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| Status |
Public on Oct 16, 2012 |
| Title |
Methylation data from glioblastoma tumor samples |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutations (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM (EGFR amplification, CDKN2A/B deletion) and/or known transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of OLIG1/2 and FOXG1, possibly reflecting different cellular origins. We identified six epigenetic and biological GBM subgroups displaying distinct global DNA methylation patterns, which harbor unique hotspot mutations, DNA copy-number alterations, and transcriptomic patterns.
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| Overall design |
We investigated a subset of childhood (n=59) and adult GBMs (n=77) using the Illumina 450k methylation array. Six non-neoplastic brain tissue samples are included as controls.
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| Contributor(s) |
Sturm D, Witt H, Hovestadt V, Khuong Quang DA, Jones DT, Konermann C, Pfaff E, Tönjes M, Sill M, Bender S, Kool M, Zapatka M, Becker N, Zucknick M, Hielscher T, Liu XY, Fontebasso AM, Ryzhova M, Albrecht S, Jacob K, Wolter M, Ebinger M, Schuhmann MU, van Meter T, Frühwald MC, Hauch H, Pekrun A, Radlwimmer B, Niehues T, von Komorowski G, Dürken M, Kulozik AE, Madden J, Donson A, Foreman NK, Drissi R, Fouladi M, Scheurlen W, von Deimling A, Monoranu C, Roggendorf W, Herold-Mende C, Unterberg A, Kramm CM, Felsberg J, Hartmann C, Wiestler B, Wick W, Milde T, Witt O, Lindroth AM, Schwartzentruber J, Faury D, Fleming A, Zakrzewska M, Liberski PP, Zakrzewski K, Hauser P, Garami M, Klekner A, Bognar L, Morrissy S, Cavalli F, Taylor MD, van Sluis P, Koster J, Versteeg R, Volckmann R, Mikkelsen T, Aldape K, Reifenberger G, Collins VP, Majewski J, Korshunov A, Lichter P, Plass C, Jabado N, Pfister SM |
| Citation(s) |
23079654 |
| Submission date |
Mar 05, 2012 |
| Last update date |
Mar 22, 2019 |
| Contact name |
Dominik Sturm |
| Organization name |
German Cancer Research Center
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (142)
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| Relations |
| BioProject |
PRJNA153007 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE36278_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE36278_unmethyl_methyl_signals_GSM886028-GSM886108.txt.gz |
332.0 Mb |
(ftp)(http) |
TXT |
| GSE36278_unmethyl_methyl_signals_GSM972672-GSM972733.txt.gz |
263.7 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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