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Hench J, Hultschig C, Brugger J, Mariani L, Guzman R, Soleman J, Leu S, Benton M, Stec IM, Hench IB, Hoffmann P, Harter P, Weber KJ, Albers A, Thomas C, Hasselblatt M, Schüller U, Restelli L, Capper D, Hewer E, Diebold J, Kolenc D, Schneider UC, Rushing E, Della Monica R, Chiariotti L, Sill M, Schrimpf D, von Deimling A, Sahm F, Kölsche C, Tolnay M, Frank S. EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics. Acta Neuropathol Commun 2024; 12:51. [PMID: 38576030 PMCID: PMC10993614 DOI: 10.1186/s40478-024-01759-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.
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Affiliation(s)
- Jürgen Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
| | - Claus Hultschig
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Jon Brugger
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Luigi Mariani
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Raphael Guzman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Jehuda Soleman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Severina Leu
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Miles Benton
- Human Genomics, Institute of Environmental Science and Research (ESR), 5022, Porirua, Wellington, New Zealand
| | - Irenäus Maria Stec
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Ivana Bratic Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Per Hoffmann
- Life&Brain GmbH, Venusberg-Campus 1, Gebäude 76, 53127, Bonn, Germany
| | - Patrick Harter
- Institute of Neuropathology, Center for Neuropathology and Prion Research, Feodor- Lynen-Str. 23, 81377, München, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital, Heinrich-Hoffmann- Straße 7, 60528, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Ulrich Schüller
- Forschungsinstitut Kinderkrebszentrum, Martinistrasse 52, 20251, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg- Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Department of Neuropathology, Department of Neuropathology, Charité- Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lisa Restelli
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - David Capper
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ekkehard Hewer
- Institut universitaire de pathologie, Lausanne University Hospital (CHUV), University of Lausanne, Rue du Bugnon 25, 1011, Lausanne, Switzerland
| | - Joachim Diebold
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Danijela Kolenc
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ulf C Schneider
- Klinik für Neurochirurgie, Luzerner Kantonsspital, Haus 31, 6000, 16, Spitalstrasse, Luzern, Switzerland
| | - Elisabeth Rushing
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
- Medica Pathologie Zentrum Zürich, Hottingerstrasse 9 / 11, 8032, Zürich, Switzerland
| | - Rosa Della Monica
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Lorenzo Chiariotti
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- , 23. DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Kölsche
- Pathologisches Institut der LMU, Thalkirchner Str. 36, 80337, München, Germany
| | - Markus Tolnay
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Stephan Frank
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
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2
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Reuss DE, Schrimpf D, Cherkezov A, Suwala AK, Lausová T, Snuderl M, Capper D, Sill M, Jones DTW, Pfister SM, Sahm F, von Deimling A. Heterogeneity of DNA methylation profiles and copy number alterations in 10782 adult-type glioblastomas, IDH-wildtype. Free Neuropathol 2024; 5:5-7. [PMID: 38532825 PMCID: PMC10964111 DOI: 10.17879/freeneuropathology-2024-5345] [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] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The morphological patterns leading to the diagnosis of glioblastoma may also commonly be observed in several other distinct tumor entities, which can result in a mixed bag of tumors subsumed under this diagnosis. The 2021 WHO Classification of CNS Tumors has separated several of these entities from the diagnosis of glioblastoma, IDH-wildtype. This study determines the DNA methylation classes most likely receiving the diagnosis glioblastoma, IDH wildtype according to the definition by the WHO 2021 Classification and provides comparative copy number analyses. We identified 10782 methylome datasets uploaded to the web page www.molecularneuropathology.org with a calibrated score of ≥0.9 by the Heidelberg Brain Tumor Classifier version v12.8. These methylation classes were characterized by the diagnosis glioblastoma being the most frequent classification encountered in each of the classes according to the WHO 2021 definition. Further, methylation classes selected for this study predominantly contained adult patients. Unsupervised clustering confirmed the presence of nine methylation classes containing tumors most likely receiving the diagnosis glioblastoma, IDH-wildtype according to the WHO 2021 definition. Copy number analysis and a focus on genes with typical numerical alterations in glioblastoma revealed clear differences between the nine methylation classes. Although great progress in diagnostic precision has been achieved over the last decade, our data clearly demonstrate that glioblastoma, IDH-wildtype still is a heterogeneous group in need of further stratification.
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Affiliation(s)
- David E. Reuss
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asan Cherkezov
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abigail K. Suwala
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tereza Lausová
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health and School of Medicine, New York, New York, USA
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T. W. Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M. Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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3
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Sturm D, Capper D, Andreiuolo F, Gessi M, Kölsche C, Reinhardt A, Sievers P, Wefers AK, Ebrahimi A, Suwala AK, Gielen GH, Sill M, Schrimpf D, Stichel D, Hovestadt V, Daenekas B, Rode A, Hamelmann S, Previti C, Jäger N, Buchhalter I, Blattner-Johnson M, Jones BC, Warmuth-Metz M, Bison B, Grund K, Sutter C, Hirsch S, Dikow N, Hasselblatt M, Schüller U, Koch A, Gerber NU, White CL, Buntine MK, Kinross K, Algar EM, Hansford JR, Gottardo NG, Schuhmann MU, Thomale UW, Hernáiz Driever P, Gnekow A, Witt O, Müller HL, Calaminus G, Fleischhack G, Kordes U, Mynarek M, Rutkowski S, Frühwald MC, Kramm CM, von Deimling A, Pietsch T, Sahm F, Pfister SM, Jones DTW. Author Correction: Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology. Nat Med 2024; 30:306. [PMID: 37875569 PMCID: PMC10803251 DOI: 10.1038/s41591-023-02652-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe Andreiuolo
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Laboratory of Neuropathology, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Brazil
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Marco Gessi
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Christian Kölsche
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Philipp Sievers
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neurological Surgery, Helen Diller Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gerrit H Gielen
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bjarne Daenekas
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Agata Rode
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Hamelmann
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christopher Previti
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ivo Buchhalter
- Omics IT and Data Management Core Facility, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Monika Warmuth-Metz
- Department of Diagnostic and Interventional Neuroradiology, University Hospital of Würzburg, Würzburg, Germany
- Neuroradiological Reference Center for the Pediatric Brain Tumor (HIT) Studies of the German Society of Pediatric Oncology and Hematology, University Hospital Würzburg, since 2021 University Hospital Augsburg, Augsburg, Germany
| | - Brigitte Bison
- Neuroradiological Reference Center for the Pediatric Brain Tumor (HIT) Studies of the German Society of Pediatric Oncology and Hematology, University Hospital Würzburg, since 2021 University Hospital Augsburg, Augsburg, Germany
- Diagnostic and Interventional Neuroradiology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Hirsch
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas U Gerber
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland
| | - Christine L White
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Parkville, VIC, Australia
| | - Molly K Buntine
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
| | - Kathryn Kinross
- Australian and New Zealand Children's Haematology and Oncology Group (ANZCHOG), Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Elizabeth M Algar
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Jordan R Hansford
- Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australia immunoGENomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | | | - Ulrich W Thomale
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Pablo Hernáiz Driever
- German HIT-LOGGIC Registry for low-grade glioma in children and adolescents, Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Astrid Gnekow
- Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, Faculty of Medicine, University Augsburg, Augsburg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hermann L Müller
- Department of Pediatrics and Pediatric Hematology/Oncology, University Children's Hospital, Klinikum Oldenburg AöR, Oldenburg, Germany
| | - Gabriele Calaminus
- Department of Pediatric Hematology and Oncology, University Childrens' Hospital Muenster, Muenster, Germany
| | - Gudrun Fleischhack
- Pediatric Hematology and Oncology, Pediatrics III, University Children's Hospital of Essen, Essen, Germany
| | - Uwe Kordes
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael C Frühwald
- Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, Faculty of Medicine, University Augsburg, Augsburg, Germany
| | - Christof M Kramm
- Department of Child and Adolescent Health, Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
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4
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Sahm K, Kessler T, Eisele P, Ratliff M, Sperk E, König L, Breckwoldt MO, Seliger C, Mildenberger I, Schrimpf D, Herold-Mende C, Zeiner PS, Tabatabai G, Meuth SG, Capper D, Bendszus M, von Deimling A, Wick W, Sahm F, Platten M. Concurrent gliomas in patients with multiple sclerosis. Commun Med (Lond) 2023; 3:186. [PMID: 38110626 PMCID: PMC10728097 DOI: 10.1038/s43856-023-00381-y] [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: 12/22/2022] [Accepted: 10/10/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Concurrent malignant brain tumors in patients with multiple sclerosis (MS) constitute a rare but paradigmatic phenomenon for studying neuroimmunological mechanisms from both molecular and clinical perspectives. METHODS A multicenter cohort of 26 patients diagnosed with both primary brain tumors and multiple sclerosis was studied for disease localization, tumor treatment-related MS activity, and molecular characteristics specific for diffuse glioma in MS patients. RESULTS MS neither predisposes nor protects from the development of gliomas. Patients with glioblastoma WHO grade 4 without isocitratdehydrogenase (IDH) mutations have a longstanding history of MS, whereas patients diagnosed with IDH-mutant astrocytoma WHO grade 2 receive multiple sclerosis diagnosis mostly at the same time or later. Concurrent MS is associated with a lesser extent of tumor resection and a worse prognosis in IDH-mutant glioma patients (PFS 32 vs. 64 months, p = 0.0206). When assessing tumor-intrinsic differences no distinct subgroup-defining methylation pattern is identified in gliomas of MS patients compared to other glioma samples. However, differential methylation of immune-related genetic loci including human leukocyte antigen locus on 6p21 and interleukin locus on 5q31 is found in MS patients vs. matched non-MS patients. In line, inflammatory disease activity increases in 42% of multiple sclerosis patients after brain tumor radiotherapy suggesting a susceptibility of multiple sclerosis brain tissue to pro-inflammatory stimuli such as ionizing radiation. CONCLUSIONS Concurrent low-grade gliomas should be considered in multiple sclerosis patients with slowly progressive, expansive T2/FLAIR lesions. Our findings of typically reduced extent of resection in MS patients and increased MS activity after radiation may inform future treatment decisions.
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Affiliation(s)
- Katharina Sahm
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences (MCTN), University of Heidelberg, Mannheim, Germany.
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Eisele
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences (MCTN), University of Heidelberg, Mannheim, Germany
| | - Miriam Ratliff
- Department of Neurosurgery, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences (MCTN), University of Heidelberg, Mannheim, Germany
| | - Elena Sperk
- Department of Radiation Oncology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Laila König
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael O Breckwoldt
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Corinna Seliger
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, Regensburg University Hospital, Regensburg, Germany
| | - Iris Mildenberger
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences (MCTN), University of Heidelberg, Mannheim, Germany
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Pia S Zeiner
- Dr Senckenberg Institute of Neurooncology, University of Frankfurt, Frankfurt, Germany
| | - Ghazaleh Tabatabai
- Department of Neurology & Interdisciplinary Neurooncology, University Hospital Tübingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sven G Meuth
- Department of Neurology, Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neurosciences (MCTN), University of Heidelberg, Mannheim, Germany.
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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5
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Rahmanzade R, Pfaff E, Banan R, Sievers P, Suwala AK, Hinz F, Bogumil H, Cherkezov A, Kaan AF, Schrimpf D, Friedel D, Göbel K, Keller F, Saenz-Sardà X, Lossos A, Sill M, Witt O, Sakowitz OW, Korshunov A, Reuss DE, Etminan N, Unterberg A, Ratliff M, Herold-Mende C, Wick W, Pfister SM, von Deimling A, Jones DTW, Sahm F. Genetical and epigenetical profiling identifies two subgroups of pineal parenchymal tumors of intermediate differentiation (PPTID) with distinct molecular, histological and clinical characteristics. Acta Neuropathol 2023; 146:853-856. [PMID: 37776353 PMCID: PMC10627898 DOI: 10.1007/s00401-023-02638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023]
Affiliation(s)
- Ramin Rahmanzade
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rouzbeh Banan
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Hinz
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henri Bogumil
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asan Cherkezov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aras Fuat Kaan
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kirsten Göbel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Keller
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xavier Saenz-Sardà
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Alexander Lossos
- Departments of Oncology and Neurology, Leslie and Michael Gaffin Center for Neuro-Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver W Sakowitz
- Neurosurgery Center Ludwigsburg-Heilbronn, RKH Klinikum Ludwigsburg, Ludwigsburg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Miriam Ratliff
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Mannheim, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
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6
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Mamatjan Y, Voisin MR, Nassiri F, Moraes FY, Bunda S, So J, Salih M, Shirahata M, Ono T, Shimizu H, Schrimpf D, von Deimling A, Aldape KD, Zadeh G. Integrated molecular analysis reveals hypermethylation and overexpression of HOX genes to be poor prognosticators in isocitrate dehydrogenase mutant glioma. Neuro Oncol 2023; 25:2028-2041. [PMID: 37474126 PMCID: PMC10628942 DOI: 10.1093/neuonc/noad126] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Diffuse gliomas represent over 80% of malignant brain tumors ranging from low-grade to aggressive high-grade lesions. Within isocitrate dehydrogenase (IDH)-mutant gliomas, there is a high variability in survival and a need to more accurately predict outcome. METHODS To identify and characterize a predictive signature of outcome in gliomas, we utilized an integrative molecular analysis (using methylation, mRNA, copy number variation (CNV), and mutation data), analyzing a total of 729 IDH-mutant samples including a test set of 99 from University Health Network (UHN) and 2 validation cohorts including the German Cancer Research Center (DKFZ) and The Cancer Genome Atlas (TCGA). RESULTS Cox regression analysis of methylation data from the UHN cohort identified CpG-based signatures that split the glioma cohort into 2 prognostic groups strongly predicting survival that were validated using 2 independent cohorts from TCGA and DKFZ (all P-values < .0001). The methylation signatures that predicted poor outcomes also exhibited high CNV instability and hypermethylation of HOX gene probes. Integrated multi-platform analyses using mRNA and methylation (iRM) showed that parallel HOX gene overexpression and simultaneous hypermethylation were significantly associated with increased mutational load, high aneuploidy, and worse survival (P-value < .0001). A 7-HOX gene signature was developed and validated using the most significantly associated HOX genes with patient outcome in both 1p/19q codeleted and non-codeleted IDHmut gliomas. CONCLUSIONS HOX gene methylation and expression provide important prognostic information in IDH-mutant gliomas that are not captured by current molecular diagnostics. A 7-HOX gene signature of outcome shows significant survival differences in both 1p/19q codeleted and non-codeleted IDH-mutant gliomas.
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Affiliation(s)
- Yasin Mamatjan
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
- Faculty of Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Mathew R Voisin
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Farshad Nassiri
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Fabio Y Moraes
- Department of Oncology, Queens University, Kingston, Ontario, Canada
| | - Severa Bunda
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Jonathan So
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mira Salih
- Mount Sinai Hospital, New York, New York, USA
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Mitsuaki Shirahata
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
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7
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Kessler T, Schrimpf D, Doerner L, Hai L, Kaulen LD, Ito J, van den Bent M, Taphoorn M, Brandes AA, Idbaih A, Dômont J, Clement PM, Campone M, Bendszus M, von Deimling A, Sahm F, Platten M, Wick W, Wick A. Prognostic Markers of DNA Methylation and Next-Generation Sequencing in Progressive Glioblastoma from the EORTC-26101 Trial. Clin Cancer Res 2023; 29:3892-3900. [PMID: 37494539 PMCID: PMC10543963 DOI: 10.1158/1078-0432.ccr-23-0926] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/07/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE The EORTC-26101 study was a randomized phase II and III clinical trial of bevacizumab in combination with lomustine versus lomustine alone in progressive glioblastoma. Other than for progression-free survival (PFS), there was no benefit from addition of bevacizumab for overall survival (OS). However, molecular data allow for the rare opportunity to assess prognostic biomarkers from primary surgery for their impact in progressive glioblastoma. EXPERIMENTAL DESIGN We analyzed DNA methylation array data and panel sequencing from 170 genes of 380 tumor samples of the EORTC-26101 study. These patients were comparable with the overall study cohort in regard to baseline characteristics, study treatment, and survival. RESULTS Of patients' samples, 295/380 (78%) were classified into one of the main glioblastoma groups, receptor tyrosine kinase (RTK)1, RTK2 and mesenchymal. There were 10 patients (2.6%) with isocitrate dehydrogenase mutant tumors in the biomarker cohort. Patients with RTK1 and RTK2 classified tumors had lower median OS compared with mesenchymal (7.6 vs. 9.2 vs. 10.5 months). O6-methylguanine DNA-methyltransferase (MGMT) promoter methylation was prognostic for PFS and OS. Neurofibromin (NF)1 mutations were predictive of response to bevacizumab treatment. CONCLUSIONS Thorough molecular classification is important for brain tumor clinical trial inclusion and evaluation. MGMT promoter methylation and RTK1 classifier assignment were prognostic in progressive glioblastoma. NF1 mutation may be a predictive biomarker for bevacizumab treatment.
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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, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Laura Doerner
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ling Hai
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Leon D. Kaulen
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Jakob Ito
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Martin Taphoorn
- Haaglanden Medical Center, The Hague, the Netherlands
- Leiden University Medical Center, Leiden, the Netherlands
| | - Alba A. Brandes
- The Medical Oncology Department, Azienda Unità Sanitaria Locale di Bologna–IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Ahmed Idbaih
- Sorbonne Université, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, DMU Neurosciences, Service de Neurologie 2-Mazarin, Paris, France
| | | | | | - Mario Campone
- Institut de Cancerologie de l'Ouest–Centre Rene Gauducheau, SaintHerblain, France
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 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, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Antje Wick
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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8
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Westphal D, Meinhardt M, Grützmann K, Schöne L, Steininger J, Neuhaus LT, Wiegel M, Schrimpf D, Aust DE, Schröck E, Baretton GB, Beissert S, Juratli TA, Schackert GG, Gravemeyer J, Becker JC, von Deimling A, Koelsche C, Klink B, Meier F, Schulz A, Muders MH, Seifert M. Identification of Epigenetically Regulated Genes Distinguishing Intracranial from Extracranial Melanoma Metastases. J Invest Dermatol 2023; 143:1233-1245.e17. [PMID: 36716920 DOI: 10.1016/j.jid.2023.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/13/2022] [Accepted: 01/09/2023] [Indexed: 01/29/2023]
Abstract
Despite remarkable advances in treating patients with metastatic melanoma, the management of melanoma brain metastases remains challenging. Recent evidence suggests that epigenetic reprogramming is an important mechanism for the adaptation of melanoma cells to the brain environment. In this study, the methylomes and transcriptomes of a cohort of matched melanoma metastases were evaluated by integrated omics data analysis. The identified 38 candidate genes displayed distinct promoter methylation and corresponding gene expression changes in intracranial compared with extracranial metastases. The 11 most promising genes were validated on protein level in both tumor and surrounding normal tissue using immunohistochemistry. In accordance with the underlying promoter methylation and gene expression changes, a significantly different protein expression was confirmed for STK10, PDXK, WDR24, CSSP1, NMB, RASL11B, phosphorylated PRKCZ, PRKCZ, and phosphorylated GRB10 in the intracranial metastases. The observed changes imply a distinct intracranial phenotype with increased protein kinase B phosphorylation and a higher frequency of proliferating cells. Knockdown of PRKCZ or GRB10 altered the expression of phosphorylated protein kinase B and decreased the viability of a brain-specific melanoma cell line. In summary, epigenetically regulated cancer-relevant alterations were identified that provide insights into the molecular mechanisms that discriminate brain metastases from other organ metastases, which could be exploited by targeting the affected signaling pathways.
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Affiliation(s)
- Dana Westphal
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.
| | - Matthias Meinhardt
- Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Konrad Grützmann
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Lisa Schöne
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Julian Steininger
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Lena T Neuhaus
- Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Miriam Wiegel
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela E Aust
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany; BioBank Dresden (BBD), Tumor and Normal Tissue Bank (TNTB), National Center for Tumor Diseases (NCT/UCC), University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Gustavo B Baretton
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany; BioBank Dresden (BBD), Tumor and Normal Tissue Bank (TNTB), National Center for Tumor Diseases (NCT/UCC), University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Stefan Beissert
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Tareq A Juratli
- Department of Neurosurgery, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Gabriele G Schackert
- Department of Neurosurgery, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Jan Gravemeyer
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen C Becker
- Translational Skin Cancer Research, German Cancer Consortium (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of General Pathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Klink
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Dresden, Germany; Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Skin Cancer Center at the University Cancer Center and National Center for Tumor Diseases, Dresden, Germany
| | - Alexander Schulz
- Department of Dermatology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Michael H Muders
- Institute of Pathology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Michael Seifert
- National Center for Tumor Diseases (NCT/UCC), Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany; Medizinische Fakultät and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute for Medical Informatics and Biometry, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
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9
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Korshunov A, Okonechnikov K, Schrimpf D, Tonn S, Mynarek M, Koster J, Sievers P, Milde T, Sahm F, Jones DTW, von Deimling A, Pfister SM, Kool M. Transcriptome analysis stratifies second-generation non-WNT/non-SHH medulloblastoma subgroups into clinically tractable subtypes. Acta Neuropathol 2023; 145:829-842. [PMID: 37093271 DOI: 10.1007/s00401-023-02575-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Medulloblastoma (MB), one of the most common malignant pediatric brain tumor, is a heterogenous disease comprised of four distinct molecular groups (WNT, SHH, Group 3, Group 4). Each of these groups can be further subdivided into second-generation MB (SGS MB) molecular subgroups, each with distinct genetic and clinical characteristics. For instance, non-WNT/non-SHH MB (Group 3/4) can be subdivided molecularly into eight distinct and clinically relevant tumor subgroups. A further molecular stratification/summarization of these SGS MB would allow for the assignment of patients to risk-associated treatment protocols. Here, we performed DNA- and RNA-based analysis of 574 non-WNT/non-SHH MB and analyzed the clinical significance of various molecular patterns within the entire cohort and the eight SGS MB, with the aim to develop an optimal risk stratification of these tumors. Multigene analysis disclosed several survival-associated genes highly specific for each molecular subgroup within this non-WNT/non-SHH MB cohort with minimal inter-subgroup overlap. These subgroup-specific and prognostically relevant genes were associated with pathways that could underlie SGS MB clinical-molecular diversity and tumor-driving mechanisms. By combining survival-associated genes within each SGS MB, distinct metagene sets being appropriate for their optimal risk stratification were identified. Defined subgroup-specific metagene sets were independent variables in the multivariate models generated for each SGS MB and their prognostic value was confirmed in a completely non-overlapping validation cohort of non-WNT/non-SHH MB (n = 377). In summary, the current results indicate that the integration of transcriptome data in risk stratification models may improve outcome prediction for each non-WNT/non-SHH SGS MB. Identified subgroup-specific gene expression signatures could be relevant for clinical implementation and survival-associated metagene sets could be adopted for further SGS MB risk stratification. Future studies should aim at validating the prognostic role of these transcriptome-based SGS MB subtypes in prospective clinical trials.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Svenja Tonn
- Pediatric Hematology and Oncology and Mildred Scheel Cancer Career Center HaTriCS4, Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Pediatric Hematology and Oncology and Mildred Scheel Cancer Career Center HaTriCS4, Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Till Milde
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
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10
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Sturm D, Capper D, Andreiuolo F, Gessi M, Kölsche C, Reinhardt A, Sievers P, Wefers AK, Ebrahimi A, Suwala AK, Gielen GH, Sill M, Schrimpf D, Stichel D, Hovestadt V, Daenekas B, Rode A, Hamelmann S, Previti C, Jäger N, Buchhalter I, Blattner-Johnson M, Jones BC, Warmuth-Metz M, Bison B, Grund K, Sutter C, Hirsch S, Dikow N, Hasselblatt M, Schüller U, Koch A, Gerber NU, White CL, Buntine MK, Kinross K, Algar EM, Hansford JR, Gottardo NG, Schuhmann MU, Thomale UW, Hernáiz Driever P, Gnekow A, Witt O, Müller HL, Calaminus G, Fleischhack G, Kordes U, Mynarek M, Rutkowski S, Frühwald MC, Kramm CM, von Deimling A, Pietsch T, Sahm F, Pfister SM, Jones DTW. Multiomic neuropathology improves diagnostic accuracy in pediatric neuro-oncology. Nat Med 2023; 29:917-926. [PMID: 36928815 PMCID: PMC10115638 DOI: 10.1038/s41591-023-02255-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/13/2023] [Indexed: 03/17/2023]
Abstract
The large diversity of central nervous system (CNS) tumor types in children and adolescents results in disparate patient outcomes and renders accurate diagnosis challenging. In this study, we prospectively integrated DNA methylation profiling and targeted gene panel sequencing with blinded neuropathological reference diagnostics for a population-based cohort of more than 1,200 newly diagnosed pediatric patients with CNS tumors, to assess their utility in routine neuropathology. We show that the multi-omic integration increased diagnostic accuracy in a substantial proportion of patients through annotation to a refining DNA methylation class (50%), detection of diagnostic or therapeutically relevant genetic alterations (47%) or identification of cancer predisposition syndromes (10%). Discrepant results by neuropathological WHO-based and DNA methylation-based classification (30%) were enriched in histological high-grade gliomas, implicating relevance for current clinical patient management in 5% of all patients. Follow-up (median 2.5 years) suggests improved survival for patients with histological high-grade gliomas displaying lower-grade molecular profiles. These results provide preliminary evidence of the utility of integrating multi-omics in neuropathology for pediatric neuro-oncology.
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Affiliation(s)
- Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe Andreiuolo
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Laboratory of Neuropathology, Paulo Niemeyer State Brain Institute, Rio de Janeiro, Brazil
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Marco Gessi
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Christian Kölsche
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Philipp Sievers
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neurological Surgery, Helen Diller Research Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gerrit H Gielen
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bjarne Daenekas
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Agata Rode
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Hamelmann
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christopher Previti
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ivo Buchhalter
- Omics IT and Data Management Core Facility, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Barbara C Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Monika Warmuth-Metz
- Department of Diagnostic and Interventional Neuroradiology, University Hospital of Würzburg, Würzburg, Germany
- Neuroradiological Reference Center for the Pediatric Brain Tumor (HIT) Studies of the German Society of Pediatric Oncology and Hematology, University Hospital Würzburg, since 2021 University Hospital Augsburg, Augsburg, Germany
| | - Brigitte Bison
- Neuroradiological Reference Center for the Pediatric Brain Tumor (HIT) Studies of the German Society of Pediatric Oncology and Hematology, University Hospital Würzburg, since 2021 University Hospital Augsburg, Augsburg, Germany
- Diagnostic and Interventional Neuroradiology, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Steffen Hirsch
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas U Gerber
- Department of Oncology, University Children's Hospital Zürich, Zürich, Switzerland
| | - Christine L White
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
- Victorian Clinical Genetics Services, Parkville, VIC, Australia
| | - Molly K Buntine
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
| | - Kathryn Kinross
- Australian and New Zealand Children's Haematology and Oncology Group (ANZCHOG), Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Elizabeth M Algar
- Genetics and Molecular Pathology Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Jordan R Hansford
- Women's and Children's Hospital, South Australia Health and Medical Research Institute, South Australia immunoGENomics Cancer Institute, University of Adelaide, Adelaide, SA, Australia
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital, Nedlands, WA, Australia
- Centre for Child Health Research, University of Western Australia, Nedlands, WA, Australia
- Brain Tumour Research Program, Telethon Kids Institute, Nedlands, WA, Australia
| | | | - Ulrich W Thomale
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Pablo Hernáiz Driever
- German HIT-LOGGIC Registry for low-grade glioma in children and adolescents, Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Astrid Gnekow
- Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, Faculty of Medicine, University Augsburg, Augsburg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hermann L Müller
- Department of Pediatrics and Pediatric Hematology/Oncology, University Children's Hospital, Klinikum Oldenburg AöR, Oldenburg, Germany
| | - Gabriele Calaminus
- Department of Pediatric Hematology and Oncology, University Childrens' Hospital Muenster, Muenster, Germany
| | - Gudrun Fleischhack
- Pediatric Hematology and Oncology, Pediatrics III, University Children's Hospital of Essen, Essen, Germany
| | - Uwe Kordes
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Mynarek
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael C Frühwald
- Swabian Children's Cancer Center, Paediatric and Adolescent Medicine, Faculty of Medicine, University Augsburg, Augsburg, Germany
| | - Christof M Kramm
- Department of Child and Adolescent Health, Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
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11
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Kommoss FKF, Chong AS, Chong AL, Pfaff E, Jones DTW, Hiemcke-Jiwa LS, Kester LA, Flucke U, Gessler M, Schrimpf D, Sahm F, Clarke BA, Stewart CJR, Wang Y, Gilks CB, Kommoss F, Huntsman DG, Schüller U, Koelsche C, Glenn McCluggage W, von Deimling A, Foulkes WD. Genomic characterization of DICER1-associated neoplasms uncovers molecular classes. Nat Commun 2023; 14:1677. [PMID: 36966138 PMCID: PMC10039902 DOI: 10.1038/s41467-023-37092-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/28/2023] [Indexed: 03/27/2023] Open
Abstract
DICER1 syndrome is a tumor predisposition syndrome that is associated with up to 30 different neoplastic lesions, usually affecting children and adolescents. Here we identify a group of mesenchymal tumors which is highly associated with DICER1 syndrome, and molecularly distinct from other DICER1-associated tumors. This group of DICER1-associated mesenchymal tumors encompasses multiple well-established clinicopathological tumor entities and can be further divided into three clinically meaningful classes designated "low-grade mesenchymal tumor with DICER1 alteration" (LGMT DICER1), "sarcoma with DICER1 alteration" (SARC DICER1), and primary intracranial sarcoma with DICER1 alteration (PIS DICER1). Our study not only provides a combined approach to classify DICER1-associated neoplasms for improved clinical management but also suggests a role for global hypomethylation and other recurrent molecular events in sarcomatous differentiation in mesenchymal tumors with DICER1 alteration. Our results will facilitate future investigations into prognostication and therapeutic approaches for affected patients.
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Affiliation(s)
- Felix K F Kommoss
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anne-Sophie Chong
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Avinguda de la Granvia de L'Hospitalet, Barcelona, Spain
| | - Anne-Laure Chong
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Elke Pfaff
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Laura S Hiemcke-Jiwa
- Department of Pathology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Lennart A Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Uta Flucke
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University & Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Blaise A Clarke
- Department of Pathology, University Health Network, Toronto, ON, Canada
| | - Colin J R Stewart
- Department of Anatomical Pathology, King Edward Memorial Hospital, Subiaco, WA, Australia
- School for Women's and Infants' Health, University of Western Australia, Perth, WA, Australia
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christian Koelsche
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - W Glenn McCluggage
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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12
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Sievers P, Sill M, Schrimpf D, Abdullaev Z, Donson AM, Lake JA, Friedel D, Scheie D, Tynninen O, Rauramaa T, Vepsäläinen KL, Samuel D, Chapman R, Grundy RG, Pajtler KW, Tauziède-Espariat A, Métais A, Varlet P, Snuderl M, Jacques TS, Aldape K, Reuss DE, Korshunov A, Wick W, Pfister SM, von Deimling A, Sahm F, Jones DTW. Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature. NPJ Precis Oncol 2023; 7:30. [PMID: 36964296 PMCID: PMC10039012 DOI: 10.1038/s41698-023-00372-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
Pediatric neoplasms in the central nervous system (CNS) show extensive clinical and molecular heterogeneity and are fundamentally different from those occurring in adults. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Here, we investigated a rare, molecularly distinct type of pediatric high-grade neuroepithelial tumor (n = 18), that was identified through unsupervised visualization of genome-wide DNA methylation array data, together with copy number profiling, targeted next-generation DNA sequencing, and RNA transcriptome sequencing. DNA and/or RNA sequencing revealed recurrent fusions involving the capicua transcriptional repressor (CIC) gene in 10/10 tumor samples analyzed, with the most common fusion being CIC::LEUTX (n = 9). In addition, a CIC::NUTM1 fusion was detected in one of the tumors. Apart from the detected fusion events, no additional oncogenic alteration was identified in these tumors. The histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. All tumors were located in the supratentorial compartment, occurred during childhood (median age 8.5 years) and typically showed early relapses. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC. Downstream functional consequences of the fusion protein CIC::LEUTX and potential therapeutic implications need to be further investigated.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew M Donson
- Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica A Lake
- Center for Cancer and Blood Disorders, Children's Hospital Colorado, Aurora, CO, USA
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Olli Tynninen
- Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
- Unit of Pathology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa L Vepsäläinen
- Department of Pediatrics, Kuopio University Hospital, University of Kuopio, Kuopio, Finland
| | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Rebecca Chapman
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Alice Métais
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris-Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Thomas S Jacques
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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13
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Bogumil H, Sill M, Schrimpf D, Ismer B, Blume C, Rahmanzade R, Hinz F, Cherkezov A, Banan R, Friedel D, Reuss DE, Selt F, Ecker J, Milde T, Pajtler KW, Schittenhelm J, Hench J, Frank S, Boldt HB, Kristensen BW, Scheie D, Melchior LC, Olesen V, Sehested A, Boué DR, Abdullaev Z, Satgunaseelan L, Kurth I, Seidlitz A, White CL, Ng HK, Shi ZF, Haberler C, Deckert M, Timmer M, Goldbrunner R, Tauziède-Espariat A, Varlet P, Brandner S, Alexandrescu S, Snuderl M, Aldape K, Korshunov A, Witt O, Herold-Mende C, Unterberg A, Wick W, Pfister SM, von Deimling A, Jones DTW, Sahm F, Sievers P. Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA): a molecularly distinct brain tumor type with recurrent NTRK gene fusions. Acta Neuropathol 2023; 145:667-680. [PMID: 36933012 PMCID: PMC10119244 DOI: 10.1007/s00401-023-02558-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023]
Abstract
Glioneuronal tumors are a heterogenous group of CNS neoplasms that can be challenging to accurately diagnose. Molecular methods are highly useful in classifying these tumors-distinguishing precise classes from their histological mimics and identifying previously unrecognized types of tumors. Using an unsupervised visualization approach of DNA methylation data, we identified a novel group of tumors (n = 20) that formed a cluster separate from all established CNS tumor types. Molecular analyses revealed ATRX alterations (in 16/16 cases by DNA sequencing and/or immunohistochemistry) as well as potentially targetable gene fusions involving receptor tyrosine-kinases (RTK; mostly NTRK1-3) in all of these tumors (16/16; 100%). In addition, copy number profiling showed homozygous deletions of CDKN2A/B in 55% of cases. Histological and immunohistochemical investigations revealed glioneuronal tumors with isomorphic, round and often condensed nuclei, perinuclear clearing, high mitotic activity and microvascular proliferation. Tumors were mainly located supratentorially (84%) and occurred in patients with a median age of 19 years. Survival data were limited (n = 18) but point towards a more aggressive biology as compared to other glioneuronal tumors (median progression-free survival 12.5 months). Given their molecular characteristics in addition to anaplastic features, we suggest the term glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA) to describe these tumors. In summary, our findings highlight a novel type of glioneuronal tumor driven by different RTK fusions accompanied by recurrent alterations in ATRX and homozygous deletions of CDKN2A/B. Targeted approaches such as NTRK inhibition might represent a therapeutic option for patients suffering from these tumors.
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Affiliation(s)
- Henri Bogumil
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Britta Ismer
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ramin Rahmanzade
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Hinz
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Asan Cherkezov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rouzbeh Banan
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jens Schittenhelm
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Eberhard-Karls-University Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, Tübingen, Germany.,Department of Neuropathology, University Hospital Tübingen, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Jürgen Hench
- Division of Neuropathology, Institute for Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Division of Neuropathology, Institute for Pathology, University Hospital Basel, Basel, Switzerland
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Bjarne Winther Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Pathology, The Bartholin Institute, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine and Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Linea C Melchior
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Viola Olesen
- Spine Unit, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel R Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital and the Ohio State University, Columbus, OH, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Ina Kurth
- Division of Radiooncology-Radiobiology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekatrin Seidlitz
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg and German Consortium for Translational Cancer Research (DKTK) Partner Site, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,Helmholtz Association/Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
| | - Christine L White
- Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Australia.,Victorian Clinical Genetics Services, Parkville, Australia
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, China
| | - Zhi-Feng Shi
- Hong Kong and Shanghai Brain Consortium (HSBC), Hong Kong, China.,Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martina Deckert
- Institute of Neuropathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Marco Timmer
- Laboratory for Neurooncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Roland Goldbrunner
- Laboratory for Neurooncology and Experimental Neurosurgery, Department of General Neurosurgery, Center for Neurosurgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Arnault Tauziède-Espariat
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France.,Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris - Psychiatry and Neuroscience, Sainte-Anne Hospital, Paris, France.,Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR S1266, INSERM, IMA-BRAIN, Paris, France
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | | | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program, National Center for Tumor Diseases (NCT), Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany. .,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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14
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Okonechnikov K, Federico A, Schrimpf D, Sievers P, Sahm F, Koster J, Jones DTW, von Deimling A, Pfister SM, Kool M, Korshunov A. Comparison of transcriptome profiles between medulloblastoma primary and recurrent tumors uncovers novel variance effects in relapses. Acta Neuropathol Commun 2023; 11:7. [PMID: 36635768 PMCID: PMC9837941 DOI: 10.1186/s40478-023-01504-1] [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: 11/25/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
Nowadays medulloblastoma (MB) tumors can be treated with risk-stratified approaches with up to 80% success rate. However, disease relapses occur in approximately 30% of patients and successful salvage treatment strategies at relapse remain scarce. Acquired copy number changes or TP53 mutations are known to occur frequently in relapses, while methylation profiles usually remain highly similar to those of the matching primary tumors, indicating that in general molecular subgrouping does not change during the course of the disease. In the current study, we have used RNA sequencing data to analyze the transcriptome profiles of 43 primary-relapse MB pairs in order to identify specific molecular features of relapses within various tumor groups. Gene variance analysis between primary and relapse samples demonstrated the impact of age in SHH-MB: the changes in gene expression relapse profiles were more pronounced in the younger patients (< 10 years old), which were also associated with increased DNA aberrations and somatic mutations at relapse probably driving this effect. For Group 3/4 MB transcriptome data analysis uncovered clear sets of genes either active or decreased at relapse that are significantly associated with survival, thus could be potential predictive markers. In addition, deconvolution analysis of bulk transcriptome data identified progression-associated differences in cell type enrichment. The proportion of undifferentiated progenitors increased in SHH-MB relapses with a concomitant decrease of differentiated neuron-like cells, while in Group 3/4 MB relapses cell cycle activity increases and differentiated neuron-like cells proportion decreases as well. Thus, our findings uncovered significant transcriptome changes in the molecular signatures of relapsed MB and could be potentially useful for further clinical purposes.
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Affiliation(s)
- Konstantin Okonechnikov
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Aniello Federico
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sievers
- grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Koster
- grid.7177.60000000084992262Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.487647.ePrincess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Andrey Korshunov
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
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15
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Reuss DE, Schrimpf D, Stichel D, Ebrahimi A, Dampier C, Aldape K, Snuderl M, Capper D, Sill M, Jones DTW, Pfister SM, Sahm F, von Deimling A. Reference on copy number variations in pleomorphic xanthoastrocytoma: Implications for diagnostic approach. Free Neuropathol 2023; 4:4-19. [PMID: 38026572 PMCID: PMC10646999 DOI: 10.17879/freeneuropathology-2023-5156] [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] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Pleomorphic xanthoastrocytoma (PXA) poses a diagnostic challenge. The present study relies on methylation-based predictions and focuses on copy number variations (CNV) in PXA. We identified 551 tumors from patients having received the histologic diagnosis or differential diagnosis pleomorphic xanthoastrocytoma (PXA) uploaded to the web page www.molecularneuropathology.org. Of these 551 tumors, 165 received the prediction "methylation class (anaplastic) pleomorphic xanthoastrocytoma" with a calibrated score >=0.9 by the brain tumor classifier version v12.8 and, therefore, were defined the PXA reference set designated mcPXAref. In addition to these 165 mcPXAref, 767 other tumors received the prediction mcPXA with a calibrated score >=0.9 but without a histological PXA diagnosis. The total number of individual tumors predicted by histology and/or by methylome based classification as PXA, mcPXA or both was 1318, and these were designated the study cohort. The selection of a control cohort was guided by methylation-based predictions recurrently observed for the other 386/551 tumors diagnosed as histologic PXA. 131/386 received predictions for another entity besides PXA with a score >=0.9. Control tumors corresponding to the 11 most common other predictions were selected, adding up to 1100 reference cases. CNV profiles were calculated from all methylation datasets of the study and control cohorts. Special attention was given to the 7/10 signature, gene amplifications and homozygous deletion of CDKN2A/B. Comparison of CNV in the subsets of the study cohort and the control cohort were used to establish relations independent of histological diagnoses. Tumors in mcPXA were highly homogenous in regard to CNV alterations, irrespective of the histological diagnoses. The 7/10 signature commonly present in glioblastoma, IDH-wildtype, was present in 15-20% of mcPXA, whereas amplification of oncogenes (likewise common in glioblastoma) was very rare in mcPXA (<1%). In contrast, the histology-based PXA group exhibited high variance in regard to methylation classes as well as to CNVs. Our data add to the notion, that histologically defined PXA likely only represent a subset of the biological disease.
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Affiliation(s)
- David E. Reuss
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Chris Dampier
- Laboratory of Pathology, National Cancer Institute, Centre for Cancer Research, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, Centre for Cancer Research, Bethesda, MD, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health and School of Medicine, New York, New York, USA
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M. Pfister
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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16
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Patel A, Dogan H, Jung A, Seferbekova Z, Payne A, Ritter M, Schrimpf D, Stichel D, Hamelmann S, Blume C, Euskirchen P, Goidts V, Sill M, Pfister S, Loose M, Wick W, von Deimling A, Jones DT, Schlesner M, Gerstung M, Sahm F. PATH-46. COMPUTATIONAL HISTOPATHOLOGY INFORMED RAPID TARGETED NANOPORE SEQUENCING ENABLES AFFORDABLE NEXT DAY REPORTING OF COMPREHENSIVE MOLECULAR MARKERS FOR CNS TUMOUR DIAGNOSTICS. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
BACKGROUND
Integrative brain tumour diagnostics indisputably requires comprehensive reporting of molecular markers. The 2021 WHO classification of central nervous system (CNS) tumours substantially increased the set of markers for routine evaluation, with greater significance to DNA methylation analysis in diagnostics. Limited by investment and batching, smaller labs and clinics might suffer major delays in delivering clinical decisions. To make precision diagnostics accessible, we introduce an integrated computational histopathology and adaptive nanopore sequencing workflow for next day CNS tumour diagnostics.
METHODS
We used CNS-CHiP- a multitask deep transfer learning model to predict key molecular alterations and methylation classification from H&E stained CNS tumour slides. For further characterisation and subtyping, we used the predictions to formulate a custom panel for each patient. Targeted sequencing and analyses were performed using Rapid-CNS2- a custom neurooncology nanopore sequencing pipeline for parallel copy-number, mutational and methylation analysis that is flexible in target selection with no additional library preparation and can be initiated upon receipt of frozen sections. Sequencing was performed on a portable MinION or GridION.
RESULTS
We demonstrate our workflow on diagnostic samples received by the Department of Neuropathology, University Hospital Heidelberg. CNS-CHiP predicted multiple pathognomonic alterations (eg. IDH mutation, 7 gain/10 loss) with reasonable accuracy. This provided basic information regarding the tumor type instantly. Personalised panels enabled small target sizes, resulting in low sequencing time (up to 24h) and competitive costs. The GPU-accelerated bioinformatics pipeline reduced analysis time from > 24h to < 3h.
CONCLUSIONS
Our workflow harnessing histology-based molecular predictions to instruct targeted nanopore sequencing can be set up with low initial investment and has the potential to facilitate reporting of molecular results on the next day of sample collection. CNS-CHiP combined with Rapid-CNS2 thus aims to make CNS tumour diagnostics affordable and accessible to smaller hospitals and labs especially in low- and middle-income countries.
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Affiliation(s)
- Areeba Patel
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ), Heidelberg , Baden-Wurttemberg , Germany
| | - Helin Dogan
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Jung
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI , Cambridge , United Kingdom
| | - Zaira Seferbekova
- Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Payne
- DeepSeq, School of Life Sciences, University of Nottingham , Nottingham , United Kingdom
| | - Michael Ritter
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan Hamelmann
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christina Blume
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Philipp Euskirchen
- Department of Neurology, Charité-Universitätsmedizin Berlin , Berlin , Germany
| | - Violaine Goidts
- Brain Tumor Translational Targets, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ) , Heidelberg , Germany
| | - Stefan Pfister
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany , Heidelberg , Germany
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham , Nottingham , United Kingdom
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg , Baden-Wurttemberg , Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - David T Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg University Hospital and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Matthias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, Augsburg University , Augsburg , Germany
| | - Moritz Gerstung
- Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
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17
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Reinhardt A, Pfister K, Schrimpf D, Stichel D, Sahm F, Reuss DE, Capper D, Wefers AK, Ebrahimi A, Sill M, Felsberg J, Reifenberger G, Becker A, Prinz M, Staszewski O, Hartmann C, Schittenhelm J, Gramatzki D, Weller M, Olar A, Rushing EJ, Bergmann M, Farrell MA, Blümcke I, Coras R, Beckervordersandforth J, Kim SH, Rogerio F, Dimova PS, Niehusmann P, Unterberg A, Platten M, Pfister SM, Wick W, Herold-Mende C, von Deimling A. Anaplastic ganglioglioma - a diagnosis comprising several distinct tumour types. Neuropathol Appl Neurobiol 2022; 48:e12847. [PMID: 35977725 DOI: 10.1111/nan.12847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 03/12/2022] [Revised: 07/20/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Anaplastic ganglioglioma is a rare tumour and diagnosis has been based on histological criteria. The 5th edition of the World Health Organization Classification of Tumours of the Central Nervous System (CNS WHO) does not list anaplastic ganglioglioma as a distinct diagnosis due to lack of molecular data in previous publications AIM: We retrospectively compiled a cohort of 54 histologically diagnosed anaplastic gangliogliomas to explore whether the molecular profiles of these tumours represent a separate type or resolve into other entities METHODS: Samples were subjected to histological review, DNA methylation profiling and next generation sequencing. Morphologic and molecular data were summarised to an integrated diagnosis RESULTS: The majority of histologically diagnosed anaplastic gangliogliomas resolved into CNS WHO diagnoses of glial tumours, most commonly pleomorphic xanthoastrocytoma (16/54), glioblastoma, IDH wildtype and diffuse paediatric-type high-grade glioma, H3 wildtype and IDH wildtype (11 and 2/54) followed by low-grade glial or glioneuronal tumours including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumour and diffuse leptomeningeal glioneuronal tumour (5/54), IDH mutant astrocytoma (4/54) and others (6/54). A subset of tumours (10/54) was not assignable to a CNS WHO diagnosis and common molecular profiles pointing to a separate entity were not evident CONCLUSION: In summary, we show that tumours histologically diagnosed as anaplastic ganglioglioma comprise a wide spectrum of CNS WHO tumour types with different prognostic and therapeutic implications. We therefore suggest assigning this designation with caution and recommend comprehensive molecular workup.
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Affiliation(s)
- Annekathrin Reinhardt
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Current address: Centre for Human Genetics Tübingen, Tübingen, Germany
| | - Kristin Pfister
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Pathology, Kantonsspital Winterthur, Winterthur, Switzerland
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Martin Sill
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Joerg Felsberg
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ori Staszewski
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Hannover Medical School, Hannover, Germany
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, University Tübingen, Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Dorothee Gramatzki
- Department of Neurology, University Hospital and University Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology, University Hospital and University Zurich, Zurich, Switzerland
| | | | | | - Markus Bergmann
- Institute of Neuropathology, Center for Pathology, Klinikum Bremen Mitte, Bremen, Germany
| | | | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Roland Coras
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Jan Beckervordersandforth
- Department of Pathology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Se Hoon Kim
- Department of Pathology, Yonsei University, College of Medicine, Seoul, South Korea
| | - Fabio Rogerio
- Department of Pathology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Petia S Dimova
- Epilepsy Surgery Center, Department of Neurosurgery, St. Ivan Rilski University Hospital, Sofia, Bulgaria
| | - Pitt Niehusmann
- Section of Neuropathology, Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Andreas Unterberg
- Clinic for Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Clinical Cooperation Unit Neuroimmunology and Brain Tumour Immunology, German Cancer Research Center (DKFZ), Heidelberg
| | - Stefan M Pfister
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Paediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Core Center Heidelberg, Germany.,Neurology Clinic, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Germany
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18
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Adeberg S, Knoll M, Koelsche C, Bernhardt D, Schrimpf D, Sahm F, König L, Harrabi SB, Hörner-Rieber J, Verma V, Bewerunge-Hudler M, Unterberg A, Sturm D, Jungk C, Herold-Mende C, Wick W, von Deimling A, Debus J, Rieken S, Abdollahi A. DNA-methylome-assisted classification of patients with poor prognostic subventricular zone associated IDH-wildtype glioblastoma. Acta Neuropathol 2022; 144:129-142. [PMID: 35660939 PMCID: PMC9217840 DOI: 10.1007/s00401-022-02443-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/04/2022] [Accepted: 05/21/2022] [Indexed: 11/25/2022]
Abstract
Glioblastoma (GBM) derived from the “stem cell” rich subventricular zone (SVZ) may constitute a therapy-refractory subgroup of tumors associated with poor prognosis. Risk stratification for these cases is necessary but is curtailed by error prone imaging-based evaluation. Therefore, we aimed to establish a robust DNA methylome-based classification of SVZ GBM and subsequently decipher underlying molecular characteristics. MRI assessment of SVZ association was performed in a retrospective training set of IDH-wildtype GBM patients (n = 54) uniformly treated with postoperative chemoradiotherapy. DNA isolated from FFPE samples was subject to methylome and copy number variation (CNV) analysis using Illumina Platform and cnAnalysis450k package. Deep next-generation sequencing (NGS) of a panel of 130 GBM-related genes was conducted (Agilent SureSelect/Illumina). Methylome, transcriptome, CNV, MRI, and mutational profiles of SVZ GBM were further evaluated in a confirmatory cohort of 132 patients (TCGA/TCIA). A 15 CpG SVZ methylation signature (SVZM) was discovered based on clustering and random forest analysis. One third of CpG in the SVZM were associated with MAB21L2/LRBA. There was a 14.8% (n = 8) discordance between SVZM vs. MRI classification. Re-analysis of these patients favored SVZM classification with a hazard ratio (HR) for OS of 2.48 [95% CI 1.35–4.58], p = 0.004 vs. 1.83 [1.0–3.35], p = 0.049 for MRI classification. In the validation cohort, consensus MRI based assignment was achieved in 62% of patients with an intraclass correlation (ICC) of 0.51 and non-significant HR for OS (2.03 [0.81–5.09], p = 0.133). In contrast, SVZM identified two prognostically distinct subgroups (HR 3.08 [1.24–7.66], p = 0.016). CNV alterations revealed loss of chromosome 10 in SVZM– and gains on chromosome 19 in SVZM– tumors. SVZM– tumors were also enriched for differentially mutated genes (p < 0.001). In summary, SVZM classification provides a novel means for stratifying GBM patients with poor prognosis and deciphering molecular mechanisms governing aggressive tumor phenotypes.
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Affiliation(s)
- Sebastian Adeberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Maximilian Knoll
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Denise Bernhardt
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Radiation Oncology, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Laila König
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Semi Ben Harrabi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juliane Hörner-Rieber
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Vivek Verma
- Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center Houston, Houston, TX, USA
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Andreas Unterberg
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Angelika Lautenschläger Children's Hospital, University Medical Center for Children and Adolescents, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Christine Jungk
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Christel Herold-Mende
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neurooncology, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- Department of Neuropathology, University Hospital of Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Juergen Debus
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Rieken
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Heidelberg Institute for Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), UKHD and DKFZ, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
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19
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Felix M, Friedel D, Jayavelu AK, Filipski K, Reinhardt A, Warnken U, Stichel D, Schrimpf D, Korshunov A, Wang Y, Kessler T, Etminan N, Unterberg A, Herold-Mende C, Heikaus L, Sahm F, Wick W, Harter PN, von Deimling A, Reuss DE. HIP1R and vimentin immunohistochemistry predict 1p/19q status in IDH-mutant glioma. Neuro Oncol 2022; 24:2121-2132. [PMID: 35511748 PMCID: PMC9713528 DOI: 10.1093/neuonc/noac111] [Citation(s) in RCA: 4] [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] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND IDH-mutant gliomas are separate based on the codeletion of the chromosomal arms 1p and 19q into oligodendrogliomas IDH-mutant 1p/19q-codeleted and astrocytomas IDH-mutant. While nuclear loss of ATRX expression excludes 1p/19q codeletion, its limited sensitivity prohibits to conclude on 1p/19q status in tumors with retained nuclear ATRX expression. METHODS Employing mass spectrometry based proteomic analysis in a discovery series containing 35 fresh frozen and 72 formalin fixed and paraffin embedded tumors with established IDH and 1p/19q status, potential biomarkers were discovered. Subsequent validation immunohistochemistry was conducted on two independent series (together 77 oligodendrogliomas IDH-mutant 1p/19q-codeleted and 92 astrocytomas IDH-mutant). RESULTS We detected highly specific protein patterns distinguishing oligodendroglioma and astrocytoma. In these patterns, high HIP1R and low vimentin levels were observed in oligodendroglioma while low HIP1R and high vimentin levels occurred in astrocytoma. Immunohistochemistry for HIP1R and vimentin expression in 35 cases from the FFPE discovery series confirmed these findings. Blinded evaluation of the validation cohorts predicted the 1p/19q status with a positive and negative predictive value as well as an accuracy of 100% in the first cohort and with a positive predictive value of 83%; negative predictive value of 100% and an accuracy of 92% in the second cohort. Nuclear ATRX loss as marker for astrocytoma increased the sensitivity to 96% and the specificity to 100%. CONCLUSIONS We demonstrate that immunohistochemistry for HIP1R, vimentin, and ATRX predict 1p/19q status with 100% specificity and 95% sensitivity and therefore, constitutes a simple and inexpensive approach to the classification of IDH-mutant glioma.
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Affiliation(s)
- Marius Felix
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Ashok Kumar Jayavelu
- Clinical Cooperation Unit Pediatric Leukemia, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany,Hopp Children’s Cancer Center Heidelberg - KiTZ, Heidelberg, Germany,Molecular Medicine Partnership Unit, EMBL, Heidelberg, Germany
| | - Katharina Filipski
- Institute of Neurology, (Edinger Institute), University Hospital, Frankfurt Am Main, Germany,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany,University Cancer Center (UCT), Frankfurt, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Yueting Wang
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg
| | - Andreas Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick N Harter
- Institute of Neurology, (Edinger Institute), University Hospital, Frankfurt Am Main, Germany,German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany,Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - David E Reuss
- Corresponding Author: David E. Reuss, MD, Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany ()
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20
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Patel A, Dogan H, Payne A, Krause E, Sievers P, Schoebe N, Schrimpf D, Blume C, Stichel D, Holmes N, Euskirchen P, Hench J, Frank S, Rosenstiel-Goidts V, Ratliff M, Etminan N, Unterberg A, Dieterich C, Herold-Mende C, Pfister SM, Wick W, Loose M, von Deimling A, Sill M, Jones DTW, Schlesner M, Sahm F. Rapid-CNS 2: rapid comprehensive adaptive nanopore-sequencing of CNS tumors, a proof-of-concept study. Acta Neuropathol 2022; 143:609-612. [PMID: 35357562 PMCID: PMC9038836 DOI: 10.1007/s00401-022-02415-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 01/01/2023]
Affiliation(s)
- Areeba Patel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Helin Dogan
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Alexander Payne
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Elena Krause
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Natalie Schoebe
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Nadine Holmes
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Philipp Euskirchen
- Department of Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jürgen Hench
- Division of Neuropathology, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Division of Neuropathology, Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Miriam Ratliff
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany
| | | | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthew Loose
- DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 224, 69120, Heidelberg, Germany.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
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21
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Lyskjær I, Kara N, De Noon S, Davies C, Rocha AM, Strobl AC, Usher I, Gerrand C, Strauss SJ, Schrimpf D, von Deimling A, Beck S, Flanagan AM. Osteosarcoma: Novel prognostic biomarkers using circulating and cell-free tumour DNA. Eur J Cancer 2022; 168:1-11. [PMID: 35421838 DOI: 10.1016/j.ejca.2022.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/03/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023]
Abstract
AIM Osteosarcoma (OS) is the most common primary bone tumour in children and adolescents. Circulating free (cfDNA) and circulating tumour DNA (ctDNA) are promising biomarkers for disease surveillance and prognostication in several cancer types; however, few such studies are reported for OS. The purpose of this study was to discover and validate methylation-based biomarkers to detect plasma ctDNA in patients with OS and explore their utility as prognostic markers. METHODS Candidate CpG markers were selected through analysis of methylation array data for OS, non-OS tumours and germline samples. Candidates were validated in two independent OS datasets (n = 162, n = 107) and the four top-performing markers were selected. Methylation-specific digital droplet PCR (ddPCR) assays were designed and experimentally validated in OS tumour samples (n = 20) and control plasma samples. Finally, ddPCR assays were applied to pre-operative plasma and where available post-operative plasma from 72 patients with OS, and findings correlated with outcome. RESULTS Custom ddPCR assays detected ctDNA in 69% and 40% of pre-operative plasma samples (n = 72), based on thresholds of one or two positive markers respectively. ctDNA was detected in 5/17 (29%) post-operative plasma samples from patients, which in four cases were associated with or preceded disease relapse. Both pre-operative cfDNA levels and ctDNA detection independently correlated with overall survival (p = 0.0015 and p = 0.0096, respectively). CONCLUSION Our findings illustrate the potential of mutation-independent methylation-based ctDNA assays for OS. This study lays the foundation for multi-institutional collaborative studies to explore the utility of plasma-derived biomarkers in the management of OS.
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Affiliation(s)
- Iben Lyskjær
- Research Department of Pathology, University College London, London, UK; Medical Genomics Research Group, University College London, London, UK
| | - Neesha Kara
- Medical Genomics Research Group, University College London, London, UK
| | - Solange De Noon
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Christopher Davies
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Ana Maia Rocha
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Anna-Christina Strobl
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | - Inga Usher
- Research Department of Pathology, University College London, London, UK
| | - Craig Gerrand
- Bone Tumour Unit, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK
| | | | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, and CCU Neuropathology, German Cancer Institute, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, and CCU Neuropathology, German Cancer Institute, Heidelberg, Germany
| | - Stephan Beck
- Medical Genomics Research Group, University College London, London, UK
| | - Adrienne M Flanagan
- Research Department of Pathology, University College London, London, UK; Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK.
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22
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Berghoff AS, Hielscher T, Ricken G, Furtner J, Schrimpf D, Widhalm G, Rajky U, Marosi C, Hainfellner JA, von Deimling A, Sahm F, Preusser M. Prognostic impact of genetic alterations and methylation classes in meningioma. Brain Pathol 2022; 32:e12970. [PMID: 35213082 PMCID: PMC8877750 DOI: 10.1111/bpa.12970] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/23/2020] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022] Open
Abstract
Meningiomas are classified based on histological features, but genetic and epigenetic features are emerging as relevant biomarkers for outcome prediction and may supplement histomorphological evaluation. We investigated meningioma‐relevant mutations and their correlation with DNA methylation clusters and patient survival times. Formalin‐fixed and paraffin‐embedded samples of 126 meningioma patients (WHO grade I 52/126; 41.3%; WHO grade II: 48/126; 38.1%; WHO grade III: 26/126; 20.6%) were investigated. We analyzed NF2, TRAF7, KLF4, ARID, SMO, AKT,TERT promotor, PIK3CA, and SUFU mutations using panel sequencing and correlated them to DNA methylation classes (MC) determined using 850k EPIC arrays. The TRAKL mutation genotype was characterized by the presence of any of the following mutations: TRAF7, AKT1, and KLF4. Survival data including progression‐free survival (PFS) and overall survival (OS) was retrieved from chart review. Mutations were evident in 90/126 (71.4%) specimens with mutations in NF2 (39/126; 31.0%), TRAF7 (39/126; 31.0%) and KLF4 (25/126; 19.8%) being the most frequent ones. Two or more mutations were observed in 35/126 (27.8%) specimens. While TRAKL was predominantly found in benign MC, NF2 was associated with malign MC (p < 0.05). TRAF7, KLF4, and TRAKL mutation genotype were associated with improved PFS and OS (p < 0.05). TERT promotor methylation, intermediate, and malign MC were associated with impaired PFS and OS (p < 0.05). Methylation cluster showed better prognostic discrimination for PFS and OS (c‐index 0.77/0.75) than each of the individual mutations (c‐index 0.63/0.68). In multivariate analysis correcting for age, gender, MC, and WHO grade, none of the individual mutations except TERT remained an independent significant prognostic factor for PFS. Molecular profiling including mutational analysis and DNA methylation classification may facilitate more precise prognostic assessment and identification of potential targets for personalized therapy in meningioma patients.
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Affiliation(s)
- Anna S Berghoff
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ, Heidelberg, Germany
| | - Gerda Ricken
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Julia Furtner
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg Widhalm
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Ursula Rajky
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christine Marosi
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | | | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Preusser
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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23
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Suwala AK, Felix M, Friedel D, Stichel D, Schrimpf D, Hinz F, Hewer E, Schweizer L, Dohmen H, Pohl U, Staszewski O, Korshunov A, Stein M, Wongsurawat T, Cheunsuacchon P, Sathornsumetee S, Koelsche C, Turner C, Le Rhun E, Mühlebner A, Schucht P, Özduman K, Ono T, Shimizu H, Prinz M, Acker T, Herold-Mende C, Kessler T, Wick W, Capper D, Wesseling P, Sahm F, von Deimling A, Hartmann C, Reuss DE. Oligosarcomas, IDH-mutant are distinct and aggressive. Acta Neuropathol 2022; 143:263-281. [PMID: 34967922 PMCID: PMC8742817 DOI: 10.1007/s00401-021-02395-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/30/2021] [Revised: 11/15/2021] [Accepted: 12/05/2021] [Indexed: 01/21/2023]
Abstract
Oligodendrogliomas are defined at the molecular level by the presence of an IDH mutation and codeletion of chromosomal arms 1p and 19q. In the past, case reports and small studies described gliomas with sarcomatous features arising from oligodendrogliomas, so called oligosarcomas. Here, we report a series of 24 IDH-mutant oligosarcomas from 23 patients forming a distinct methylation class. The tumors were recurrences from prior oligodendrogliomas or developed de novo. Precursor tumors of 12 oligosarcomas were histologically and molecularly indistinguishable from conventional oligodendrogliomas. Oligosarcoma tumor cells were embedded in a dense network of reticulin fibers, frequently showing p53 accumulation, positivity for SMA and CALD1, loss of OLIG2 and gain of H3K27 trimethylation (H3K27me3) as compared to primary lesions. In 5 oligosarcomas no 1p/19q codeletion was detectable, although it was present in the primary lesions. Copy number neutral LOH was determined as underlying mechanism. Oligosarcomas harbored an increased chromosomal copy number variation load with frequent CDKN2A/B deletions. Proteomic profiling demonstrated oligosarcomas to be highly distinct from conventional CNS WHO grade 3 oligodendrogliomas with consistent evidence for a smooth muscle differentiation. Expression of several tumor suppressors was reduced with NF1 being lost frequently. In contrast, oncogenic YAP1 was aberrantly overexpressed in oligosarcomas. Panel sequencing revealed mutations in NF1 and TP53 along with IDH1/2 and TERT promoter mutations. Survival of patients was significantly poorer for oligosarcomas as first recurrence than for grade 3 oligodendrogliomas as first recurrence. These results establish oligosarcomas as a distinct group of IDH-mutant gliomas differing from conventional oligodendrogliomas on the histologic, epigenetic, proteomic, molecular and clinical level. The diagnosis can be based on the combined presence of (a) sarcomatous histology, (b) IDH-mutation and (c) TERT promoter mutation and/or 1p/19q codeletion, or, in unresolved cases, on its characteristic DNA methylation profile.
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24
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Ebrahimi A, Korshunov A, Reifenberger G, Capper D, Felsberg J, Trisolini E, Pollo B, Calatozzolo C, Prinz M, Staszewski O, Schweizer L, Schittenhelm J, Harter PN, Paulus W, Thomas C, Kohlhof-Meinecke P, Seiz-Rosenhagen M, Milde T, Casalini BM, Suwala A, Wefers AK, Reinhardt A, Sievers P, Kramm CM, Etminam N, Unterberg A, Wick W, Herold-Mende C, Sturm D, Pfister SM, Sill M, Jones DTW, Schrimpf D, Reuss DE, Aldape K, Abdullaev Z, Sahm F, von Deimling A, Stichel D. Pleomorphic xanthoastrocytoma is a heterogeneous entity with pTERT mutations prognosticating shorter survival. Acta Neuropathol Commun 2022; 10:5. [PMID: 35012690 PMCID: PMC8751269 DOI: 10.1186/s40478-021-01308-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/26/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
Pleomorphic xanthoastrocytoma (PXA) in its classic manifestation exhibits distinct morphological features and is assigned to CNS WHO grade 2 or grade 3. Distinction from glioblastoma variants and lower grade glial and glioneuronal tumors is a common diagnostic challenge. We compared a morphologically defined set of PXA (histPXA) with an independent set, defined by DNA methylation analysis (mcPXA). HistPXA encompassed 144 tumors all subjected to DNA methylation array analysis. Sixty-two histPXA matched to the methylation class mcPXA. These were combined with the cases that showed the mcPXA signature but had received a histopathological diagnosis other than PXA. This cohort constituted a set of 220 mcPXA. Molecular and clinical parameters were analyzed in these groups. Morphological parameters were analyzed in a subset of tumors with FFPE tissue available. HistPXA revealed considerable heterogeneity in regard to methylation classes, with methylation classes glioblastoma and ganglioglioma being the most frequent mismatches. Similarly, the mcPXA cohort contained tumors of diverse histological diagnoses, with glioblastoma constituting the most frequent mismatch. Subsequent analyses demonstrated the presence of canonical pTERT mutations to be associated with unfavorable prognosis among mcPXA. Based on these data, we consider the tumor type PXA to be histologically more varied than previously assumed. Histological approach to diagnosis will predominantly identify cases with the established archetypical morphology. DNA methylation analysis includes additional tumors in the tumor class PXA that share similar DNA methylation profile but lack the typical morphology of a PXA. DNA methylation analysis also assist in separating other tumor types with morphologic overlap to PXA. Our data suggest the presence of canonical pTERT mutations as a robust indicator for poor prognosis in methylation class PXA.
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25
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Sievers P, Sill M, Schrimpf D, Friedel D, Sturm D, Gardberg M, Kurian KM, Krskova L, Vicha A, Schaller T, Hagel C, Abdullaev Z, Aldape K, Jacques TS, Korshunov A, Wick W, Pfister SM, von Deimling A, Jones DTW, Sahm F. Epigenetic profiling reveals a subset of pediatric-type glioneuronal tumors characterized by oncogenic gene fusions involving several targetable kinases. Acta Neuropathol 2022; 144:1049-1052. [PMID: 36070143 PMCID: PMC9547789 DOI: 10.1007/s00401-022-02492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 01/26/2023]
Affiliation(s)
- Philipp Sievers
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dennis Friedel
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Gardberg
- grid.410552.70000 0004 0628 215XDepartment of Pathology, Turku University Hospital, Turku, Finland ,grid.1374.10000 0001 2097 1371Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kathreena M. Kurian
- grid.5337.20000 0004 1936 7603Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lenka Krskova
- grid.412826.b0000 0004 0611 0905Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic ,grid.412826.b0000 0004 0611 0905Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- grid.412826.b0000 0004 0611 0905Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic ,grid.412826.b0000 0004 0611 0905Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Tina Schaller
- grid.7307.30000 0001 2108 9006Pathology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Christian Hagel
- grid.13648.380000 0001 2180 3484Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Zied Abdullaev
- grid.48336.3a0000 0004 1936 8075Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Kenneth Aldape
- grid.48336.3a0000 0004 1936 8075Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Thomas S. Jacques
- grid.83440.3b0000000121901201Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK ,grid.451052.70000 0004 0581 2008Department of Histopathology, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Andrey Korshunov
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- grid.5253.10000 0001 0328 4908Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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Korshunov A, Okonechnikov K, Stichel D, Schrimpf D, Delaidelli A, Tonn S, Mynarek M, Sievers P, Sahm F, Jones DTW, von Deimling A, Pfister SM, Kool M. Gene expression profiling of Group 3 medulloblastomas defines a clinically tractable stratification based on KIRREL2 expression. Acta Neuropathol 2022; 144:339-352. [PMID: 35771282 PMCID: PMC9288368 DOI: 10.1007/s00401-022-02460-1] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
Medulloblastomas (MB) molecularly designated as Group 3 (Grp 3) MB represent a more clinically aggressive tumor variant which, as a group, displays heterogeneous molecular characteristics and disease outcomes. Reliable risk stratification of Grp 3 MB would allow for appropriate assignment of patients to aggressive treatment protocols and, vice versa, for sparing adverse effects of high-dose radio-chemotherapy in patients with standard or low-risk tumors. Here we performed RNA-based analysis on an international cohort of 179 molecularly designated Grp 3 MB treated with HIT protocols. We analyzed the clinical significance of differentially expressed genes, thereby developing optimal prognostic subdivision of this MB molecular group. We compared the transcriptome profiles of two Grp 3 MB subsets with various outcomes (76 died within the first 60 months vs. 103 survived this period) and identified 224 differentially expressed genes (DEG) between these two clinical groups (Limma R algorithm, adjusted p-value < 0.05). We selected the top six DEG overexpressed in the unfavorable cohort for further survival analysis and found that expression of all six genes strongly correlated with poor outcomes. However, only high expression of KIRREL2 was identified as an independent molecular prognostic indicator of poor patients' survival. Based on clinical and molecular patterns, four risk categories were outlined for Grp 3 MB patients: i. low-risk: M0-1/MYC non-amplified/KIRREL2 low (n = 48; 5-year OS-95%); ii. standard-risk: M0-1/MYC non-amplified/KIRREL2 high or M2-3/MYC non-amplified/KIRREL2 low (n = 65; 5-year OS-70%); iii. high-risk: M2-3/MYC non-amplified/KIRREL2 high (n = 36; 5-year OS-30%); iv. very high risk-all MYC amplified tumors (n = 30; 5-year OS-0%). Cross-validated survival models incorporating KIRREL2 expression with clinical features allowed for the reclassification of up to 50% of Grp 3 MB patients into a more appropriate risk category. Finally, KIRREL2 immunopositivity was also identified as a predictive indicator of Grp 3 MB poor survival, thus suggesting its application as a possible prognostic marker in routine clinical settings. Our results indicate that integration of KIRREL2 expression in risk stratification models may improve Grp 3 MB outcome prediction. Therefore, simple gene and/or protein expression analyses for this molecular marker could be easily adopted for Grp 3 MB prognostication and may help in assigning patients to optimal therapeutic approaches in prospective clinical trials.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany. .,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Konstantin Okonechnikov
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC Canada ,Department of Pathology and Laboratory Medicine, British Columbia Cancer Research Centre, Vancouver, BC Canada
| | - Svenja Tonn
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Martin Mynarek
- Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David T. W. Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Glioma Research (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany ,German Cancer Consortium (DKTK), Heidelberg, Germany ,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Stefan M. Pfister
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany ,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- German Cancer Consortium (DKTK), Heidelberg, Germany ,Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany ,Division of Pediatric Neuro-Oncology (B062), German Cancer Research Center (DKFZ), Heidelberg, Germany ,Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
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27
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Maas SLN, Stichel D, Hielscher T, Sievers P, Berghoff AS, Schrimpf D, Sill M, Euskirchen P, Blume C, Patel A, Dogan H, Reuss D, Dohmen H, Stein M, Reinhardt A, Suwala AK, Wefers AK, Baumgarten P, Ricklefs F, Rushing EJ, Bewerunge-Hudler M, Ketter R, Schittenhelm J, Jaunmuktane Z, Leu S, Greenway FEA, Bridges LR, Jones T, Grady C, Serrano J, Golfinos J, Sen C, Mawrin C, Jungk C, Hänggi D, Westphal M, Lamszus K, Etminan N, Jungwirth G, Herold-Mende C, Unterberg A, Harter PN, Wirsching HG, Neidert MC, Ratliff M, Platten M, Snuderl M, Aldape KD, Brandner S, Hench J, Frank S, Pfister SM, Jones DTW, Reifenberger G, Acker T, Wick W, Weller M, Preusser M, von Deimling A, Sahm F. Integrated Molecular-Morphologic Meningioma Classification: A Multicenter Retrospective Analysis, Retrospectively and Prospectively Validated. J Clin Oncol 2021; 39:3839-3852. [PMID: 34618539 PMCID: PMC8713596 DOI: 10.1200/jco.21.00784] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Meningiomas are the most frequent primary intracranial tumors. Patient outcome varies widely from benign to highly aggressive, ultimately fatal courses. Reliable identification of risk of progression for individual patients is of pivotal importance. However, only biomarkers for highly aggressive tumors are established (CDKN2A/B and TERT), whereas no molecularly based stratification exists for the broad spectrum of patients with low- and intermediate-risk meningioma. METHODS DNA methylation data and copy-number information were generated for 3,031 meningiomas (2,868 patients), and mutation data for 858 samples. DNA methylation subgroups, copy-number variations (CNVs), mutations, and WHO grading were analyzed. Prediction power for outcome was assessed in a retrospective cohort of 514 patients, validated on a retrospective cohort of 184, and on a prospective cohort of 287 multicenter cases. RESULTS Both CNV- and methylation family-based subgrouping independently resulted in increased prediction accuracy of risk of recurrence compared with the WHO classification (c-indexes WHO 2016, CNV, and methylation family 0.699, 0.706, and 0.721, respectively). Merging all risk stratification approaches into an integrated molecular-morphologic score resulted in further substantial increase in accuracy (c-index 0.744). This integrated score consistently provided superior accuracy in all three cohorts, significantly outperforming WHO grading (c-index difference P = .005). Besides the overall stratification advantage, the integrated score separates more precisely for risk of progression at the diagnostically challenging interface of WHO grade 1 and grade 2 tumors (hazard ratio 4.34 [2.48-7.57] and 3.34 [1.28-8.72] retrospective and prospective validation cohorts, respectively). CONCLUSION Merging these layers of histologic and molecular data into an integrated, three-tiered score significantly improves the precision in meningioma stratification. Implementation into diagnostic routine informs clinical decision making for patients with meningioma on the basis of robust outcome prediction.
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Affiliation(s)
- Sybren L N Maas
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Damian Stichel
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Hielscher
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna S Berghoff
- Institute of Neurology, Medical University of Vienna, Vienna, Austria.,Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Daniel Schrimpf
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Philipp Euskirchen
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christina Blume
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Areeba Patel
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Helin Dogan
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Reuss
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hildegard Dohmen
- Department of Neuropathology, University Hospital Gießen, Giessen, Germany
| | - Marco Stein
- Department of Neuropathology, University Hospital Gießen, Giessen, Germany.,Department of Neurosurgery, University Hospital Gießen, Giessen, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Baumgarten
- Department of Neurosurgery, University Hospital Frankfurt, Frankfurt, Germany
| | - Franz Ricklefs
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Elisabeth J Rushing
- Department of Neuropathology, University Hospital Zurich, Zürich, Switzerland
| | | | - Ralf Ketter
- Department of Neurosurgery, University Hospital Homburg, Homburg, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Zane Jaunmuktane
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, United Kingdom.,Department of Clinical and Movement Neurosciences and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Severina Leu
- Department of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Fay E A Greenway
- Department of Neurosurgery, St George's Hospital, London, United Kingdom
| | - Leslie R Bridges
- Department of Cellular Pathology, St George's Hospital, London, United Kingdom
| | - Timothy Jones
- Department of Neurosurgery, St George's Hospital, London, United Kingdom
| | - Conor Grady
- Department of Neurosurgery, NYU Langone Hospital, New York, NY
| | | | - John Golfinos
- Department of Neurosurgery, NYU Langone Hospital, New York, NY
| | - Chandra Sen
- Department of Neurosurgery, NYU Langone Hospital, New York, NY
| | - Christian Mawrin
- Department of Neuropathology, University Hospital Magdeburg, Magdeburg, Germany
| | - Christine Jungk
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Medicine Mannheim, Mannheim, Germany
| | - Gerhard Jungwirth
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Exp. Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt, Germany.,Frankfurt Cancer Institute (FCI) and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Heidelberg, Germany
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Marian C Neidert
- Department of Neurosurgery, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Miriam Ratliff
- Department of Neurosurgery, University Medicine Mannheim, Mannheim, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, MCTN, Heidelberg University, Heidelberg, Germany
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY
| | | | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London, United Kingdom.,Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jürgen Hench
- Department of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Department of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.,Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University Medical Faculty, Düsseldorf, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Germany
| | - Till Acker
- Department of Neuropathology, University Hospital Gießen, Giessen, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Matthias Preusser
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg and CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
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28
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Sievers P, Stichel D, Sill M, Schrimpf D, Sturm D, Selt F, Ecker J, Kazdal D, Miele E, Kranendonk MEG, Tops BBJ, Kohlhof-Meinecke P, Beschorner R, Kramm CM, Hasselblatt M, Reifenberger G, Capper D, Wesseling P, Stenzinger A, Milde T, Korshunov A, Witt O, Pfister SM, Wick W, von Deimling A, Jones DTW, Sahm F. GOPC:ROS1 and other ROS1 fusions represent a rare but recurrent drug target in a variety of glioma types. Acta Neuropathol 2021; 142:1065-1069. [PMID: 34536122 PMCID: PMC8568855 DOI: 10.1007/s00401-021-02369-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
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29
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Patel A, Dogan H, Payne A, Sievers P, Schoebe N, Schrimpf D, Stichel D, Holmes N, Euskirchen P, Hench J, Frank S, Rosenstiel-Goidts V, Dieterich C, Herold-Mende C, Pfister S, Wick W, Schlesner M, Loose M, Jones D, von Deimling A, Sill M, Sahm F. PATH-48. RAPID-CNS2: RAPID COMPREHENSIVE ADAPTIVE NANOPORE-SEQUENCING OF CNS TUMORS, A PROOF OF CONCEPT STUDY. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
The WHO classification 2021 includes multiple molecular markers for routine diagnostics in addition to histology. Sequencing setup for complete molecular profiling requires considerable investment, while batching samples for sequencing and methylation profiling can delay turnaround time. We introduce RAPID-CNS2, a nanopore adaptive sequencing pipeline that enables comprehensive mutational, methylation and copy number profiling of CNS tumours with a single third generation sequencing assay. It can be run for single samples and offers highly flexible target selection requiring no additional library preparation.
METHODS
Utilising ReadFish, a toolkit enabling targeted nanopore sequencing, we sequenced DNA from 22 diffuse glioma patient samples on a MinION device. Target regions comprised our Heidelberg brain tumour NGS panel and pre-selected CpG sites for methylation classification by an adapted random forest classifier. Pathognomonic alterations, copy number profiles, and methylation classes were called using a custom bioinformatics pipeline. Results were compared to their corresponding NGS panel-seq and EPIC array outputs.
RESULTS
Complete concordance with the EPIC array was found for copy number profiles from RAPID-CNS2. 94% pathognomonic mutations were congruent with NGS panel-seq. MGMT promoter status was correctly identified in all samples. Methylation families were detected with 96% congruence. Among the alterations decisive for rendering a classification-compatible integrated diagnosis, 97% of the alterations were consistent over the entire cohort (completely congruent in 19/22 cases and sufficient for unequivocal diagnosis in all).
CONCLUSIONS
RAPID-CNS2 provides a swift and highly flexible alternative to conventional NGS and array- based methods for SNV/Indel analysis, detection of copy number alterations and methylation classification. The turnaround time of ~4 days can be further shortened to < 12h by altering target sizes. It offers a low-capital approach that would be cost-efficient for low throughput settings and invaluable in cases requiring immediate diagnoses.
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Affiliation(s)
- Areeba Patel
- German Cancer Research Center, Heidelberg, Baden-Wurttemberg, Germany
| | - Helin Dogan
- German Cancer Research Center, Heidelberg, Baden-Wurttemberg, Germany
| | | | - Philipp Sievers
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Daniel Schrimpf
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Damian Stichel
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Jürgen Hench
- Dept. of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Dept. of Neuropathology, University Hospital Basel, Basel, Switzerland
| | | | | | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, Ruprechts-Karls-University, Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | | | | | - David Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Felix Sahm
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
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30
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Maas S, Stichel D, Hielscher T, Sievers P, Berghoff A, Schrimpf D, Sill M, Euskirchen P, Reuss D, Dohmen H, Stein M, Baumgarten P, Ricklefs F, Rushing E, Bewerunge-Hudler M, Ketter R, Schittenhelm J, Jaunmuktane Z, Leu S, Grady C, Serrano J, Golfinos J, Sen C, Mawrin C, Jungk C, Hänggi D, Westphal M, Lamszus K, Etminan N, Unterberg A, Harter P, Wirsching HG, Neidert MC, Ratliff M, Platten M, Snuderl M, Aldape K, Brandner S, Hench J, Frank S, Pfister S, Jones D, Reifenberger G, Acker T, Wick W, Weller M, Preusser M, von Deimling A, Sahm F. PATH-39. INTEGRATED MOLECULAR-MORPHOLOGICAL MENINGIOMA CLASSIFICATION: A MULTICENTER RETROSPECTIVE ANALYSIS, RETRO- AND PROSPECTIVELY VALIDATED. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
PURPOSE
Meningiomas are the most frequent primary intracranial tumors. Patient outcome varies widely from cases with benign to highly aggressive, ultimately fatal courses. Reliable identification of risk of progression for the individual patient is of pivotal importance in clinical management. However, only biomarkers for highly aggressive tumors are established at present (CDKN2A/B and TERT), while no molecularly-based stratification exists for the broad spectrum of low- and intermediate-risk meningioma patients.
PATIENTS AND METHODS
DNA methylation data and copy-number information were generated for 3,031 meningiomas of 2,868 individual patients, with mutation data for 858 samples. DNA methylation subgroups, copy-number variations (CNV), mutations and WHO grading were comparatively analyzed. Prediction power for outcome of these parameters was assessed in an initial retrospective cohort of 514 patients, and validated on a retrospective cohort of 184, and on a prospective cohort of 287 multi-center cases, respectively.
RESULTS
Both CNV and methylation family- (MF)-based subgrouping independently resulted in an increase in prediction accuracy of risk of recurrence compared to the WHO classification (c-indexes WHO 2016, CNV, and MF 0.699, 0.706 and 0.721, respectively). Merging all independently powerful risk stratification approaches into an integrated molecular-morphological score resulted in a further, substantial increase in accuracy (c-index 0.744). This integrated score consistently provided superior accuracy in all three cohorts, significantly outperforming WHO grading (c-index difference p=0.005). Besides the overall stratification advantage, the integrated score separates more precisely for risk of progression at the diagnostically challenging interface of WHO grade 1 and grade 2 tumors (HR 4.56 [2.97;7.00], 4.34 [2.48;7.57] and 3.34 [1.28; 8.72] for discovery, retrospective, and prospective validation cohort, respectively).
CONCLUSIONS
Merging these layers of histological and molecular data into an integrated, three-tiered score significantly improves the precision in meningioma stratification. Implementation into diagnostic routine informs clinical decision-making for meningioma patients on the basis of robust outcome prediction.
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Affiliation(s)
- Sybren Maas
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Damian Stichel
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Hielscher
- Dept. of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna Berghoff
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Daniel Schrimpf
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | | | - David Reuss
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hildegard Dohmen
- Dept. of Neuropathology, University Hospital Gießen, Gießen, Germany
| | - Marco Stein
- Dept. of Neurosurgery, University Hospital Giessen, Germany, Gießen, Germany
| | - Peter Baumgarten
- Dept. of Neurosurgery, University Hospital Frankfurt, Frankfurt, Germany
| | - Franz Ricklefs
- Dept. of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Elizabeth Rushing
- Dept. of Neuropathology, University Hospital Zurich, Zürich, Switzerland
| | | | - Ralf Ketter
- Dept. of Neurosurgery, University Hospital Homburg, Homburg, Germany
| | - Jens Schittenhelm
- Eberhard-Karls University Tübingen, Department of Neuropathology, Tübingen, Germany
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences and Queen Square Brain Bank for Neurological Disorders, University College London, London, United Kingdom
| | - Severina Leu
- Dept. of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Conor Grady
- Department of Neurosurgery, NYU Langone Hospital, New York, USA
| | | | - John Golfinos
- Department of Neurosurgery, NYU Langone Hospital, New York, USA
| | - Chandra Sen
- Department of Neurosurgery, NYU Langone Hospital, New York, USA
| | - Christian Mawrin
- Dept. of Neuropathology, University Hospital Magdeburg, Magdeburg, Germany
| | - Christine Jungk
- Dept. of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Hänggi
- Dept. of Neurosurgery, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg-Eppendorf, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nima Etminan
- Dept. of Neurosurgery, University Medicine Mannheim, Mannheim, Germany
| | - Andreas Unterberg
- Division of Experimental Neurosurgery, Department of Neurosurgery, Ruprechts-Karls-University Heidelberg, Heidelberg, Germany
| | - Patrick Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt, Germany
| | - Hans-Georg Wirsching
- Dept. of Neurology, University Hospital and University of Zurich, Zürich, Switzerland
| | | | - Miriam Ratliff
- Dept. of Neurosurgery, University Medicine Mannheim, Mannheim, Germany
| | - Michael Platten
- Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matija Snuderl
- Department of Pathology at NYU Grossman School of Medicine, New York City, NY, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
| | - Jürgen Hench
- Dept. of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Dept. of Neuropathology, University Hospital Basel, Basel, Switzerland
| | - Stefan Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - David Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| | - Till Acker
- Dept. of Neuropathology, University Hospital Gießen, Gießen, Germany
| | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Michael Weller
- University Hospital and University of Zurich, Zurich, Switzerland
| | - Matthias Preusser
- Dept. of Medicine, Clinical Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
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Suwala AK, Felix M, Friedel D, Stichel D, Schrimpf D, Hewer E, Schweizer L, Dohmen H, Pohl U, Erny D, Koelsche C, Turner C, Özduman K, Prinz M, Acker T, Herold-Mende C, Wick W, Capper D, Wesseling P, Sahm F, von Deimling A, Hartmann C, Reuss D. PATH-23. OLIGOSARCOMA, IDH-MUTANT IS A DISTINCT AGGRESSIVE TYPE. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Oligodendrogliomas are defined by IDH-mutations and the co-deletion of chromosomal arms 1p and 19q. In the past, case reports and small series described gliomas with sarcomatous features arising from oligodendrogliomas, so called oligosarcomas. Here, we report a group of 23 IDH-mutant oligosarcomas that form a distinct methylation group. The tumors were recurrences from prior oligodendrogliomas or developed de novo. Precursor tumors of 11 oligosarcomas were histologically and molecularly indistinguishable from conventional oligodendrogliomas. Tumor cells were embedded in a reticulin fibers network in all oligosarcomas, frequently showing p53 accumulation, positivity for SMA, and regain of H3K27me3 as compared to primary lesions. In 5 oligosarcomas no 1p/19q co-deletion was detectable, even though it was present in the primary lesions. Oligosarcomas harbored an increased chromosomal copy number variation load with frequent CDKN2A/B deletions. Proteomic profiling demonstrated oligosarcomas to be highly distinct from conventional grade 3 oligodendrogliomas with consistent evidence for smooth muscle differentiation. Expression of several tumor suppressors including NF1 and STAG2 was lost whereas oncogenic YAP1 was aberrantly overexpressed in oligosarcomas. Panel sequencing revealed mutations in TP53 and NF1 along with IDH1/2 and TERT promoter mutations. Survival of patients was significantly poorer for oligosarcomas as for grade 3 oligodendrogliomas but comparable to grade 4 IDH-mutant astrocytomas. These results establish oligosarcoma as a distinct type of IDH-mutant glioma differing from conventional oligodendrogliomas on the histologic, epigenetic, proteomic, molecular and clinical level. Diagnosis can be based on the characteristic DNA methylation profile or the combined evidence of sarcomatous histology, IDH-mutation and TERT promoter mutation with or without 1p/19q co-deletion.
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Affiliation(s)
- Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, DKFZ, Heidelberg, Germany
| | - Marius Felix
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Dennis Friedel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Damian Stichel
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Schrimpf
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ekkehard Hewer
- Institute of Pathology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Leonille Schweizer
- Institute for Neuropathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hildegard Dohmen
- Dept. of Neuropathology, University Hospital Gießen, Gießen, Germany
| | - Ute Pohl
- Department of Pathology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Daniel Erny
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christian Koelsche
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Clinton Turner
- Centre for Brain Research, Department of Anatomy and Medical Imaging, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Koray Özduman
- Department of Neurosurgery, Acıbadem University, School of Medicine, Istanbul, Istanbul, Turkey
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Till Acker
- Dept. of Neuropathology, University Hospital Gießen, Gießen, Germany
| | | | - Wolfgang Wick
- Department of Neurology, Heidelberg University Hospital and National Center for Tumor Diseases (NCT), Heidelberg, USA
| | - David Capper
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | | | - Felix Sahm
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - David Reuss
- Dept. of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
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32
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Sievers P, Henneken SC, Blume C, Sill M, Schrimpf D, Stichel D, Okonechnikov K, Reuss DE, Benzel J, Maaß KK, Kool M, Sturm D, Zheng T, Ghasemi DR, Kohlhof-Meinecke P, Cruz O, Suñol M, Lavarino C, Ruf V, Boldt HB, Pagès M, Pouget C, Schweizer L, Kranendonk MEG, Akhtar N, Bunkowski S, Stadelmann C, Schüller U, Mueller WC, Dohmen H, Acker T, Harter PN, Mawrin C, Beschorner R, Brandner S, Snuderl M, Abdullaev Z, Aldape K, Gilbert MR, Armstrong TS, Ellison DW, Capper D, Ichimura K, Reifenberger G, Grundy RG, Jabado N, Krskova L, Zapotocky M, Vicha A, Varlet P, Wesseling P, Rutkowski S, Korshunov A, Wick W, Pfister SM, Jones DTW, von Deimling A, Pajtler KW, Sahm F. Recurrent fusions in PLAGL1 define a distinct subset of pediatric-type supratentorial neuroepithelial tumors. Acta Neuropathol 2021; 142:827-839. [PMID: 34355256 PMCID: PMC8500895 DOI: 10.1007/s00401-021-02356-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Ependymomas encompass a heterogeneous group of central nervous system (CNS) neoplasms that occur along the entire neuroaxis. In recent years, extensive (epi-)genomic profiling efforts have identified several molecular groups of ependymoma that are characterized by distinct molecular alterations and/or patterns. Based on unsupervised visualization of a large cohort of genome-wide DNA methylation data, we identified a highly distinct group of pediatric-type tumors (n = 40) forming a cluster separate from all established CNS tumor types, of which a high proportion were histopathologically diagnosed as ependymoma. RNA sequencing revealed recurrent fusions involving the pleomorphic adenoma gene-like 1 (PLAGL1) gene in 19 of 20 of the samples analyzed, with the most common fusion being EWSR1:PLAGL1 (n = 13). Five tumors showed a PLAGL1:FOXO1 fusion and one a PLAGL1:EP300 fusion. High transcript levels of PLAGL1 were noted in these tumors, with concurrent overexpression of the imprinted genes H19 and IGF2, which are regulated by PLAGL1. Histopathological review of cases with sufficient material (n = 16) demonstrated a broad morphological spectrum of tumors with predominant ependymoma-like features. Immunohistochemically, tumors were GFAP positive and OLIG2- and SOX10 negative. In 3/16 of the cases, a dot-like positivity for EMA was detected. All tumors in our series were located in the supratentorial compartment. Median age of the patients at the time of diagnosis was 6.2 years. Median progression-free survival was 35 months (for 11 patients with data available). In summary, our findings suggest the existence of a novel group of supratentorial neuroepithelial tumors that are characterized by recurrent PLAGL1 fusions and enriched for pediatric patients.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sophie C Henneken
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christina Blume
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Benzel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kendra K Maaß
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tuyu Zheng
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - David R Ghasemi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Ofelia Cruz
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mariona Suñol
- Department of Pathology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Cinzia Lavarino
- Laboratory of Molecular Oncology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Viktoria Ruf
- Institute of Neuropathology, Ludwig-Maximilian University, Munich, Germany
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mélanie Pagès
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
- Laboratory of Translational Research in Pediatric Oncology, SIREDO, INSERM U830, Institut Curie, Paris Sciences Lettres University, Paris, France
| | | | - Leonille Schweizer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mariëtte E G Kranendonk
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Noreen Akhtar
- Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, UK
- Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Stephanie Bunkowski
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Christine Stadelmann
- Institute for Neuropathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Wolf C Mueller
- Paul-Flechsig Institute of Neuropathology, University Hospital and Faculty of Medicine, Leipzig, Germany
| | - Hildegard Dohmen
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Patrick N Harter
- Frankfurt Cancer Institute (FCI), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institute of Neurology (Edinger-Institute), University Hospital, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto-Von-Guericke University, Magdeburg, Germany
| | - Rudi Beschorner
- Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | | | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neuropathology, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Koichi Ichimura
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen/Düsseldorf, Germany
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- Department of Pediatrics, McGill University, Montreal, QC, H4A 3J1, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, H4A 3J1, Canada
| | - Lenka Krskova
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michal Zapotocky
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Haematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Pascale Varlet
- Department of Neuropathology, GHU Paris Psychiatry and Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
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33
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Delaidelli A, Dunham C, Santi M, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, Ellison DW, von Deimling A, Kool M, Pfister SM, Ramaswamy V, Korshunov A, Taylor MD, Sorensen PH. Clinically Tractable Outcome Prediction of non-WNT/non-SHH Medulloblastoma Based on TPD52 Immunohistochemistry in a Multicohort Study. Clin Cancer Res 2021; 28:116-128. [PMID: 34702771 DOI: 10.1158/1078-0432.ccr-21-2057] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/12/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE International consensus and the 2021 WHO classification recognize eight molecular subgroups among non-WNT/non-SHH (Group 3/4) medulloblastoma, representing ~60% of tumors. However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation profiles or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk stratification. EXPERIMENTAL DESIGN We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. RESULTS TPD52 IHC positivity represented a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67-26.7 [95% CIs between 1.00-706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing state-of-the-art risk stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity was a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53-45.40], p < 0.0001), suggesting important implication for therapeutic choices. CONCLUSIONS The current study redefines the approach to risk stratification in Group 3/4 medulloblastoma in global practice. Since integration of TPD52 IHC in classification algorithms significantly improved outcome prediction, this test could be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
- Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, and University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariarita Santi
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Joanna Triscott
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Olga Zheludkova
- St Luka's Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
| | - Daniel Schrimpf
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andreas von Deimling
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)
- Department of Pediatric Hematology and Oncology, University Hospital, Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrey Korshunov
- Department of Neuropathology of Heidelberg University and CCU Neuropathology, German Cancer Research Center, Heidelberg, Germany
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Korshunov A, Okonechnikov K, Stichel D, Ryzhova M, Schrimpf D, Sahm F, Sievers P, Absalyamova O, Zheludkova O, Golanov A, Jones DTW, Pfister SM, von Deimling A, Kool M. Integrated molecular analysis of adult sonic hedgehog (SHH)-activated medulloblastomas reveals two clinically relevant tumor subsets with VEGFA as potent prognostic indicator. Neuro Oncol 2021; 23:1576-1585. [PMID: 33589929 PMCID: PMC8408884 DOI: 10.1093/neuonc/noab031] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Up to now, adult medulloblastoma (MB) patients are treated according to the protocols elaborated for pediatric MB although these tumors are different in terms of clinical outcomes and biology. Approximately 70% of adult MB disclose a sonic hedgehog (SHH) molecular signature in contrast to about 30% in pediatric cohorts. In addition, adult SHH-MB (aSHH-MB) are clinically heterogeneous but there is consensus neither on their optimal treatment nor on risk stratification. Thus, the identification of clinically relevant molecular subsets of aSHH-MB and identification of potential treatment targets remains inconclusive. METHODS We analyzed 96 samples of institutionally diagnosed aSHH-MB through genome-wide DNA methylation profiling, targeted DNA sequencing, and RNA sequencing to identify molecular subcategories of these tumors and assess their prognostic significance. RESULTS We defined two aSHH-MB numerically comparable epigenetic subsets with clinical and molecular variability. The subset "aSHH-MBI" (46%/48%) was associated with PTCH1/SMO (54%/46%) mutations, "neuronal" transcriptional signatures, and favorable outcomes after combined radio-chemotherapy (5-year PFS = 80% and OS = 92%). The clinically unfavorable "aSHH-MBII" subset (50%/52%; 5-year PFS = 24% and OS = 45%) disclosed GLI2 amplifications (8%), loss of 10q (22%), and gene expression signatures associated with angiogenesis and embryonal development. aSHH-MBII tumors revealed strong and ubiquitous expression of VEGFA both at transcript and protein levels that was correlated with unfavorable outcome. CONCLUSIONS (1) The histologically uniform aSHH-MB cohort exhibits clear molecular heterogeneity separating these tumors into two molecular subsets (aSHH-MBI and aSHH-MBII), which are associated with different cytogenetics, mutational landscapes, gene expression signatures, and clinical course. (2) VEGFA appears to be a promising biomarker to predict clinical course, which needs further prospective validation as its potential role in the pathogenesis of this subset.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Konstantin Okonechnikov
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Marina Ryzhova
- N.N. Burdenko Neurosurgical Research Centre, Moscow, Russia
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Philipp Sievers
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | | | - Olga Zheludkova
- Department of Neuro-Oncology, Russian Scientific Center of Radiology, Moscow, Russia
| | - Andrey Golanov
- N.N. Burdenko Neurosurgical Research Centre, Moscow, Russia
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group (B360), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Suwala AK, Stichel D, Schrimpf D, Maas SLN, Sill M, Dohmen H, Banan R, Reinhardt A, Sievers P, Hinz F, Blattner-Johnson M, Hartmann C, Schweizer L, Boldt HB, Kristensen BW, Schittenhelm J, Wood MD, Chotard G, Bjergvig R, Das A, Tabori U, Hasselblatt M, Korshunov A, Abdullaev Z, Quezado M, Aldape K, Harter PN, Snuderl M, Hench J, Frank S, Acker T, Brandner S, Winkler F, Wesseling P, Pfister SM, Reuss DE, Wick W, von Deimling A, Jones DTW, Sahm F. Glioblastomas with primitive neuronal component harbor a distinct methylation and copy-number profile with inactivation of TP53, PTEN, and RB1. Acta Neuropathol 2021; 142:179-189. [PMID: 33876327 PMCID: PMC8217054 DOI: 10.1007/s00401-021-02302-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 12/11/2022]
Abstract
Glioblastoma IDH-wildtype presents with a wide histological spectrum. Some features are so distinctive that they are considered as separate histological variants or patterns for the purpose of classification. However, these usually lack defined (epi-)genetic alterations or profiles correlating with this histology. Here, we describe a molecular subtype with overlap to the unique histological pattern of glioblastoma with primitive neuronal component. Our cohort consists of 63 IDH-wildtype glioblastomas that harbor a characteristic DNA methylation profile. Median age at diagnosis was 59.5 years. Copy-number variations and genetic sequencing revealed frequent alterations in TP53, RB1 and PTEN, with fewer gains of chromosome 7 and homozygous CDKN2A/B deletions than usually described for IDH-wildtype glioblastoma. Gains of chromosome 1 were detected in more than half of the cases. A poorly differentiated phenotype with frequent absence of GFAP expression, high proliferation index and strong staining for p53 and TTF1 often caused misleading histological classification as carcinoma metastasis or primitive neuroectodermal tumor. Clinically, many patients presented with leptomeningeal dissemination and spinal metastasis. Outcome was poor with a median overall survival of only 12 months. Overall, we describe a new molecular subtype of IDH-wildtype glioblastoma with a distinct histological appearance and genetic signature.
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Affiliation(s)
- Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Sybren L N Maas
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hildegard Dohmen
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Rouzbeh Banan
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Felix Hinz
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Henning B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Bjarne Winther Kristensen
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine and Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jens Schittenhelm
- Institute of Pathology and Neuropathology, Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Matthew D Wood
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Guillaume Chotard
- Department of Pathology, Hospital Center University of Bordeaux, Bordeaux, France
| | - Rolf Bjergvig
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Anirban Das
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
| | - Uri Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Munster, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute Centre for Cancer Research, Bethesda, MD, USA
| | - Martha Quezado
- Laboratory of Pathology, National Cancer Institute Centre for Cancer Research, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute Centre for Cancer Research, Bethesda, MD, USA
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matija Snuderl
- Division of Neuropathology, NYU Langone Health, New York, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, USA
- Division of Molecular Pathology and Diagnostics, NYU Langone Health, New York, USA
| | - Jürgen Hench
- Division of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Stephan Frank
- Division of Neuropathology, Institute of Pathology, Basel University Hospital, Basel, Switzerland
| | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
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Lyskjær I, De Noon S, Tirabosco R, Rocha AM, Lindsay D, Amary F, Ye H, Schrimpf D, Stichel D, Sill M, Koelsche C, Pillay N, Von Deimling A, Beck S, Flanagan AM. DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the 'DKFZ Sarcoma Classifier'. J Pathol Clin Res 2021; 7:350-360. [PMID: 33949149 PMCID: PMC8185366 DOI: 10.1002/cjp2.215] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/26/2021] [Accepted: 03/18/2021] [Indexed: 01/01/2023]
Abstract
Diagnosing bone and soft tissue neoplasms remains challenging because of the large number of subtypes, many of which lack diagnostic biomarkers. DNA methylation profiles have proven to be a reliable basis for the classification of brain tumours and, following this success, a DNA methylation-based sarcoma classification tool from the Deutsches Krebsforschungszentrum (DKFZ) in Heidelberg has been developed. In this study, we assessed the performance of their classifier on DNA methylation profiles of an independent data set of 986 bone and soft tissue tumours and controls. We found that the 'DKFZ Sarcoma Classifier' was able to produce a diagnostic prediction for 55% of the 986 samples, with 83% of these predictions concordant with the histological diagnosis. On limiting the validation to the 820 cases with histological diagnoses for which the DKFZ Classifier was trained, 61% of cases received a prediction, and the histological diagnosis was concordant with the predicted methylation class in 88% of these cases, findings comparable to those reported in the DKFZ Classifier paper. The classifier performed best when diagnosing mesenchymal chondrosarcomas (CHSs, 88% sensitivity), chordomas (85% sensitivity), and fibrous dysplasia (83% sensitivity). Amongst the subtypes least often classified correctly were clear cell CHSs (14% sensitivity), malignant peripheral nerve sheath tumours (27% sensitivity), and pleomorphic liposarcomas (29% sensitivity). The classifier predictions resulted in revision of the histological diagnosis in six of our cases. We observed that, although a higher tumour purity resulted in a greater likelihood of a prediction being made, it did not correlate with classifier accuracy. Our results show that the DKFZ Classifier represents a powerful research tool for exploring the pathogenesis of sarcoma; with refinement, it has the potential to be a valuable diagnostic tool.
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Affiliation(s)
- Iben Lyskjær
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Solange De Noon
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Roberto Tirabosco
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Ana Maia Rocha
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Daniel Lindsay
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Fernanda Amary
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Hongtao Ye
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
| | - Daniel Schrimpf
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Martin Sill
- Hopp‐Children's Cancer Center (KiTZ)HeidelbergGermany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Christian Koelsche
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of General PathologyUniversity of HeidelbergHeidelbergGermany
| | - Nischalan Pillay
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
| | - Andreas Von Deimling
- Department of NeuropathologyUniversity of HeidelbergHeidelbergGermany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Stephan Beck
- Medical Genomics Research GroupUniversity College London, UCL Cancer InstituteLondonUK
| | - Adrienne M Flanagan
- Research Department of PathologyUniversity College London, UCL Cancer InstituteLondonUK
- Department of HistopathologyRoyal National Orthopaedic HospitalStanmoreUK
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Delaidelli A, Dunham C, Santi MR, Negri GL, Triscott J, Zheludkova O, Golanov A, Ryzhova M, Okonechnikov K, Schrimpf D, Stichel D, von Deimling A, Kool M, Pfister S, Ramaswamy V, Korshunov A, Taylor M, Sorensen P. EMBR-21. CLINICALLY TRACTABLE OUTCOME PREDICTION OF GROUP 3/4 MEDULLOBLASTOMA BASED ON TPD52 IMMUNOHISTOCHEMISTRY: A MULTICOHORT STUDY. Neuro Oncol 2021. [PMCID: PMC8168220 DOI: 10.1093/neuonc/noab090.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background International consensus and the 2021 WHO classification recognize eight molecular subtypes among Group 3/4 medulloblastoma (representing ~60% of tumors). However, very few clinical centers worldwide possess the technical capabilities to determine DNA-methylation patterns or other molecular parameters of high-risk for Group 3/4 tumors. As a result, biomarker-driven risk stratification and therapy assignment constitutes a major challenge in medulloblastoma research. Here, we identify an immunohistochemistry (IHC) marker as a clinically tractable method for improved medulloblastoma risk-stratification. Patients and Methods We bioinformatically analyzed published medulloblastoma transcriptomes and proteomes identifying as a potential biomarker TPD52, whose IHC prognostic value was validated across three Group 3/4 medulloblastoma clinical cohorts (n = 387) treated with conventional therapies. Risk stratification and prediction capability were computed utilizing uni- and multivariate survival analysis. Newly developed risk classifiers including TPD52 IHC were compared to state-of-the-art risk stratification schemes in terms of prediction error, area under the time-dependent receiver operating characteristic (ROC) curves and C-statistic. Biomarker-driven prognostic stratification models identified were cross validated in different cohorts. Results TPD52 IHC positivity represents a significant independent predictor of early relapse and death for Group 3/4 medulloblastoma (HRs between 3.67–26.7 [95% CIs between 1.00–706.23], p = 0.05, 0.017 and 0.0058). Cross-validated survival models incorporating TPD52 IHC with clinical features outperformed existing disease risk-stratification schemes, and reclassified ~50% of patients into more appropriate risk categories. Finally, TPD52 immunopositivity is a predictive indicator of poor response to chemotherapy (HR 12.66 [95% CI 3.53–45.40], p < 0.0001), suggesting important implication for therapeutic choices. Conclusion The current study redefines the approach to risk-stratification in Group 3/4 medulloblastoma. Integration of TPD52 IHC in classification algorithms significantly improves outcome prediction and can be rapidly adopted for risk stratification on a global scale, independently of advanced but technically challenging molecular profiling techniques.
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Affiliation(s)
| | | | | | | | | | - Olga Zheludkova
- St Luka’s Clinical Research Center for Children, Moscow, Russian Federation
| | - Andrey Golanov
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | - Marina Ryzhova
- Neurosurgical NN Burdenko Institute, Moscow, Russian Federation
| | | | | | - Damian Stichel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Marcel Kool
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vijay Ramaswamy
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
| | | | - Michael Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON, Canada
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Korshunov A, Okonechnikov K, Schmitt-Hoffner F, Ryzhova M, Sahm F, Stichel D, Schrimpf D, Reuss DE, Sievers P, Suwala AK, Kumirova E, Zheludkova O, Golanov A, Jones DTW, Pfister SM, Kool M, von Deimling A. Molecular analysis of pediatric CNS-PNET revealed nosologic heterogeneity and potent diagnostic markers for CNS neuroblastoma with FOXR2-activation. Acta Neuropathol Commun 2021; 9:20. [PMID: 33536079 PMCID: PMC7860633 DOI: 10.1186/s40478-021-01118-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022] Open
Abstract
Primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) are highly malignant neoplasms posing diagnostic challenge due to a lack of defining molecular markers. CNS neuroblastoma with forkhead box R2 (FOXR2) activation (CNS_NBL) emerged as a distinct pediatric brain tumor entity from a pool previously diagnosed as primitive neuroectodermal tumors of the central nervous system (CNS-PNETs). Current standard of identifying CNS_NBL relies on molecular analysis. We set out to establish immunohistochemical markers allowing safely distinguishing CNS_NBL from morphological mimics. To this aim we analyzed a series of 84 brain tumors institutionally diagnosed as CNS-PNET. As expected, epigenetic analysis revealed different methylation groups corresponding to the (1) CNS-NBL (24%), (2) glioblastoma IDH wild-type subclass H3.3 G34 (26%), (3) glioblastoma IDH wild-type subclass MYCN (21%) and (4) ependymoma with RELA_C11orf95 fusion (29%) entities. Transcriptome analysis of this series revealed a set of differentially expressed genes distinguishing CNS_NBL from its mimics. Based on RNA-sequencing data we established SOX10 and ANKRD55 expression as genes discriminating CNS_NBL from other tumors exhibiting CNS-PNET. Immunohistochemical detection of combined expression of SOX10 and ANKRD55 clearly identifies CNS_NBL discriminating them to other hemispheric CNS neoplasms harboring “PNET-like” microscopic appearance. Owing the rarity of CNS_NBL, a confirmation of the elaborated diagnostic IHC algorithm will be necessary in prospective patient series.
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39
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Sievers P, Sill M, Schrimpf D, Stichel D, Reuss DE, Sturm D, Hench J, Frank S, Krskova L, Vicha A, Zapotocky M, Bison B, Castel D, Grill J, Debily MA, Harter PN, Snuderl M, Kramm CM, Reifenberger G, Korshunov A, Jabado N, Wesseling P, Wick W, Solomon DA, Perry A, Jacques TS, Jones C, Witt O, Pfister SM, von Deimling A, Jones DTW, Sahm F. A subset of pediatric-type thalamic gliomas share a distinct DNA methylation profile, H3K27me3 loss and frequent alteration of EGFR. Neuro Oncol 2021; 23:34-43. [PMID: 33130881 PMCID: PMC7850075 DOI: 10.1093/neuonc/noaa251] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Malignant astrocytic gliomas in children show a remarkable biological and clinical diversity. Small in-frame insertions or missense mutations in the epidermal growth factor receptor gene (EGFR) have recently been identified in a distinct subset of pediatric-type bithalamic gliomas with a unique DNA methylation pattern. METHODS Here, we investigated an epigenetically homogeneous cohort of malignant gliomas (n = 58) distinct from other subtypes and enriched for pediatric cases and thalamic location, in comparison with this recently identified subtype of pediatric bithalamic gliomas. RESULTS EGFR gene amplification was detected in 16/58 (27%) tumors, and missense mutations or small in-frame insertions in EGFR were found in 20/30 tumors with available sequencing data (67%; 5 of them co-occurring with EGFR amplification). Additionally, 8 of the 30 tumors (27%) harbored an H3.1 or H3.3 K27M mutation (6 of them with a concomitant EGFR alteration). All tumors tested showed loss of H3K27me3 staining, with evidence of overexpression of the EZH inhibitory protein (EZHIP) in the H3 wildtype cases. Although some tumors indeed showed a bithalamic growth pattern, a significant proportion of tumors occurred in the unilateral thalamus or in other (predominantly midline) locations. CONCLUSIONS Our findings present a distinct molecular class of pediatric-type malignant gliomas largely overlapping with the recently reported bithalamic gliomas characterized by EGFR alteration, but additionally showing a broader spectrum of EGFR alterations and tumor localization. Global H3K27me3 loss in this group appears to be mediated by either H3 K27 mutation or EZHIP overexpression. EGFR inhibition may represent a potential therapeutic strategy in these highly aggressive gliomas.
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Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jürgen Hench
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephan Frank
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Lenka Krskova
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Ales Vicha
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Michal Zapotocky
- Prague Brain Tumor Research Group, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
- Department of Pediatric Hematology and Oncology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Brigitte Bison
- Institute of Diagnostic and Interventional Neuroradiology, University Hospital Würzburg, Würzburg, Germany
| | - David Castel
- Molecular Predictors and New Targets in Oncology, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jacques Grill
- Molecular Predictors and New Targets in Oncology, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Cancérologie de l’Enfant et de l’Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Marie-Anne Debily
- Molecular Predictors and New Targets in Oncology, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Département de Biologie, Univ. Evry, Université Paris-Saclay, Evry, France
| | - Patrick N Harter
- Institute of Neurology (Edinger Institute), Goethe University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Matija Snuderl
- Department of Pathology, NYU Langone Medical Center, New York, New York, USA
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada (N.J.)
| | - Pieter Wesseling
- Department of Pathology, Amsterdam University Medical Centers, Location VUmc and Brain Tumor Center Amsterdam, Amsterdam, the Netherlands (P.W.)
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands (P.W.)
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - David A Solomon
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, California, USA (D.A.S., A.P.)
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, California, USA (D.A.S.)
| | - Arie Perry
- Department of Pathology, University of California San Francisco (UCSF), San Francisco, California, USA (D.A.S., A.P.)
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA (A.P.)
| | - Thomas S Jacques
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Olaf Witt
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology, and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany (O.W.)
| | - Stefan M Pfister
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
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40
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Stichel D, Schrimpf D, Sievers P, Reinhardt A, Suwala AK, Sill M, Reuss DE, Korshunov A, Casalini BM, Sommerkamp AC, Ecker J, Selt F, Sturm D, Gnekow A, Koch A, Simon M, Hernáiz Driever P, Schüller U, Capper D, van Tilburg CM, Witt O, Milde T, Pfister SM, Jones DTW, von Deimling A, Sahm F, Wefers AK. Accurate calling of KIAA1549-BRAF fusions from DNA of human brain tumours using methylation array-based copy number and gene panel sequencing data. Neuropathol Appl Neurobiol 2021; 47:406-414. [PMID: 33336421 DOI: 10.1111/nan.12683] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/10/2020] [Revised: 10/14/2020] [Accepted: 12/13/2020] [Indexed: 12/20/2022]
Abstract
AIMS KIAA1549-BRAF fusions occur in certain brain tumours and provide druggable targets due to a constitutive activation of the MAP-kinase pathway. We introduce workflows for calling the KIAA1549-BRAF fusion from DNA methylation array-derived copy number as well as DNA panel sequencing data. METHODS Copy number profiles were analysed by automated screening and visual verification of a tandem duplication on chromosome 7q34, indicative of the KIAA1549-BRAF fusion. Pilocytic astrocytomas of the ICGC cohort with known fusion status were used for validation. KIAA1549-BRAF fusions were called from DNA panel sequencing data using the fusion callers Manta, Arriba with modified filtering criteria and deFuse. We screened DNA methylation and panel sequencing data of 7790 specimens from brain tumour and sarcoma entities. RESULTS We identified the fusion in 337 brain tumours with both DNA methylation and panel sequencing data. Among these, we detected the fusion from copy number data in 84% and from DNA panel sequencing data in more than 90% using Arriba with modified filters. While in 74% the KIAA1549-BRAF fusion was detected from both methylation array-derived copy number and panel sequencing data, in 9% it was detected from copy number data only and in 16% from panel data only. The fusion was almost exclusively found in pilocytic astrocytomas, diffuse leptomeningeal glioneuronal tumours and high-grade astrocytomas with piloid features. CONCLUSIONS The KIAA1549-BRAF fusion can be reliably detected from either DNA methylation array or DNA panel data. The use of both methods is recommended for the most sensitive detection of this diagnostically and therapeutically important marker.
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Affiliation(s)
- Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Belén M Casalini
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander C Sommerkamp
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Florian Selt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Astrid Gnekow
- Swabian Children's Cancer Center, University Hospital Augsburg, Augsburg, Germany
| | - Arend Koch
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK, Partner Site Berlin, German Cancer Research Center (DKFZ, Heidelberg, Germany
| | - Michèle Simon
- Department of Pediatric Oncology/Hematology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology/Hematology and Stem Cell Transplantation, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK, Partner Site Berlin, German Cancer Research Center (DKFZ, Heidelberg, Germany
| | - Cornelis M van Tilburg
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
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41
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Suwala AK, Stichel D, Schrimpf D, Kloor M, Wefers AK, Reinhardt A, Maas SLN, Kratz CP, Schweizer L, Hasselblatt M, Snuderl M, Abedalthagafi MSJ, Abdullaev Z, Monoranu CM, Bergmann M, Pekrun A, Freyschlag C, Aronica E, Kramm CM, Hinz F, Sievers P, Korshunov A, Kool M, Pfister SM, Sturm D, Jones DTW, Wick W, Unterberg A, Hartmann C, Dodgshun A, Tabori U, Wesseling P, Sahm F, von Deimling A, Reuss DE. Primary mismatch repair deficient IDH-mutant astrocytoma (PMMRDIA) is a distinct type with a poor prognosis. Acta Neuropathol 2021; 141:85-100. [PMID: 33216206 PMCID: PMC7785563 DOI: 10.1007/s00401-020-02243-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 01/05/2023]
Abstract
Diffuse IDH-mutant astrocytoma mostly occurs in adults and carries a favorable prognosis compared to IDH-wildtype malignant gliomas. Acquired mismatch repair deficiency is known to occur in recurrent IDH-mutant gliomas as resistance mechanism towards alkylating chemotherapy. In this multi-institutional study, we report a novel epigenetic group of 32 IDH-mutant gliomas with proven or suspected hereditary mismatch repair deficiency. None of the tumors exhibited a combined 1p/19q deletion. These primary mismatch repair-deficient IDH-mutant astrocytomas (PMMRDIA) were histologically high-grade and were mainly found in children, adolescents and young adults (median age 14 years). Mismatch repair deficiency syndromes (Lynch or Constitutional Mismatch Repair Deficiency Syndrom (CMMRD)) were clinically diagnosed and/or germline mutations in DNA mismatch repair genes (MLH1, MSH6, MSH2) were found in all cases, except one case with a family and personal history of colon cancer and another case with MSH6-deficiency available only as recurrent tumor. Loss of at least one of the mismatch repair proteins was detected via immunohistochemistry in all, but one case analyzed. Tumors displayed a hypermutant genotype and microsatellite instability was present in more than half of the sequenced cases. Integrated somatic mutational and chromosomal copy number analyses showed frequent inactivation of TP53, RB1 and activation of RTK/PI3K/AKT pathways. In contrast to the majority of IDH-mutant gliomas, more than 60% of the samples in our cohort presented with an unmethylated MGMT promoter. While the rate of immuno-histochemical ATRX loss was reduced, variants of unknown significance were more frequently detected possibly indicating a higher frequency of ATRX inactivation by protein malfunction. Compared to reference cohorts of other IDH-mutant gliomas, primary mismatch repair-deficient IDH-mutant astrocytomas have by far the worst clinical outcome with a median survival of only 15 months irrespective of histological or molecular features. The findings reveal a so far unknown entity of IDH-mutant astrocytoma with high prognostic relevance. Diagnosis can be established by aligning with the characteristic DNA methylation profile, by DNA-sequencing-based proof of mismatch repair deficiency or immunohistochemically demonstrating loss-of-mismatch repair proteins.
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Affiliation(s)
- Abigail K Suwala
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Sybren L N Maas
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Matija Snuderl
- Division of Neuropathology, NYU Langone Health, New York, USA
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, USA
- Division of Molecular Pathology and Diagnostics, NYU Langone Health, New York, USA
| | - Malak Sameer J Abedalthagafi
- Pathology Department, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Camelia M Monoranu
- Institute of Pathology, Julius-Maximilians-University, Würzburg, Germany
| | - Markus Bergmann
- Institute of Clinical Neuropathology, Bremen-Mitte Medical Center, Bremen, Germany
| | - Arnulf Pekrun
- Professor Hess Children's Hospital, Klinikum Bremen-Mitte, Bremen, Germany
| | | | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, University Medical Center Goettingen, Goettingen, Germany
| | - Felix Hinz
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Andrew Dodgshun
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
- Children's Haematology and Oncology Center, Christchurch Hospital, Christchurch, New Zealand
| | - Uri Tabori
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
- Division of Haematology and Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Pieter Wesseling
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, Amsterdam University Medical Centers/VUmc and Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
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Sill M, Sahm F, Schrimpf D, Capper D, Pfister SM, von Deimling A, Jones DTW. PATH-04. AN ENHANCED AI-DRIVEN PLATFORM FOR PRECISION MOLECULAR BRAIN TUMOR DIANOSTICS. Neuro Oncol 2020. [PMCID: PMC7715562 DOI: 10.1093/neuonc/noaa222.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Tumors of the CNS represent one of the most complex groups of human cancer, with a vast number of different entities occurring across a spectrum of ages and anatomic locations. This heterogeneity makes accurate diagnosis challenging, with the current gold standard relying on multiple subjective elements. We recently proposed a classification algorithm based on tumor DNA methylation profiling as an objective way to assign samples to over 80 distinct molecular classes. Here we present a substantial update to our machine learning-based algorithm, with more than 170 molecular classes now being represented amongst the 5,915 samples in our reference cohort. These new classes include further subclassification of known groups such as medulloblastoma and ependymoma, as well as multiple new molecular entities described here for the first time. A further improvement is the introduction of a more rationally layered output, making use of ‘families’ of closely-related molecular classes to improve the compatibility with the current WHO classification of CNS tumors. This approach is designed to increase the clinical relevance of the primary output, while also retaining the full information content from the random forest-driven classification. Benchmarking our new algorithm by cross-validation and on an independent validation cohort indicates a retention of the excellent accuracy of diagnosis (error-rate < 4%), with a significant improvement in the proportion of confidently classifiable tumors compared with our previous tool. We believe that this approach, freely accessible through an online web portal, has the potential to enhance diagnostic precision and thereby support clinical care for brain tumor patients.
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Affiliation(s)
- Martin Sill
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Capper
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Stichel D, Schrimpf D, Meyer J, Wefers A, Sievers P, Pfister SM, Wick W, Jones DTW, von Deimling A, Sahm F. PATH-26. RNA SEQUENCING OF FORMALIN-FIXED PARAFFIN-EMBEDDED SPECIMENS IN DIAGNOSTIC ROUTINE IDENTIFIES CLINICALLY RELEVANT GENE FUSIONS. Neuro Oncol 2020. [PMCID: PMC7715156 DOI: 10.1093/neuonc/noaa222.661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pediatric brain tumor entities harbor a variety of gene fusions. Whilst other molecular parameters like somatic mutations and copy number alterations have become pivotal for brain tumor diagnostics, gene fusions are only less well covered by routinely applied methylation arrays or targeted next-generation sequencing of DNA. In a routine diagnostic setting we established and optimized a workflow for investigation of gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by using RNA sequencing. Assessing different tools for calling fusions from raw data, we found relevant fusions in 66 out of 101 (65%) analyzed cases in a prospective cohort collected over 26 months. In 43 (43%) cases the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. Besides the relevance of pathognomonic fusions for diagnostics, especially the detection of druggable gene fusions yields direct benefit to the patients. This approach allows for an unbiased search for fusion events in the tested samples. Besides rare variants of established fusions which were not detected by prior targeted analyses, we identified previously unreported fusion events. Exemplified on KIAA1549:BRAF fusion, we in addition provide an overview of the detection accuracy of different methods, including breakpoint detection in DNA methylation array data and fusion gene detection in DNA panel sequencing data. Our data show that RNA sequencing has great diagnostic as well as therapeutic value by clinically detecting relevant alterations.
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Affiliation(s)
- Damian Stichel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jochen Meyer
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Wefers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wefers AK, Stichel D, Schrimpf D, Sahm F, von Deimling A, Blumcke I, Jones DTW, Capper D. LGG-33. ISOMORPHIC DIFFUSE GLIOMA HAS RECURRENT GENE FUSIONS OF MYBL1 OR MYB AND CAN BE DISTINGUISHED FROM OTHER MYB/MYBL1 ALTERED GLIOMAS BASED ON A DISTINCT MORPHOLOGY AND DNA METHYLATION PROFILE. Neuro Oncol 2020. [PMCID: PMC7715088 DOI: 10.1093/neuonc/noaa222.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Isomorphic diffuse glioma (IDG) was first described in 2004 as an epilepsy-associated supratentorial diffuse glioma with low cellularity, low proliferation and very monomorphic tumour cells. Most patients had seizures since childhood but were operated on as adults. To study the position of these lesions among brain tumours we histologically, molecularly and clinically analysed 26 histologically typical IDGs. Tumour cells were GFAP-positive, MAP2-, OLIG2- and CD34-negative and the nuclear ATRX-expression was retained. Proliferation was very low. Sequencing of 24 cases revealed an IDH-wildtype status. Cluster analyses of DNA methylation data showed that IDG has a DNA methylation profile distinct from those of different glial/glio-neuronal brain tumours and normal hemispheric tissue. About half of IDGs had copy number alterations of MYBL1 or MYB (13/25) and half of the cases analysed by RNA-sequencing had gene fusions of MYBL1 or MYB with various gene partners (11/22), often associated with an increased RNA-expression of the respective MYB-family gene. Integrating all data available, 77% of IDGs had either MYBL1 (54%) or MYB (23%) alterations. All patients had a good outcome and most were seizure-free after surgery. In summary, we show that isomorphic diffuse glioma is a distinct benign tumour in the family of MYB/MYBL1-altered gliomas. DNA methylation analysis is very helpful for their identification. More recent analyses of a large cohort of MYB/MYBL1-altered brain tumours suggest the presence of a third methylation group that primarily contains paediatric cases and seems to be distinct from IDG and angiocentric gliomas. Further histological, molecular and clinical analyses are ongoing.
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Affiliation(s)
- Annika K Wefers
- Institute of Pathology, Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Damian Stichel
- Institute of Pathology, Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Daniel Schrimpf
- Institute of Pathology, Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Felix Sahm
- Institute of Pathology, Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Andreas von Deimling
- Institute of Pathology, Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Clinical Cooperation Unit Neuropathology, Heidelberg, Germany
| | - Ingmar Blumcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Pediatric Glioma Research Group, Heidelberg, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology, Berlin, Germany
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Banan R, Stichel D, Bleck A, Hong B, Lehmann U, Suwala A, Reinhardt A, Schrimpf D, Buslei R, Stadelmann C, Ehlert K, Prinz M, Acker T, Schittenhelm J, Kaul D, Schweizer L, Capper D, Harter PN, Etminan N, Jones DTW, Pfister SM, Herold-Mende C, Wick W, Sahm F, von Deimling A, Hartmann C, Reuss DE. Infratentorial IDH-mutant astrocytoma is a distinct subtype. Acta Neuropathol 2020; 140:569-581. [PMID: 32776277 DOI: 10.1007/s00401-020-02194-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 06/26/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Abstract
Diffuse IDH-mutant astrocytic tumors are rarely diagnosed in the cerebellum or brainstem. In this multi-institutional study, we characterized a series of primary infratentorial IDH-mutant astrocytic tumors with respect to clinical and molecular parameters. We report that about 80% of IDH mutations in these tumors are of non-IDH1-R132H variants which are rare in supratentorial astrocytomas. Most frequently, IDH1-R132C/G and IDH2-R172S/G mutations were present. Moreover, the frequencies of ATRX-loss and MGMT promoter methylation, which are typically associated with IDH mutations in supratentorial astrocytic tumors, were significantly lower in the infratentorial compartment. Gene panel sequencing revealed two samples with IDH1-R132C/H3F3A-K27M co-mutations. Genome-wide DNA methylation as well as chromosomal copy number profiling provided further evidence for a molecular distinctiveness of infratentorial IDH-mutant astrocytomas. Clinical outcome of patients with infratentorial IDH-mutant astrocytomas is significantly better than that of patients with diffuse midline gliomas, H3K27M-mutant (p < 0.005) and significantly worse than that of patients with supratentorial IDH-mutant astrocytomas (p = 0.028). The presented data highlight the very existence and distinctiveness of infratentorial IDH-mutant astrocytomas that have important implications for diagnostics and prognostication. They imply that molecular testing is critical for detection of these tumors, since many of these tumors cannot be identified by immunohistochemistry applied for the mutated IDH1-R132H protein or loss of ATRX.
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Affiliation(s)
- Rouzbeh Banan
- Department of Neuropathology, Institute of Pathology, Hannover Medical School (MHH), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Anja Bleck
- Department of Neuropathology, Institute of Pathology, Hannover Medical School (MHH), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Bujung Hong
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Abigail Suwala
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Annekathrin Reinhardt
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rolf Buslei
- Institute of Pathology, Klinikum Bamberg, Klinikum, Germany
| | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Karoline Ehlert
- Department of Pediatric Oncology and Hematology, University of Greifswald, Greifswald, Germany
| | - Marco Prinz
- Institute of Neuropathology, University of Freiburg, Freiburg, Germany
| | - Till Acker
- Institute of Neuropathology, University of Gießen, Gießen, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - David Kaul
- Department of Radiation Oncology and Radiotherapy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Berlin, Heidelberg, Germany
| | - Patrick N Harter
- Institute of Neurology (Edinger Institute), Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Frankfurt, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Frankfurt, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Hospital Mannheim, University of Heidelberg, Heidelberg, Germany
| | - David T W Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Childrens Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Childrens Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Department of Neurosurgery, Division of Experimental Neurosurgery, University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Neurology Clinic, University of Heidelberg Medical Center, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christian Hartmann
- Department of Neuropathology, Institute of Pathology, Hannover Medical School (MHH), Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - David E Reuss
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.
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Sievers P, Hielscher T, Schrimpf D, Stichel D, Reuss DE, Berghoff AS, Neidert MC, Wirsching HG, Mawrin C, Ketter R, Paulus W, Reifenberger G, Lamszus K, Westphal M, Etminan N, Ratliff M, Herold-Mende C, Pfister SM, Jones DTW, Weller M, Harter PN, Wick W, Preusser M, von Deimling A, Sahm F. CDKN2A/B homozygous deletion is associated with early recurrence in meningiomas. Acta Neuropathol 2020; 140:409-413. [PMID: 32642869 PMCID: PMC7423850 DOI: 10.1007/s00401-020-02188-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna S Berghoff
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Marian C Neidert
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Hans-Georg Wirsching
- Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Christian Mawrin
- Department of Neuropathology, Otto-von-Guericke University, Magdeburg, Germany
| | - Ralf Ketter
- Department of Neurosurgery, University Hospital Homburg Saar, Homburg, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nima Etminan
- Department of Neurosurgery, University Medical Centre Mannheim, University of Heidelberg, Mannheim, Germany
| | - Miriam Ratliff
- Department of Neurosurgery, University Medical Centre Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, University Hospital Heidelberg, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Patrick N Harter
- Institute of Neurology (Edinger Institute), Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Matthias Preusser
- Department of Medicine I, Clinical Division of Oncology and Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology (B300), German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
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47
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Korshunov A, Sahm F, Zheludkova O, Golanov A, Stichel D, Schrimpf D, Ryzhova M, Potapov A, Habel A, Meyer J, Lichter P, Jones DTW, von Deimling A, Pfister SM, Kool M. DNA methylation profiling is a method of choice for molecular verification of pediatric WNT-activated medulloblastomas. Neuro Oncol 2020; 21:214-221. [PMID: 30252101 DOI: 10.1093/neuonc/noy155] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Wingless-activated medulloblastoma (WNT MB) represents a well-characterized molecular variant accounting for 10-15% of all MB and is associated with a favorable clinical outcome. Patients with localized WNT MBs could benefit from de-intensification of combined treatment, which would require an accurate diagnosis of these tumors. However, despite the presence of molecular features related with a WNT MB signature (nuclear ß-catenin immunoexpression, CTNNB1 mutation, and monosomy 6), a prompt and reliable diagnostic verification of these tumors is not yet feasible. METHODS In the current study, we analyzed 78 samples of WNT MB treated in a single institute through genome-wide DNA methylation and targeted next generation sequencing to elaborate an optimal method for WNT MB molecular verification. RESULTS We found that DNA methylation profiling discloses significant advantages for molecular diagnostic of WNT MB. All other "routine" methods applied, such as ß-catenin immunohistochemistry, CTNNB1 mutation analysis, and detection of monosomy 6, failed to identify all WNT MB cases. Survival analysis revealed that application of a reduced radiotherapy protocol for WNT MB treatment had no influence on patients' survival. Only one patient died due to local relapse but recurrent tumor was pathologically and molecularly diagnosed as a secondary glioblastoma. CONCLUSIONS DNA methylation analysis should be considered as a method of choice for further clinically relevant stratification of WNT MB and for correct diagnosis of the recurrent tumors. WNT MB patients with localized disease could benefit from treatment de-intensification.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Olga Zheludkova
- Department of Neuro-Oncology, Russian Scientific Center of Radiology, Moscow, Russia
| | - Andrey Golanov
- Department of Neuroradiology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Alexander Potapov
- Department of Neuroradiology, NN Burdenko Neurosurgical Institute, Moscow, Russia
| | - Antje Habel
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jochen Meyer
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Lichter
- Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany.,Division of Molecular Genetics (B060), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology (G380), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.,Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the National Center for Tumor Diseases Heidelberg, Heidelberg, Germany.,Division of Pediatric Neurooncology (B062), German Cancer Research Center and German Cancer Consortium, Heidelberg, Germany
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48
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Wefers AK, Stichel D, Schrimpf D, Coras R, Pages M, Tauziède-Espariat A, Varlet P, Schwarz D, Söylemezoglu F, Pohl U, Pimentel J, Meyer J, Hewer E, Japp A, Joshi A, Reuss DE, Reinhardt A, Sievers P, Casalini MB, Ebrahimi A, Huang K, Koelsche C, Low HL, Rebelo O, Marnoto D, Becker AJ, Staszewski O, Mittelbronn M, Hasselblatt M, Schittenhelm J, Cheesman E, de Oliveira RS, Queiroz RGP, Valera ET, Hans VH, Korshunov A, Olar A, Ligon KL, Pfister SM, Jaunmuktane Z, Brandner S, Tatevossian RG, Ellison DW, Jacques TS, Honavar M, Aronica E, Thom M, Sahm F, von Deimling A, Jones DTW, Blumcke I, Capper D. Isomorphic diffuse glioma is a morphologically and molecularly distinct tumour entity with recurrent gene fusions of MYBL1 or MYB and a benign disease course. Acta Neuropathol 2020; 139:193-209. [PMID: 31563982 PMCID: PMC7477753 DOI: 10.1007/s00401-019-02078-w] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
The "isomorphic subtype of diffuse astrocytoma" was identified histologically in 2004 as a supratentorial, highly differentiated glioma with low cellularity, low proliferation and focal diffuse brain infiltration. Patients typically had seizures since childhood and all were operated on as adults. To define the position of these lesions among brain tumours, we histologically, molecularly and clinically analysed 26 histologically prototypical isomorphic diffuse gliomas. Immunohistochemically, they were GFAP-positive, MAP2-, OLIG2- and CD34-negative, nuclear ATRX-expression was retained and proliferation was low. All 24 cases sequenced were IDH-wildtype. In cluster analyses of DNA methylation data, isomorphic diffuse gliomas formed a group clearly distinct from other glial/glio-neuronal brain tumours and normal hemispheric tissue, most closely related to paediatric MYB/MYBL1-altered diffuse astrocytomas and angiocentric gliomas. Half of the isomorphic diffuse gliomas had copy number alterations of MYBL1 or MYB (13/25, 52%). Gene fusions of MYBL1 or MYB with various gene partners were identified in 11/22 (50%) and were associated with an increased RNA-expression of the respective MYB-family gene. Integrating copy number alterations and available RNA sequencing data, 20/26 (77%) of isomorphic diffuse gliomas demonstrated MYBL1 (54%) or MYB (23%) alterations. Clinically, 89% of patients were seizure-free after surgery and all had a good outcome. In summary, we here define a distinct benign tumour class belonging to the family of MYB/MYBL1-altered gliomas. Isomorphic diffuse glioma occurs both in children and adults, has a concise morphology, frequent MYBL1 and MYB alterations and a specific DNA methylation profile. As an exclusively histological diagnosis may be very challenging and as paediatric MYB/MYBL1-altered diffuse astrocytomas may have the same gene fusions, we consider DNA methylation profiling very helpful for their identification.
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Affiliation(s)
- Annika K Wefers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Coras
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Mélanie Pages
- Department of Neuropathology, Sainte-Anne Hospital, Descartes University, Paris, France
| | | | - Pascale Varlet
- Department of Neuropathology, Sainte-Anne Hospital, Descartes University, Paris, France
| | - Daniel Schwarz
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
- Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Figen Söylemezoglu
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ute Pohl
- Department of Cellular Pathology, Queen's Hospital BHRUT, Romford, UK
- Department of Cellular Pathology, Queen Elizabeth Hospital Birmingham/University Hospitals Birmingham, Birmingham, UK
| | - José Pimentel
- Department of Neurosciences and Mental Health, Laboratory of Neuropathology, Hospital de Santa Maria (CHULN, EPE), Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Jochen Meyer
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Anna Japp
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Abhijit Joshi
- Department of Neuropathology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annekathrin Reinhardt
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Belén Casalini
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Azadeh Ebrahimi
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Huang
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hu Liang Low
- Department of Neurosurgery, Queen's Hospital BHRUT, Romford, UK
| | - Olinda Rebelo
- Neuropathology Unit, Centro Hospitalar de Universidades de Coimbra, Coimbra, Portugal
| | - Dina Marnoto
- Neuropathology Unit, Centro Hospitalar de Universidades de Coimbra, Coimbra, Portugal
| | - Albert J Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Ori Staszewski
- Institute of Neuropathology, University of Freiburg, Freiburg, Germany
| | - Michel Mittelbronn
- Edinger Institute, Institute of Neurology, University of Frankfurt am Main, Frankfurt, Germany
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Laboratoire National de Santé (LNS), National Center of Pathology (NCP), Dudelange, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg City, Luxembourg
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University Hospital of Tübingen, Tübingen, Germany
- Center for CNS Tumours, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital of Tübingen, Tübingen, Germany
| | - Edmund Cheesman
- Department of Paediatric Histopathology, Royal Manchester Children's Hospital Manchester, Manchester, UK
| | - Ricardo Santos de Oliveira
- Division of Pediatric Neurosurgery, Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Rosane Gomes P Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Volkmar H Hans
- Abteilung Neuropathologie, Institut für klinische Pathologie, Dietrich-Bonhoeffer-Klinikum, Neubrandenburg, Germany
- Institut für Neuropathologie, Evangelisches Klinikum Bethel gGmbH, Bielefeld, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Adriana Olar
- Departments of Pathology and Laboratory Medicine and Neurosurgery, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Charleston, SC, USA
| | - Keith L Ligon
- Department of Oncologic Pathology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Zane Jaunmuktane
- Division of Neuropathology, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
| | - Sebastian Brandner
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Ruth G Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thomas S Jacques
- Developmental Biology and Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mrinalini Honavar
- Department of Pathology, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Eleonora Aronica
- Amsterdam UMC, Department of (Neuro)Pathology, University of Amsterdam, Amsterdam and Stichting Epilepsie Instellingen Nederland, Heemstede, The Netherlands
| | - Maria Thom
- Division of Neuropathology, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingmar Blumcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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49
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Kommoss FKF, Stichel D, Schrimpf D, Kriegsmann M, Tessier-Cloutier B, Talhouk A, McAlpine JN, Chang KTE, Sturm D, Pfister SM, Romero-Pérez L, Kirchner T, Grünewald TGP, Buslei R, Sinn HP, Mechtersheimer G, Schirmacher P, Schmidt D, Lehr HA, Sahm F, Huntsman DG, Gilks CB, Kommoss F, von Deimling A, Koelsche C. DNA methylation-based profiling of uterine neoplasms: a novel tool to improve gynecologic cancer diagnostics. J Cancer Res Clin Oncol 2019; 146:97-104. [PMID: 31768620 DOI: 10.1007/s00432-019-03093-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
PURPOSE Uterine neoplasms comprise a broad spectrum of lesions, some of which may pose a diagnostic challenge even to experienced pathologists. Recently, genome-wide DNA methylation-based classification of central nervous system tumors has been shown to increase diagnostic precision in clinical practice when combined with standard histopathology. In this study, we describe DNA methylation patterns of a diverse set of uterine neoplasms and test the applicability of array-based DNA methylation profiling. METHODS A multicenter cohort including prototypical epithelial and mesenchymal uterine neoplasms was collected. Tumors were subject to pathology review and array-based DNA methylation profiling (Illumina Infinium HumanMethylation450 or EPIC [850k] BeadChip). Methylation data were analyzed by unsupervised hierarchical clustering and t-SNE analysis. RESULTS After sample retrieval and pathology review the study cohort consisted of 49 endometrial carcinomas (EC), 5 carcinosarcomas (MMMT), 8 uterine leiomyomas (ULMO), 7 uterine leiomyosarcomas (ULMS), 15 uterine tumor resembling ovarian sex cord tumors (UTROSCT), 17 low-grade endometrial stromal sarcomas (LGESS) and 9 high-grade endometrial stromal sarcomas (HGESS). Analysis of methylation data identified distinct methylation clusters, which correlated with established diagnostic categories of uterine neoplasms. MMMT clustered together with EC, while ULMO, ULMS and UTROSCT each formed distinct clusters. The LGESS cluster differed from that of HGESS, and within the branch of HGESS, we observed a notable subgrouping of YWHAE- and BCOR-rearranged tumors. CONCLUSION Herein, we describe distinct DNA methylation signatures in uterine neoplasms and show that array-based DNA methylation analysis holds promise as an ancillary tool to further characterize uterine neoplasms, especially in cases which are diagnostically challenging by conventional techniques.
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Affiliation(s)
- Felix K F Kommoss
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Damian Stichel
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark Kriegsmann
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Aline Talhouk
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Jessica N McAlpine
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada
| | - Kenneth T E Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, Singapore
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Rolf Buslei
- Institute of Pathology, Sozialstiftung Bamberg, Bamberg, Germany
| | - Hans-Peter Sinn
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Gunhild Mechtersheimer
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | - Peter Schirmacher
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany
| | | | - Hans-Anton Lehr
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, University of British Columbia and BC Cancer Agency, Vancouver, BC, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Pathology, Institute of Pathology, Heidelberg University Hospital, INF 224, 69120, Heidelberg, Germany.
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50
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Wirsching HG, Tabatabai G, Roelcke U, Hottinger AF, Jörger F, Schmid A, Plasswilm L, Schrimpf D, Mancao C, Capper D, Conen K, Hundsberger T, Caparrotti F, von Moos R, Riklin C, Felsberg J, Roth P, Jones DTW, Pfister S, Rushing EJ, Abrey L, Reifenberger G, Held L, von Deimling A, Ochsenbein A, Weller M. Bevacizumab plus hypofractionated radiotherapy versus radiotherapy alone in elderly patients with glioblastoma: the randomized, open-label, phase II ARTE trial. Ann Oncol 2019; 29:1423-1430. [PMID: 29648580 DOI: 10.1093/annonc/mdy120] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background The addition of bevacizumab to temozolomide-based chemoradiotherapy (TMZ/RT → TMZ) did not prolong overall survival (OS) in patients with newly diagnosed glioblastoma in phase III trials. Elderly and frail patients are underrepresented in clinical trials, but early reports suggested preferential benefit in this population. Patients and methods ARTE was a 2 : 1 randomized, multi-center, open-label, non-comparative phase II trial of hypofractionated RT (40 Gy in 15 fractions) with bevacizumab (10 mg/kg×14 days) (arm A, N = 50) or without bevacizumab (arm B, N = 25) in patients with newly diagnosed glioblastoma aged ≥65 years. The primary objective was to obtain evidence for prolongation of median OS by the addition of bevacizumab to RT. Response was assessed by RANO criteria. Quality of life (QoL) was monitored by the EORTC QLQ-C30/BN20 modules. Exploratory studies included molecular subtyping by 450k whole methylome and gene expression analyses. Results Median PFS was longer in arm A than in arm B (7.6 and 4.8 months, P = 0.003), but OS was similar (12.1 and 12.2 months, P = 0.77). Clinical deterioration was delayed and more patients came off steroids in arm A. Prolonged PFS in arm A was confined to tumors with the receptor tyrosine kinase (RTK) I methylation subtype (HR 0.25, P = 0.014) and proneural gene expression (HR 0.29, P = 0.025). In a Cox model of OS controlling for established prognostic factors, associations with more favorable outcome were identified for age <70 years (HR 0.52, P = 0.018) and Karnofsky performance score 90%-100% (HR 0.51, P = 0.026). Including molecular subtypes into that model identified an association of the RTK II gene methylation subtype with inferior OS (HR 1.73, P = 0.076). Conclusion Efficacy outcomes and exploratory analyses of ARTE do not support the hypothesis that the addition of bevacizumab to RT generally prolongs survival in elderly glioblastoma patients. Molecular biomarkers may identify patients with preferential benefit from bevacizumab. Clinical trial registration number NCT01443676.
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Affiliation(s)
- H-G Wirsching
- Brain Tumor Center Zurich, University Hospital and University of Zurich, Zurich, Switzerland; Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - G Tabatabai
- Brain Tumor Center Zurich, University Hospital and University of Zurich, Zurich, Switzerland; Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - U Roelcke
- Department of Neurology, Brain Tumor Center Aarau, Cantonal Hospital Aarau, Aarau, Switzerland
| | - A F Hottinger
- Department of Clinical Neurosciences, University Hospital Lausanne, Lausanne, Switzerland; Department of Medical Oncology, University Hospital Lausanne, Lausanne, Switzerland
| | - F Jörger
- Department of Clinical Trials Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - A Schmid
- Department of Medical Oncology, University Hospital Bern, Bern, Switzerland
| | - L Plasswilm
- Department of Radiation Oncology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - D Schrimpf
- Department of Neuropathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - C Mancao
- Genentech, Oncology Biomarker Development, Basel, Switzerland
| | - D Capper
- Department of Neuropathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - K Conen
- Department of Medical Oncology, University Hospital Basel, Basel, Switzerland
| | - T Hundsberger
- Department of Neurology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - F Caparrotti
- Department of Radiation Oncology, University Hospital Geneva, Geneva, Switzerland
| | - R von Moos
- Department of Medical Oncology, Cantonal Hospital Chur, Chur, Switzerland
| | - C Riklin
- Department of Medical Oncology, Cantonal Hospital Lucerne, Lucerne Switzerland
| | - J Felsberg
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - P Roth
- Brain Tumor Center Zurich, University Hospital and University of Zurich, Zurich, Switzerland; Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - D T W Jones
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - S Pfister
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Hematology and Oncology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - E J Rushing
- Brain Tumor Center Zurich, University Hospital and University of Zurich, Zurich, Switzerland; Department of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - L Abrey
- F. Hoffmann-La Roche, Pharma Division, Product Development Oncology, Basel, Switzerland
| | - G Reifenberger
- Department of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; German Cancer Research Center, Essen/Düsseldorf, Germany
| | - L Held
- Biostatistics Department, University of Zurich, Zurich, Switzerland
| | - A von Deimling
- Department of Neuropathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Ochsenbein
- Department of Medical Oncology, University Hospital Bern, Bern, Switzerland
| | - M Weller
- Brain Tumor Center Zurich, University Hospital and University of Zurich, Zurich, Switzerland; Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland.
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