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Zhang L, Fritah S, Nazarov PV, Kaoma T, Van Dyck E. Impact of IDH Mutations, the 1p/19q Co-Deletion and the G-CIMP Status on Alternative Splicing in Diffuse Gliomas. Int J Mol Sci 2023; 24:9825. [PMID: 37372972 DOI: 10.3390/ijms24129825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
By generating protein diversity, alternative splicing provides an important oncogenic pathway. Isocitrate dehydrogenase (IDH) 1 and 2 mutations and 1p/19q co-deletion have become crucial for the novel molecular classification of diffuse gliomas, which also incorporates DNA methylation profiling. In this study, we have carried out a bioinformatics analysis to examine the impact of the IDH mutation, as well as the 1p/19q co-deletion and the glioma CpG island methylator phenotype (G-CIMP) status on alternative splicing in a cohort of 662 diffuse gliomas from The Cancer Genome Atlas (TCGA). We identify the biological processes and molecular functions affected by alternative splicing in the various glioma subgroups and provide evidence supporting the important contribution of alternative splicing in modulating epigenetic regulation in diffuse gliomas. Targeting the genes and pathways affected by alternative splicing might provide novel therapeutic opportunities against gliomas.
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Affiliation(s)
- Lu Zhang
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Cancer Research (DoCR), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
- Multiomics Data Science Research Group, DoCR, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit (DIA), Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
| | - Eric Van Dyck
- DNA Repair and Chemoresistance Group, DoCR, Luxembourg Institute of Health (LIH), L-1445 Strassen, Luxembourg
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2
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Ozair A, Bhat V, Alisch RS, Khosla AA, Kotecha RR, Odia Y, McDermott MW, Ahluwalia MS. DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets. Cancers (Basel) 2023; 15:cancers15041342. [PMID: 36831683 PMCID: PMC9954183 DOI: 10.3390/cancers15041342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.
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Affiliation(s)
- Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Faculty of Medicine, King George’s Medical University, Lucknow 226003, India
| | - Vivek Bhat
- St. John’s Medical College, Bangalore 560034, India
| | - Reid S. Alisch
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Atulya A. Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Rupesh R. Kotecha
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Michael W. McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
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3
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Noor H, Zaman A, Teo C, Sughrue ME. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. Int J Mol Sci 2021; 22:ijms222212572. [PMID: 34830454 PMCID: PMC8625785 DOI: 10.3390/ijms222212572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Lower-grade glioma (LGG) is a diffuse infiltrative tumor of the central nervous system, which lacks targeted therapy. We investigated the role of Podocan-like 1 (PODNL1) methylation in LGG clinical outcomes using the TCGA-LGG transcriptomics dataset. We identified four PODNL1 CpG sites, cg07425555, cg26969888, cg18547299, and cg24354933, which were associated with unfavorable overall survival (OS) and disease-free survival (DFS) in univariate and multivariate analysis after adjusting for age, gender, tumor-grade, and IDH1-mutation. In multivariate analysis, the OS and DFS hazard ratios ranged from 0.44 to 0.58 (p < 0.001) and 0.62 to 0.72 (p < 0.001), respectively, for the four PODNL1 CpGs. Enrichment analysis of differential gene and protein expression and analysis of 24 infiltrating immune cell types showed significantly increased infiltration in LGGs and its histological subtypes with low-methylation levels of the PODNL1 CpGs. High PODNL1 expression and low-methylation subgroups of the PODNL1 CpG sites were associated with significantly increased PD-L1, PD-1, and CTLA4 expressions. PODNL1 methylation may thus be a potential indicator of immune checkpoint blockade response, and serve as a biomarker for determining prognosis and immune subtypes in LGG.
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Affiliation(s)
- Humaira Noor
- Cure Brain Cancer Biomarkers and Translational Research Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2031, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Randwick, NSW 2031, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Correspondence:
| | - Ashraf Zaman
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Charles Teo
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Michael E. Sughrue
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
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4
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J Dabrowski M, Wojtas B. Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications. Int J Mol Sci 2019; 20:E3478. [PMID: 31311166 DOI: 10.3390/ijms20143478] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/04/2019] [Accepted: 07/09/2019] [Indexed: 01/08/2023] Open
Abstract
During the last two decades, several international consortia have been established to unveil the molecular background of human cancers including gliomas. As a result, a huge outbreak of new genetic and epigenetic data appeared. It was not only shown that gliomas share some specific DNA sequence aberrations, but they also present common alterations of chromatin. Many researchers have reported specific epigenetic features, such as DNA methylation and histone modifications being involved in tumor pathobiology. Unlike mutations in DNA, epigenetic changes are more global in nature. Moreover, many studies have shown an interplay between different types of epigenetic changes. Alterations in DNA methylation in gliomas are one of the best described epigenetic changes underlying human pathology. In the following work, we present the state of knowledge about global DNA methylation patterns in gliomas and their interplay with histone modifications that may affect transcription factor binding, global gene expression and chromatin conformation. Apart from summarizing the impact of global DNA methylation on glioma pathobiology, we provide an extract of key mechanisms of DNA methylation machinery.
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Abstract
Adult diffuse gliomas form a heterogeneous group of tumors of the central nervous system that vary greatly in histology and prognosis. A significant advance during the last decade has been the identification of a set of genetic lesions that correlate well with histology and clinical outcome in diffuse gliomas. Most characteristic driver mutations consist of isocitrate dehydrogenase 1 (IDH1) and IDH2, and H3 histone family member 3A, which are strongly associated with DNA and histone methylation patterns. A well-characterized DNA methylation aberration is on the O6-methylguanine-DNA methyltransferase promoter. This aberration is associated with an improved response to the DNA alkylating agent, temozolomide. Methylation alterations are used for classification or treatment decisions of diffuse gliomas. This supports the importance of considering epigenomic aberrations in the pathogenesis of gliomas. Recent DNA methylation analyses revealed a small group of IDH mutant diffuse gliomas exhibiting decreased DNA hypermethylation resulting in substantial unfavorable prognosis comparable to glioblastoma. Thus, DNA methylation patterns may become a new standard that replaces the conventional grading system based on histological diagnosis. In this review, we summarize recent developments regarding the contributions of methylation patterns to the pathogenesis of adult diffuse glioma, the interactions between methylation patterns and driver mutations, and potential epigenomic targeted therapies.
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Affiliation(s)
- Kosuke Aoki
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Atsushi Natsume
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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6
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Patil V, Mahalingam K. Comprehensive analysis of Reverse Phase Protein Array data reveals characteristic unique proteomic signatures for glioblastoma subtypes. Gene 2018; 685:85-95. [PMID: 30401645 DOI: 10.1016/j.gene.2018.10.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/11/2022]
Abstract
The most common and lethal type of intracranial tumors include the astrocytomas. Grade IV astrocytoma or Glioblastoma (GBM) is highly aggressive and treatment-refractory with a median survival of only 14 to 16 months. Molecular profiling of GBMs reveals a high degree of intra- and inter-tumoral heterogeneity, and hence it is important to understand the important signalling axes that get deregulated in different GBM subtypes to provide effective tailor-made therapies. In this study, we have carried out extensive analysis of Reverse Phase Protein Array (RPPA) data from TCGA cohort to develop protein signatures that define glioma grades or subtypes. The protein signatures that distinguished Grade II or III from GBM had largely overlapped, and pathway analysis revealed the positive enrichment of extracellular matrix proteins (ECM), MYC pathway, uPAR pathway and G2/M checkpoint genes in GBM. We also identified protein signatures for GBMs with genetic alterations (IDH mutation, p53 mutation, EGFR amplification or mutation, CDKN2A/CDKN2B deletion, and PTEN mutation) that occur at high frequency. G-CIMP positive GBM-specific protein signature showed a large similarity with IDH1-mutant protein signature, thus signifying the importance of IDH1 mutation driving the G-CIMP. Gene expression subtype analysis revealed an association of specific proteins to classical (EGFR and phosphor variants), mesenchymal (SERPINE1, TAZ, and Myosin-IIa_pS1943), neural (TUBA1B), and proneural (GSK3_pS9) types. Univariate Cox regression analysis identified several proteins showing significant correlation with GBM survival. Multivariate analysis revealed that IGFBP2 and RICTOR_pT1135 are independent predictors of survival. Overall, our analyses reveal that specific proteins are regulated in different glioma subtypes underscoring the importance of diverse signalling axes playing important role in the pathogenesis of glioma tumors.
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Affiliation(s)
- Vikas Patil
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - Kulandaivelu Mahalingam
- Department of Bio-Medical Sciences, School of Biosciences and Technology, VIT University, Vellore 632014, India.
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7
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Glowacka WK, Jain H, Okura M, Maimaitiming A, Mamatjan Y, Nejad R, Farooq H, Taylor MD, Aldape K, Kongkham P. 5-Hydroxymethylcytosine preferentially targets genes upregulated in isocitrate dehydrogenase 1 mutant high-grade glioma. Acta Neuropathol 2018; 135:617-634. [PMID: 29428975 PMCID: PMC5978937 DOI: 10.1007/s00401-018-1821-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/18/2018] [Accepted: 02/07/2018] [Indexed: 01/12/2023]
Abstract
Gliomas demonstrate epigenetic dysregulation exemplified by the Glioma CpG Island Methylator Phenotype (G-CIMP) seen in IDH1 mutant tumors. 5-Hydroxymethylcytosine (5hmC) is implicated in glioma pathogenesis; however, its role in IDH1 mutant gliomas is incompletely understood. To characterize 5hmC in IDH1 mutant gliomas further, we examine 5hmC in a cohort of IDH1 mutant and wild-type high-grade gliomas (HGG) using a quantitative locus-specific approach. Regions demonstrating high 5hmC abundance and differentially hydroxymethylated regions (DHMR) enrich for enhancers implicated in glioma pathogenesis. Among these regions, IDH1 mutant tumors possess greater 5hmC compared to wild type. 5hmC contributes to overall methylation status of G-CIMP genes. 5hmC targeting gene body regions correlates significantly with increased gene expression. In particular, a strong correlation between increased 5hmC and increased gene expression is identified for genes highly expressed in the IDH1 mutant cohort. Overall, locus-specific gain of 5hmC targeting regulatory regions and associated with overexpressed genes suggests a significant role for 5hmC in IDH1 mutant HGG.
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8
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Heiland DH, Ferrarese R, Claus R, Dai F, Masilamani AP, Kling E, Weyerbrock A, Kling T, Nelander S, Carro MS. c-Jun-N-terminal phosphorylation regulates DNMT1 expression and genome wide methylation in gliomas. Oncotarget 2018; 8:6940-6954. [PMID: 28036297 PMCID: PMC5351681 DOI: 10.18632/oncotarget.14330] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 12/15/2016] [Indexed: 12/19/2022] Open
Abstract
High-grade gliomas (HGG) are the most common brain tumors, with an average survival time of 14 months. A glioma-CpG island methylator phenotype (G-CIMP), associated with better clinical outcome, has been described in low and high-grade gliomas. Mutation of IDH1 is known to drive the G-CIMP status. In some cases, however, the hypermethylation phenotype is independent of IDH1 mutation, suggesting the involvement of other mechanisms. Here, we demonstrate that DNMT1 expression is higher in low-grade gliomas compared to glioblastomas and correlates with phosphorylated c-Jun. We show that phospho-c-Jun binds to the DNMT1 promoter and causes DNA hypermethylation. Phospho-c-Jun activation by Anisomycin treatment in primary glioblastoma-derived cells attenuates the aggressive features of mesenchymal glioblastomas and leads to promoter methylation and downregulation of key mesenchymal genes (CD44, MMP9 and CHI3L1). Our findings suggest that phospho-c-Jun activates an important regulatory mechanism to control DNMT1 expression and regulate global DNA methylation in Glioblastoma.
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Affiliation(s)
- Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roberto Ferrarese
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Department of Hematology, Oncology, and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany
| | - Fangping Dai
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anie P Masilamani
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kling
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Teresia Kling
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Maria S Carro
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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9
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Mock A, Geisenberger C, Orlik C, Warta R, Schwager C, Jungk C, Dutruel C, Geiselhart L, Weichenhan D, Zucknick M, Nied AK, Friauf S, Exner J, Capper D, Hartmann C, Lahrmann B, Grabe N, Debus J, von Deimling A, Popanda O, Plass C, Unterberg A, Abdollahi A, Schmezer P, Herold-Mende C. LOC283731 promoter hypermethylation prognosticates survival after radiochemotherapy in IDH1 wild-type glioblastoma patients. Int J Cancer 2016; 139:424-32. [PMID: 26934681 DOI: 10.1002/ijc.30069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/16/2016] [Indexed: 01/15/2023]
Abstract
MGMT promoter methylation status is currently the only established molecular prognosticator in IDH wild-type glioblastoma multiforme (GBM). Therefore, we aimed to discover novel therapy-associated epigenetic biomarkers. After enrichment for hypermethylated fractions using methyl-CpG-immunoprecipitation (MCIp), we performed global DNA methylation profiling for 14 long-term (LTS; >36 months) and 15 short-term (STS; 6-10 months) surviving GBM patients. Even after exclusion of the G-CIMP phenotype, we observed marked differences between the LTS and STS methylome. A total of 1,247 probes in 706 genes were hypermethylated in LTS and 463 probes in 305 genes were found to be hypermethylated in STS patients (p values < 0.05, log2 fold change ± 0.5). We identified 13 differentially methylated regions (DMRs) with a minimum of four differentially methylated probes per gene. Indeed, we were able to validate a subset of these DMRs through a second, independent method (MassARRAY) in our LTS/STS training set (ADCY1, GPC3, LOC283731/ISLR2). These DMRs were further assessed for their prognostic capability in an independent validation cohort (n = 62) of non-G-CIMP GBMs from the TCGA. Hypermethylation of multiple CpGs mapping to the promoter region of LOC283731 correlated with improved patient outcome (p = 0.03). The prognostic performance of LOC283731 promoter hypermethylation was confirmed in a third independent study cohort (n = 89), and was independent of gender, performance (KPS) and MGMT status (p = 0.0485, HR = 0.63). Intriguingly, the prediction was most pronounced in younger GBM patients (<60 years). In conclusion, we provide compelling evidence that promoter methylation status of this novel gene is a prognostic biomarker in IDH1 wild-type/non-G-CIMP GBMs.
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Affiliation(s)
- Andreas Mock
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany.,Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany.,Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Geisenberger
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Orlik
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Rolf Warta
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Schwager
- Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christine Jungk
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Céline Dutruel
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Lea Geiselhart
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Manuela Zucknick
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ann-Katrin Nied
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Sara Friauf
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Janina Exner
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Bernd Lahrmann
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Medical Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Medical Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Debus
- Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Odilia Popanda
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Andreas Unterberg
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Amir Abdollahi
- Molecular and Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Institute for Radiation Oncology (HIRO), Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Schmezer
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
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10
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Wiestler B, Capper D, Hovestadt V, Sill M, Jones DTW, Hartmann C, Felsberg J, Platten M, Feiden W, Keyvani K, Pfister SM, Wiestler OD, Meyermann R, Reifenberger G, Pietsch T, von Deimling A, Weller M, Wick W. 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 Oncol 2014; 16:1630-8. [PMID: 25028501 DOI: 10.1093/neuonc/nou138] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Molecular biomarkers including isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation, 1p/19q codeletion, and O(6)-methylguanine-DNA-methyltransferase (MGMT) promoter methylation may improve prognostication and guide treatment decisions for patients with World Health Organization (WHO) anaplastic gliomas. At present, each marker is individually tested by distinct assays. Illumina Infinium HumanMethylation450 BeadChip arrays (HM450) enable the determination of large-scale methylation profiles and genome-wide DNA copy number changes. Algorithms have been developed to detect the glioma CpG island methylator phenotype (G-CIMP) associated with IDH1/2 mutation, 1p/19q codeletion, and MGMT promoter methylation using a single assay. METHODS Here, we retrospectively investigated the diagnostic and prognostic performance of these algorithms in comparison to individual marker testing and patient outcome in the biomarker cohort (n = 115 patients) of the NOA-04 trial. RESULTS Concordance for IDH and 1p/19q status was very high: In 92% of samples, the HM450 and reference data agreed. In discordant samples, survival analysis by Kaplan-Meier and Cox regression analyses suggested a more accurate assessment of biological phenotype by the HM450 analysis. The HM450-derived MGMT-STP27 model to calculate MGMT promoter methylation probability revealed this aberration in a significantly higher fraction of samples than conventional methylation-specific PCR, with 87 of 91 G-CIMP tumors predicted as MGMT promoter-methylated. Pyrosequencing of discordant samples confirmed the HM450 assessment in 14 of 17 cases. CONCLUSIONS G-CIMP and 1p/19q codeletion are reliably detectable by HM450 analysis and are associated with prognosis in the NOA-04 trial. For MGMT, HM450 suggests promoter methylation in the vast majority of G-CIMP tumors, which is supported by pyrosequencing.
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Affiliation(s)
- Benedikt Wiestler
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - David Capper
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Volker Hovestadt
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Martin Sill
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - David T W Jones
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Christian Hartmann
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Joerg Felsberg
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Michael Platten
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Wolfgang Feiden
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Kathy Keyvani
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Stefan M Pfister
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Otmar D Wiestler
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Richard Meyermann
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Guido Reifenberger
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Thorsten Pietsch
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Andreas von Deimling
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Michael Weller
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
| | - Wolfgang Wick
- Department of Neurooncology (B.W., M.P., W.W.); Department of Neuropathology (D.C., A.v.D.); Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital (S.M.P.); Clinical Cooperation Units Neurooncology (B.W., W.W.), Neuropathology (D.C, A.v.D.); Neuroimmunology and Brain Tumor Immunology (M.P.); Division of Molecular Genetics (V.H.); Division of Biostatistics (M.S.); Division of Pediatric Neurooncology (S.M.P., D.T.W.J.), German Cancer Research Center (DKFZ), Heidelberg, Germany (O.D.W.) and German Cancer Consortium (DKTK); Department for Neuropathology, Institute of Pathology, Medical University of Hannover, Hannover, Germany (C.H.); Department of Neuropathology, Heinrich-Heine-University, Düsseldorf, Germany (J.F., G.R.); German Consortium for Translational Cancer Research (DKTK), Düsseldorf, Germany (M.P., G.R.); Institute for Neuropathology, Saarland University, 66421 Saarbrücken, Germany (W.F.); Institute for Neuropathology, University of Essen Medical School, Essen, Germany (K.K.); Institute for Neuropathology, University of Tübingen, Tübingen, Germany (R.M.); Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany (T.P.); Department of Neurology, University Hospital Zurich, Zürich, Switzerland (M.W.)
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Jha P, Pia Patric IR, Shukla S, Pathak P, Pal J, Sharma V, Thinagararanjan S, Santosh V, Suri V, Sharma MC, Arivazhagan A, Suri A, Gupta D, Somasundaram K, Sarkar C. Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation. Neuro Oncol 2014; 16:1607-17. [PMID: 24997139 DOI: 10.1093/neuonc/nou113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH)1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. METHODS Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. RESULTS Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. CONCLUSIONS Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation.
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Affiliation(s)
- Prerana Jha
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Irene Rosita Pia Patric
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Sudhanshu Shukla
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Pankaj Pathak
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Jagriti Pal
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vikas Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Sivaarumugam Thinagararanjan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vani Santosh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Arimappamagan Arivazhagan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Ashish Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Deepak Gupta
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Kumaravel Somasundaram
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India (P.J., P.P., VI.S., VA.S., M.C.S., C.S.); Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India (I.R.P.P., S.S., J.P., S.T., K.S.); Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, India (VAI.S.); Department of Neurosurgery, National Institute of Mental Health and Neurosciences, Bangalore, India (A.A.); Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India (A.S., D.G.)
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Wiestler B, Claus R, Hartlieb SA, Schliesser MG, Weiss EK, Hielscher T, Platten M, Dittmann LM, Meisner C, Felsberg J, Happold C, Simon M, Nikkhah G, Papsdorf K, Steinbach JP, Sabel M, Grimm C, Weichenhan D, Tews B, Reifenberger G, Capper D, Müller W, Plass C, Weller M, Wick W. Malignant astrocytomas of elderly patients lack favorable molecular markers: an analysis of the NOA-08 study collective. Neuro Oncol 2013; 15:1017-26. [PMID: 23595628 DOI: 10.1093/neuonc/not043] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The number of patients age >65 years with malignant gliomas is increasing. Prognosis of these patients is worse compared with younger patients. To determine biological differences among malignant gliomas of different age groups and help to explain the survival heterogeneity seen in the NOA-08 trial, the prevalence and impact of recently established biomarkers for outcome in younger patients were characterized in elderly patients. METHODS Prevalences of mutations of isocitrate dehydrogenase 1 (IDH1) and histone H3.3 (H3F3A), the glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and methylation of alkylpurine DNA N-glycosylase (APNG) and peroxiredoxin 1 (PRDX1) promoters were determined in a representative biomarker subset (n = 126 patients with anaplastic astrocytoma or glioblastoma) from the NOA-08 trial. RESULTS IDH1 mutations (R132H) were detected in only 3/126 patients, precluding determination of an association between IDH mutation and outcome. These 3 patients also displayed the G-CIMP phenotype. None of the IDH1 wild-type tumors were G-CIMP positive. Mutations in H3F3A were absent in all 103 patients sequenced for H3F3A. MassARRAY analysis of the APNG promoter revealed generally low methylation levels and failed to confirm any predictive properties for benefit from alkylating chemotherapy. Neither did PRDX1 promoter methylation show differential methylation or association with outcome in this cohort. In a 170-patient cohort from The Cancer Genome Atlas database matched for relevant prognostic factors, age ≥65 years was strongly associated with shorter survival. CONCLUSIONS Despite an age-independent stable frequency of O(6)-methylguanine-DNA methyltransferase (MGMT) promoter hypermethylation, tumors in this age group largely lack prognostically favorable markers established in younger glioblastoma patients, which likely contributes to the overall worse prognosis of elderly patients. However, the survival differences hint at fundamental further differences among malignant gliomas of different age groups.
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