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Kessler T, Berberich A, Sadik A, Sahm F, Gorlia T, Meisner C, Hoffmann DC, Wick A, Kickingereder P, Rübmann P, Bendszus M, Opitz C, Weller M, van den Bent M, Stupp R, Winkler F, Brandes A, von Deimling A, Platten M, Wick W. Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes. Cancer Med 2020; 9:8373-8385. [PMID: 32991787 PMCID: PMC7666733 DOI: 10.1002/cam4.3447] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/30/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Gliomas evade current therapies through primary and acquired resistance and the effect of temozolomide is mainly restricted to methylguanin-O6-methyltransferase promoter (MGMT) promoter hypermethylated tumors. Further resistance markers are largely unknown and would help for better stratification. METHODS Clinical data and methylation profiles from the NOA-08 (104, elderly glioblastoma) and the EORTC 26101 (297, glioblastoma) studies and 398 patients with glioblastoma from the Heidelberg Neuro-Oncology center have been analyzed focused on the predictive effect of DNA damage response (DDR) gene methylation. Candidate genes were validated in vitro. RESULTS Twenty-eight glioblastoma 5'-cytosine-phosphat-guanine-3' (CpGs) from 17 DDR genes negatively correlated with expression and were used together with telomerase reverse transcriptase (TERT) promoter mutations in further analysis. CpG methylation of DDR genes shows highest association with the mesenchymal (MES) and receptor tyrosine kinase (RTK) II glioblastoma subgroup. MES tumors have lower tumor purity compared to RTK I and II subgroup tumors. CpG hypomethylation of DDR genes TP73 and PRPF19 correlated with worse patient survival in particular in MGMT promoter unmethylated tumors. TERT promoter mutation is most frequent in RTK I and II subtypes and associated with worse survival. Primary glioma cells show methylation patterns that resemble RTK I and II glioblastoma and long term established glioma cell lines do not match with glioblastoma subtypes. Silencing of selected resistance genes PRPF19 and TERT increase sensitivity to temozolomide in vitro. CONCLUSION Hypomethylation of DDR genes and TERT promoter mutations is associated with worse tumor prognosis, dependent on the methylation cluster and MGMT promoter methylation status in IDH wild-type glioblastoma.
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Affiliation(s)
- Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Anne Berberich
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Ahmed Sadik
- Brain Tumor Metabolism, DKTK, DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Thierry Gorlia
- European Organization for Research and Treatment of Cancer Headquarters, Brussels, Belgium
| | | | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Antje Wick
- Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Petra Rübmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Martin van den Bent
- The Brain Tumor Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Roger Stupp
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Alba Brandes
- Department of Medical Oncology, Azienda USL-IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neurology, Medical Faculty Mannheim, MCTN, Heidelberg University, Mannheim, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program of the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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