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Sahm F, Schrimpf D, Stichel D, Jones DTW, Hielscher T, Schefzyk S, Okonechnikov K, Koelsche C, Reuss DE, Capper D, Sturm D, Wirsching HG, Berghoff AS, Baumgarten P, Kratz A, Huang K, Wefers AK, Hovestadt V, Sill M, Ellis HP, Kurian KM, Okuducu AF, Jungk C, Drueschler K, Schick M, Bewerunge-Hudler M, Mawrin C, Seiz-Rosenhagen M, Ketter R, Simon M, Westphal M, Lamszus K, Becker A, Koch A, Schittenhelm J, Rushing EJ, Collins VP, Brehmer S, Chavez L, Platten M, Hänggi D, Unterberg A, Paulus W, Wick W, Pfister SM, Mittelbronn M, Preusser M, Herold-Mende C, Weller M, von Deimling A. DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis. Lancet Oncol 2017; 18:682-694. [PMID: 28314689 DOI: 10.1016/s1470-2045(17)30155-9] [Citation(s) in RCA: 497] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND The WHO classification of brain tumours describes 15 subtypes of meningioma. Nine of these subtypes are allotted to WHO grade I, and three each to grade II and grade III. Grading is based solely on histology, with an absence of molecular markers. Although the existing classification and grading approach is of prognostic value, it harbours shortcomings such as ill-defined parameters for subtypes and grading criteria prone to arbitrary judgment. In this study, we aimed for a comprehensive characterisation of the entire molecular genetic landscape of meningioma to identify biologically and clinically relevant subgroups. METHODS In this multicentre, retrospective analysis, we investigated genome-wide DNA methylation patterns of meningiomas from ten European academic neuro-oncology centres to identify distinct methylation classes of meningiomas. The methylation classes were further characterised by DNA copy number analysis, mutational profiling, and RNA sequencing. Methylation classes were analysed for progression-free survival outcomes by the Kaplan-Meier method. The DNA methylation-based and WHO classification schema were compared using the Brier prediction score, analysed in an independent cohort with WHO grading, progression-free survival, and disease-specific survival data available, collected at the Medical University Vienna (Vienna, Austria), assessing methylation patterns with an alternative methylation chip. FINDINGS We retrospectively collected 497 meningiomas along with 309 samples of other extra-axial skull tumours that might histologically mimic meningioma variants. Unsupervised clustering of DNA methylation data clearly segregated all meningiomas from other skull tumours. We generated genome-wide DNA methylation profiles from all 497 meningioma samples. DNA methylation profiling distinguished six distinct clinically relevant methylation classes associated with typical mutational, cytogenetic, and gene expression patterns. Compared with WHO grading, classification by individual and combined methylation classes more accurately identifies patients at high risk of disease progression in tumours with WHO grade I histology, and patients at lower risk of recurrence among WHO grade II tumours (p=0·0096) from the Brier prediction test). We validated this finding in our independent cohort of 140 patients with meningioma. INTERPRETATION DNA methylation-based meningioma classification captures clinically more homogenous groups and has a higher power for predicting tumour recurrence and prognosis than the WHO classification. The approach presented here is potentially very useful for stratifying meningioma patients to observation-only or adjuvant treatment groups. We consider methylation-based tumour classification highly relevant for the future diagnosis and treatment of meningioma. FUNDING German Cancer Aid, Else Kröner-Fresenius Foundation, and DKFZ/Heidelberg Institute of Personalized Oncology/Precision Oncology Program.
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Affiliation(s)
- Felix Sahm
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Schefzyk
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | | | - Peter Baumgarten
- Neurological Institute (Edinger-Institute), Goethe University, Frankfurt, Germany
| | - Annekathrin Kratz
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Huang
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hayley P Ellis
- Brain Tumour Research Group, Institute of Clinical Neurosciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Ali Fuat Okuducu
- Department of Pathology, University Hospital Nürnberg, Nürnberg, Germany
| | - Christine Jungk
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Matthias Schick
- Genomics and Proteomics Core Facility, Micro-Array Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, Micro-Array Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | | | - Ralf Ketter
- Department of Neurosurgery, Saarland University, Homburg, Germany
| | - Matthias Simon
- Department of Neurosurgery, Evangelische Krankenhaus Bielefeld, Bielefeld, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Arend Koch
- Department of Neuropathology, Charité Medical University, Berlin, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Elisabeth J Rushing
- Department of Neuropathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - V Peter Collins
- Department of Molecular Histopathology, University of Cambridge, Cambridge, UK
| | - Stefanie Brehmer
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany; Neurology Clinic, University Hospital Mannheim, Mannheim, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michel Mittelbronn
- Neurological Institute (Edinger-Institute), Goethe University, Frankfurt, Germany
| | - Matthias Preusser
- Department of Medicine I, CNS Tumours Unit, Medical University of Vienna, Vienna, Austria
| | | | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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