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Schoof M, Spohn M, Dorostkar M, Neyazi S, Bockmayr M, Swartling F, Kawauchi D, Gilbertson R, Taylor J, Pei Y, Glass R, Cheng J, Galarza NM, Hench J, Herms J, Jurmeister P, Schweizer L, Capper D, Harter P, Thomas C, Hasselblatt M, Blattner-Johnson M, Jones D, Frank S, Kerl K, Schüller U. PATH-04. Array-based global DNA Methylation profiling of mouse brain tumors allows comparison to human tumors. Neuro Oncol 2022. [PMCID: PMC9164802 DOI: 10.1093/neuonc/noac079.588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The classification of human brain tumors by global DNA methylation profiling has become an essential part of modern integrated neuropathological diagnostics. It has proven to reliably identify known and novel brain tumor (sub-)types that are biologically and clinically distinct. Therefore, this technique has critically improved diagnostic accuracy and risk stratification of brain tumor patients. Although indispensable for the understanding of tumor biology and for preclinical drug trials, the comparison of genetically engineered mouse models to human brain tumors is still difficult. The assessment of tumor morphology only provides an approximate picture, and transcriptomic data from human brain tumors are sparse and suffer from platform-related technical incomparability. Here, we show array-based DNA methylation profiling of well-established murine brain tumors, such as Wnt and Shh medulloblastoma, YAP and RELA ependymoma, ETMR, and AT/RT. Similar to human brain tumors, unbiased clustering methods revealed distinct methylation profiles and mean methylation levels for mouse brain tumors types. Analyses were possible for fresh-frozen as well as for paraffin-embedded tissue, and copy number alterations could be inferred from methylation profiles. Most importantly, first results suggest that inter-species comparisons allow the classification of brain tumors from known or novel mouse models based on the constantly growing spectrum of human brain tumor types and subtypes with hundreds of thousands of available datasets. As an example, upon DNA methylation profiling, cerebellar tumors arising in Math1-cre::SmoM2Fl/+ mice display the highest similarity to human SHH medulloblastoma when compared to multiple human brain tumor entities including WNT and Non-WNT/Non-SHH medulloblastoma. These results suggest that global DNA methylation profiling may add another very important level of information to the characterization of genetically engineered mouse models.
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Affiliation(s)
- Melanie Schoof
- Research Insitute Children`s Cancer Center Hamburg , Hamburg , Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Michael Spohn
- Research Insitute Children`s Cancer Center Hamburg , Hamburg , Germany
- Bioinformatics Facility, Faculty of Medicine, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Mario Dorostkar
- Center for Neuropathology and Prion Research, Institute of Neuropathology, LMU Munich , Munich , Germany
| | - Sina Neyazi
- Research Insitute Children`s Cancer Center Hamburg , Hamburg , Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Michael Bockmayr
- Research Insitute Children`s Cancer Center Hamburg , Hamburg , Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Fredrik Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University , Uppsala , Sweden
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology National Center of Neurology and Psychiatry (NCNP) National Institute of Neuroscience , Tokyo , Japan
| | - Richard Gilbertson
- Dept. of Oncology, Cancer Research UK Cambridge Centre, CRUK Cambridge Institute, Li Ka Shing Centre , Cambridge , United Kingdom
| | - Jessica Taylor
- Dept. of Oncology, Cancer Research UK Cambridge Centre, CRUK Cambridge Institute, Li Ka Shing Centre , Cambridge , United Kingdom
| | - Yanxin Pei
- Center for Cancer and Immunology Research Children’s National Hospital , Washigton DC , USA
| | - Rainer Glass
- Neurosurgical Research, Department of Neurosurgery, University Hospital, LMU Munich , Munich , Germany
- German Cancer Consortium (DKTK) partner site Munich and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jiying Cheng
- Neurosurgical Research, Department of Neurosurgery, University Hospital, LMU Munich , Munich , Germany
| | - Natalia Moreno Galarza
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University , Muenster , Germany
| | - Juergen Hench
- Department of Neuropathology, Institute of Pathology, Basel University Hospital , Basel , Switzerland
| | - Jochen Herms
- Center for Neuropathology and Prion Research, Institute of Neuropathology, LMU Munich , Munich , Germany
| | - Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health LMU , Berlin , Germany
| | - Leonille Schweizer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology , Berlin , Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Neuropathology , Berlin , Germany
| | - Patrick Harter
- Edinger-Institute (Neurological Institute) Goethe-University Medical School , Frankfurt , Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster , Muenster , Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster , Muenster , Germany
| | - Mirjam Blattner-Johnson
- Hopp Children's Cancer Center (KiTZ) , Heidelberg , Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - David Jones
- Hopp Children's Cancer Center (KiTZ) , Heidelberg , Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Frank
- Department of Neuropathology, Institute of Pathology, Basel University Hospital , Basel , Switzerland
| | - Kornelius Kerl
- Pediatric Hematology and Oncology, University Children's Hospital Muenster , Muenster , Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf , Hamburg , Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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Galarza NM, Holdhof D, Interlandi M, Melcher V, Graf M, Kastrati D, Meisterernst M, Johann P, Kool M, Frühwald M, Schüller U, Kerl K. ATRT-07. MURINE SOX2-POSITIVE EARLY PRECURSOR CELLS GIVE RISE TO RHABDOID TUMORS WITH FEATURES OF THE HUMAN ATRT-MYC GROUP. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Natalia Moreno Galarza
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
| | - Dörthe Holdhof
- Research Institute Children’s Cancer Center Hamburg, Eppendorf University Hospital, University of Hamburg, Hamburg, Germany
| | - Marta Interlandi
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
| | - Viktoria Melcher
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
| | - Monika Graf
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
| | - Dennis Kastrati
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
| | - Michael Meisterernst
- Institute of Molecular Tumor Biology Muenster, University Hospital Muenster, Muenster, Germany
| | - Pascal Johann
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Frühwald
- Children’s Hospital Augsburg, Swabian Children’s Cancer Center, Augsburg, Germany
| | - Ulrich Schüller
- Research Institute Children’s Cancer Center Hamburg, Eppendorf University Hospital, University of Hamburg, Hamburg, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children’s Hospital, Westfalian-Wilhelms-University, Muenster, Germany
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