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Schepke E, Löfgren M, Pietsch T, Kling T, Nordborg C, Olsson Bontell T, Holm S, Öberg A, Nyman P, Eliasson-Hofvander M, Sabel M, Lannering B, Carén H. Supratentorial CNS-PNETs in children; a Swedish population-based study with molecular re-evaluation and long-term follow-up. Clin Epigenetics 2023; 15:40. [PMID: 36895035 PMCID: PMC9996973 DOI: 10.1186/s13148-023-01456-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/23/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Molecular analyses have shown that tumours diagnosed as supratentorial primitive neuro-ectodermal tumours of the central nervous system (CNS-PNETs) in the past represent a heterogenous group of rare childhood tumours including high-grade gliomas (HGG), ependymomas, atypical teratoid/rhabdoid tumours (AT/RT), CNS neuroblastoma with forkhead box R2 (FOXR2) activation and embryonal tumour with multi-layered rosettes (ETMR). All these tumour types are rare and long-term clinical follow-up data are sparse. We retrospectively re-evaluated all children (0-18 years old) diagnosed with a CNS-PNET in Sweden during 1984-2015 and collected clinical data. METHODS In total, 88 supratentorial CNS-PNETs were identified in the Swedish Childhood Cancer Registry and from these formalin-fixed paraffin-embedded tumour material was available for 71 patients. These tumours were histopathologically re-evaluated and, in addition, analysed using genome-wide DNA methylation profiling and classified by the MNP brain tumour classifier. RESULTS The most frequent tumour types, after histopathological re-evaluation, were HGG (35%) followed by AT/RT (11%), CNS NB-FOXR2 (10%) and ETMR (8%). DNA methylation profiling could further divide the tumours into specific subtypes and with a high accuracy classify these rare embryonal tumours. The 5 and 10-year overall survival (OS) for the whole CNS-PNET cohort was 45% ± 12% and 42% ± 12%, respectively. However, the different groups of tumour types identified after re-evaluation displayed very variable survival patterns, with a poor outcome for HGG and ETMR patients with 5-year OS 20% ± 16% and 33% ± 35%, respectively. On the contrary, high PFS and OS was observed for patients with CNS NB-FOXR2 (5-year 100% for both). Survival rates remained stable even after 15-years of follow-up. CONCLUSIONS Our findings demonstrate, in a national based setting, the molecular heterogeneity of these tumours and show that DNA methylation profiling of these tumours provides an indispensable tool in distinguishing these rare tumours. Long-term follow-up data confirms previous findings with a favourable outcome for CNS NB-FOXR2 tumours and poor chances of survival for ETMR and HGG.
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Affiliation(s)
- Elizabeth Schepke
- grid.1649.a000000009445082XChildhood Cancer Centre, Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Maja Löfgren
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Torsten Pietsch
- grid.15090.3d0000 0000 8786 803XDepartment of Neuropathology, DGNN Brain Tumour Reference Centre, University of Bonn Medical Center, Bonn, Germany
| | - Teresia Kling
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
| | - Claes Nordborg
- grid.1649.a000000009445082XDepartment of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- grid.1649.a000000009445082XDepartment of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- grid.8761.80000 0000 9919 9582Departmentof Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Holm
- grid.24381.3c0000 0000 9241 5705Department of Paediatric Haematology and Oncology, Astrid Lindgrens Childrens Hospital, Karolinska University, Stockholm, Sweden
| | - Anders Öberg
- grid.8993.b0000 0004 1936 9457Department of Woman’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Per Nyman
- grid.5640.70000 0001 2162 9922Department of Paediatrics, Linköping University, Linköping, Sweden
| | - Marie Eliasson-Hofvander
- grid.411843.b0000 0004 0623 9987Department of Paediatric Oncology and Haematology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Magnus Sabel
- grid.1649.a000000009445082XChildhood Cancer Centre, Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- grid.8761.80000 0000 9919 9582Department of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Birgitta Lannering
- grid.8761.80000 0000 9919 9582Department of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30 Gothenburg, Sweden
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Schepke E, Löfgren M, Pietsch T, Bontell TO, Kling T, Wenger A, Vega SF, Danielsson A, Dosa S, Holm S, Öberg A, Nyman P, Eliasson-Hofvander M, Sandström PE, Pfister SM, Lannering B, Sabel M, Carén H. DNA methylation profiling improves routine diagnosis of paediatric CNS tumours: a prospective population-based study. Neuropathol Appl Neurobiol 2022; 48:e12838. [PMID: 35892159 PMCID: PMC9543790 DOI: 10.1111/nan.12838] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 02/16/2022] [Revised: 05/05/2022] [Accepted: 07/02/2022] [Indexed: 11/28/2022]
Abstract
AIMS Paediatric brain tumours are rare and establishing a precise diagnosis can be challenging. Analysis of DNA methylation profiles has been shown to be a reliable method to classify central nervous system (CNS) tumours with high accuracy. We aimed to prospectively analyse CNS tumours diagnosed in Sweden, to assess the clinical impact of adding DNA methylation-based classification to standard paediatric brain tumour diagnostics in an unselected cohort. METHODS All CNS tumours diagnosed in children (0-18 years) during 2017-2020 were eligible for inclusion provided sufficient tumour material was available. Tumours were analysed using genome-wide DNA methylation profiling and classified by the MNP brain tumour classifier. The initial histopathological diagnosis was compared to the DNA methylation-based classification. For incongruent results, a blinded re-evaluation was performed by an experienced neuropathologist. RESULTS 240 tumours with a histopathology-based diagnosis were profiled. A high-confidence methylation score of 0.84 or more was reached in 78% of the cases. In 69%, the histopathological diagnosis was confirmed and for some of these also refined, 6% were incongruent and the re-evaluation favoured the methylation-based classification. In the remaining 3% of cases, the methylation class was non-contributory. The change in diagnosis would have had a direct impact on the clinical management in 5% of all patients. CONCLUSIONS Integrating DNA methylation-based tumour classification into routine clinical analysis improves diagnostics and provides molecular information that is important for treatment decisions. The results from methylation profiling should be interpreted in the context of clinical and histopathological information.
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Affiliation(s)
- Elizabeth Schepke
- Childhood Cancer Centre, Queen Silvia Children´s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden.,Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maja Löfgren
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumour Reference Centre, University of Bonn Medical Centre, Bonn, Germany
| | - Thomas Olsson Bontell
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Anna Danielsson
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandor Dosa
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Holm
- Department of Paediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Öberg
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Per Nyman
- Department of Paediatrics, Linköping University, Linköping, Sweden
| | - Marie Eliasson-Hofvander
- Department of Paediatric Oncology and Haematology, Lund University, Skane University Hospital, Lund, Sweden
| | | | - Stefan M Pfister
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Paediatric Neuro-oncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Birgitta Lannering
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Sabel
- Childhood Cancer Centre, Queen Silvia Children´s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Schepke E, Löfgren M, Pietsch T, Bontell TO, Kling T, Wenger A, Vega SF, Danielsson A, Dosa S, Holm S, Öberg A, Nyman P, Eliasson-Hofvander M, Sandström PE, Pfister SM, Lannering B, Sabel M, Carén H. PATH-08. DNA methylation profiling improves routine diagnostics of paediatric CNS tumours: a prospective population-based study. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.592] [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: 11/12/2022] Open
Abstract
Abstract
AIMS: Paediatric brain tumours are rare and establishing a precise diagnosis can be challenging. Analysis of DNA methylation profiles has been shown to be a reliable method to classify central nervous system (CNS) tumours with high accuracy. We aimed to prospectively analyse CNS tumours diagnosed in Sweden, to assess the clinical impact of adding DNA methylation-based classification to standard paediatric brain tumour diagnostics in an unselected cohort. Methods: All CNS tumours diagnosed in children (0-18 years) during 2017-2020 were eligible for inclusion provided sufficient tumour material was available. Tumours were analysed using genome-wide DNA methylation profiling and classified by the MNP brain tumour classifier. The initial histopathological diagnosis was compared to the DNA methylation-based classification. For incongruent results, a blinded re-evaluation was performed by an experienced neuropathologist. Results: 240 tumours with a histopathology-based diagnosis were profiled. A high-confidence methylation score of 0.84 or more was reached in 78% of the cases. In 69%, the histopathological diagnosis was confirmed and for some of these also refined, 6% were incongruent and the re-evaluation favoured the methylation-based classification. In the remaining 3% of cases, the methylation class was non-contributory or could not be predicted. The change in diagnosis would have had a direct impact on the clinical management in 5% of all patients.Conclusions: Integrating DNA methylation-based tumour classification into routine clinical analysis improves diagnostics and molecular information important for treatment decisions. The results from methylation profiling should be interpreted in the context of clinical and histopathological information.
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Affiliation(s)
- Elizabeth Schepke
- Childhood Cancer Centre, Queen Silvia Children′s Hospital, Sahlgrenska University Hospital , Gothenburg , Sweden
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Maja Löfgren
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumour Reference Centre, University of Bonn Medical Centre, Venusberg-Campus , Bonn , Germany
| | - Thomas Olsson Bontell
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital , Gothenburg , Sweden
| | - Teresia Kling
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Anna Wenger
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Anna Danielsson
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Sandor Dosa
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital , Gothenburg , Sweden
| | - Stefan Holm
- Department of Paediatrics, Karolinska University Hospital , Stockholm , Sweden
| | - Anders Öberg
- Department of Women's and Children's Health, Uppsala University , Uppsala , Sweden
| | - Per Nyman
- Department of Paediatrics, Linköping University, Linköping, Sweden
| | - Marie Eliasson-Hofvander
- Department of Paediatric Oncology and Haematology, Lund University, Skane University Hospital , Lund , Sweden
| | | | - Stefan M Pfister
- Department of Paediatric Haematology and Oncology, Heidelberg University Hospital , Heidelberg , Germany
- Division of Paediatric Neuro-oncology, German Cancer Research Centre (DKFZ) , Heidelberg , Germany
| | - Birgitta Lannering
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Magnus Sabel
- Childhood Cancer Centre, Queen Silvia Children′s Hospital, Sahlgrenska University Hospital , Gothenburg , Sweden
- Department of Paediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Helena Carén
- Sahlgrenska Centre for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
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Schepke E, Löfgren M, Pietsch T, Kling T, Nordborg C, Bontell TO, Holm S, Öberg A, Nyman P, Eliasson-Hofvander M, Sabel M, Lannering B, Carén H. ETMR-10. Retrospective molecular re-evaluation of CNS PNETs; a population-based study. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
BACKGROUND: The heterogeneous group of tumors, primitive neuro-ectodermal tumors of the central nervous system (CNS-PNETs), is a group of rare childhood embryonal tumors associated with a poor prognosis. In recent years, molecular analyzes have shown that CNS-PNETs consist of high-grade gliomas (HGG), ependymomas, different embryonal entities like atypical teratoid /rhabdoid tumors (AT/RT), CNS neuroblastoma FOXR2 and embryonal tumor with multi-layered rosettes (ETMR). Each of these tumor types is unusual and long-term clinical follow-up data are sparse. METHODS: We retrospectively re-evaluated all children (0-18 years old) diagnosed with a CNS-PNET in Sweden during 1984-2015. In total, 88 supratentorial CNS-PNETs were identified in the Swedish Childhood Cancer Registry and from these formalin-fixed paraffin-embedded tumor material was available for 69 patients. All tumors were reviewed histopathologically by an experienced neuropathologist and were analyzed using genome-wide DNA methylation profiling and classified by the MNP brain tumor classifier. RESULTS: The largest entities, after re-evaluation, were HGG (30%), CNS NB-FOXR2 (12%), AT/RT (10%) and ETMR (8%). Some tumors were difficult to classify and will be further evaluated molecularly. Some examples: Best treatment results were seen for patients with CNS-NB FOXR2 (5-year PFS: 100%) where all patients had received craniospinal radiotherapy (CSI). Patients with ETMR were all very young and survival data show early progression and poor survival (5-year OS 34%). CONCLUSIONS: Although the patient material is relatively small, it is population-based with long follow-up times. Our findings are in line with other studies and shows that CSI is important for cure for CNS-NB FOXR2 and that intensive multi-modal therapies needs to be evaluated in up-front studies for these rare embryonal tumors.
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Affiliation(s)
- Elizabeth Schepke
- Childhood Cancer Centre, Queen Silvia Children′s Hospital, Sahlgrenska University Hospital , Gothenburg , Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Maja Löfgren
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Centre, University of Bonn Medical Centre, Venusberg-Campus , Bonn , Germany
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Claes Nordborg
- Childhood Cancer Centre, Queen Silvia Children′s Hospital, Sahlgrenska University Hospital , Gothenburg , Sweden
| | | | - Stefan Holm
- Department of Woman’s and Children’s Health, Uppsala University , Uppsala , Sweden
| | - Anders Öberg
- Department of Pediatrics, Linköping University, Linköping, Sweden
| | - Per Nyman
- Department of Pediatric Oncology and Hematology, Lund University , Lund , Sweden
| | - Marie Eliasson-Hofvander
- Department of Clinical Science, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Magnus Sabel
- Childhood Cancer Centre, Queen Silvia Children′s Hospital, Sahlgrenska University Hospital , Gothenburg , Sweden
- Department of Clinical Science, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Birgitta Lannering
- Department of Clinical Science, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , Gothenburg , Sweden
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