of sALS may not be limited to the genotype of patients, but may be influenced by exposure to environmental factors. Alterations in epigenetic modifications are likely to play a role in disease onset and progression in ALS, as aberrant epigenetic patterns may be acquired throughout life. The aim of this study was to identify epigenetic marks associated with sALS. We hypothesize that epigenetic modifications may alter the expression of pathogenesis-related genes leading to the onset and progression of sALS. Using ELISA assays, we observed alterations in global methylation (5 mC) and hydroxymethylation (5 HmC) in postmortem sALS spinal cord but not in whole blood. Loci-specific differentially methylated and expressed genes in sALS spinal cord were identified by genome-wide 5mC and expression profiling using high-throughput microarrays. Concordant direction, hyper- or hypo-5mC with parallel changes in gene expression (under- or over-expression), was observed in 112 genes highly associated with biological functions related to immune and inflammation response. Furthermore, literature-based analysis identified potential associations among the epigenes. Integration of methylomics and transcriptomics data successfully revealed methylation changes in sALS spinal cord. This study represents an initial identification of epigenetic regulatory mechanisms in sALS which may improve our understanding of sALS pathogenesis for the identification of biomarkers and new therapeutic targets.
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Affiliation(s)
- Claudia Figueroa-Romero
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Junguk Hur
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Diane E. Bender
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Colin E. Delaney
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael D. Cataldo
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea L. Smith
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raymond Yung
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Douglas M. Ruden
- Institute of Environmental Health Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Brian C. Callaghan
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Eva L. Feldman
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, United States of America
- National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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