Assessing CpG island methylator phenotype, 1p/19q codeletion, and MGMT promoter methylation from epigenome-wide data in the biomarker cohort of the NOA-04 trial

Neuro-Oncology

Volumn 16, Issue 12, 2014, Pages 1630-1638

  Wiestler, Benedikt ^a,c   Capper, David ^b,d   Hovestadt, Volker ^e   Sill, Martin ^f   Jones, David T W ^g   Hartmann, Christian ⁱ   Felsberg, Joerg ^j   Platten, Michael ^a,d,k   Feiden, Wolfgang ^l   Keyvani, Kathy ^m   Pfister, Stefan M ^b,g   Wiestler, Otmar D ^h   Meyermann, Richard ⁿ   Reifenberger, Guido ^j,k   Pietsch, Thorsten ^o   Von Deimling, Andreas ^b,d   Weller, Michael ^p   Wick, Wolfgang ^a,c  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b UNIVERSITY HOSPITAL HEIDELBERG   (Germany)

^c Clinical Cooperation Units Neurooncology   (Germany)

^d Department of Neuropathology ^*  (Germany)

^e Division of Molecular Genetics   (Germany)

^f DKFZ   (Germany)

^g Division of Pediatric Neurooncology   (Germany)

^h GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

ⁱ HANNOVER MEDICAL SCHOOL   (Germany)

^j HEINRICH HEINE UNIVERSITY   (Germany)

^k partner site Essen Düsseldorf   (Germany)

^l SAARLAND UNIVERSITY   (Germany)

^m UNIVERSITY OF DUISBURG ESSEN   (Germany)

ⁿ UNIVERSITY OF TÜBINGEN   (Germany)

^o UNIVERSITY HOSPITAL BONN   (Germany)

^p UNIVERSITY HOSPITAL ZURICH   (Switzerland)

more..

Author keywords

1p 19q; 450k; Anaplastic glioma; G CIMP; MGMT

Indexed keywords

BIOLOGICAL MARKER; ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; LOMUSTINE; METHYLATED DNA PROTEIN CYSTEINE METHYLTRANSFERASE; PROCARBAZINE; TEMOZOLOMIDE; VINCRISTINE; DNA METHYLTRANSFERASE; ISOCITRATE DEHYDROGENASE; MGMT PROTEIN, HUMAN; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; TUMOR SUPPRESSOR PROTEIN;

ARTICLE; ASTROCYTOMA; CANCER PROGNOSIS; CANCER SURVIVAL; CHROMOSOME 19Q; CHROMOSOME 1P; COMPARATIVE STUDY; CONTROLLED STUDY; COPY NUMBER VARIATION; CPG ISLAND; DIAGNOSTIC TEST ACCURACY STUDY; DNA DETERMINATION; DNA METHYLATION; EPIGENETICS; GENE DELETION; GENETIC ASSOCIATION; GLIOBLASTOMA; HUMAN; HUMAN TISSUE; IDH GENE; MAJOR CLINICAL STUDY; MGMT GENE; OLIGODENDROGLIOMA; PHASE 3 CLINICAL TRIAL (TOPIC); PHENOTYPE; PROMOTER REGION; PYROSEQUENCING; RECEIVER OPERATING CHARACTERISTIC; RETROSPECTIVE STUDY; SENSITIVITY AND SPECIFICITY; ADULT; AGED; ALGORITHM; BRAIN NEOPLASMS; CHROMOSOME 1; CHROMOSOME 19; FEMALE; GENETICS; GLIOMA; MALE; MIDDLE AGED; YOUNG ADULT;

ADULT; AGED; ALGORITHMS; BIOLOGICAL MARKERS; BRAIN NEOPLASMS; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 19; CPG ISLANDS; DNA METHYLATION; DNA MODIFICATION METHYLASES; DNA REPAIR ENZYMES; FEMALE; GENE DELETION; GLIOMA; HUMANS; ISOCITRATE DEHYDROGENASE; MALE; MIDDLE AGED; PHENOTYPE; PROMOTER REGIONS, GENETIC; RETROSPECTIVE STUDIES; TUMOR SUPPRESSOR PROTEINS; YOUNG ADULT;

EID: 84929712250     PISSN: 15228517     EISSN: 15235866     Source Type: Journal    
DOI: 10.1093/neuonc/nou138     Document Type: Article

References (40)

1. Weller M, Pfister SM, Wick W, et al. Molecular neuro-oncology in clinical practice: a new horizon. Lancet Oncol. 2013;14(9):e370-e379.
2. Smith JS, Perry A, Borell TJ, et al. Alterations of chromosome arms 1p and 19q as predictors of survival in oligodendrogliomas, astrocytomas, and mixed oligoastrocytomas. J Clin Oncol. 2000;18(3):636-645.
3. Van Den Bent MJ, Brandes AA, Taphoorn MJB, et al. Adjuvant procarbazine, lomustine, and vincristine chemotherapy in newly diagnosed anaplastic oligodendroglioma: long-term follow-up of EORTC brain tumor group study 26951. J Clin Oncol. 2013;31(3):344-350.
4. Cairncross G, Wang M, Shaw E, et al. Phase III trial of chemoradiotherapy for anaplastic oligodendroglioma: long-term results of RTOG 9402. J Clin Oncol. 2013;31(3):337-343.
5. Bettegowda C, Agrawal N, Jiao Y, et al. Mutations in CIC and FUBP1 contribute to human oligodendroglioma. Science. 2011;333(6048):1453-1455.
6. Parsons DW, Jones S, Zhang X, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008;321(5897):1807-1812.
7. Yan H, Parsons DW, Jin G, et al. IDH1 and IDH2 mutations in gliomas. N Engl J Med. 2009;360(8):765-773.
8. Labussière M, Idbaih A, Wang X-W, et al. All the 1p19q codeleted gliomas are mutated on IDH1 or IDH2. Neurology. 2010;74(23):1886-1890.
9. Turcan S, Rohle D, Goenka A, et al. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature. 2012;483(7390):479-483.
10. 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.
11. Lai A, Kharbanda S, Pope WB, et al. Evidence for sequenced molecular evolution of IDH1 mutant glioblastoma from a distinct cell of origin. J Clin Oncol. 2011;29(34):4482-4490.
12. Wick W, Hartmann C, Engel C, et al. NOA-04 randomized phase III trial of sequential radiochemotherapy of anaplastic glioma with procarbazine, lomustine, and vincristine or temozolomide. J Clin Oncol. 2009;27(35):5874-5880.
13. Sanson M, Marie Y, Paris S, et al. Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomas. J Clin Oncol. 2009;27(25):4150-4154.
14. Hegi ME, Diserens A-C, Gorlia T, et al. MGMT gene silencing and benefit from temozolomide in glioblastoma. N Engl J Med. 2005;352(10):997-1003.
15. Wick W, Platten M, Meisner C, et al. Temozolomide chemotherapy alone versus radiotherapy alone for malignant astrocytoma in the elderly: the NOA-08 randomised, phase 3 trial. Lancet Oncol. 2012;13(7):707-715.
16. Gilbert MR, Wang M, Aldape KD, et al. Dose-dense temozolomide for newly diagnosed glioblastoma: a randomized phase III clinical trial. J Clin Oncol. 2013;31(32):4085-4091.
17. Vlassenbroeck I, Califice S, Diserens A-C, et al. Validation of real-time methylation-specific PCR to determine O6-methylguanine-DNA methyltransferase gene promoter methylation in glioma. J Mol Diagn. 2008;10(4):332-337.
18. Van Den Bent MJ, Dubbink HJ, Sanson M, et al. MGMT promoter methylation is prognostic but not predictive for outcome to adjuvant PCV chemotherapy in anaplastic oligodendroglial tumors: a report from EORTC Brain Tumor Group Study 26951. J Clin Oncol. 2009;27(35):5881-5886.
19. Wick W, Meisner C, Hentschel B, et al. Prognostic or predictive value of MGMT promoter methylation in gliomas depends on IDH1 mutation. Neurology. 2013;81(17):1515-1522.
20. Sturm D, Witt H, Hovestadt V, et al. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell. 2012;22(4):425-437.
21. Bady P, Sciuscio D, Diserens A-C, et al. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathol. 2012;124(4):547-560.
22. Hovestadt V, Remke M, Kool M, et al. Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays. Acta Neuropathol. 2013;125(6):913-916.
23. Krex D, Klink B, Hartmann C, et al. Long-term survival with glioblastoma multiforme. Brain. 2007;130(10):2596-2606.
24. Capper D, Weissert S, Balss J, et al. Characterization of R132H mutation-specific IDH1 antibody binding in brain tumors. Brain Pathol. 2010;20(1):245-254.
25. Quillien V, Lavenu A, Karayan-Tapon L, et al. Comparative assessment of 5 methods (methylation-specific PCR, MethyLight, pyrosequencing, methylation-sensitive high-resolution melting, and immunohistochemistry) to analyze O6-methylguanine-DNA-methyltranferase in a series of 100 glioblastoma patients. Cancer. 2012;118(17):4201-4211.
26. Koelsche C, Sahm F, Capper D, et al. Distribution of TERT promoter mutations in pediatric and adult tumors of the nervous system. Acta Neuropathol. 2013;126(6):907-915.
27. Wiestler B, Capper D, Holland-Letz T, et al. ATRX loss refines the classification of anaplastic gliomas and identifies a subgroup of IDH mutant astrocytic tumors with better prognosis. Acta Neuropathol. 2013;126(3):443-451.
28. Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;1277:0-0.
29. R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/. 2013.
30. Weller M, Wick W. Neuro-oncology in 2013: improving outcome in newly diagnosed malignant glioma. Nat Rev Neurol. 2014;10(2):68-70.
31. 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.
32. Frattini V, Trifonov V, Chan JM, et al. The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet. 2013;45(10):1141-1149.
33. Preusser M, Capper D, Hartmann C. IDH testing in diagnostic neuropathology: review and practical guideline article invited by the Euro-CNS research committee. Clin Neuropathol. 2011;30(5):217-230.
34. Horbinski C, Miller CR, Perry A. Gone FISHing: clinical lessons learned in brain tumor molecular diagnostics over the last decade. Brain Pathol. 2011;21(1):57-73.
35. Natté R, Van Eijk R, Eilers P, et al. Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol. 2005;15(3):192-197.
36. Franco-Hernández C, Martýnez-Glez V, De Campos JM, et al. Allelic status of 1p and 19q in oligodendrogliomas and glioblastomas: multiplex ligation-dependent probe amplification versus loss of heterozygosity. Cancer Genet Cytogenet. 2009;190(2):93-96.
37. Weller M, Stupp R, Reifenberger G, et al. MGMTpromoter methylation in malignant gliomas: ready for personalized medicine? Nat. Rev Neurol. 2010;6(1):39-51.
38. Killela PJ, Reitman ZJ, Jiao Y, et al. TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal. Proc Natl Acad Sci USA. 2013;110(15):6021-6026.
39. Mulholland S, Pearson DM, Hamoudi RA, et al. MGMT CpG island is invariably methylated in adult astrocytic and oligodendroglial tumors with IDH1 or IDH2 mutations. Int J Cancer. 2012;131(5):1104-1113.
40. Malley DS, Hamoudi RA, Kocialkowski S, et al. A distinct region of the MGMT CpG island critical for transcriptional regulation is preferentially methylated in glioblastoma cells and xenografts. Acta Neuropathol. 2011;121(5):651-661.