1
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Hey F, Andreadi C, Noble C, Patel B, Jin H, Kamata T, Straatman K, Luo J, Balmanno K, Jones DT, Collins VP, Cook SJ, Caunt CJ, Pritchard C. Over-expressed, N-terminally truncated BRAF is detected in the nucleus of cells with nuclear phosphorylated MEK and ERK. Heliyon 2018; 4:e01065. [PMID: 30603699 PMCID: PMC6304467 DOI: 10.1016/j.heliyon.2018.e01065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/12/2018] [Accepted: 12/14/2018] [Indexed: 12/31/2022] Open
Abstract
BRAF is a cytoplasmic protein kinase, which activates the MEK-ERK signalling pathway. Deregulation of the pathway is associated with the presence of BRAF mutations in human cancer, the most common being V600E BRAF, although structural rearrangements, which remove N-terminal regulatory sequences, have also been reported. RAF-MEK-ERK signalling is normally thought to occur in the cytoplasm of the cell. However, in an investigation of BRAF localisation using fluorescence microscopy combined with subcellular fractionation of Green Fluorescent Protein (GFP)-tagged proteins expressed in NIH3T3 cells, surprisingly, we detected N-terminally truncated BRAF (ΔBRAF) in both nuclear and cytoplasmic compartments. In contrast, ΔCRAF and full-length, wild-type BRAF (WTBRAF) were detected at lower levels in the nucleus while full-length V600EBRAF was virtually excluded from this compartment. Similar results were obtained using ΔBRAF tagged with the hormone-binding domain of the oestrogen receptor (hbER) and with the KIAA1549-ΔBRAF translocation mutant found in human pilocytic astrocytomas. Here we show that GFP-ΔBRAF nuclear translocation does not involve a canonical Nuclear Localisation Signal (NLS), but is suppressed by N-terminal sequences. Nuclear GFP-ΔBRAF retains MEK/ERK activating potential and is associated with the accumulation of phosphorylated MEK and ERK in the nucleus. In contrast, full-length GFP-WTBRAF and GFP-V600EBRAF are associated with the accumulation of phosphorylated ERK but not phosphorylated MEK in the nucleus. These data have implications for cancers bearing single nucleotide variants or N-terminal deleted structural variants of BRAF.
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Affiliation(s)
- Fiona Hey
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Catherine Andreadi
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Catherine Noble
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Bipin Patel
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Hong Jin
- Department of Molecular Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Tamihiro Kamata
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Kees Straatman
- Core Biotechnology Services, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Jinli Luo
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Kathryn Balmanno
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - David T.W. Jones
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - V. Peter Collins
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Simon J. Cook
- Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Christopher J. Caunt
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Catrin Pritchard
- Leicester Cancer Research Centre, Clinical Sciences Building, University of Leicester, Leicester Royal Infirmary, Leicester LE2 7LX, UK
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2
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Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U. An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures. Sci Rep 2018; 8:13537. [PMID: 30202034 PMCID: PMC6131140 DOI: 10.1038/s41598-018-31659-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 04/30/2018] [Accepted: 08/16/2018] [Indexed: 12/21/2022] Open
Abstract
Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Aggressive disease was further characterised by transcriptional evidence of increased PRC2 activity, stemness and epithelial-to-mesenchymal transition. Our analyses discern biologically distinct variants of anaplastic meningioma with prognostic and therapeutic significance.
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Affiliation(s)
- Grace Collord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Patrick Tarpey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Natalja Kurbatova
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Manuel Castro
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Tibor Nagy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Graham Bignell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Francesco Maura
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jorge Berna
- Mobile Genomes and Disease, Molecular Medicine and Chronic diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, 15706, Spain
| | - Jose M C Tubio
- Mobile Genomes and Disease, Molecular Medicine and Chronic diseases Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, 15706, Spain
| | - Chris E McMurran
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Adam M H Young
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Mathijs Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Erasmus University Medical Center, Department of Hematology, Rotterdam, The Netherlands
| | - Imran Noorani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Stephen J Price
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Colin Watts
- Department of Neurosurgery, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elke Leipnitz
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Matthias Kirsch
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Gabriele Schackert
- Klinik und Poliklink für Neurochirurgie, "Carl Gustav Carus" Universitätsklinikum, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Danita Pearson
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Abel Devadass
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Zvi Ram
- Department of Neurosurgery, Tel-Aviv Medical Center, Tel-Aviv, Israel
| | - V Peter Collins
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Kieren Allinson
- Department of Pathology, Cambridge University Hospital, CB2 0QQ, Cambridge, UK
| | - Michael D Jenkinson
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Translational Medicine, University of Liverpool, Liverpool, L9 7LJ, UK
| | - Rasheed Zakaria
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L9 7LJ, UK
| | - Khaja Syed
- Department of Neurosurgery, The Walton Centre, Liverpool, L9 7LJ, UK
- Institute of Integrative Biology, University of Liverpool, Liverpool, L9 7LJ, UK
| | - C Oliver Hanemann
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, Devon, PL4 8AA, UK
| | - Jemma Dunn
- Institute of Translational and Stratified Medicine, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, Devon, PL4 8AA, UK
| | - Michael W McDermott
- Department of Neurosurgery, UCSF Medical Center, San Francisco, CA, 94143-0112, USA
| | - Ramez W Kirollos
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, CB2 0QQ, UK
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Thomas Santarius
- Department of Neurosurgery, Department of Clinical Neuroscience, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - Ultan McDermott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Institute of Translational Medicine, University of Liverpool, Liverpool, L9 7LJ, UK.
- AstraZeneca, CRUK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.
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3
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Harewood L, Kishore K, Eldridge MD, Wingett S, Pearson D, Schoenfelder S, Collins VP, Fraser P. Hi-C as a tool for precise detection and characterisation of chromosomal rearrangements and copy number variation in human tumours. Genome Biol 2017; 18:125. [PMID: 28655341 PMCID: PMC5488307 DOI: 10.1186/s13059-017-1253-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [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: 12/09/2016] [Accepted: 06/08/2017] [Indexed: 12/02/2022] Open
Abstract
Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, is troublesome, which is particularly detrimental in oncology where rearrangements play diagnostic and prognostic roles. Here we describe the use of Hi-C as a tool for detection of both balanced and unbalanced chromosomal rearrangements in primary human tumour samples, with the potential to define chromosome breakpoints to bp resolution. In addition, we show copy number profiles can also be obtained from the same data, all at a significantly lower cost than standard sequencing approaches.
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Affiliation(s)
- Louise Harewood
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Steven Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Danita Pearson
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | | | - V Peter Collins
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.
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4
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Sahm F, Schrimpf D, Stichel D, Jones DTW, Hielscher T, Schefzyk S, Okonechnikov K, Koelsche C, Reuss DE, Capper D, Sturm D, Wirsching HG, Berghoff AS, Baumgarten P, Kratz A, Huang K, Wefers AK, Hovestadt V, Sill M, Ellis HP, Kurian KM, Okuducu AF, Jungk C, Drueschler K, Schick M, Bewerunge-Hudler M, Mawrin C, Seiz-Rosenhagen M, Ketter R, Simon M, Westphal M, Lamszus K, Becker A, Koch A, Schittenhelm J, Rushing EJ, Collins VP, Brehmer S, Chavez L, Platten M, Hänggi D, Unterberg A, Paulus W, Wick W, Pfister SM, Mittelbronn M, Preusser M, Herold-Mende C, Weller M, von Deimling A. DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis. Lancet Oncol 2017; 18:682-694. [PMID: 28314689 DOI: 10.1016/s1470-2045(17)30155-9] [Citation(s) in RCA: 497] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND The WHO classification of brain tumours describes 15 subtypes of meningioma. Nine of these subtypes are allotted to WHO grade I, and three each to grade II and grade III. Grading is based solely on histology, with an absence of molecular markers. Although the existing classification and grading approach is of prognostic value, it harbours shortcomings such as ill-defined parameters for subtypes and grading criteria prone to arbitrary judgment. In this study, we aimed for a comprehensive characterisation of the entire molecular genetic landscape of meningioma to identify biologically and clinically relevant subgroups. METHODS In this multicentre, retrospective analysis, we investigated genome-wide DNA methylation patterns of meningiomas from ten European academic neuro-oncology centres to identify distinct methylation classes of meningiomas. The methylation classes were further characterised by DNA copy number analysis, mutational profiling, and RNA sequencing. Methylation classes were analysed for progression-free survival outcomes by the Kaplan-Meier method. The DNA methylation-based and WHO classification schema were compared using the Brier prediction score, analysed in an independent cohort with WHO grading, progression-free survival, and disease-specific survival data available, collected at the Medical University Vienna (Vienna, Austria), assessing methylation patterns with an alternative methylation chip. FINDINGS We retrospectively collected 497 meningiomas along with 309 samples of other extra-axial skull tumours that might histologically mimic meningioma variants. Unsupervised clustering of DNA methylation data clearly segregated all meningiomas from other skull tumours. We generated genome-wide DNA methylation profiles from all 497 meningioma samples. DNA methylation profiling distinguished six distinct clinically relevant methylation classes associated with typical mutational, cytogenetic, and gene expression patterns. Compared with WHO grading, classification by individual and combined methylation classes more accurately identifies patients at high risk of disease progression in tumours with WHO grade I histology, and patients at lower risk of recurrence among WHO grade II tumours (p=0·0096) from the Brier prediction test). We validated this finding in our independent cohort of 140 patients with meningioma. INTERPRETATION DNA methylation-based meningioma classification captures clinically more homogenous groups and has a higher power for predicting tumour recurrence and prognosis than the WHO classification. The approach presented here is potentially very useful for stratifying meningioma patients to observation-only or adjuvant treatment groups. We consider methylation-based tumour classification highly relevant for the future diagnosis and treatment of meningioma. FUNDING German Cancer Aid, Else Kröner-Fresenius Foundation, and DKFZ/Heidelberg Institute of Personalized Oncology/Precision Oncology Program.
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Affiliation(s)
- Felix Sahm
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Schefzyk
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Konstantin Okonechnikov
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Koelsche
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David E Reuss
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | | | - Peter Baumgarten
- Neurological Institute (Edinger-Institute), Goethe University, Frankfurt, Germany
| | - Annekathrin Kratz
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Huang
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika K Wefers
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hayley P Ellis
- Brain Tumour Research Group, Institute of Clinical Neurosciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, Southmead Hospital, University of Bristol, Bristol, UK
| | - Ali Fuat Okuducu
- Department of Pathology, University Hospital Nürnberg, Nürnberg, Germany
| | - Christine Jungk
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Matthias Schick
- Genomics and Proteomics Core Facility, Micro-Array Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Bewerunge-Hudler
- Genomics and Proteomics Core Facility, Micro-Array Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | | | - Ralf Ketter
- Department of Neurosurgery, Saarland University, Homburg, Germany
| | - Matthias Simon
- Department of Neurosurgery, Evangelische Krankenhaus Bielefeld, Bielefeld, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Albert Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Arend Koch
- Department of Neuropathology, Charité Medical University, Berlin, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Elisabeth J Rushing
- Department of Neuropathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - V Peter Collins
- Department of Molecular Histopathology, University of Cambridge, Cambridge, UK
| | - Stefanie Brehmer
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany; Neurology Clinic, University Hospital Mannheim, Mannheim, Germany
| | - Daniel Hänggi
- Department of Neurosurgery, University Hospital Mannheim, Mannheim, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Neurology Clinic, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Pediatric Oncology, Haematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Michel Mittelbronn
- Neurological Institute (Edinger-Institute), Goethe University, Frankfurt, Germany
| | - Matthias Preusser
- Department of Medicine I, CNS Tumours Unit, Medical University of Vienna, Vienna, Austria
| | | | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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5
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Fontebasso AM, Shirinian M, Khuong-Quang DA, Bechet D, Gayden T, Kool M, De Jay N, Jacob K, Gerges N, Hutter B, Şeker-Cin H, Witt H, Montpetit A, Brunet S, Lepage P, Bourret G, Klekner A, Bognár L, Hauser P, Garami M, Farmer JP, Montes JL, Atkinson J, Lambert S, Kwan T, Korshunov A, Tabori U, Collins VP, Albrecht S, Faury D, Pfister SM, Paulus W, Hasselblatt M, Jones DTW, Jabado N. Non-random aneuploidy specifies subgroups of pilocytic astrocytoma and correlates with older age. Oncotarget 2016; 6:31844-56. [PMID: 26378811 PMCID: PMC4741644 DOI: 10.18632/oncotarget.5571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/15/2015] [Indexed: 11/25/2022] Open
Abstract
Pilocytic astrocytoma (PA) is the most common brain tumor in children but is rare in adults, and hence poorly studied in this age group. We investigated 222 PA and report increased aneuploidy in older patients. Aneuploid genomes were identified in 45% of adult compared with 17% of pediatric PA. Gains were non-random, favoring chromosomes 5, 7, 6 and 11 in order of frequency, and preferentially affecting non-cerebellar PA and tumors with BRAF V600E mutations and not with KIAA1549-BRAF fusions or FGFR1 mutations. Aneuploid PA differentially expressed genes involved in CNS development, the unfolded protein response, and regulators of genomic stability and the cell cycle (MDM2, PLK2),whose correlated programs were overexpressed specifically in aneuploid PA compared to other glial tumors. Thus, convergence of pathways affecting the cell cycle and genomic stability may favor aneuploidy in PA, possibly representing an additional molecular driver in older patients with this brain tumor.
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Affiliation(s)
- Adam M Fontebasso
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Margret Shirinian
- Department of Experimental Pathology, Immunology and Microbiology, American University Of Beirut, Beirut, Lebanon
| | - Dong-Anh Khuong-Quang
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Denise Bechet
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Tenzin Gayden
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Marcel Kool
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Nicolas De Jay
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Karine Jacob
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Noha Gerges
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Barbara Hutter
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Huriye Şeker-Cin
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Alexandre Montpetit
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Sébastien Brunet
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Lepage
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Geneviève Bourret
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - László Bognár
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Peter Hauser
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklós Garami
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Jean-Pierre Farmer
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Jose-Luis Montes
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Jeffrey Atkinson
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Sally Lambert
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Tony Kwan
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uri Tabori
- Division of Pediatric Hematology-Oncology and The Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - V Peter Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Damien Faury
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nada Jabado
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, Quebec, Canada.,Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
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6
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Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DTW, Capper D, Sill M, Buchhalter I, Northcott PA, Leis I, Ryzhova M, Koelsche C, Pfaff E, Allen SJ, Balasubramanian G, Worst BC, Pajtler KW, Brabetz S, Johann PD, Sahm F, Reimand J, Mackay A, Carvalho DM, Remke M, Phillips JJ, Perry A, Cowdrey C, Drissi R, Fouladi M, Giangaspero F, Łastowska M, Grajkowska W, Scheurlen W, Pietsch T, Hagel C, Gojo J, Lötsch D, Berger W, Slavc I, Haberler C, Jouvet A, Holm S, Hofer S, Prinz M, Keohane C, Fried I, Mawrin C, Scheie D, Mobley BC, Schniederjan MJ, Santi M, Buccoliero AM, Dahiya S, Kramm CM, von Bueren AO, von Hoff K, Rutkowski S, Herold-Mende C, Frühwald MC, Milde T, Hasselblatt M, Wesseling P, Rößler J, Schüller U, Ebinger M, Schittenhelm J, Frank S, Grobholz R, Vajtai I, Hans V, Schneppenheim R, Zitterbart K, Collins VP, Aronica E, Varlet P, Puget S, Dufour C, Grill J, Figarella-Branger D, Wolter M, Schuhmann MU, Shalaby T, Grotzer M, van Meter T, Monoranu CM, Felsberg J, Reifenberger G, Snuderl M, Forrester LA, Koster J, Versteeg R, Volckmann R, van Sluis P, Wolf S, Mikkelsen T, Gajjar A, Aldape K, Moore AS, Taylor MD, Jones C, Jabado N, Karajannis MA, Eils R, Schlesner M, Lichter P, von Deimling A, Pfister SM, Ellison DW, Korshunov A, Kool M. New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell 2016; 164:1060-1072. [PMID: 26919435 DOI: 10.1016/j.cell.2016.01.015] [Citation(s) in RCA: 577] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/22/2015] [Accepted: 01/08/2016] [Indexed: 12/11/2022]
Abstract
Primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) are highly aggressive, poorly differentiated embryonal tumors occurring predominantly in young children but also affecting adolescents and adults. Herein, we demonstrate that a significant proportion of institutionally diagnosed CNS-PNETs display molecular profiles indistinguishable from those of various other well-defined CNS tumor entities, facilitating diagnosis and appropriate therapy for patients with these tumors. From the remaining fraction of CNS-PNETs, we identify four new CNS tumor entities, each associated with a recurrent genetic alteration and distinct histopathological and clinical features. These new molecular entities, designated "CNS neuroblastoma with FOXR2 activation (CNS NB-FOXR2)," "CNS Ewing sarcoma family tumor with CIC alteration (CNS EFT-CIC)," "CNS high-grade neuroepithelial tumor with MN1 alteration (CNS HGNET-MN1)," and "CNS high-grade neuroepithelial tumor with BCOR alteration (CNS HGNET-BCOR)," will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by poorly differentiated CNS tumors.
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Affiliation(s)
- Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Umut H Toprak
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ) Heidelberg and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Irina Leis
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marina Ryzhova
- NN Burdenko Neurosurgical Institute, Moscow, 125047 Russia
| | - Christian Koelsche
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Elke Pfaff
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sariah J Allen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Gnanaprakash Balasubramanian
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara C Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Sebastian Brabetz
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Pascal D Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Jüri Reimand
- Ontario Institute for Cancer Research, M5G 0A3, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alan Mackay
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Diana M Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Marc Remke
- Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M4N 1X8, Canada
| | - Joanna J Phillips
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA.,Neuropathology, Department of Pathology, University of California, San Francisco, CA 94143-0102, USA.,Department of Neurological Surgery, University of California, San Francisco, CA 94143-0112, USA
| | - Arie Perry
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA.,Neuropathology, Department of Pathology, University of California, San Francisco, CA 94143-0102, USA.,Department of Neurological Surgery, University of California, San Francisco, CA 94143-0112, USA
| | - Cynthia Cowdrey
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA
| | - Rachid Drissi
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Maryam Fouladi
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomic-Pathological Sciences, Sapienza University of Rome, 00185 Rome, Italy.,IRCCS Neuromed, 86077 Pozzilli, Molise, Italy
| | - Maria Łastowska
- Department of Pathology, Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Wolfram Scheurlen
- Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, 90419 Nürnberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical School, 53105 Bonn, Germany
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria.,Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Lötsch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Institute of Neurology, Medical University of Vienna, 1097 Vienna, Austria
| | - Anne Jouvet
- Neuro-Oncology and Neuro-Inflammation Team, Inserm U1028, CNRS UMR 5292, University Lyon-1, Neuroscience Center, 69000 Lyon, France, and Centre de Pathologie et de Neuropathologie Est, Hospices Civils de Lyon, 69003 Lyon, France
| | - Stefan Holm
- Department of Women's and Children's Health (KBH), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Silvia Hofer
- Department of Oncology, Luzerner Kantonsspital, 6000 Luzern 16, Luzern, Switzerland
| | - Marco Prinz
- Institute of Neuropathology, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany
| | - Catherine Keohane
- Department of Pathology, University College Cork and Cork University Hospital Wilton, Cork, Ireland
| | - Iris Fried
- Department of Pediatric Hematology and Oncology, Hadassah Medical Center, Jerusalem, Israel
| | - Christian Mawrin
- Institute of Neuropathology, University Hospital, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - David Scheie
- Department of Pathology, Copenhagen University Hospital, 2100 København Ø, Denmark
| | - Bret C Mobley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J Schniederjan
- Department of Pathology and Laboratory Administration, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mariarita Santi
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna M Buccoliero
- Pathology Unit, Anna Meyer Children's University Hospital, 50141 Florence, Italy
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Christof M Kramm
- Division of Pediatric Hematology and Oncology, Department of Child and Adolescent Health, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - André O von Bueren
- Division of Pediatric Hematology and Oncology, Department of Child and Adolescent Health, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Katja von Hoff
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christel Herold-Mende
- Department of Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | | | - Till Milde
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) Heidelberg, 69120 Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Center Amsterdam, 1008 MB Amsterdam, The Netherlands.,Department of Pathology, Radboud University Nijmegen Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jochen Rößler
- Department of Pediatric Hematology/Oncology, Center of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Ulrich Schüller
- Department of Neuropathology, Ludwig-Maximilians-University, and German Cancer Consortium (DKTK) partner site Munich, 81377 Munich, Germany
| | - Martin Ebinger
- Department of Hematology and Oncology, Children's University Hospital Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University of Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Stephan Frank
- Department of Neuropathology, Institute of Pathology, Basel University Hospital, 4031 Basel, Switzerland
| | - Rainer Grobholz
- Department of Pathology, Medical Center Aarau, 5001 Aarau, Switzerland
| | - Istvan Vajtai
- Department of Pathology, University Hospital Bern, 3010 Bern, Switzerland
| | - Volkmar Hans
- Department of Neuropathology, Medical Center Bielefeld, 33617 Bielefeld, Germany
| | - Reinhard Schneppenheim
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Karel Zitterbart
- Department of Pediatric Oncology, University Hospital Brno and Masaryk University, Faculty of Medicine, 613 00 Brno, Czech Republic
| | - V Peter Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Eleonora Aronica
- Department of Neuropathology, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Pascale Varlet
- Department of Neuropathology, Hôpital Sainte-Anne, 75674, Paris, France
| | - Stephanie Puget
- Pediatric Neurosurgery Department, Necker Enfants Malades Hospital, 75015, Paris, France
| | - Christelle Dufour
- Brain Tumor Program, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris Sud, 94805, Villejuif, France
| | - Jacques Grill
- Brain Tumor Program, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris Sud, 94805, Villejuif, France
| | - Dominique Figarella-Branger
- Department of Pathology and Neuropathology, la Timone Hospital, AP-HM and UMR911 CR02, Aix-Marseille University, 13385 Marseille, France
| | - Marietta Wolter
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Martin U Schuhmann
- Department of Neurosurgery, Section of Pediatric Neurosurgery, University Hospital Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Tarek Shalaby
- Neuro-Oncology Program, Division of Oncology, University Children's Hospital Zurich, 8032 Zürich, Switzerland
| | - Michael Grotzer
- Neuro-Oncology Program, Division of Oncology, University Children's Hospital Zurich, 8032 Zürich, Switzerland
| | | | - Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center (CCC) Mainfranken, University and University Hospital, 97080 Würzburg, Germany
| | - Jörg Felsberg
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Matija Snuderl
- Department of Pathology, Division of Neuropathology, NYU Langone Medical Center, New York, NY 10016, USA
| | | | - Jan Koster
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Peter van Sluis
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, High Throughput Sequencing Unit, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Tom Mikkelsen
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kenneth Aldape
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, Translational Research Institute; UQ Child Health Research Centre, The University of Queensland; Queensland Children's Medical Research Institute, Children's Health Queensland Hospital and Health Service; Brisbane, Australia
| | - Michael D Taylor
- Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M4N 1X8, Canada
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Nada Jabado
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Matthias A Karajannis
- Departments of Pediatrics and Otolaryngology, Division of Pediatric Hematology/Oncology, NYU Langone Medical Center and Laura and Isaac Perlmutter Cancer Center, NY 10016, New York, USA
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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7
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Qaddoumi I, Orisme W, Wen J, Santiago T, Gupta K, Dalton JD, Tang B, Haupfear K, Punchihewa C, Easton J, Mulder H, Boggs K, Shao Y, Rusch M, Becksfort J, Gupta P, Wang S, Lee RP, Brat D, Peter Collins V, Dahiya S, George D, Konomos W, Kurian KM, McFadden K, Serafini LN, Nickols H, Perry A, Shurtleff S, Gajjar A, Boop FA, Klimo PD, Mardis ER, Wilson RK, Baker SJ, Zhang J, Wu G, Downing JR, Tatevossian RG, Ellison DW. Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology. Acta Neuropathol 2016; 131:833-45. [PMID: 26810070 DOI: 10.1007/s00401-016-1539-z] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 01/16/2016] [Accepted: 01/17/2016] [Indexed: 12/24/2022]
Abstract
Low-grade neuroepithelial tumors (LGNTs) are diverse CNS tumors presenting in children and young adults, often with a history of epilepsy. While the genetic profiles of common LGNTs, such as the pilocytic astrocytoma and 'adult-type' diffuse gliomas, are largely established, those of uncommon LGNTs remain to be defined. In this study, we have used massively parallel sequencing and various targeted molecular genetic approaches to study alterations in 91 LGNTs, mostly from children but including young adult patients. These tumors comprise dysembryoplastic neuroepithelial tumors (DNETs; n = 22), diffuse oligodendroglial tumors (d-OTs; n = 20), diffuse astrocytomas (DAs; n = 17), angiocentric gliomas (n = 15), and gangliogliomas (n = 17). Most LGNTs (84 %) analyzed by whole-genome sequencing (WGS) were characterized by a single driver genetic alteration. Alterations of FGFR1 occurred frequently in LGNTs composed of oligodendrocyte-like cells, being present in 82 % of DNETs and 40 % of d-OTs. In contrast, a MYB-QKI fusion characterized almost all angiocentric gliomas (87 %), and MYB fusion genes were the most common genetic alteration in DAs (41 %). A BRAF:p.V600E mutation was present in 35 % of gangliogliomas and 18 % of DAs. Pathogenic alterations in FGFR1/2/3, BRAF, or MYB/MYBL1 occurred in 78 % of the series. Adult-type d-OTs with an IDH1/2 mutation occurred in four adolescents, the youngest aged 15 years at biopsy. Despite a detailed analysis, novel genetic alterations were limited to two fusion genes, EWSR1-PATZ1 and SLMAP-NTRK2, both in gangliogliomas. Alterations in BRAF, FGFR1, or MYB account for most pathogenic alterations in LGNTs, including pilocytic astrocytomas, and alignment of these genetic alterations and cytologic features across LGNTs has diagnostic implications. Additionally, therapeutic options based upon targeting the effects of these alterations are already in clinical trials.
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8
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Brodbelt A, Greenberg D, Williams M, Karabatsou T, Miller S, Collins VP. PO395 YEAR SURVIVAL WITH GLIOBLASTOMA: A NATIONAL PERSPECTIVE. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov284.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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9
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Geisenberger C, Mock A, Warta R, Rapp C, Schwager C, Korshunov A, Nied AK, Capper D, Brors B, Jungk C, Jones D, Collins VP, Ichimura K, Bäcklund LM, Schnabel E, Mittelbron M, Lahrmann B, Zheng S, Verhaak RGW, Grabe N, Pfister SM, Hartmann C, von Deimling A, Debus J, Unterberg A, Abdollahi A, Herold-Mende C. Molecular profiling of long-term survivors identifies a subgroup of glioblastoma characterized by chromosome 19/20 co-gain. Acta Neuropathol 2015; 130:419-34. [PMID: 25931051 DOI: 10.1007/s00401-015-1427-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/04/2015] [Accepted: 04/18/2015] [Indexed: 01/07/2023]
Abstract
Glioblastoma (GBM) is a devastating tumor and few patients survive beyond 3 years. Defining the molecular determinants underlying long-term survival is essential for insights into tumor biology and biomarker identification. We therefore investigated homogeneously treated, IDH (wt) long-term (LTS, n = 10) and short-term survivors (STS, n = 6) by microarray transcription profiling. While there was no association of clinical parameters and molecular subtypes with long-term survival, STS tumors were characterized by differential polarization of infiltrating microglia with predominance of the M2 phenotype detectable both on the mRNA and protein level. Furthermore, transcriptional signatures of LTS and STS predicted patient outcome in a large, IDH (wt) cohort (n = 468). Interrogation of overlapping genomic alterations identified concurrent gain of chromosomes 19 and 20 as a favorable prognostic marker. The strong association of this co-gain with survival was validated by aCGH in a second, independent cohort (n = 124). Finally, FISH and gene expression data revealed gains to constitute low-amplitude, clonal events with a strong impact on transcription. In conclusion, these findings provide important insights into the manipulation of the innate immune system by particularly aggressive GBM tumors. Furthermore, we genomically characterize a previously unknown, clinically relevant subgroup of glioblastoma, which can easily be identified through modern neuropathological workup.
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10
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Riegman PHJ, de Jong B, Daidone MG, Söderström T, Thompson J, Hall JA, Mendy M, Ten Hoeve J, Broeks A, Reed W, Morente MM, López-Guerrero JA, Collins VP, Rogan J, Ringborg U. Optimizing sharing of hospital biobank samples. Sci Transl Med 2015; 7:297fs31. [PMID: 26203078 DOI: 10.1126/scitranslmed.3009279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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] [Indexed: 12/19/2022]
Abstract
Implementing technical guidelines and standards as well as ways to boost cooperation should facilitate sharing of hospital biobank samples.
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Affiliation(s)
- Peter H J Riegman
- Department of Pathology, Erasmus Medical Center, 3015 CE Rotterdam, Netherlands.
| | - Bas de Jong
- Department of Pathology, Erasmus Medical Center, 3015 CE Rotterdam, Netherlands
| | - Maria Grazia Daidone
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Tommy Söderström
- Karolinska Healthcare Research Biobank, Clinical Pathology/Cytology, Karolinska University Hospital, T5:01, SE-171 76 Stockholm, Sweden
| | - James Thompson
- Karolinska Institutet Biobank, Karolinska Institutet SE-171 77 Stockholm, Sweden
| | - Jacqueline A Hall
- Translational Research, Imaging and Radiotherapy Department, European Organisation for Research and Treatment of Cancer, 1200 Brussels, Belgium
| | - Maimuna Mendy
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, F-69372 Lyon Cedex 08, France
| | - Jelle Ten Hoeve
- Research IT, Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Annegien Broeks
- Research IT, Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Wenche Reed
- Research, Innovation and Education Unit, Oslo University Hospital, 0424 Oslo, Norway
| | - Manuel M Morente
- Biobanco, Centro Nacional de Investigaciones Oncológicas, 28029 Madrid, Spain
| | - José Antonio López-Guerrero
- Laboratory of Molecular Biology and Biobank, Fundacion Instituto Valenciano de Oncologia, 46009 Valencia, Spain
| | - V Peter Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Jane Rogan
- Manchester Cancer Research Centre Biobank, Paterson Institute for Cancer Research, The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Ulrik Ringborg
- Cancer Center Karolinska, Karolinska University Hospital Solna, SE-171 76 Stockholm, Sweden
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11
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Collins VP, Jones DTW, Giannini C. Pilocytic astrocytoma: pathology, molecular mechanisms and markers. Acta Neuropathol 2015; 129:775-88. [PMID: 25792358 PMCID: PMC4436848 DOI: 10.1007/s00401-015-1410-7] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [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: 11/21/2014] [Revised: 02/17/2015] [Accepted: 03/06/2015] [Indexed: 01/19/2023]
Abstract
Pilocytic astrocytomas (PAs) were recognized as a discrete clinical entity over 70 years ago. They are relatively benign (WHO grade I) and have, as a group, a 10-year survival of over 90%. Many require merely surgical removal and only very infrequently do they progress to more malignant gliomas. While most show classical morphology, they may present a spectrum of morphological patterns, and there are difficult cases that show similarities to other gliomas, some of which are malignant and require aggressive treatment. Until recently, almost nothing was known about the molecular mechanisms involved in their development. The use of high-throughput sequencing techniques interrogating the whole genome has shown that single abnormalities of the mitogen-activating protein kinase (MAPK) pathway are exclusively found in almost all cases, indicating that PA represents a one-pathway disease. The most common mechanism is a tandem duplication of a ≈2 Mb-fragment of #7q, giving rise to a fusion between two genes, resulting in a transforming fusion protein, consisting of the N-terminus of KIAA1549 and the kinase domain of BRAF. Additional infrequent fusion partners have been identified, along with other abnormalities of the MAP-K pathway, affecting tyrosine kinase growth factor receptors at the cell surface (e.g., FGFR1) as well as BRAF V600E, KRAS, and NF1 mutations among others. However, while the KIAA1549-BRAF fusion occurs in all areas, the incidence of the various other mutations identified differs in PAs that develop in different regions of the brain. Unfortunately, from a diagnostic standpoint, almost all mutations found have been reported in other brain tumor types, although some retain considerable utility. These molecular abnormalities will be reviewed, and the difficulties in their potential use in supporting a diagnosis of PA, when the histopathological findings are equivocal or in the choice of individualized therapy, will be discussed.
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Affiliation(s)
- V Peter Collins
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK,
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12
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Pajtler KW, Witt H, Sill M, Jones DTW, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM. Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. Cancer Cell 2015; 27:728-43. [PMID: 25965575 PMCID: PMC4712639 DOI: 10.1016/j.ccell.2015.04.002] [Citation(s) in RCA: 753] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/26/2015] [Accepted: 04/08/2015] [Indexed: 12/17/2022]
Abstract
Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.
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Affiliation(s)
- Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, 45147 Essen, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Fabian Kratochwil
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruth Tatevossian
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jüri Reimand
- The Donnelly Center, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hans-Jörg Warnatz
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, 125047 Moscow, Russia
| | - Steve Mack
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Vijay Ramaswamy
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - David Capper
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Leonille Schweizer
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Laura Sieber
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Andrea Wittmann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Zhiqin Huang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Daniel Fults
- University of Utah, Salt Lake City, UT 84132, USA
| | - Helen Toledano
- Pediatric Hematology Oncology, Schneider Children's Medical Center of Israel, 49202 Petah Tikva, Israel
| | - Smadar Avigad
- Department of Molecular Oncology, Schneider Children's Medical Center of Israel, Tel Aviv University, 49202 Tel Aviv, Israel
| | - Lindsey M Hoffman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Andrew M Donson
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Nicholas Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Ekkehard Hewer
- Department of Pathology, University of Bern, 3010 Bern, Switzerland
| | - Karel Zitterbart
- Department of Pediatric Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, 61300 Brno, Czech Republic; Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 65653 Brno, Czech Republic
| | - Mark Gilbert
- Division of Cancer Medicine, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Terri S Armstrong
- Division of Cancer Medicine, Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Family Health, University of Texas Health Science Center-SON, Houston, TX 77030, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey C Allen
- Departments of Pediatrics and Neurology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Matthias A Karajannis
- Division of Pediatric Hematology and Oncology, Departments of Pediatrics and Otolaryngology, NYU Langone Medical Center, New York, NY 10016, USA
| | - David Zagzag
- Department of Pathology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Martin Hasselblatt
- Institute for Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany
| | - Olaf Witt
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - V Peter Collins
- Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Katja von Hoff
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn, 53127 Bonn, Germany
| | - Gary Bader
- The Donnelly Center, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Peter Lichter
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Richard Gilbertson
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kenneth Aldape
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Andrey Korshunov
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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13
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Witt H, Sill M, Wani K, Mack S, Capper D, Heim S, Johann P, Lambert S, Rhyzova M, Hovestadt V, Tzaridis T, Pajtler K, Bender S, Milde T, Northcott PA, Kulozik AE, Witt O, Lichter P, Collins VP, Deimling AV, Kool M, Taylor MD, Hasselblatt M, Jones DT, Korshunov A, Aldape K, Pfister S. Abstract 3094: Epigenetic classification of ependymal brain tumors across age groups. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3094] [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]
Abstract
Abstract
Since it has become evident that histopathological grading of ependymoma according to the WHO classification of CNS tumors is not capable of accurately classifying patients into meaningful strata, a broadly accepted molecular classification scheme with prognostic significance is desperately needed. In recent years, ependymomas were classified into molecular subgroups based on transcriptomic alterations. In tumors localized within the posterior fossa, two distinct biological entities of ependymoma were delineated by several studies (designated posterior fossa A and posterior fossa B), which show striking differences in genetic characteristics and clinical outcome. A similar consensus for supratentorial and spinal ependymoma is lacking.
We studied genome-wide DNA methylation (Illumina HumanMethylation450 (450k) array) in 180 primary ependymal tumors (80 with corresponding gene expression profiling data generated by Affymetrix 133plus2.0 arrays), including ependymomas (posterior fossa, supratentorial, spinal), subependymomas (SE), myxopapillary ependymoma (MPE), pineal parenchymal tumors of intermediate differentiation (PPTID), and papillary tumors of the pineal region (PTPR). We performed hierarchical clustering to identify robust molecular subgroups. Independent gene expression profiling datasets from previously published ependymoma studies (Johnson et al.; Wani et al.; Witt et al.) were used as validation cohorts.
DNA methylation data showed that ependymal brain tumors can be classified into eight molecular subgroups. Notably, MPE, SE, PPTID and PTPR tumors formed robust distinct clusters, as did posterior fossa Group A and Group B ependymomas. Supratentorial ependymomas can be classified into two principle molecular subgroups, one of which displays a dismal prognosis, and comprises predominantly children and infants, and is associated with highly recurrent gene fusion. Notably, a significant number of ependymomas previously classified by histology as WHO Grade II/III look like SE by methylation, and also have extremely good survival.
In summary, using genome-wide DNA methylation and transcriptome analysis we could decipher robust molecular subgroups of ependymal brain tumors including supratentorial ependymoma. Diagnoses of tumors with challenging histopathological features can now be supported by this technology. Hence, this approach offers the possibility to replace the unambiguous histological grading system that is currently in use with a robust molecular classification that readily distinguishes biologically, genetically, and clinically meaningful subgroups of ependymal brain tumors.
Citation Format: Hendrik Witt, Martin Sill, Khalida Wani, Steve Mack, David Capper, Stephanie Heim, Pascal Johann, Sally Lambert, Marina Rhyzova, Volker Hovestadt, Theophilos Tzaridis, Kristian Pajtler, Sebastian Bender, Till Milde, Paul A. Northcott, Andreas E. Kulozik, Olaf Witt, Peter Lichter, V Peter Collins, Andreas von Deimling, Marcel Kool, Michael D. Taylor, Martin Hasselblatt, David TW Jones, Andrey Korshunov, Ken Aldape, Stefan Pfister. Epigenetic classification of ependymal brain tumors across age groups. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3094. doi:10.1158/1538-7445.AM2014-3094
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Affiliation(s)
- Hendrik Witt
- 1German Cancer Research Center, Heidelberg, Germany
| | - Martin Sill
- 1German Cancer Research Center, Heidelberg, Germany
| | - Khalida Wani
- 2MD Anderson, Divison of Neuropathology, Houston, TX
| | - Steve Mack
- 3Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Capper
- 4Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Stephanie Heim
- 5Department of Neuropathology, University of Münster, Heidelberg, Germany
| | | | - Sally Lambert
- 6Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marina Rhyzova
- 7NN Burdenko Neurosurgical Institute, Moscow, Russian Federation
| | - Volker Hovestadt
- 8German Cancer Research Center, Molecular Genetics, Heidelberg, Germany
| | | | | | | | - Till Milde
- 1German Cancer Research Center, Heidelberg, Germany
| | | | - Andreas E. Kulozik
- 9Department of Pediatric Oncology, University of Heidelberg, Heidelberg, Germany
| | - Olaf Witt
- 1German Cancer Research Center, Heidelberg, Germany
| | | | - V Peter Collins
- 6Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Marcel Kool
- 1German Cancer Research Center, Heidelberg, Germany
| | - Michael D. Taylor
- 3Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martin Hasselblatt
- 5Department of Neuropathology, University of Münster, Heidelberg, Germany
| | | | - Andrey Korshunov
- 4Department of Neuropathology, University of Heidelberg, Heidelberg, Germany
| | - Ken Aldape
- 2MD Anderson, Divison of Neuropathology, Houston, TX
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14
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Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A, Bolli N, Behjati S, Tarpey PS, Nangalia J, Massie CE, Butler AP, Teague JW, Vassiliou GS, Green AR, Du MQ, Unnikrishnan A, Pimanda JE, Teh BT, Munshi N, Greaves M, Vyas P, El-Naggar AK, Santarius T, Collins VP, Grundy R, Taylor JA, Hayes DN, Malkin D, Foster CS, Warren AY, Whitaker HC, Brewer D, Eeles R, Cooper C, Neal D, Visakorpi T, Isaacs WB, Bova GS, Flanagan AM, Futreal PA, Lynch AG, Chinnery PF, McDermott U, Stratton MR, Campbell PJ. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. eLife 2014; 3:e02935. [PMID: 25271376 PMCID: PMC4371858 DOI: 10.7554/elife.02935] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [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: 03/28/2014] [Accepted: 09/26/2014] [Indexed: 01/04/2023] Open
Abstract
Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are unclear. In this study, we analyzed somatic alterations in mtDNA from 1675 tumors. We identified 1907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C > T and A > G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. A number of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria and is fundamentally linked to mtDNA replication.
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Affiliation(s)
- Young Seok Ju
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Ludmil B Alexandrov
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Moritz Gerstung
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Inigo Martincorena
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Serena Nik-Zainal
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Manasa Ramakrishna
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Helen R Davies
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Elli Papaemmanuil
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Gunes Gundem
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Adam Shlien
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Niccolo Bolli
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Sam Behjati
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Patrick S Tarpey
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Jyoti Nangalia
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Charles E Massie
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Adam P Butler
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Jon W Teague
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - George S Vassiliou
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Anthony R Green
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
| | - Ming-Qing Du
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Ashwin Unnikrishnan
- Lowy Cancer Research
Centre, University of New South Wales,
Sydney, Australia
| | - John E Pimanda
- Lowy Cancer Research
Centre, University of New South Wales,
Sydney, Australia
| | - Bin Tean Teh
- Laboratory of Cancer
Epigenome, National Cancer Centre,
Singapore, Singapore
- Duke-NUS Graduate Medical School,
Singapore, Singapore
| | - Nikhil Munshi
- Department of Hematologic
Oncology, Dana-Farber Cancer Institute,
Boston, United States
| | - Mel Greaves
- Institute of Cancer Research, Sutton,
London, United Kingdom
| | - Paresh Vyas
- Weatherall Institute for Molecular
Medicine, University of Oxford,
Oxford, United Kingdom
| | - Adel K El-Naggar
- Department of Pathology,
MD Anderson Cancer Center, Houston, United
States
| | - Tom Santarius
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - V Peter Collins
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Richard Grundy
- Children's Brain Tumour Research
Centre, University of Nottingham,
Nottingham, United Kingdom
| | - Jack A Taylor
- National Institute of Environmental
Health Sciences, National Institute of
Health, Triangle,
North Carolina, United
States
| | - D Neil Hayes
- Department of Internal
Medicine, University of North Carolina,
Chapel
Hill, United States
| | - David Malkin
- Hospital for Sick
Children, University of Toronto,
Toronto, Canada
| | - Christopher S Foster
- Department of Molecular and Clinical
Cancer Medicine, University of Liverpool,
London, United Kingdom
- HCA Pathology Laboratories,
London, United Kingdom
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Hayley C Whitaker
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Daniel Brewer
- Institute of Cancer Research, Sutton,
London, United Kingdom
- School of Biological
Sciences, University of East Anglia,
Norwich, United Kingdom
| | - Rosalind Eeles
- Institute of Cancer Research, Sutton,
London, United Kingdom
| | - Colin Cooper
- Institute of Cancer Research, Sutton,
London, United Kingdom
- School of Biological
Sciences, University of East Anglia,
Norwich, United Kingdom
| | - David Neal
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Tapio Visakorpi
- Institute of Biosciences and Medical
Technology - BioMediTech and Fimlab Laboratories,
University of Tampere and Tampere University Hospital,
Tampere, Finland
| | - William B Isaacs
- Department of Oncology,
Johns Hopkins University, Baltimore, United
States
| | - G Steven Bova
- Institute of Biosciences and Medical
Technology - BioMediTech and Fimlab Laboratories,
University of Tampere and Tampere University Hospital,
Tampere, Finland
| | - Adrienne M Flanagan
- Department of
Histopathology, Royal National Orthopaedic
Hospital, Middlesex, United Kingdom
- University College London Cancer
Institute, University College London,
London, United Kingdom
| | - P Andrew Futreal
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Department of Genomic
Medicine, The University of Texas, MD Anderson Cancer
Center, Houston, Texas, United States
| | - Andy G Lynch
- Cancer Research UK Cambridge
Institute, University of Cambridge,
Cambridge, United Kingdom
| | - Patrick F Chinnery
- Wellcome Trust Centre for Mitochondrial
Research, Institute of Genetic Medicine, Newcastle
University, Newcastle-upon-tyne, United
Kingdom
| | - Ultan McDermott
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
| | - Michael R Stratton
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
| | - Peter J Campbell
- Cancer Genome Project,
Wellcome Trust Sanger Institute,
Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation
Trust, Cambridge, United Kingdom
- Department of Haematology,
University of Cambridge, Cambridge, United
Kingdom
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15
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Louis DN, Perry A, Burger P, Ellison DW, Reifenberger G, von Deimling A, Aldape K, Brat D, Collins VP, Eberhart C, Figarella‐Branger D, Fuller GN, Giangaspero F, Giannini C, Hawkins C, Kleihues P, Korshunov A, Kros JM, Beatriz Lopes M, Ng H, Ohgaki H, Paulus W, Pietsch T, Rosenblum M, Rushing E, Soylemezoglu F, Wiestler O, Wesseling P. International Society Of Neuropathology--Haarlem consensus guidelines for nervous system tumor classification and grading. Brain Pathol 2014; 24:429-35. [PMID: 24990071 PMCID: PMC8029490 DOI: 10.1111/bpa.12171] [Citation(s) in RCA: 422] [Impact Index Per Article: 42.2] [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] [Indexed: 11/26/2022] Open
Abstract
Major discoveries in the biology of nervous system tumors have raised the question of how non-histological data such as molecular information can be incorporated into the next World Health Organization (WHO) classification of central nervous system tumors. To address this question, a meeting of neuropathologists with expertise in molecular diagnosis was held in Haarlem, the Netherlands, under the sponsorship of the International Society of Neuropathology (ISN). Prior to the meeting, participants solicited input from clinical colleagues in diverse neuro-oncological specialties. The present "white paper" catalogs the recommendations of the meeting, at which a consensus was reached that incorporation of molecular information into the next WHO classification should follow a set of provided "ISN-Haarlem" guidelines. Salient recommendations include that (i) diagnostic entities should be defined as narrowly as possible to optimize interobserver reproducibility, clinicopathological predictions and therapeutic planning; (ii) diagnoses should be "layered" with histologic classification, WHO grade and molecular information listed below an "integrated diagnosis"; (iii) determinations should be made for each tumor entity as to whether molecular information is required, suggested or not needed for its definition; (iv) some pediatric entities should be separated from their adult counterparts; (v) input for guiding decisions regarding tumor classification should be solicited from experts in complementary disciplines of neuro-oncology; and (iv) entity-specific molecular testing and reporting formats should be followed in diagnostic reports. It is hoped that these guidelines will facilitate the forthcoming update of the fourth edition of the WHO classification of central nervous system tumors.
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Affiliation(s)
- David N. Louis
- Department of PathologyMassachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Arie Perry
- Department of PathologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Peter Burger
- Department of PathologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | - David W. Ellison
- Department of PathologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Guido Reifenberger
- Department of NeuropathologyHeinrich Heine UniversityDuesseldorfGermany
- Clinical Cooperation Unit NeuropathologyGerman Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Andreas von Deimling
- Clinical Cooperation Unit NeuropathologyGerman Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuropathologyInstitute of PathologyRuprecht‐Karls‐UniversityHeidelbergGermany
| | - Kenneth Aldape
- Department of PathologyPrincess Margaret HospitalTorontoCanada
| | - Daniel Brat
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGAUSA
| | | | - Charles Eberhart
- Department of PathologyThe Johns Hopkins University School of MedicineBaltimoreMDUSA
| | | | - Gregory N. Fuller
- Department of PathologyThe University of Texas M. D. Anderson Cancer CenterHoustonTXUSA
| | - Felice Giangaspero
- Department of RadiologicalOncological and Anatomo‐Pathological SciencesUniversity La SapienzaRome
- IRCCS NeuromedPozzilliItaly
| | - Caterina Giannini
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cynthia Hawkins
- Department of Paediatric Laboratory MedicineThe Hospital for Sick ChildrenUniversity of TorontoTorontoCanada
| | | | - Andrey Korshunov
- Clinical Cooperation Unit NeuropathologyGerman Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuropathologyHeidelberg University HospitalHeidelbergGermany
| | - Johan M. Kros
- Department of PathologyErasmus Medical CenterRotterdamThe Netherlands
| | - M. Beatriz Lopes
- Department of PathologyUniversity of Virginia School of MedicineCharlottesvilleVAUSA
| | - Ho‐Keung Ng
- Department of Anatomical Pathology and Cellular PathologyThe Chinese University of Hong KongHong Kong
| | - Hiroko Ohgaki
- International Agency for Research on Cancer (IARC)LyonFrance
| | - Werner Paulus
- Institute of NeuropathologyUniversity Hospital MünsterMünsterGermany
| | - Torsten Pietsch
- Institute of NeuropathologyBrain Tumor Reference CenterUniversity of BonnBonnGermany
| | - Marc Rosenblum
- Department of PathologyMemorial Sloan‐Kettering Cancer CenterNew YorkNYUSA
| | - Elisabeth Rushing
- Institute for NeuropathologyUniversity Hospital of ZurichZurichSwitzerland
| | | | | | - Pieter Wesseling
- Department of PathologyVU University Medical CenterAmsterdamThe Netherlands
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
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16
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Spence T, Sin-Chan P, Picard D, Barszczyk M, Hoss K, Lu M, Kim SK, Ra YS, Nakamura H, Fangusaro J, Hwang E, Kiehna E, Toledano H, Wang Y, Shi Q, Johnston D, Michaud J, La Spina M, Buccoliero AM, Adamek D, Camelo-Piragua S, Peter Collins V, Jones C, Kabbara N, Jurdi N, Varlet P, Perry A, Scharnhorst D, Fan X, Muraszko KM, Eberhart CG, Ng HK, Gururangan S, Van Meter T, Remke M, Lafay-Cousin L, Chan JA, Sirachainan N, Pomeroy SL, Clifford SC, Gajjar A, Shago M, Halliday W, Taylor MD, Grundy R, Lau CC, Phillips J, Bouffet E, Dirks PB, Hawkins CE, Huang A. CNS-PNETs with C19MC amplification and/or LIN28 expression comprise a distinct histogenetic diagnostic and therapeutic entity. Acta Neuropathol 2014; 128:291-303. [PMID: 24839957 PMCID: PMC4159569 DOI: 10.1007/s00401-014-1291-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [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: 11/26/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 10/26/2022]
Abstract
Amplification of the C19MC oncogenic miRNA cluster and high LIN28 expression has been linked to a distinctly aggressive group of cerebral CNS-PNETs (group 1 CNS-PNETs) arising in young children. In this study, we sought to evaluate the diagnostic specificity of C19MC and LIN28, and the clinical and biological spectra of C19MC amplified and/or LIN28+ CNS-PNETs. We interrogated 450 pediatric brain tumors using FISH and IHC analyses and demonstrate that C19MC alteration is restricted to a sub-group of CNS-PNETs with high LIN28 expression; however, LIN28 immunopositivity was not exclusive to CNS-PNETs but was also detected in a proportion of other malignant pediatric brain tumors including rhabdoid brain tumors and malignant gliomas. C19MC amplified/LIN28+ group 1 CNS-PNETs arose predominantly in children <4 years old; a majority arose in the cerebrum but 24 % (13/54) of tumors had extra-cerebral origins. Notably, group 1 CNS-PNETs encompassed several histologic classes including embryonal tumor with abundant neuropil and true rosettes (ETANTR), medulloepithelioma, ependymoblastoma and CNS-PNETs with variable differentiation. Strikingly, gene expression and methylation profiling analyses revealed a common molecular signature enriched for primitive neural features, high LIN28/LIN28B and DNMT3B expression for all group 1 CNS-PNETs regardless of location or tumor histology. Our collective findings suggest that current known histologic categories of CNS-PNETs which include ETANTRs, medulloepitheliomas, ependymoblastomas in various CNS locations, comprise a common molecular and diagnostic entity and identify inhibitors of the LIN28/let7/PI3K/mTOR axis and DNMT3B as promising therapeutics for this distinct histogenetic entity.
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Affiliation(s)
- Tara Spence
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Patrick Sin-Chan
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Daniel Picard
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
| | - Mark Barszczyk
- Department of Pathology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katharina Hoss
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
| | - Mei Lu
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Young-Shin Ra
- Department of Neurosurgery, Asan Medical Center, Seoul, South Korea
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan
| | - Jason Fangusaro
- Division of Pediatric Hematology/Oncology and Stem Cell Transplantation, Children’s Memorial Hospital, Chicago, IL USA
| | - Eugene Hwang
- Center for Cancer and Blood Disorders, Children’s National Medical Center, Washington, DC USA
| | - Erin Kiehna
- Department of Neurosurgery, Children’s Hospital of Los Angeles, Los Angeles, CA USA
| | - Helen Toledano
- Oncology Department, Schneider Hospital, Petach Tikva, Israel
| | - Yin Wang
- Department of Neuropathology Huashan Hospital, Fudan University, Shanghai, China
| | - Qing Shi
- Department of Pathology, Shanghai Children’s Hospital Affiliated Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Donna Johnston
- Department of Pediatrics, Children’s Hospital of Eastern Ontario, Ottawa, ON Canada
| | - Jean Michaud
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Eastern Ontario, Ottawa, ON Canada
| | - Milena La Spina
- Paediatric Haematology and Oncology Division, University of Catania, Sicily, Italy
| | | | - Dariusz Adamek
- Department of Pathomorphology, Jagiellonian University Medical College, Krakow, Poland
| | | | | | - Chris Jones
- Department of Paediatric Molecular Pathology, Institute of Cancer Research, Sutton, UK
| | - Nabil Kabbara
- Division of Pediatric Hematology Oncology, Rafic Hariri University Hospital, Beirut, Lebanon
| | - Nawaf Jurdi
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pascale Varlet
- Medical and Department of Neuropathology, Sainte-Anne Hospital, University Paris V Descartes, Paris, France
| | - Arie Perry
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA USA
| | - David Scharnhorst
- Department of Pathology, Children’s Hospital Central California, Madera, CA USA
| | - Xing Fan
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI USA
| | - Karin M. Muraszko
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI USA
| | - Charles G. Eberhart
- Division of Pathology, John Hopkins University School of Medicine, Baltimore, MD USA
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Physiology, Chinese University of Hong Kong, Hong Kong, China
| | | | - Timothy Van Meter
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA USA
| | - Marc Remke
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON Canada
| | - Lucie Lafay-Cousin
- Department of Pediatric Oncology, Alberta Children’s Hospital, Calgary, AB Canada
| | - Jennifer A. Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB Canada
| | - Nongnuch Sirachainan
- Departments of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Bangkok, Thailand
| | - Scott L. Pomeroy
- Department of Neurology, Children’s Hospital Boston, Boston, MA USA
| | - Steven C. Clifford
- Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - Amar Gajjar
- Neuro-oncology Division, St Jude Children’s Research Hospital, Memphis, TN USA
| | - Mary Shago
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - William Halliday
- Department of Pathology, The Hospital for Sick Children, Toronto, ON Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON Canada
| | - Richard Grundy
- Children’s Brain Tumor Research Centre, Queen’s Medical Centre University of Nottingham, Nottingham, UK
| | - Ching C. Lau
- Texas Children’s Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Joanna Phillips
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA USA
| | - Eric Bouffet
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
| | - Peter B. Dirks
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, ON Canada
| | - Cynthia E. Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
- Department of Pathology, The Hospital for Sick Children, Toronto, ON Canada
| | - Annie Huang
- Division of Hematology-Oncology, Department of Pediatrics, The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Peter Gilgan CRL,686 Bay Street, 17th Floor, 179712, Toronto, ON M5G0A4 Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
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17
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Kwiecinska A, Ichimura K, Berglund M, Dinets A, Sulaiman L, Collins VP, Larsson C, Porwit A, Lagercrantz SB. Amplification of 2p as a genomic marker for transformation in lymphoma. Genes Chromosomes Cancer 2014; 53:750-68. [PMID: 24832791 PMCID: PMC4369132 DOI: 10.1002/gcc.22184] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/19/2014] [Accepted: 04/22/2014] [Indexed: 12/22/2022] Open
Abstract
To outline further genetic mechanisms of transformation from follicular lymphoma (FL) to diffuse large B-cell lymphoma (DLBCL), we have performed whole genome array-CGH in 81 tumors from 60 patients [29 de novo DLBCL (dnDLBCL), 31 transformed DLBCL (tDLBCL), and 21 antecedent FL]. In 15 patients, paired tumor samples (primary FL and a subsequent tDLBCL) were available, among which three possessed more than two subsequent tumors, allowing us to follow specific genetic alterations acquired before, during, and after the transformation. Gain of 2p15–16.1 encompassing, among others, the REL, BCL11A, USP34, COMMD1, and OTX1 genes was found to be more common in the tDLBCL compared with dnDLBCL (P < 0.001). Furthermore, a high-level amplification of 2p15–16.1 was also detected in the FL stage prior to transformation, indicating its importance during the transformation event. Quantitative real-time PCR showed a higher level of amplification of REL, USP34, and COMMD1 (all involved in the NFκΒ-pathway) compared with BCL11A, which indicates that the altered genes disrupting the NFκΒ pathway may be the driver genes of transformation rather than the previously suggested BCL11A. Moreover, a 17q21.33 amplification was exclusively found in tDLBCL, never in FL (P < 0.04) or dnDLBCL, indicating an upregulation of genes of importance during the later phase of transformation. Taken together, our study demonstrates potential genomic markers for disease progression to clinically more aggressive forms. We also confirm the importance of the TP53-, CDKN2A-, and NFκΒ-pathways for the transformation from FL to DLBCL. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Anna Kwiecinska
- Department of Oncology-Pathology, Karolinska Institutet, CCK Karolinska University Hospital, Solna, Sweden
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18
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Kool M, Jones DTW, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, McCabe MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM. Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. Cancer Cell 2014; 25:393-405. [PMID: 24651015 PMCID: PMC4493053 DOI: 10.1016/j.ccr.2014.02.004] [Citation(s) in RCA: 548] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/19/2013] [Accepted: 02/13/2014] [Indexed: 01/07/2023]
Abstract
Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.
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Affiliation(s)
- Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany.
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Natalie Jäger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Trevor J Pugh
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Rosario M Piro
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | | | | | - Marc Remke
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Till Milde
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Franck Bourdeaut
- Institut Curie, 75005 Paris, France; Institut Curie/INSERM U830, 75248 Paris, France
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, Moscow 125047, Russia
| | - Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Elke Pfaff
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sebastian Stark
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sonja Hutter
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Huriye Seker-Cin
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Pascal Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Christin Schmidt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - David Shih
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Jüri Reimand
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Laura Sieber
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Andrea Wittmann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Linda Linke
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Ursula D Weber
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Rainer König
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany; Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), 07745 Jena, Germany
| | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Guillaume Bergthold
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA; UMR 8203, CNRS Vectorology and Anticancer Therapeutics, Gustave Roussy Cancer Institute, University Paris XI, 94805 Villejuif Cedex, France
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam 1105 AZ, the Netherlands
| | - Sabine Schmidt
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Chris Lawerenz
- Data Management Facility, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Cynthia C Bartholomae
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Christof von Kalle
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Andreas Unterberg
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Translational Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69121 Heidelberg, Germany
| | - Silvia Hofer
- Department of Oncology, University Hospital Zürich, 8006 Zürich, Switzerland
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Wolfram Scheurlen
- Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, 90419 Nürnberg, Germany
| | - Jörg Felsberg
- Department of Neuropathology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Martin Hasselblatt
- Institute for Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - John R Crawford
- Departments of Pediatrics and Neurosciences, University of California San Diego, La Jolla, CA 92093; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Gerald A Grant
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Nada Jabado
- Departments of Pediatrics and Human Genetics, McGill University Health Centre Research Institute, Montreal, QC H3H 1P3, Canada
| | - Arie Perry
- Departments of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cynthia Cowdrey
- Departments of Pathology and Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sydney Croul
- Department of Neuropathology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON M5G 1L7, Canada
| | - Gelareh Zadeh
- Department of Neuropathology, The Arthur and Sonia Labatt Brain Tumour Research Centre, Toronto, ON M5G 1L7, Canada
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Francois Doz
- Institut Curie, 75005 Paris, France; Université Paris Descartes, 75006 Paris, France
| | - Olivier Delattre
- Institut Curie, 75005 Paris, France; Institut Curie/INSERM U830, 75248 Paris, France
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Martin G McCabe
- Manchester Academic Health Science Centre, Manchester M13 9NT, UK
| | - V Peter Collins
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Mark W Kieran
- Pediatric Medical Neuro-Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA
| | - Yoon-Jae Cho
- Department of Neurology and Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott L Pomeroy
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Olaf Witt
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Ulrich Schüller
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Andrey Korshunov
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Neuropathology, University of Heidelberg, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany; Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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Bender S, Tang Y, Lindroth AM, Hovestadt V, Jones DTW, Kool M, Zapatka M, Northcott PA, Sturm D, Wang W, Radlwimmer B, Højfeldt JW, Truffaux N, Castel D, Schubert S, Ryzhova M, Seker-Cin H, Gronych J, Johann PD, Stark S, Meyer J, Milde T, Schuhmann M, Ebinger M, Monoranu CM, Ponnuswami A, Chen S, Jones C, Witt O, Collins VP, von Deimling A, Jabado N, Puget S, Grill J, Helin K, Korshunov A, Lichter P, Monje M, Plass C, Cho YJ, Pfister SM. Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas. Cancer Cell 2013; 24:660-72. [PMID: 24183680 DOI: 10.1016/j.ccr.2013.10.006] [Citation(s) in RCA: 525] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/09/2013] [Accepted: 10/04/2013] [Indexed: 11/30/2022]
Abstract
Two recurrent mutations, K27M and G34R/V, within histone variant H3.3 were recently identified in ∼50% of pHGGs. Both mutations define clinically and biologically distinct subgroups of pHGGs. Here, we provide further insight about the dominant-negative effect of K27M mutant H3.3, leading to a global reduction of the repressive histone mark H3K27me3. We demonstrate that this is caused by aberrant recruitment of the PRC2 complex to K27M mutant H3.3 and enzymatic inhibition of the H3K27me3-establishing methyltransferase EZH2. By performing chromatin immunoprecipitation followed by next-generation sequencing and whole-genome bisulfite sequencing in primary pHGGs, we show that reduced H3K27me3 levels and DNA hypomethylation act in concert to activate gene expression in K27M mutant pHGGs.
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Affiliation(s)
- Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
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20
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Sahm F, Bissel J, Koelsche C, Schweizer L, Capper D, Reuss D, Böhmer K, Lass U, Göck T, Kalis K, Meyer J, Habel A, Brehmer S, Mittelbronn M, Jones DTW, Schittenhelm J, Urbschat S, Ketter R, Heim S, Mawrin C, Hainfellner JA, Berghoff AS, Preusser M, Becker A, Herold-Mende C, Unterberg A, Hartmann C, Kickingereder P, Collins VP, Pfister SM, von Deimling A. AKT1E17K mutations cluster with meningothelial and transitional meningiomas and can be detected by SFRP1 immunohistochemistry. Acta Neuropathol 2013; 126:757-62. [PMID: 24096618 DOI: 10.1007/s00401-013-1187-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
Abstract
The activating E17K mutation in the AKT1 gene has been detected in several tumor entities. Currently several clinical studies with specific AKT1 inhibitors are under way. To determine whether AKT1 mutations are involved in human tumors of the nervous system, we examined a series of 1,437 tumors including 391 primary intracranial brain tumors and 1,046 tumors of the coverings of the central and peripheral nervous system. AKT1E17K mutations were exclusively seen in meningiomas and occurred in 65 of 958 of these tumors. A strong preponderance was seen in the variant of meningothelial meningioma WHO grade I of basal and spinal localization. In contrast, AKT1E17K mutations were rare in WHO grade II and absent in WHO grade III meningiomas. In order to more effectively detect this mutation, we tested for immunohistochemical markers associated with this alteration. We observed strong up-regulation of SFRP1 expression in all meningiomas with AKT1E17K mutation and in HEK293 cells after transfection with mutant AKT1E17K, but not in meningiomas and HEK293 cells lacking this mutation.
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21
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Jones DTW, Hutter B, Jäger N, Korshunov A, Kool M, Warnatz HJ, Zichner T, Lambert SR, Ryzhova M, Quang DAK, Fontebasso AM, Stütz AM, Hutter S, Zuckermann M, Sturm D, Gronych J, Lasitschka B, Schmidt S, Seker-Cin H, Witt H, Sultan M, Ralser M, Northcott PA, Hovestadt V, Bender S, Pfaff E, Stark S, Faury D, Schwartzentruber J, Majewski J, Weber UD, Zapatka M, Raeder B, Schlesner M, Worth CL, Bartholomae CC, von Kalle C, Imbusch CD, Radomski S, Lawerenz C, van Sluis P, Koster J, Volckmann R, Versteeg R, Lehrach H, Monoranu C, Winkler B, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, Ebinger M, Schuhmann MU, Cho YJ, Pomeroy SL, von Deimling A, Witt O, Taylor MD, Wolf S, Karajannis MA, Eberhart CG, Scheurlen W, Hasselblatt M, Ligon KL, Kieran MW, Korbel JO, Yaspo ML, Brors B, Felsberg J, Reifenberger G, Collins VP, Jabado N, Eils R, Lichter P, Pfister SM. Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet 2013; 45:927-32. [PMID: 23817572 DOI: 10.1038/ng.2682] [Citation(s) in RCA: 561] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/03/2013] [Indexed: 02/08/2023]
Abstract
Pilocytic astrocytoma, the most common childhood brain tumor, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression and often becoming a chronic disease with substantial morbidities. Here we describe whole-genome sequencing of 96 pilocytic astrocytomas, with matched RNA sequencing (n = 73), conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. We identified recurrent activating mutations in FGFR1 and PTPN11 and new NTRK2 fusion genes in non-cerebellar tumors. New BRAF-activating changes were also observed. MAPK pathway alterations affected all tumors analyzed, with no other significant mutations identified, indicating that pilocytic astrocytoma is predominantly a single-pathway disease. Notably, we identified the same FGFR1 mutations in a subset of H3F3A-mutated pediatric glioblastoma with additional alterations in the NF1 gene. Our findings thus identify new potential therapeutic targets in distinct subsets of pilocytic astrocytoma and childhood glioblastoma.
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Affiliation(s)
- David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Lambert SR, Witt H, Hovestadt V, Zucknick M, Kool M, Pearson D, Korshnov A, Pfister S, Collins VP, Jones DTW. Abstract 3807: Integrative genomic profiling of pilocytic astrocytomas reveals location specific differential methylation and expression of brain developmental genes. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3807] [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]
Abstract
Abstract
Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and cause significant morbidity, particularly related to chronic neurological deficiencies. They are characterized by activating alterations in the mitogen activated protein kinase (MAPK) pathway, but little else is known about their development. To map the methylation profile of these tumors, we have performed a global DNA methylation analysis on 62 PAs and 7 normal cerebellum samples using Illumina 450K microarrays. Based on these data we have found two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and have identified key neural developmental genes that are differentially methylated between the two groups, including NR2E1 and EN2. Integration with gene expression microarray data revealed significant expression differences that were typically associated with a strong positive correlation between methylation and expression. Differential methylation was most commonly identified within the gene body and/or 10 kb upstream/downstream of the gene body, and was, in part, accounted for by differences in the level of 5-hydroxymethylcytosine. We also identified a large number of differentially methylated genes between cerebellar PAs and normal cerebellum, which were again enriched for developmental genes. In addition, we found a significant association between differential methylation and SUZ12 binding sites, suggesting potential disruption of the polycomb repressor complex 2 (PRC2) in PA development. Taken together these data suggest the methylation profile of PA may reflect the cell of origin from which the tumors are derived, and highlights the potential disruption of key developmental regulators during tumorigenesis. These findings have implications for future clinical trials, as they suggest drug sensitivity and response may differ according to tumor location.
Citation Format: Sally R. Lambert, Hendrik Witt, Volker Hovestadt, Manuela Zucknick, Marcel Kool, Danita Pearson, Andrey Korshnov, Stefan Pfister, V. Peter Collins, David T. W. Jones. Integrative genomic profiling of pilocytic astrocytomas reveals location specific differential methylation and expression of brain developmental genes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3807. doi:10.1158/1538-7445.AM2013-3807
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Jones DTW, Hutter B, Jäger N, Korshunov A, Kool M, Lambert SR, Khuong Quang DA, Fontebasso AM, Ryzhova M, Warnatz HJ, Zichner T, Korbel JO, Wolf S, Yaspo ML, Ligon KL, Kieran MW, Brors B, Felsberg J, Reifenberger G, Collins VP, Jabado N, Eils R, Lichter P, Pfister SM. Abstract 4594: Recurrent FGFR1 hotspot mutations represent a novel therapeutic target in childhood astrocytoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4594] [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]
Abstract
Abstract
Introduction: Pilocytic astrocytoma (PA) is the most common childhood brain tumor. This tumor can occur throughout the central nervous system, with roughly 50% of cases arising outside of the cerebellum. Tumors in these non-cerebellar locations are often difficult to treat surgically, leading to multiple tumor recurrences. PA can therefore become a chronic disease, with patients experiencing substantial morbidities. Alterations in the MAPK pathway, particularly BRAF, have previously been identified in ∼80% of PAs. Interestingly, however, the majority of those cases without a recognized change are non-cerebellar.
Methods: To investigate the full range of genetic alterations occurring in PA, we used Illumina HiSeq technologies to perform whole-genome sequencing of matched tumor and germline DNA from 47 patients, with corresponding RNA sequencing data for 35 tumors.
Results: The average somatic mutation rate in PA was extremely low, at 0.065/Mb, with an average of only 1.8 non-synonymous coding single nucleotide variants (SNVs) per tumor - almost ten times lower than we have recently reported for medulloblastoma. We found several novel alterations in known PA-related genes, including two new oncogenic BRAF fusions. Most strikingly, however, we identified mutations at two hotspots in the FGFR1 receptor tyrosine kinase in 4/6 centrally located PAs lacking any other MAPK pathway change. Two of these cases also carried a mutation in a downstream adaptor protein, PTPN11 (Shp2). Interestingly, germline mutations of PTPN11 are associated with Noonan syndrome (NS), and there are case reports of NS patients developing PAs. Screening of additional non-cerebellar PAs revealed four further cases with an FGFR1 mutation. All PAs, regardless of MAPK pathway alteration, displayed highly elevated expression of FGF2, indicating a general role for ligand-mediated activation of the FGFR1/MAPK pathway in PA tumorigenesis. Notably, the same FGFR1 mutations were also identified in four midline pediatric glioblastomas (GBM), a highly malignant brain tumor, suggesting a possible common origin for a subset of these two entities, despite their dramatically different clinical course.
Conclusion: Altogether, MAPK alterations were identified in 96% of PAs, with very few other changes, confirming the concept of PA as a single-pathway disease. Our results also suggest that a subset of centrally located, FGFR1-driven pediatric PAs and GBMs may share common origins. Most importantly, they reveal a novel therapeutic target in clinically relevant subsets of childhood glioma.
Citation Format: David TW Jones, Barbara Hutter, Natalie Jäger, Andrey Korshunov, Marcel Kool, Sally R. Lambert, Dong Anh Khuong Quang, Adam M. Fontebasso, Marina Ryzhova, Hans-Jörg Warnatz, Thomas Zichner, Jan O. Korbel, Stephan Wolf, Marie-Laure Yaspo, Keith L. Ligon, Mark W. Kieran, Benedikt Brors, Jörg Felsberg, Guido Reifenberger, V. Peter Collins, Nada Jabado, Roland Eils, Peter Lichter, Stefan M. Pfister, ICGC PedBrain Tumor Project. Recurrent FGFR1 hotspot mutations represent a novel therapeutic target in childhood astrocytoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4594. doi:10.1158/1538-7445.AM2013-4594
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Affiliation(s)
| | | | | | | | - Marcel Kool
- 1German Cancer Research Center, Heidelberg, Germany
| | | | | | - Adam M. Fontebasso
- 4McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Marina Ryzhova
- 5Burdenko Neurosurgical Institute, Moscow, Russian Federation
| | | | - Thomas Zichner
- 7European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan O. Korbel
- 7European Molecular Biology Laboratory, Heidelberg, Germany
| | - Stephan Wolf
- 1German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | - Jörg Felsberg
- 9Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | - Nada Jabado
- 4McGill University Health Center Research Institute, Montreal, Quebec, Canada
| | - Roland Eils
- 1German Cancer Research Center, Heidelberg, Germany
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Korshunov A, Ryzhova M, Jones DTW, Northcott PA, van Sluis P, Volckmann R, Koster J, Versteeg R, Cowdrey C, Perry A, Picard D, Rosenblum M, Giangaspero F, Aronica E, Schüller U, Hasselblatt M, Collins VP, von Deimling A, Lichter P, Huang A, Pfister SM, Kool M. LIN28A immunoreactivity is a potent diagnostic marker of embryonal tumor with multilayered rosettes (ETMR). Acta Neuropathol 2012; 124:875-81. [PMID: 23161096 PMCID: PMC3508282 DOI: 10.1007/s00401-012-1068-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 11/06/2012] [Accepted: 11/06/2012] [Indexed: 01/13/2023]
Abstract
Embryonal tumor with multilayered rosettes (ETMR, previously known as ETANTR) is a highly aggressive embryonal CNS tumor, which almost exclusively affects infants and is associated with a dismal prognosis. Accurate diagnosis is of critical clinical importance because of its poor response to current treatment protocols and its distinct biology. Amplification of the miRNA cluster at 19q13.42 has been identified previously as a genetic hallmark for ETMR, but an immunohistochemistry-based assay for clinical routine diagnostics [such as INI-1 for atypical teratoid rhabdoid tumor (AT/RT)] is still lacking. In this study, we screened for an ETMR-specific marker using a gene-expression profiling dataset of more than 1,400 brain tumors and identified LIN28A as a highly specific marker for ETMR. The encoded protein binds small RNA and has been implicated in stem cell pluripotency, metabolism and tumorigenesis. Using an LIN28A specific antibody, we carried out immunohistochemical analysis of LIN28A in more than 800 childhood brain-tumor samples and confirmed its high specificity for ETMR. Strong LIN28A immunoexpression was found in all 37 ETMR samples tested, whereas focal reactivity was only present in a small (6/50) proportion of AT/RT samples. All other pediatric brain tumors were completely LIN28A-negative. In summary, we established LIN28A immunohistochemistry as a highly sensitive and specific, rapid, inexpensive diagnostic tool for routine pathological verification of ETMR.
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Affiliation(s)
- Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, NN Burdenko Neurosurgical Institute, 4th Tverskaya-Yamskaya 16, Moscow, 125047 Russia
| | - David T. W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg Germany
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg Germany
| | - Peter van Sluis
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, The Netherlands
| | - Cynthia Cowdrey
- Departments of Pathology and Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, USA
| | - Arie Perry
- Departments of Pathology and Neurological Surgery, Brain Tumor Research Center, University of California, San Francisco, USA
| | - Daniel Picard
- Division of Hematology-Oncology, Department of Pediatrics, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomic Pathology Sciences, Università Sapienza, Rome, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Eleonora Aronica
- Department of Neuropathology, Academic Medical Center, Amsterdam, The Netherlands
| | - Ulrich Schüller
- Center of Neuropathology, Ludwig-Maximilians University, Munich, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | | | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter Lichter
- Divison of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annie Huang
- Division of Hematology-Oncology, Department of Pediatrics, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON Canada
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg Germany
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Sturm D, Witt H, Hovestadt V, Khuong-Quang DA, Jones DTW, Konermann C, Pfaff E, Tönjes M, Sill M, Bender S, Kool M, Zapatka M, Becker N, Zucknick M, Hielscher T, Liu XY, Fontebasso AM, Ryzhova M, Albrecht S, Jacob K, Wolter M, Ebinger M, Schuhmann MU, van Meter T, Frühwald MC, Hauch H, Pekrun A, Radlwimmer B, Niehues T, von Komorowski G, Dürken M, Kulozik AE, Madden J, Donson A, Foreman NK, Drissi R, Fouladi M, Scheurlen W, von Deimling A, Monoranu C, Roggendorf W, Herold-Mende C, Unterberg A, Kramm CM, Felsberg J, Hartmann C, Wiestler B, Wick W, Milde T, Witt O, Lindroth AM, Schwartzentruber J, Faury D, Fleming A, Zakrzewska M, Liberski PP, Zakrzewski K, Hauser P, Garami M, Klekner A, Bognar L, Morrissy S, Cavalli F, Taylor MD, van Sluis P, Koster J, Versteeg R, Volckmann R, Mikkelsen T, Aldape K, Reifenberger G, Collins VP, Majewski J, Korshunov A, Lichter P, Plass C, Jabado N, Pfister SM. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 2012; 22:425-37. [PMID: 23079654 DOI: 10.1016/j.ccr.2012.08.024] [Citation(s) in RCA: 1303] [Impact Index Per Article: 108.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/03/2012] [Accepted: 08/24/2012] [Indexed: 12/30/2022]
Abstract
Glioblastoma (GBM) is a brain tumor that carries a dismal prognosis and displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical amino acids (K27 and G34) of histone H3.3 in one-third of pediatric GBM. Here, we show that each H3F3A mutation defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and that they are mutually exclusive with IDH1 mutations, which characterize a third mutation-defined subgroup. Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM and/or established transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of transcription factors OLIG1, OLIG2, and FOXG1, possibly reflecting different cellular origins.
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Affiliation(s)
- Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, 69120 Heidelberg, Germany
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Jones DTW, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, Wang Q, Lasitschka B, Bartholomae CC, Schmidt M, von Kalle C, Ast V, Lawerenz C, Eils J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Betts MJ, Russell RB, Coco S, Tonini GP, Schüller U, Hans V, Graf N, Kim YJ, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Rössler J, Ebinger M, Schuhmann MU, Frühwald MC, Hasselblatt M, Jabado N, Rutkowski S, von Bueren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P. Dissecting the genomic complexity underlying medulloblastoma. Nature 2012; 488:100-5. [PMID: 22832583 DOI: 10.1038/nature11284] [Citation(s) in RCA: 647] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 06/06/2012] [Indexed: 12/31/2022]
Abstract
Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.
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Affiliation(s)
- David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany
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Piccirillo SGM, Dietz S, Madhu B, Griffiths J, Price SJ, Collins VP, Watts C. Fluorescence-guided surgical sampling of glioblastoma identifies phenotypically distinct tumour-initiating cell populations in the tumour mass and margin. Br J Cancer 2012; 107:462-8. [PMID: 22722315 PMCID: PMC3405212 DOI: 10.1038/bjc.2012.271] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [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: 04/27/2012] [Revised: 05/22/2012] [Accepted: 05/23/2012] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Acquiring clinically annotated, spatially stratified tissue samples from human glioblastoma (GBM) is compromised by haemorrhage, brain shift and subjective identification of 'normal' brain. We tested the use of 5-aminolevulinic acid (5-ALA) fluorescence to objective tissue sampling and to derive tumour-initiating cells (TICs) from mass and margin. METHODS The 5-ALA was administered to 30 GBM patients. Samples were taken from the non-fluorescent necrotic core, fluorescent tumour mass and non-fluorescent margin. We compared the efficiency of isolating TICs from these areas in 5-ALA versus control patients. HRMAS (1)H NMR was used to reveal metabolic alterations due to 5-ALA. We then characterised TICs for self-renewal in vitro and tumorigenicity in vivo. RESULTS The derivation of TICs was not compromised by 5-ALA and the metabolic profile was similar between tumours from 5-ALA patients and controls. The TICs from the fluorescent mass were self-renewing in vitro and tumour-forming in vivo, whereas TICs from non-fluorescent margin did not self-renew in vitro but did form tumours in vivo. CONCLUSION Our data show that 5-ALA does not compromise the derivation of TICs. It also reveals that the margin contains TICs, which are phenotypically different from those isolated from the corresponding mass.
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Affiliation(s)
- S G M Piccirillo
- Department of Clinical Neurosciences, Cambridge Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK
| | - S Dietz
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - B Madhu
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - J Griffiths
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - S J Price
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - V P Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - C Watts
- Department of Clinical Neurosciences, Cambridge Centre for Brain Repair, University of Cambridge, Forvie Site, Robinson Way, Cambridge CB2 0PY, UK
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
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Shaw E, Tuff A, Sharpe R, Jones LK, Turtiaien T, Griffiths M, Butler R, Gonzalez de Castro D, Mason MD, Collins VP, Rae F, Evans TJ, Johnston SRD, Rogan J, Hanby A, Peach J, Johnson PWM. Emerging findings in the Cancer Research UK stratified medicine program. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.tps10633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
TPS10633^ Background: Molecular analysis of tumours may be used to identify those predicted to benefit from novel targeted therapies. The Cancer Research UK programme is piloting plans to apply such testing broadly across the UK healthcare system, linking molecular phenotype to clinical outcomes. Methods: The Stratified Medicine Programme (SMP) aims to develop a model for high quality, large-scale molecular characterization of cancer specimens through an initiative developed in partnership with AstraZeneca, Pfizer, the UK Department of Health and academic researchers. Phase One of the SMP is a two year feasibility study. It aims to demonstrate the submission of consented blood samples and sections of surplus diagnostic formalin-fixed paraffin-embedded tumour tissue from 9,000 patients at centres across the UK to one of three ‘technology hubs’ for mutation testing of genes of potential clinical interest (KRAS, BRAF, NRAS, PIK3CA, TP53, PTEN, TMPRSS2-ERG, EGFR, EML4-ALK and KIT) in six selected tumour types. The tests are technically validated and will be completed in clinically relevant timescales. Data including pathological and treatment information and clinical outcome is also collected for the recruited patients, linked to the genetic data and stored in a central data repository hosted within the National Cancer Registration Service. The study opened in September 2011 at 7 sites across the UK and by the end of 2011, 760 patientswith breast, lung, prostate, colorectal, ovarian cancer or metastatic malignant melanoma had consented to participate. 142 sets of molecular results had been returned to clinical teams. Updated figures will be presented at the meeting, by which time the programme is projected to have accrued 4000 subjects. By 2013, we hope to have developed a scalable model for routine, high quality, prospective molecular characterisation of tumours for NHS cancer patients, with consent for the collection, storage and research use of population-scale genetic and clinical outcome data. We will report the emerging results from the Stratified Medicines Programme and early insights into implications for wider implementation across the UK healthcare system.
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Affiliation(s)
- Emily Shaw
- Cancer Research UK, London, United Kingdom
| | - Alice Tuff
- Cancer Research UK, London, United Kingdom
| | | | | | | | - Michael Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham, United Kingdom
| | - Rachel Butler
- Institute of Medical Genetics, Cardiff, United Kingdom
| | | | | | - V. Peter Collins
- Department of Pathology and Molecular Histopathology, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Frances Rae
- Laboratory Medicine, NHS Lothian, Edinburgh, United Kingdom
| | | | | | - Jane Rogan
- Manchester Cancer Research Centre, Manchester, United Kingdom
| | - Andrew Hanby
- Leeds Institute of Molecular Medicine, Leeds, United Kingdom
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Qureshi AA, Collins VP, Jani P. Genomic differences in benign and malignant follicular thyroid tumours using 1-Mb array-comparative genomic hybridisation. Eur Arch Otorhinolaryngol 2012; 270:325-35. [PMID: 22526578 DOI: 10.1007/s00405-012-2017-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/27/2012] [Indexed: 11/30/2022]
Abstract
Currently there is a lack of objective markers that can reliably differentiate benign and malignant follicular thyroid tumours. Such markers are needed to avoid the morbidity and cost of diagnosing these lesions by a thyroid lobectomy and then a second operation to remove the remaining half of thyroid if cancer is found. The aim of this research was to look for genomic markers that might solve this important problem. Ethical approval for the project was obtained. DNA was extracted from formalin-fixed paraffin-embedded specimens and copy number analysed using an in-house produced 1-megabase genomic array by comparative genomic hybridization (1Mb-aCGH). Acceptable quality data were obtained in 25/26 (96 %) of adenomas and 17/28 (61 %) of carcinomas. Among the carcinomas, 11 were minimally invasive (MI), 5 widely invasive (WI) and there was one metastasis. Recurrent copy number changes distinguishing benign and malignant included +1p34.2-36.33, +1q, +13q12.11-14.3, +14q22.1-32.33, +20q and -22. +20q became more sensitive (36.4 %) for MI carcinomas, whereas +13q12.11-14.3 and +14q22.1-32.33 became more sensitive (66.7 %) for identifying WI cancers from adenomas. Only in the context of aneuploidy (3 adenomas, 3 MI, 3 WI) there were some specific copy number changes that could differentiate all aneuploid adenomas from carcinomas. This research is the first using 1Mb-aCGH to study benign and malignant follicular thyroid tumours. Overall, the incidence of any copy number changes is low, but there are a number of changes associated with different tumour types. Further research with a larger sample and better quality DNA will clarify these findings.
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Affiliation(s)
- Abdul A Qureshi
- Department of Otolaryngology, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.
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30
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Wu X, Northcott PA, Dubuc A, Dupuy AJ, Shih DJH, Witt H, Croul S, Bouffet E, Fults DW, Eberhart CG, Garzia L, Van Meter T, Zagzag D, Jabado N, Schwartzentruber J, Majewski J, Scheetz TE, Pfister SM, Korshunov A, Li XN, Scherer SW, Cho YJ, Akagi K, MacDonald TJ, Koster J, McCabe MG, Sarver AL, Collins VP, Weiss WA, Largaespada DA, Collier LS, Taylor MD. Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature 2012; 482:529-33. [PMID: 22343890 PMCID: PMC3288636 DOI: 10.1038/nature10825] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2010] [Accepted: 01/03/2012] [Indexed: 12/15/2022]
Abstract
Medulloblastoma, the most common malignant paediatric brain tumour, arises in the cerebellum and disseminates through the cerebrospinal fluid in the leptomeningeal space to coat the brain and spinal cord. Dissemination, a marker of poor prognosis, is found in up to 40% of children at diagnosis and in most children at the time of recurrence. Affected children therefore are treated with radiation to the entire developing brain and spinal cord, followed by high-dose chemotherapy, with the ensuing deleterious effects on the developing nervous system. The mechanisms of dissemination through the cerebrospinal fluid are poorly studied, and medulloblastoma metastases have been assumed to be biologically similar to the primary tumour. Here we show that in both mouse and human medulloblastoma, the metastases from an individual are extremely similar to each other but are divergent from the matched primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted subclone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize. Failure to account for the bicompartmental nature of metastatic medulloblastoma could be a major barrier to the development of effective targeted therapies.
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Affiliation(s)
- Xiaochong Wu
- Arthur and Sonia Labatt Brain Tumour Research Center, Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
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Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012. [PMID: 22286061 DOI: 10.1038/nature11026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.
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Mulholland S, Pearson DM, Hamoudi RA, Malley DS, Smith CM, Weaver JMJ, Jones DTW, Kocialkowski S, Bäcklund LM, Collins VP, Ichimura K. MGMT CpG island is invariably methylated in adult astrocytic and oligodendroglial tumors with IDH1 or IDH2 mutations. Int J Cancer 2012; 131:1104-13. [PMID: 22020830 DOI: 10.1002/ijc.26499] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 08/14/2011] [Accepted: 09/09/2011] [Indexed: 11/10/2022]
Abstract
We have previously identified a region containing 16 CpGs within the MGMT CpG islands which is critical for the transcriptional control of MGMT (Malley, Acta Neuropathol 2011). To investigate the patterns and incidence of MGMT methylation in astrocytic and oligodendroglial tumors, we quantitatively assessed methylation at these 16 CpGs using bisulfite modification followed by pyrosequencing of 362 gliomas not treated with temozolomide, and correlated the findings with previously identified patterns of genetic abnormalities, patients' age and survival. The MGMT gene was considered to be methylated when the mean methylation of the 16 CpGs was 10% or higher. This cut-off value distinguished diffuse astrocytomas with high and low MGMT expression. Within each tumor type, the patterns of methylation were highly variable and also highly heterogeneous across the 16 CpGs. A high incidence of MGMT methylation was observed in all subtypes of gliomas included in this study. Among a subset of 97 tumors where conventional methylation-specific PCR (MSP) was also applied, methylation was detected by both methods in 54 tumors, while the pyrosequencing results identified a further 17 tumors. No additional cases were found using MSP alone, indicating that pyrosequencing is a robust method for methylation analysis. All tumors with IDH1/IDH2 mutations except two had MGMT methylation, while there were many tumors with MGMT methylation, particularly primary glioblastomas, which had no mutations of IDH1/2. We suggest that MGMT methylation may be one of the earliest events in the development of astrocytic and oligodendroglial tumors.
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Affiliation(s)
- Shani Mulholland
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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Cin H, Meyer C, Herr R, Janzarik WG, Lambert S, Jones DTW, Jacob K, Benner A, Witt H, Remke M, Bender S, Falkenstein F, Van Anh TN, Olbrich H, Deimling AV, Pekrun A, Kulozik AE, Gnekow A, Scheurlen W, Witt O, Omran H, Jabado N, Collins VP, Brummer T, Marschalek R, Lichter P, Korshunov A, Pfister SM. FAM131B-BRAF Fusion Gene Resulting From 7q34 Deletion Leads to MAPK Pathway Activation in Pilocytic Astrocytoma. Klin Padiatr 2011. [DOI: 10.1055/s-0031-1292584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Al-Mayhani MTF, Grenfell R, Narita M, Piccirillo S, Kenney-Herbert E, Fawcett JW, Collins VP, Ichimura K, Watts C. NG2 expression in glioblastoma identifies an actively proliferating population with an aggressive molecular signature. Neuro Oncol 2011; 13:830-45. [PMID: 21798846 PMCID: PMC3145476 DOI: 10.1093/neuonc/nor088] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [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: 12/20/2010] [Accepted: 05/13/2011] [Indexed: 12/18/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common type of primary brain tumor and a highly malignant and heterogeneous cancer. Current conventional therapies fail to eradicate or curb GBM cell growth. Hence, exploring the cellular and molecular basis of GBM cell growth is vital to develop novel therapeutic approaches. Neuroglia (NG)-2 is a transmembrane proteoglycan expressed by NG2+ progenitors and is strongly linked to cell proliferation in the normal brain. By using NG2 as a biomarker we identify a GBM cell population (GBM NG2+ cells) with robust proliferative, clonogenic, and tumorigenic capacity. We show that a significant proportion (mean 83%) of cells proliferating in the tumor mass express NG2 and that over 50% of GBM NG2+ cells are proliferating. Compared with the GBM NG2- cells from the same tumor, the GBM of NG2+ cells overexpress genes associated with aggressive tumorigenicity, including overexpression of Mitosis and Cell Cycling Module genes (e.g., MELK, CDC, MCM, E2F), which have been previously shown to correlate with poor survival in GBM. We also show that the coexpression pattern of NG2 with other glial progenitor markers in GBM does not recapitulate that described in the normal brain. The expression of NG2 by such an aggressive and actively cycling GBM population combined with its location on the cell surface identifies this cell population as a potential therapeutic target in a subset of patients with GBM.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Colin Watts
- Cambridge Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge (M.T.F.A-M., S.P., E.K-H., J.W.F., C.W.); MRC Laboratory of Molecular Biology, University of Cambridge (R.G.); CRUK Cancer Research Institute, University of Cambridge (M.N.); Division of Molecular Histopathology, Department of Pathology, University of Cambridge (V.P.C., K.I.); Department of Neurosurgery, University of Cambridge (C.W.), Cambridge, UK
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35
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Cin H, Meyer C, Herr R, Janzarik WG, Lambert S, Jones DTW, Jacob K, Benner A, Witt H, Remke M, Bender S, Falkenstein F, Van Anh TN, Olbrich H, von Deimling A, Pekrun A, Kulozik AE, Gnekow A, Scheurlen W, Witt O, Omran H, Jabado N, Collins VP, Brummer T, Marschalek R, Lichter P, Korshunov A, Pfister SM. Oncogenic FAM131B-BRAF fusion resulting from 7q34 deletion comprises an alternative mechanism of MAPK pathway activation in pilocytic astrocytoma. Acta Neuropathol 2011; 121:763-74. [PMID: 21424530 DOI: 10.1007/s00401-011-0817-z] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [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: 01/28/2011] [Revised: 02/18/2011] [Accepted: 02/19/2011] [Indexed: 01/01/2023]
Abstract
Activation of the MAPK signaling pathway has been shown to be a unifying molecular feature in pilocytic astrocytoma (PA). Genetically, tandem duplications at chromosome 7q34 resulting in KIAA1549-BRAF fusion genes constitute the most common mechanism identified to date. To elucidate alternative mechanisms of aberrant MAPK activation in PA, we screened 125 primary tumors for RAF fusion genes and mutations in KRAS, NRAS, HRAS, PTPN11, BRAF and RAF1. Using microarray-based comparative genomic hybridization (aCGH), we identified in three cases an interstitial deletion of ~2.5 Mb as a novel recurrent mechanism forming BRAF gene fusions with FAM131B, a currently uncharacterized gene on chromosome 7q34. This deletion removes the BRAF N-terminal inhibitory domains, giving a constitutively active BRAF kinase. Functional characterization of the novel FAM131B-BRAF fusion demonstrated constitutive MEK phosphorylation potential and transforming activity in vitro. In addition, our study confirmed previously reported BRAF and RAF1 fusion variants in 72% (90/125) of PA. Mutations in BRAF (8/125), KRAS (2/125) and NF1 (4/125) and the rare RAF1 gene fusions (2/125) were mutually exclusive with BRAF rearrangements, with the exception of two cases in our series that concomitantly harbored more than one hit in the MAPK pathway. In summary, our findings further underline the fundamental role of RAF kinase fusion products as a tumor-specific marker and an ideally suited drug target for PA.
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Affiliation(s)
- Huriye Cin
- Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
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Jones DTW, Mulholland SA, Pearson DM, Malley DS, Openshaw SWS, Lambert SR, Liu L, Bäcklund LM, Ichimura K, Collins VP. Adult grade II diffuse astrocytomas are genetically distinct from and more aggressive than their paediatric counterparts. Acta Neuropathol 2011; 121:753-61. [PMID: 21327941 DOI: 10.1007/s00401-011-0810-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [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: 11/24/2010] [Revised: 01/31/2011] [Accepted: 02/06/2011] [Indexed: 12/17/2022]
Abstract
Diffuse astrocytomas (WHO grade II) typically present as slow-growing tumours showing significant cellular differentiation, but possessing a tendency towards malignant progression. They account for ~10% of all astrocytic tumours, with a peak incidence between 30 and 40 years of age. Median survival is reported as around 6-8 years. Mutations of TP53 and IDH1 have been described as genetic hallmarks, while copy number alterations are also relatively common. However, there is some evidence to suggest that these characteristics may vary with age. Here, we present an integrated clinicopathologic, genomic and transcriptomic analysis suggesting that paediatric and adult tumours are associated with distinct genetic signatures. For example, no childhood tumour showed mutation of IDH1/2 or TP53, virtually no copy number changes were seen, and MGMT methylation was absent. In contrast, adult tumours showed IDH1/2 mutation in 94% and TP53 mutation in 69% of cases, with multiple copy number alterations per case and hypermethylation of MGMT in the majority of tumours. These differences were associated with a worse prognosis in the adult patients. The expression array data also revealed a significant difference in the expression of a number of genes putatively involved in neural stem cell maintenance and CNS development, including DLL3, HES5, BMP2, TIMP1 and BAMBI. Genes involved in DNA replication and the cell cycle were also enriched in the adult tumours, suggesting that their more aggressive behaviour may be due to derivation from a more rapidly dividing, less differentiated cell type.
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Affiliation(s)
- David T W Jones
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, UK.
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37
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Jacob K, Quang-Khuong DA, Jones DTW, Witt H, Lambert S, Albrecht S, Witt O, Vezina C, Shirinian M, Faury D, Garami M, Hauser P, Klekner A, Bognar L, Farmer JP, Montes JL, Atkinson J, Hawkins C, Korshunov A, Collins VP, Pfister SM, Tabori U, Jabado N. Genetic aberrations leading to MAPK pathway activation mediate oncogene-induced senescence in sporadic pilocytic astrocytomas. Clin Cancer Res 2011; 17:4650-60. [PMID: 21610151 DOI: 10.1158/1078-0432.ccr-11-0127] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [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]
Abstract
PURPOSE Oncogenic BRAF/Ras or NF1 loss can potentially trigger oncogene-induced senescence (OIS) through activation of the mitogen-activated protein kinase (MAPK) pathway. Somatic genetic abnormalities affecting this pathway occur in the majority of pilocytic astrocytomas (PA), the most prevalent brain neoplasm in children. We investigated whether OIS is induced in PA. EXPERIMENTAL DESIGN We tested expression of established senescence markers in three independent cohorts of sporadic PA. We also assessed for OIS in vitro, using forced expression of wild-type and V600E-mutant BRAF in two astrocytic cell lines: human telomerase reverse transcriptase (hTERT)-immortalized astrocytes and fetal astrocytes. RESULTS Our results indicate that PAs are senescent as evidenced by marked senescence-associated acidic β-galactosidase activity, low KI-67 index, and induction of p16(INK4a) but not p53 in the majority of 52 PA samples (46 of 52; 88.5%). Overexpression of a number of senescence-associated genes [CDKN2A (p16), CDKN1A (p21), CEBPB, GADD45A, and IGFBP7] was shown at the mRNA level in two independent PA tumor series. In vitro, sustained activation of wild-type or mutant BRAF induced OIS in both astrocytic cell lines. Loss of p16(INK4a) in immortalized astrocytes abrogated OIS, indicative of the role of this pathway in mediating this phenomenon in astrocytes. OIS is a mechanism of tumor suppression that restricts the progression of benign tumors. We show that it is triggered in PAs through p16(INK4a) pathway induction following aberrant MAPK activation. CONCLUSIONS OIS may account for the slow growth pattern in PA, the lack of progression to higher-grade astrocytomas, and the high overall survival of affected patients.
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Affiliation(s)
- Karine Jacob
- Department of Human Genetics, McGill University Health Center Research Institute, Montreal, Canada
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Cin H, Meyer C, Herr R, Janzarik WG, Lambert S, Jones DTW, Jacob K, Witt H, Remke M, Bender S, Scheurlen W, Witt O, Omran H, Jabado N, Collins VP, Brummer T, Marschalek R, Lichter P, Korshunov A, Pfister SM. FAM131B-BRAF Fusion Gene Resulting From 7q34 Deletion Leads to MAPK Pathway Activation in Pilocytic Astrocytoma. Klin Padiatr 2011. [DOI: 10.1055/s-0031-1277077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Mulholland SA, Hamoudi RA, Malley DS, Collins VP, Ichimura K. Abstract LB-181: Genome-wide DNA methylation analysis reveals novel hypermethylated genes in astrocytic tumors. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-lb-181] [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]
Abstract
Abstract
Introduction:
Astrocytomas are the most common subtype of glioma, accounting for about 70% of all malignant tumors found in the central nervous system. Genetic alterations in gliomas have been extensively researched, but epigenetic changes are less well investigated. The aim of this study is to analyze genome-wide patterns of DNA methylation in a set of astrocytic tumors to identify aberrantly methylated genes, which could serve as candidates for new diagnostic markers and/or therapeutic targets.
Material & Methods:
DNA methylation was investigated genome-wide by methyl-DNA immunoprecipitation (MeDIP) and hybridization to customized Agilent Human CpG island (250K) oligonucleotide arrays. In total, 18 glioblastoma cell lines, 59 astrocytic tumor samples (4 diffuse astrocytomas WHO grade II, 17 anaplastic astrocytomas grade III and 38 glioblastomas grade IV) and 5 normal whole brain samples were analyzed. Data quality control, normalization and analysis was performed through the arrayQuality and LIMMA packages of R. Statistical comparisons were made between tumors grouped according to various parameters including tumor vs normal, malignancy grades and known genotypes such as IDH mutations using an empirical Bayes t-test. Methylation levels were validated by pyrosequencing and compared with mRNA expression measured by real-time-qPCR (RT-QPCR).
Results:
A number of differentially methylated genes (Log2 fold change > 1.5, adjusted p value < 0.001 after Benjamini & Hochberg multiple test correction) were identified in tumors as compared to normal brain samples. A selection of hypermethylated candidates were confirmed by pyrosequencing. The normalized array data significantly (p<0.0001) correlated to methylation (Pearson's correlation test) for SIM1 (r = 0.84), OTX2 (r = 0.78), NEFM (r = 0.88) and CDYL (r = 0.82). RT-QPCR was performed for NEFM and confirmed correlation between DNA methylation and mRNA expression (r = −0.76, p < 0.0001). SIM1 and OTX2 are transcription factors that play a key role in neurogenesis. NEFM encodes for a neurofilament and is expressed during neuronal differentiation. CDYL has recently been shown to be a REST/NRSF corepressor and key in the repression of the proto-oncogene TrkC. Functional annotation of the candidate gene lists indicated the significant (p<0.0001) enrichment of binding sites for the following transcription factors: E2F, PAX4, PAX5 and STAT5A.
Conclusion:
We have demonstrated the effectiveness of using MeDIP and the Agilent array platform to profile DNA methylation genome-wide in astrocytic tumors and identified a number of aberrantly hypermethylated genes in astrocytic tumors. Some of these genes are involved in transcriptional control of neuronal differentiation, suggesting that suppression of this pathway may be involved in the pathogenesis of these tumors.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-181. doi:10.1158/1538-7445.AM2011-LB-181
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Cin H, Meyer C, Herr R, Janzarik WG, Lambert S, Jones DTW, Benner A, Witt H, Remke M, Bender S, Falkenstein F, Anh TNV, Olbrich H, von Deimling A, Kulozik AE, Gnekow A, Scheurlen W, Witt O, Omran H, Collins VP, Brummer T, Marschalek R, Lichter P, Korshunov A, Pfister SM. Abstract 4699: Oncogenic fusion genes resulting from 7q34 deletions constitute a novel mechanism of MAPK pathway activation in pilocytic astrocytoma. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4699] [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]
Abstract
Abstract
Pilocytic astrocytoma (PA) is the most common brain tumor in children. Underlying genetic driver aberrations can currently be determined for 75-80% of cases. In particular, we and others have recently shown that tandem duplication at 7q34, resulting in BRAF fusion genes and constitutive activation of the MAPK signaling pathway, is a hallmark genetic lesion in PA development. Alternative mechanisms of MAPK activation include BRAF and KRAS point mutations, RAF1 fusions, and Neurofibromatosis-associated NF1 mutations.
In order to examine more precisely the spectrum of alterations in PA, we screened 79 tumor samples for RAF fusion genes and mutations in KRAS, NRAS, PTPN11, BRAF and RAF1. We used multiplex and long-distance inverse (LDI) PCR to identify BRAF and RAF1 fusion genes and direct sequencing for detailed breakpoint mapping.
Strikingly, LDI-PCR revealed a novel BRAF fusion gene with an uncharacterized gene, FAM131B, as a partner. Array-based comparative genomic hybridization (aCGH), revealed an interstitial deletion of ∼2.5 Mb as a novel mechanism forming the FAM131B-BRAF fusion. As with the more common duplication, this deletion removes the N-terminal auto-inhibitory domain of BRAF kinase, resulting in constitutive kinase activity. Functional characterization of the novel fusion gene demonstrated constitutive MEK phosphorylation potential and transforming activity in NIH 3T3 cells. The same fusion gene was also identified in one PA in an additional series from Cambridge, UK (n=7, with no previously identified alteration). Furthermore, we have detected a larger deletion at 7q in one additional case from our series, in which the alternative fusion partner is currently being identified.
Overall, gene fusions targeting RAF kinases were identified in 68% (54/79) of PA. Detailed analysis of genomic DNA mapped 96% (52/54) of the breakpoints to the same breakpoint cluster region in intron 8 of the BRAF gene. Moreover, we identified the first non-intronic breakpoint in exon 8 of BRAF and two novel SRGAP3-RAF1 fusion variants. BRAF, KRAS or NF1 mutations were observed as alternative mechanisms of MAPK activation in 9 tumors in which no RAF duplication was detected, as well as in two cases in our series which concomitantly harbored two or even three hits in the MAPK pathway.
In summary, we have identified a novel, recurrent BRAF fusion gene resulting in MAPK pathway activation in PA caused by a genomic deletion rather than amplification at 7q34, suggesting the possibility of further undiscovered fusion variants targeting RAF genes in this and other tumor types. Being a hallmark of PA tumorigenesis, these RAF fusion genes are expected to have clinical utility as both a specific marker for PA and a tumor-specific therapeutic target, which offers promise for applying novel treatment strategies in the near future.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4699. doi:10.1158/1538-7445.AM2011-4699
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Affiliation(s)
- Huriye Cin
- 1German Cancer Research Center, Heidelberg, Germany
| | - Claus Meyer
- 2Institute of Pharmaceutical Biology, Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt, Germany
| | - Ricarda Herr
- 3Centre for Biological Systems Analysis (ZBSA), Centre for Biological Signalling Studies BIOSS and Faculty of Biology, Albert-Ludwigs-University Freiburg, Germany
| | | | - Sally Lambert
- 5Division of Molecular Histopathology, Department of Pathology, University of Cambridge, United Kingdom
| | | | - Axel Benner
- 6Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Hendrik Witt
- 1German Cancer Research Center, Heidelberg, Germany
| | - Marc Remke
- 1German Cancer Research Center, Heidelberg, Germany
| | | | | | - Ton Nu Van Anh
- 8Department of Pediatric Neurology and Muscle Disorders, University Hospital Freiburg, Germany
| | - Heike Olbrich
- 8Department of Pediatric Neurology and Muscle Disorders, University Hospital Freiburg, Germany
| | | | - Andreas E. Kulozik
- 10Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Germany
| | - Astrid Gnekow
- 7Department of Pediatrics, Klinikum Augsburg, Germany
| | | | - Olaf Witt
- 10Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Germany
| | - Heymut Omran
- 12Clinic and Polyclinic for Pediatrics, Department of General Pediatrics, University Hospital Muenster, Germany
| | - V Peter Collins
- 5Division of Molecular Histopathology, Department of Pathology, University of Cambridge, United Kingdom
| | - Tilman Brummer
- 3Centre for Biological Systems Analysis (ZBSA), Centre for Biological Signalling Studies BIOSS and Faculty of Biology, Albert-Ludwigs-University Freiburg, Germany
| | - Rolf Marschalek
- 2Institute of Pharmaceutical Biology, Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt, Germany
| | | | - Andrey Korshunov
- 9Department of Neuropathology, University Hospital Heidelberg, Germany
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McCabe MG, Bäcklund LM, Leong HS, Ichimura K, Collins VP. Chromosome 17 alterations identify good-risk and poor-risk tumors independently of clinical factors in medulloblastoma. Neuro Oncol 2011; 13:376-83. [PMID: 21292688 PMCID: PMC3064691 DOI: 10.1093/neuonc/noq192] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Current risk stratification schemas for medulloblastoma, based on combinations of clinical variables and histotype, fail to accurately identify particularly good- and poor-risk tumors. Attempts have been made to improve discriminatory power by combining clinical variables with cytogenetic data. We report here a pooled analysis of all previous reports of chromosomal copy number related to survival data in medulloblastoma. We collated data from previous reports that explicitly quoted survival data and chromosomal copy number in medulloblastoma. We analyzed the relative prognostic significance of currently used clinical risk stratifiers and the chromosomal aberrations previously reported to correlate with survival. In the pooled dataset metastatic disease, incomplete tumor resection and severe anaplasia were associated with poor outcome, while young age at presentation was not prognostically significant. Of the chromosomal variables studied, isolated 17p loss and gain of 1q correlated with poor survival. Gain of 17q without associated loss of 17p showed a trend to improved outcome. The most commonly reported alteration, isodicentric chromosome 17, was not prognostically significant. Sequential multivariate models identified isolated 17p loss, isolated 17q gain, and 1q gain as independent prognostic factors. In a historical dataset, we have identified isolated 17p loss as a marker of poor outcome and 17q gain as a novel putative marker of good prognosis. Biological markers of poor-risk and good-risk tumors will be critical in stratifying treatment in future trials. Our findings should be prospectively validated independently in future clinical studies.
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Affiliation(s)
- Martin G McCabe
- Manchester Academic Health Science Centre, School of Cancer and Enabling Sciences, University of Manchester, The Christie NHS Foundation Trust, Withington, Manchester M20 4BX, UK.
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Kullar PJ, Pearson DM, Malley DS, Collins VP, Ichimura K. CpG island hypermethylation of the neurofibromatosis type 2 (NF2) gene is rare in sporadic vestibular schwannomas. Neuropathol Appl Neurobiol 2011; 36:505-14. [PMID: 20831745 DOI: 10.1111/j.1365-2990.2010.01090.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Loss of both wild-type copies of the neurofibromatosis type 2 (NF2) gene is found in both sporadic and neurofibromatosis type 2-associated vestibular schwannomas (VS). Previous studies have identified a subset of VS with no loss or mutation of NF2. We hypothesized that methylation of NF2 resulting in gene silencing may play a role in such tumours. METHODS Forty sporadic VS were analysed by array comparative genomic hybridization using 1 Mb whole genome and chromosome 22 tile path arrays. The NF2 genes were sequenced and methylation of NF2 examined by pyrosequencing. RESULTS Monosomy 22 was the only recurrent change found. Twelve tumours had NF2 mutations. Eight tumours had complete loss of wild-type NF2, four had one mutated and one wild-type allele, 11 had only one wild-type allele and 17 showed no abnormalities. Methylation analysis showed low-level methylation in four tumours at a limited number of CpGs. No high-level methylation was found. CONCLUSIONS This study shows that a significant proportion of sporadic VS (>40%) have unmethylated wild-type NF2 genes. This indicates that other mechanisms, yet to be identified, are operative in the oncogenesis of these VSs.
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Affiliation(s)
- P J Kullar
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
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Brada M, Stenning S, Gabe R, Thompson LC, Levy D, Rampling R, Erridge S, Saran F, Gattamaneni R, Hopkins K, Beall S, Collins VP, Lee SM. Temozolomide Versus Procarbazine, Lomustine, and Vincristine in Recurrent High-Grade Glioma. J Clin Oncol 2010; 28:4601-8. [PMID: 20855843 DOI: 10.1200/jco.2009.27.1932] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [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 Temozolomide (TMZ) is an alkylating agent licensed for treatment of high-grade glioma (HGG). No prospective comparison with nitrosourea-based chemotherapy exists. We report, to our knowledge, the first randomized trial of procarbazine, lomustine, and vincristine (PCV) versus TMZ in chemotherapy-naive patients with recurrent HGG. Patients and Methods Four hundred forty-seven patients were randomly assigned to PCV (224 patients) or TMZ (sub–random assignment: TMZ-5 [200 mg/m2 for 5 days, 112 patients] or TMZ-21 [100 mg/m2 for 21 days, 111 patients]) for up to 9 months or until progression. The primary outcomes were survival (PCV v TMZ) and 12-week progression-free survival (PFS; TMZ-5 v TMZ-21). This study is registered as ISRCTN83176944. Results Percentages of patients completing 9 months of treatment in the PCV, TMZ-5, and TMZ-21 arms were 17%, 26%, and 13%, respectively. Major toxicity was similar across all three groups. With a median follow-up time of 12 months and 382 deaths, there was no clear survival benefit when comparing PCV with TMZ (hazard ratio [HR], 0.91; 95% CI, 0.74 to 1.11; P = .350). For TMZ-5 versus TMZ-21, 12-week PFS rates were similar (63.6% and 65.7%, respectively; P = .745), but TMZ-5 improved overall PFS (HR, 1.38; 95% CI, 1.05 to 1.82; P = .023), survival (HR, 1.32; 95% CI, 0.99 to 1.75; P = .056), and global quality of life (49% v 19% improved > 10 points at 6 months, respectively; P = .005). Conclusion Although TMZ (both arms combined) did not show a clear benefit compared with PCV, comparison of the TMZ schedules demonstrated that the 21-day schedule was inferior to the 5-day schedule in this setting. This challenges the current understanding of increasing TMZ dose-intensity by prolonged scheduling.
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Affiliation(s)
- Michael Brada
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Sally Stenning
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Rhian Gabe
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Lindsay C. Thompson
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - David Levy
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Roy Rampling
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Sara Erridge
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Frank Saran
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Rao Gattamaneni
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Kirsten Hopkins
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Sarah Beall
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - V. Peter Collins
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
| | - Siow-Ming Lee
- From The Institute of Cancer Research and The Royal Marsden National Health Service Foundation Trust, Sutton; Medical Research Council Clinical Trials Unit; University College Hospital and University College London Cancer Institute, London; Weston Park Hospital, Sheffield; University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow; Western General Hospital, Edinburgh; The Christie Hospital, Manchester; Bristol Haematology and Oncology Centre, Bristol; and Addenbrookes Hospital, Cambridge,
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Vogazianou AP, Chan R, Bäcklund LM, Pearson DM, Liu L, Langford CF, Gregory SG, Collins VP, Ichimura K. Distinct patterns of 1p and 19q alterations identify subtypes of human gliomas that have different prognoses. Neuro Oncol 2010; 12:664-78. [PMID: 20164239 PMCID: PMC2940668 DOI: 10.1093/neuonc/nop075] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [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: 09/02/2009] [Accepted: 11/15/2009] [Indexed: 11/13/2022] Open
Abstract
We studied the status of chromosomes 1 and 19 in 363 astrocytic and oligodendroglial tumors. Whereas the predominant pattern of copy number abnormality was a concurrent loss of the entire 1p and 19q regions (total 1p/19q loss) among oligodendroglial tumors and partial deletions of 1p and/or 19q in astrocytic tumors, a subset of apparently astrocytic tumors also had total 1p/19q loss. The presence of total 1p/19q loss was associated with longer survival of patients with all types of adult gliomas independent of age and diagnosis (P = .041). The most commonly deleted region on 19q in astrocytic tumors spans 885 kb in 19q13.33-q13.41, which is telomeric to the previously proposed region. Novel regions of homozygous deletion, including a part of DPYD (1p21.3) or the KLK cluster (19q13.33), were observed in anaplastic oligodendrogliomas. Amplifications encompassing AKT2 (19q13.2) or CCNE1 (19q12) were identified in some glioblastomas. Deletion mapping of the centromeric regions of 1p and 19q in the tumors that had total 1p/19q loss, indicating that the breakpoints lie centromeric to NOTCH2 within the pericentromeric regions of 1p and 19q. Thus, we show that the copy number abnormalities of 1p and 19q in human gliomas are complex and have distinct patterns that are prognostically predictive independent of age and pathological diagnosis. An accurate identification of total 1p/19q loss and discriminating this from other 1p/19q changes is, however, critical when the 1p/19q copy number status is used to stratify patients in clinical trials.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Koichi Ichimura
- Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke's Hospital, Cambridge (A.P.V., R.C., D.M.P., L.L., V.P.C., K.I.); Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden (L.M.B.); The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge (C.F.L., S.G.G.); Duke Center for Human Genetics, Duke University Medical Center, Durham, North Carolina (S.G.G.)
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Pohl U, Dean AF, Ichimura K, Liu L, Nicholson J, Cross J, Collins VP. Genomic analysis of chromosome 22 in synchronous and histologically distinct intracranial tumours in a child. Neuropathol Appl Neurobiol 2010; 36:359-63. [PMID: 20345646 DOI: 10.1111/j.1365-2990.2010.01085.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Li M, Lee KF, Lu Y, Clarke I, Shih D, Eberhart C, Collins VP, Van Meter T, Picard D, Zhou L, Boutros PC, Modena P, Liang ML, Scherer SW, Bouffet E, Rutka JT, Pomeroy SL, Lau CC, Taylor MD, Gajjar A, Dirks PB, Hawkins CE, Huang A. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell 2009; 16:533-46. [PMID: 19962671 PMCID: PMC3431561 DOI: 10.1016/j.ccr.2009.10.025] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 08/03/2009] [Accepted: 10/23/2009] [Indexed: 12/19/2022]
Abstract
We discovered a high-level amplicon involving the chr19q13.41 microRNA (miRNA) cluster (C19MC) in 11/45 ( approximately 25%) primary CNS-PNET, which results in striking overexpression of miR-517c and 520g. Constitutive expression of miR-517c or 520g promotes in vitro and in vivo oncogenicity, modulates cell survival, and robustly enhances growth of untransformed human neural stem cells (hNSCs) in part by upregulating WNT pathway signaling and restricting differentiation of hNSCs. Remarkably, the C19MC amplicon, which is very rare in other brain tumors (1/263), identifies an aggressive subgroup of CNS-PNET with distinct gene-expression profiles, characteristic histology, and dismal survival. Our data implicate miR-517c and 520g as oncogenes and promising biological markers for CNS-PNET and provide important insights into oncogenic properties of the C19MC locus.
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Affiliation(s)
- Meihua Li
- Division of Hematology-Oncology, Hospital for Sick Children, Toronto, ON M5G 0A3, Canada
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Ichimura K, Pearson DM, Kocialkowski S, Bäcklund LM, Chan R, Jones DTW, Collins VP. IDH1 mutations are present in the majority of common adult gliomas but rare in primary glioblastomas. Neuro Oncol 2009; 11:341-7. [PMID: 19435942 PMCID: PMC2743214 DOI: 10.1215/15228517-2009-025] [Citation(s) in RCA: 429] [Impact Index Per Article: 28.6] [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: 11/21/2008] [Accepted: 02/23/2009] [Indexed: 12/15/2022] Open
Abstract
We screened exon 4 of the gene isocitrate dehydrogenase 1 (NADP+), soluble (IDH1) for mutations in 596 primary intracranial tumors of all major types. Codon 132 mutation was seen in 54% of astrocytomas and 65% of oligodendroglial tumors but in only 6% of glioblastomas (3% of primary and 50% of secondary glioblastomas). There were no mutations in any other type of tumor studied. While mutations in the tumor protein p53 gene (TP53) and total 1p/19q deletions were mutually exclusive, IDH1 mutations were strongly correlated with these genetic abnormalities. All four types of mutant IDH1 proteins showed decreased enzymatic activity. The data indicate that IDH1 mutation combined with either TP53 mutation or total 1p/19q loss is a frequent and early change in the majority of oligodendroglial tumors, diffuse astrocytomas, anaplastic astrocytomas, and secondary glioblastomas but not in primary glioblastomas.
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Affiliation(s)
- Koichi Ichimura
- Molecular Histopathology, Level 3, Lab Block, Addenbrooke's Hospital, Box 231, Cambridge CB20QQ, UK.
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Thelander EF, Ichimura K, Corcoran M, Barbany G, Nordgren A, Heyman M, Berglund M, Mungall A, Rosenquist R, Collins VP, Grandér D, Larsson C, Lagercrantz S. Characterization of 6q deletions in mature B cell lymphomas and childhood acute lymphoblastic leukemia. Leuk Lymphoma 2009; 49:477-87. [DOI: 10.1080/10428190701817282] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chanudet E, Ye H, Ferry J, Bacon CM, Adam P, Müller-Hermelink HK, Radford J, Pileri SA, Ichimura K, Collins VP, Hamoudi RA, Nicholson AG, Wotherspoon AC, Isaacson PG, Du MQ. A20 deletion is associated with copy number gain at the TNFA/B/C locus and occurs preferentially in translocation-negative MALT lymphoma of the ocular adnexa and salivary glands. J Pathol 2009; 217:420-30. [PMID: 19006194 DOI: 10.1002/path.2466] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The genetic basis of MALT lymphoma is largely unknown. Characteristic chromosomal translocations are frequently associated with gastric and pulmonary cases, but are rare at other sites. We compared the genetic profiles of 33 ocular adnexal and 25 pulmonary MALT lymphomas by 1 Mb array-comparative genomic hybridization (CGH) and revealed recurrent 6q23 losses and 6p21.2-6p22.1 gains exclusive to ocular cases. High-resolution chromosome 6 tile-path array-CGH identified NF-kappaB inhibitor A20 as the target of 6q23.3 deletion and TNFA/B/C locus as a putative target of 6p21.2-22.1 gain. Interphase fluorescence in situ hybridization showed that A20 deletion occurred in MALT lymphoma of the ocular adnexa (8/42=19%), salivary gland (2/24=8%), thyroid (1/9=11%) and liver (1/2), but not in the lung (26), stomach (45) and skin (13). Homozygous deletion was observed in three cases. A20 deletion and TNFA/B/C gain were significantly associated (p<0.001) and exclusively found in cases without characteristic translocation. In ocular cases, A20 deletion was associated with concurrent involvement of different adnexal tissues or extraocular sites at diagnosis (p=0.007), a higher proportion of relapse (67% versus 37%) and a shorter relapse-free survival (p=0.033). A20 deletion and gain at TNFA/B/C locus may thus play an important role in the development of translocation-negative MALT lymphoma.
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Affiliation(s)
- E Chanudet
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, UK
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McCabe MG, Ichimura K, Pearson DM, Liu L, Clifford SC, Ellison DW, Collins VP. Novel mechanisms of gene disruption at the medulloblastoma isodicentric 17p11 breakpoint. Genes Chromosomes Cancer 2009; 48:121-31. [DOI: 10.1002/gcc.20625] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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