Skip to main content
Top
Published in: Current Neurology and Neuroscience Reports 3/2011

01-06-2011

Genomic Profiles of Glioma

Author: Cameron Brennan

Published in: Current Neurology and Neuroscience Reports | Issue 3/2011

Login to get access

Abstract

Recent large-scale genomic profiling studies of glioma have yielded a proliferation of candidate subclasses, biomarkers and therapeutic targets for investigation. Some findings, such as that of IDH mutation in low-grade gliomas and secondary glioblastoma (GBM), fit well into established notions of different routes of gliomagenesis. Other results, such as the division of primary GBM based on signaling pathway alterations, suggest new pathogenetic routes with implications for treatment. The analysis of this data is still in the early stage. Nonetheless, several preliminary findings merit consideration in the development and interpretation of current clinical trials.
Literature
1.
go back to reference The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061–8.CrossRef The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061–8.CrossRef
2.
go back to reference Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008;321:1807–12.PubMedCrossRef Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008;321:1807–12.PubMedCrossRef
3.
go back to reference Louis DN, Ohgaki H, Wiestler OD, et al. The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007;114(2):97–109.PubMedCrossRef Louis DN, Ohgaki H, Wiestler OD, et al. The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007;114(2):97–109.PubMedCrossRef
4.
go back to reference Huse JT, Holland EC. Targeting brain cancer: advances in the molecular pathology of malignant glioma and medulloblastoma. Nat Rev Cancer. 2010;10(5):319–31.PubMedCrossRef Huse JT, Holland EC. Targeting brain cancer: advances in the molecular pathology of malignant glioma and medulloblastoma. Nat Rev Cancer. 2010;10(5):319–31.PubMedCrossRef
5.
go back to reference Jaeckle KA, Decker PA, Ballman KV, et al. Transformation of low grade glioma and correlation with outcome: an NCCTG database analysis. Journal of neuro-oncology. Dec 12 2010. Jaeckle KA, Decker PA, Ballman KV, et al. Transformation of low grade glioma and correlation with outcome: an NCCTG database analysis. Journal of neuro-oncology. Dec 12 2010.
6.
go back to reference Furnari FB, Fenton T, Bachoo RM, et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev. 2007;21(21):2683–710.PubMedCrossRef Furnari FB, Fenton T, Bachoo RM, et al. Malignant astrocytic glioma: genetics, biology, and paths to treatment. Genes Dev. 2007;21(21):2683–710.PubMedCrossRef
7.
go back to reference Attolini CS, Cheng YK, Beroukhim R, et al. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci USA. 2010;107(41):17604–9.PubMedCrossRef Attolini CS, Cheng YK, Beroukhim R, et al. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci USA. 2010;107(41):17604–9.PubMedCrossRef
8.
go back to reference Caskey L, Wang R, Bruner J, Yung W, Zhang W. Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling. Cancer Research. Jan 1 1999. Caskey L, Wang R, Bruner J, Yung W, Zhang W. Reactivation of insulin-like growth factor binding protein 2 expression in glioblastoma multiforme: a revelation by parallel gene expression profiling. Cancer Research. Jan 1 1999.
9.
go back to reference Fuller GN, Hess KR, Rhee C, et al. Molecular Classification of Human Diffuse Gliomas by Multidimensional Scaling Analysis of Gene Expression Profiles Parallels Morphology-Based Classification, Correlates with Survival, and Reveals Clinically-Relevant Novel Glioma Subsets. Brain Pathol. 2002;12:108–16.PubMedCrossRef Fuller GN, Hess KR, Rhee C, et al. Molecular Classification of Human Diffuse Gliomas by Multidimensional Scaling Analysis of Gene Expression Profiles Parallels Morphology-Based Classification, Correlates with Survival, and Reveals Clinically-Relevant Novel Glioma Subsets. Brain Pathol. 2002;12:108–16.PubMedCrossRef
10.
go back to reference Kim S, Dougherty ER, Shmulevich I, et al. Identification of combination gene sets for glioma classification. Mol Cancer Ther. 2002;1:1229–36.PubMed Kim S, Dougherty ER, Shmulevich I, et al. Identification of combination gene sets for glioma classification. Mol Cancer Ther. 2002;1:1229–36.PubMed
11.
go back to reference Rickman D, Bobek M, Misek D, Kuick R, Blaivas M. Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. Cancer Research. Jan 1 2001. Rickman D, Bobek M, Misek D, Kuick R, Blaivas M. Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis. Cancer Research. Jan 1 2001.
12.
go back to reference Sallinen S, Sallinen P, Haapasalo H, Helin H. Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Research. Jan 1 2000. Sallinen S, Sallinen P, Haapasalo H, Helin H. Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Research. Jan 1 2000.
13.
go back to reference Shai R, Shi T, Kremen T, Horvath S, Liau L. Gene expression profiling identifies molecular subtypes of gliomas. Oncogene. 2003;22:4918–23.PubMedCrossRef Shai R, Shi T, Kremen T, Horvath S, Liau L. Gene expression profiling identifies molecular subtypes of gliomas. Oncogene. 2003;22:4918–23.PubMedCrossRef
14.
go back to reference Somasundaram K, Reddy SP, Vinnakota K, et al. Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene. 2005;24(47):7073–83.PubMedCrossRef Somasundaram K, Reddy SP, Vinnakota K, et al. Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene. 2005;24(47):7073–83.PubMedCrossRef
15.
go back to reference Tanwar M, Gilbert M, Holland E. Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. Cancer Research. Jan 1 2002. Tanwar M, Gilbert M, Holland E. Gene expression microarray analysis reveals YKL-40 to be a potential serum marker for malignant character in human glioma. Cancer Research. Jan 1 2002.
16.
go back to reference Phillips HS, Kharbanda S, Chen R, et al. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell. 2006;9(3):157–73.PubMedCrossRef Phillips HS, Kharbanda S, Chen R, et al. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell. 2006;9(3):157–73.PubMedCrossRef
17.
go back to reference Freije W, Castro-Vargas F, Fang Z, et al. Gene expression profiling of gliomas strongly predicts survival. Cancer Res. 2004;64(18):6503.PubMedCrossRef Freije W, Castro-Vargas F, Fang Z, et al. Gene expression profiling of gliomas strongly predicts survival. Cancer Res. 2004;64(18):6503.PubMedCrossRef
18.
go back to reference Nigro J, Misra A, Zhang L, Smirnov I, Colman H. Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Research. Jan 1 2005. Nigro J, Misra A, Zhang L, Smirnov I, Colman H. Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Research. Jan 1 2005.
19.
go back to reference • Verhaak RGW, Hoadley KA, Purdom E, et al. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98–110. This paper defines the major transcriptomal and molecular subclasses of primary GBM arising from TCGA preliminary analysis.PubMedCrossRef • Verhaak RGW, Hoadley KA, Purdom E, et al. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010;17(1):98–110. This paper defines the major transcriptomal and molecular subclasses of primary GBM arising from TCGA preliminary analysis.PubMedCrossRef
20.
go back to reference Brennan C, Momota H, Hambardzumyan D, et al. Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations. PLoS ONE. 2009;4(11):1–10.CrossRef Brennan C, Momota H, Hambardzumyan D, et al. Glioblastoma Subclasses Can Be Defined by Activity among Signal Transduction Pathways and Associated Genomic Alterations. PLoS ONE. 2009;4(11):1–10.CrossRef
21.
go back to reference Chen G, Gharib TG, Huang CC, et al. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics. 2002;1(4):304–13.PubMedCrossRef Chen G, Gharib TG, Huang CC, et al. Discordant protein and mRNA expression in lung adenocarcinomas. Mol Cell Proteomics. 2002;1(4):304–13.PubMedCrossRef
22.
go back to reference Guo Y, Xiao P, Lei S, et al. How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai). 2008;40(5):426–36.CrossRef Guo Y, Xiao P, Lei S, et al. How is mRNA expression predictive for protein expression? A correlation study on human circulating monocytes. Acta Biochim Biophys Sin (Shanghai). 2008;40(5):426–36.CrossRef
23.
go back to reference Huse J, Phillips H, Brennan C. Molecular Subclassification of Diffuse Gliomas: Seeing Order in the Chaos. Glia. 2011;in press. Huse J, Phillips H, Brennan C. Molecular Subclassification of Diffuse Gliomas: Seeing Order in the Chaos. Glia. 2011;in press.
24.
go back to reference Paugh BS, Qu C, Jones C, et al. Integrated Molecular Genetic Profiling of Pediatric High-Grade Gliomas Reveals Key Differences With the Adult Disease. J Clin Oncol. 2010;28(18):3061–8.PubMedCrossRef Paugh BS, Qu C, Jones C, et al. Integrated Molecular Genetic Profiling of Pediatric High-Grade Gliomas Reveals Key Differences With the Adult Disease. J Clin Oncol. 2010;28(18):3061–8.PubMedCrossRef
25.
go back to reference • Dang L, White DW, Gross S, et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2009;462(7274):739–744. This paper describes the nature of IDH mutation in cancer and investigates the biological effects.CrossRef • Dang L, White DW, Gross S, et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2009;462(7274):739–744. This paper describes the nature of IDH mutation in cancer and investigates the biological effects.CrossRef
26.
go back to reference Bleeker FE, Atai NA, Lamba S, et al. The prognostic IDH1(R132) mutation is associated with reduced NADP+−dependent IDH activity in glioblastoma. Acta Neuropathol. 2010;119(4):487–94.PubMedCrossRef Bleeker FE, Atai NA, Lamba S, et al. The prognostic IDH1(R132) mutation is associated with reduced NADP+−dependent IDH activity in glioblastoma. Acta Neuropathol. 2010;119(4):487–94.PubMedCrossRef
27.
go back to reference Balss J, Meyer J, Mueller W, Korshunov A, Hartmann C, von Deimling A. Analysis of the IDH1 codon 132 mutation in brain tumors. Acta Neuropathol. 2008;116(6):597–602.PubMedCrossRef Balss J, Meyer J, Mueller W, Korshunov A, Hartmann C, von Deimling A. Analysis of the IDH1 codon 132 mutation in brain tumors. Acta Neuropathol. 2008;116(6):597–602.PubMedCrossRef
28.
go back to reference Yan H, Parsons DW, Jin G, et al. IDH1 and IDH2 mutations in gliomas. N Engl J Med. 2009;360(8):765–73.PubMedCrossRef Yan H, Parsons DW, Jin G, et al. IDH1 and IDH2 mutations in gliomas. N Engl J Med. 2009;360(8):765–73.PubMedCrossRef
29.
go back to reference Hartmann C, Meyer J, Balss J, et al. Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas. Acta Neuropathol. 2009;118(4):469–74.PubMedCrossRef Hartmann C, Meyer J, Balss J, et al. Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas. Acta Neuropathol. 2009;118(4):469–74.PubMedCrossRef
30.
go back to reference Labussiere M, Idbaih A, Wang XW, et al. All the 1p19q codeleted gliomas are mutated on IDH1 or IDH2. Neurology. 2010;74(23):1886–90.PubMedCrossRef Labussiere M, Idbaih A, Wang XW, et al. All the 1p19q codeleted gliomas are mutated on IDH1 or IDH2. Neurology. 2010;74(23):1886–90.PubMedCrossRef
31.
go back to reference Dang L, Jin S, Su SM. IDH mutations in glioma and acute myeloid leukemia. Trends Mol Med. 2010;16(9):387–97.PubMedCrossRef Dang L, Jin S, Su SM. IDH mutations in glioma and acute myeloid leukemia. Trends Mol Med. 2010;16(9):387–97.PubMedCrossRef
32.
go back to reference • Noushmehr H, Weisenberger DJ, Diefes K, et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010;17(5):510–522. This paper discusses the discovery of G-CIMP of GBM, its prognostic power, and its relationship to IDH mutation.PubMedCrossRef • Noushmehr H, Weisenberger DJ, Diefes K, et al. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell. 2010;17(5):510–522. This paper discusses the discovery of G-CIMP of GBM, its prognostic power, and its relationship to IDH mutation.PubMedCrossRef
33.
go back to reference Figueroa ME, Abdel-Wahab O, Lu C, et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553–67.PubMedCrossRef Figueroa ME, Abdel-Wahab O, Lu C, et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553–67.PubMedCrossRef
34.
go back to reference Weller M, Felsberg J, Hartmann C, et al. Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J Clin Oncol. 2009;27(34):5743–50.PubMedCrossRef Weller M, Felsberg J, Hartmann C, et al. Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J Clin Oncol. 2009;27(34):5743–50.PubMedCrossRef
35.
go back to reference •• Hartmann C, Hentschel B, Wick W, et al. Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas. Acta Neuropathol. 2010;120(6):707–718. This study investigates the prognostic power of IDH mutation in relation to established prognostic variables in 382 patients with anaplastic astrocytoma or GBM. The results suggest that IDH mutation may be the most significant predictor of survival, comparable to or surpassing WHO III/IV histologic grade.PubMedCrossRef •• Hartmann C, Hentschel B, Wick W, et al. Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas. Acta Neuropathol. 2010;120(6):707–718. This study investigates the prognostic power of IDH mutation in relation to established prognostic variables in 382 patients with anaplastic astrocytoma or GBM. The results suggest that IDH mutation may be the most significant predictor of survival, comparable to or surpassing WHO III/IV histologic grade.PubMedCrossRef
36.
go back to reference Houillier C, Wang X, Kaloshi G, et al. IDH1 or IDH2 mutations predict longer survival and response to temozolomide in low-grade gliomas. Neurology. 2010;75(17):1560–6.PubMedCrossRef Houillier C, Wang X, Kaloshi G, et al. IDH1 or IDH2 mutations predict longer survival and response to temozolomide in low-grade gliomas. Neurology. 2010;75(17):1560–6.PubMedCrossRef
37.
go back to reference van den Bent MJ, Dubbink HJ, Marie Y, et al. IDH1 and IDH2 mutations are prognostic but not predictive for outcome in anaplastic oligodendroglial tumors: a report of the European Organization for Research and Treatment of Cancer Brain Tumor Group. Clin Cancer Res. 2010;16(5):1597–604.PubMedCrossRef van den Bent MJ, Dubbink HJ, Marie Y, et al. IDH1 and IDH2 mutations are prognostic but not predictive for outcome in anaplastic oligodendroglial tumors: a report of the European Organization for Research and Treatment of Cancer Brain Tumor Group. Clin Cancer Res. 2010;16(5):1597–604.PubMedCrossRef
38.
go back to reference Capper D, Weissert S, Balss J, et al. Characterization of R132H mutation-specific IDH1 antibody binding in brain tumors. Brain Pathol. 2010;20(1):245–54.PubMedCrossRef Capper D, Weissert S, Balss J, et al. Characterization of R132H mutation-specific IDH1 antibody binding in brain tumors. Brain Pathol. 2010;20(1):245–54.PubMedCrossRef
39.
go back to reference Capper D, Zentgraf H, Balss J, Hartmann C, von Deimling A. Monoclonal antibody specific for IDH1 R132H mutation. Acta Neuropathol. 2009;118(5):599–601.PubMedCrossRef Capper D, Zentgraf H, Balss J, Hartmann C, von Deimling A. Monoclonal antibody specific for IDH1 R132H mutation. Acta Neuropathol. 2009;118(5):599–601.PubMedCrossRef
40.
go back to reference Kato Y, Jin G, Kuan CT, McLendon RE, Yan H, Bigner DD. A monoclonal antibody IMab-1 specifically recognizes IDH1R132H, the most common glioma-derived mutation. Biochem Biophys Res Commun. 2009;390(3):547–51.PubMedCrossRef Kato Y, Jin G, Kuan CT, McLendon RE, Yan H, Bigner DD. A monoclonal antibody IMab-1 specifically recognizes IDH1R132H, the most common glioma-derived mutation. Biochem Biophys Res Commun. 2009;390(3):547–51.PubMedCrossRef
41.
go back to reference Camelo-Piragua S, Jansen M, Ganguly A, Kim JC, Louis DN, Nutt CL. Mutant IDH1-specific immunohistochemistry distinguishes diffuse astrocytoma from astrocytosis. Acta Neuropathol. 2010;119(4):509–11.PubMedCrossRef Camelo-Piragua S, Jansen M, Ganguly A, Kim JC, Louis DN, Nutt CL. Mutant IDH1-specific immunohistochemistry distinguishes diffuse astrocytoma from astrocytosis. Acta Neuropathol. 2010;119(4):509–11.PubMedCrossRef
42.
go back to reference Stupp R, Hegi ME, Mason WP, et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 2009;10(5):459–66.PubMedCrossRef Stupp R, Hegi ME, Mason WP, et al. Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 2009;10(5):459–66.PubMedCrossRef
43.
go back to reference Weller M, Stupp R, Reifenberger G, et al. MGMT promoter methylation in malignant gliomas: ready for personalized medicine? Nat Rev Neurol. 2010;6(1):39–51.PubMedCrossRef Weller M, Stupp R, Reifenberger G, et al. MGMT promoter methylation in malignant gliomas: ready for personalized medicine? Nat Rev Neurol. 2010;6(1):39–51.PubMedCrossRef
44.
go back to reference Brandes AA, Franceschi E, Tosoni A, et al. MGMT promoter methylation status can predict the incidence and outcome of pseudoprogression after concomitant radiochemotherapy in newly diagnosed glioblastoma patients. J Clin Oncol. 2008;26(13):2192–7.PubMedCrossRef Brandes AA, Franceschi E, Tosoni A, et al. MGMT promoter methylation status can predict the incidence and outcome of pseudoprogression after concomitant radiochemotherapy in newly diagnosed glioblastoma patients. J Clin Oncol. 2008;26(13):2192–7.PubMedCrossRef
45.
go back to reference Brandsma D, van den Bent MJ. Pseudoprogression and pseudoresponse in the treatment of gliomas. Curr Opin Neurol. 2009;22(6):633–8.PubMedCrossRef Brandsma D, van den Bent MJ. Pseudoprogression and pseudoresponse in the treatment of gliomas. Curr Opin Neurol. 2009;22(6):633–8.PubMedCrossRef
46.
go back to reference Allingham-Hawkins D, Lea A, Levine S. DecisionDx-GBM gene expression assay for prognostic testing in glioblastoma multiform. PLoS Curr. 2010;2:RRN1186.PubMedCrossRef Allingham-Hawkins D, Lea A, Levine S. DecisionDx-GBM gene expression assay for prognostic testing in glioblastoma multiform. PLoS Curr. 2010;2:RRN1186.PubMedCrossRef
Metadata
Title
Genomic Profiles of Glioma
Author
Cameron Brennan
Publication date
01-06-2011
Publisher
Current Science Inc.
Published in
Current Neurology and Neuroscience Reports / Issue 3/2011
Print ISSN: 1528-4042
Electronic ISSN: 1534-6293
DOI
https://doi.org/10.1007/s11910-011-0198-7

Other articles of this Issue 3/2011

Current Neurology and Neuroscience Reports 3/2011 Go to the issue