1
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Kling T, Ferreyra Vega S, Suman M, Dénes A, Lipatnikova A, Lagerström S, Olsson Bontell T, Jakola AS, Carén H. Refinement of prognostication for IDH-mutant astrocytomas using DNA methylation-based classification. Brain Pathol 2024:e13233. [PMID: 38168467 DOI: 10.1111/bpa.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The 2021 World Health Organization (WHO) grading system of isocitrate dehydrogenase (IDH)-mutant astrocytomas relies on histological features and the presence of homozygous deletion of the cyclin-dependent kinase inhibitor 2A and 2B (CDKN2A/B). DNA methylation profiling has become highly relevant in the diagnosis of central nervous system (CNS) tumors including gliomas, and it has been incorporated into routine clinical diagnostics in some countries. In this study, we, therefore, examined the value of DNA methylation-based classification for prognostication of patients with IDH-mutant astrocytomas. We analyzed histopathological diagnoses, genome-wide DNA methylation array data, and chromosomal copy number alteration profiles from a cohort of 385 adult-type IDH-mutant astrocytomas, including a local cohort of 127 cases and 258 cases from public repositories. Prognosis based on WHO 2021 CNS criteria (histological grade and CDKN2A/B homozygous deletion status), other relevant chromosomal/gene alterations in IDH-mutant astrocytomas and DNA methylation-based subclassification according to the molecular neuropathology classifier were assessed. We demonstrate that DNA methylation-based classification of IDH-mutant astrocytomas can be used to predict outcome of the patients equally well as WHO 2021 CNS criteria. In addition, methylation-based subclassification enabled the identification of IDH-mutant astrocytoma patients with poor survival among patients with grade 3 tumors and patients with grade 4 tumors with a more favorable outcome. In conclusion, DNA methylation-based subclassification adds prognostic information for IDH-mutant astrocytomas that can further refine the current WHO 2021 grading scheme for these patients.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Medha Suman
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Dénes
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Lipatnikova
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stina Lagerström
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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2
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Wenger A, Karlsson I, Kling T, Carén H. CRISPR-Cas9 knockout screen identifies novel treatment targets in childhood high-grade glioma. Clin Epigenetics 2023; 15:80. [PMID: 37161535 PMCID: PMC10170782 DOI: 10.1186/s13148-023-01498-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Brain tumours are the leading cause of cancer-related death in children, and there is no effective treatment. A growing body of evidence points to deregulated epigenetics as a tumour driver, particularly in paediatric cancers as they have relatively few genomic alterations, and key driver mutations have been identified in histone 3 (H3). Cancer stem cells (CSC) are implicated in tumour development, relapse and therapy resistance and thus particularly important to target. We therefore aimed to identify novel epigenetic treatment targets in CSC derived from H3-mutated high-grade glioma (HGG) through a CRISPR-Cas9 knockout screen. RESULTS The knockout screen identified more than 100 novel genes essential for the growth of CSC derived from paediatric HGG with H3K27M mutation. We successfully validated 12 of the 13 selected hits by individual knockout in the same two CSC lines, and for the top six hits we included two additional CSC lines derived from H3 wild-type paediatric HGG. Knockout of these genes led to a significant decrease in CSC growth, and altered stem cell and differentiation markers. CONCLUSIONS The screen robustly identified essential genes known in the literature, but also many novel genes essential for CSC growth in paediatric HGG. Six of the novel genes (UBE2N, CHD4, LSM11, KANSL1, KANSL3 and EED) were validated individually thus demonstrating their importance for CSC growth in H3-mutated and wild-type HGG. These genes should be further studied and evaluated as novel treatment targets in paediatric HGG.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska 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
| | - Ida Karlsson
- Sahlgrenska 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
| | - Teresia Kling
- Sahlgrenska 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
| | - Helena Carén
- Sahlgrenska 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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3
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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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4
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Ferreyra Vega S, Olsson Bontell T, Kling T, Jakola AS, Carén H. Longitudinal DNA methylation analysis of adult-type IDH-mutant gliomas. Acta Neuropathol Commun 2023; 11:23. [PMID: 36739454 PMCID: PMC9899392 DOI: 10.1186/s40478-023-01520-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 02/06/2023] Open
Abstract
Diffuse gliomas are the most prevalent malignant primary brain tumors in adults and remain incurable despite standard therapy. Tumor recurrence is currently inevitable, which contributes to a persistent high morbidity and mortality in these patients. In this study, we examined the genome-wide DNA methylation profiles of primary and recurrent adult-type IDH-mutant gliomas to elucidate DNA methylation changes associated with tumor progression (with or without malignant transformation). We analyzed DNA methylation profiles of 37 primary IDH-mutant gliomas and 42 paired recurrences using the DNA methylation EPIC beadChip array. DNA methylation-based classification reflected the tumor progression over time. We observed a methylation subtype switch in a proportion of IDH-mutant astrocytomas; the primary tumors were subclassified as low-grade astrocytomas, which progressed to high-grade astrocytomas in the recurrent tumors. The CNS WHO grade 4 IDH-mutant astrocytomas did not always resemble methylation subclasses of higher grades. The number of differentially methylated CpG sites increased over time, and astrocytomas accumulated more differentially methylated CpG sites than oligodendrogliomas during tumor progression. Few differentially methylated CpG sites were shared between patients. We demonstrated that DNA methylation profiles are mostly maintained during IDH-mutant glioma progression, but CpG site-specific methylation alterations can occur.
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Affiliation(s)
- Sandra Ferreyra Vega
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 7, 413 45 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, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- grid.8761.80000 0000 9919 9582Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - 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, Gothenburg, Sweden
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 7, 413 45, Gothenburg, Sweden. .,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden. .,Department of Neurosurgery, St. Olavs University Hospital, Trondheim, Norway.
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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5
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Kling T, Barnes D. 138 The Effect of Changes in Physician Shift Times and Physical Patient Coverage Areas on Resident Sign-out Burden in an Academic Emergency Department. Ann Emerg Med 2022. [DOI: 10.1016/j.annemergmed.2022.08.162] [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: 11/25/2022]
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6
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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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7
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Wenger A, Ferreyra Vega S, Schepke E, Löfgren M, Olsson Bontell T, Tisell M, Nilsson D, Kling T, Carén H. DNA methylation alterations across time and space in paediatric brain tumours. Acta Neuropathol Commun 2022; 10:105. [PMID: 35842717 PMCID: PMC9287974 DOI: 10.1186/s40478-022-01406-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/07/2022] [Indexed: 11/10/2022] Open
Abstract
DNA methylation is increasingly used for tumour classification and has expanded upon the > 100 currently known brain tumour entities. A correct diagnosis is the basis for suitable treatment for patients with brain tumours, which is the leading cause of cancer-related death in children. DNA methylation profiling is required for diagnosis of certain tumours, and used clinically for paediatric brain tumours in several countries. We therefore evaluated if the methylation-based classification is robust in different locations of the same tumour, and determined how the methylation pattern changed over time to relapse. We sampled 3-7 spatially separated biopsies per patient, and collected samples from paired primary and relapse brain tumours from children. Altogether, 121 samples from 46 paediatric patients with brain tumours were profiled with EPIC methylation arrays. The methylation-based classification was mainly homogeneous for all included tumour types that were successfully classified, which is promising for clinical diagnostics. There were indications of multiple subclasses within tumours and switches in the relapse setting, but not confirmed as the classification scores were below the threshold. Site-specific methylation alterations did occur within the tumours and varied significantly between tumour types for the temporal samples, and as a trend in spatial samples. More alterations were present in high-grade tumours compared to low-grade, and significantly more alterations with longer relapse times. The alterations in the spatial and temporal samples were significantly depleted in CpG islands, exons and transcription start sites, while enriched in OpenSea and regions not affiliated with a gene, suggesting a random location of the alterations in less conserved regions. In conclusion, more DNA methylation changes accumulated over time and more alterations occurred in high-grade tumours. The alterations mainly occurred in regions without gene affiliation, and did not affect the methylation-based classification, which largely remained homogeneous in paediatric brain tumours.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.,Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elizabeth Schepke
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.,Childhood Cancer Centre, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maja Löfgren
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Daniel Nilsson
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.
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8
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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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9
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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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10
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Ferreyra Vega S, Wenger A, Kling T, Olsson Bontell T, Jakola AS, Carén H. Spatial heterogeneity in DNA methylation and chromosomal alterations in diffuse gliomas and meningiomas. Mod Pathol 2022; 35:1551-1561. [PMID: 35701666 PMCID: PMC9596370 DOI: 10.1038/s41379-022-01113-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023]
Abstract
Adult-type diffuse gliomas and meningiomas are the most common primary intracranial tumors of the central nervous system. DNA methylation profiling is a novel diagnostic technique increasingly used also in the clinic. Although molecular heterogeneity is well described in these tumors, DNA methylation heterogeneity is less studied. We therefore investigated the intratumor genetic and epigenetic heterogeneity in diffuse gliomas and meningiomas, with focus on potential clinical implications. We further investigated tumor purity as a source for heterogeneity in the tumors. We analyzed genome-wide DNA methylation profiles generated from 126 spatially separated tumor biopsies from 39 diffuse gliomas and meningiomas. Moreover, we evaluated five methods for measurement of tumor purity and investigated intratumor heterogeneity by assessing DNA methylation-based classification, chromosomal copy number alterations and molecular markers. Our results demonstrated homogeneous methylation-based classification of IDH-mutant gliomas and further corroborates subtype heterogeneity in glioblastoma IDH-wildtype and high-grade meningioma patients after excluding samples with low tumor purity. We detected a large number of differentially methylated CpG sites within diffuse gliomas and meningiomas, particularly in tumors of higher grades. The presence of CDKN2A/B homozygous deletion differed in one out of two patients with IDH-mutant astrocytomas, CNS WHO grade 4. We conclude that diffuse gliomas and high-grade meningiomas are characterized by intratumor heterogeneity, which should be considered in clinical diagnostics and in the assessment of methylation-based and molecular markers.
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Affiliation(s)
- Sandra Ferreyra Vega
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- grid.8761.80000 0000 9919 9582Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- grid.8761.80000 0000 9919 9582Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Asgeir Store Jakola
- grid.8761.80000 0000 9919 9582Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden ,grid.52522.320000 0004 0627 3560Department of Neurosurgery, St.Olavs University Hospital, Trondheim, Norway
| | - 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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11
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, 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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12
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Wenger A, Ferreyra Vega S, Kling T, Bontell TO, Jakola AS, Carén H. Intratumor DNA methylation heterogeneity in glioblastoma: implications for DNA methylation-based classification. Neuro Oncol 2020; 21:616-627. [PMID: 30668814 PMCID: PMC6502500 DOI: 10.1093/neuonc/noz011] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND A feature of glioblastoma (GBM) is cellular and molecular heterogeneity, both within and between tumors. This variability causes a risk for sampling bias and potential tumor escape from future targeted therapy. Heterogeneous intratumor gene expression in GBM is well documented, but little is known regarding the epigenetic heterogeneity. Variability in DNA methylation within tumors would have implications for diagnostics, as methylation can be used for tumor classification, subtyping, and determination of the clinically used biomarker O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation. We therefore aimed to profile the intratumor DNA methylation heterogeneity in GBM and its effect on diagnostic properties. METHODS Three to 4 spatially separated biopsies per tumor were collected from 12 GBM patients. We performed genome-wide DNA methylation analysis and investigated intratumor variation. RESULTS All samples were classified as GBM isocitrate dehydrogenase (IDH) wild type (wt)/mutated by methylation profiling, but the subclass differed within 5 tumors. Some GBM samples exhibited higher DNA methylation differences within tumors than between, and many cytosine-phosphate-guanine (CpG) sites (mean: 17 000) had different methylation levels within the tumors. MGMT methylation status differed in IDH mutated patients (1/1). CONCLUSIONS We demonstrated that intratumor DNA methylation heterogeneity is a feature of GBM. Although all biopsies were classified as GBM IDH wt/mutated by methylation analysis, the assigned subclass differed in samples from the same patient. The observed heterogeneity within tumors is important to consider for methylation-based biomarkers and future improvements in stratification of GBM patients.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - 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
| | - Asgeir Store Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Neurosurgery, St Olavs University Hospital, Trondheim, Norway
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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13
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Danielsson A, Barreau K, Kling T, Tisell M, Carén H. Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation. Clin Epigenetics 2020; 12:26. [PMID: 32046773 PMCID: PMC7014676 DOI: 10.1186/s13148-020-0817-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/19/2019] [Accepted: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Radiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells. METHODS We examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel. RESULTS Few fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure. CONCLUSIONS DNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.
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Affiliation(s)
- Anna Danielsson
- Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Kristell Barreau
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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14
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Larsson S, Wenger A, Dósa S, Sabel M, Kling T, Carén H. Cell line-based xenograft mouse model of paediatric glioma stem cells mirrors the clinical course of the patient. Carcinogenesis 2019; 39:1304-1309. [PMID: 29982329 PMCID: PMC6175027 DOI: 10.1093/carcin/bgy091] [Citation(s) in RCA: 11] [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: 02/15/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
The leading cause of cancer-related mortality among children is brain tumour, and glioblastoma multiforme (GBM) has the worst prognosis. New treatments are urgently needed, but with few cases and clinical trials in children, pre-clinical models such as patient-derived tumour xenografts (PDTX) are important. To generate these, tumour tissue is transplanted into mice, but this yields highly variable results and requires serial passaging in mice, which is time-consuming and expensive. We therefore aimed to establish a cell line-based orthotopic mouse model representative of the patient tumour. Glioma stem cell (GSC) lines derived from paediatric GBM were orthotopically transplanted into immunodeficient mice. Overall survival data were collected and histological analysis of the resulting neoplasias was performed. Genome-wide DNA methylation arrays were used for methylation and copy-number alterations (CNA) profiling. All GSC lines initiated tumours on transplantation and the survival of the mice correlated well with the survival of the patients. Xenograft tumours presented histological hallmarks of GBM, and were also classified as GBM by methylation profiling. Each xenograft tumour clustered together with its respective injected GSC line and patient tumour based on the methylation data. We have established a robust and reproducible cell line-based xenograft paediatric GBM model. The xenograft tumours accurately reflected the patient tumours and mirrored the clinical course of the patient. This model can therefore be used to assess patient response in pre-clinical studies.
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Affiliation(s)
- Susanna Larsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Sándor Dósa
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg.,The Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg
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15
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Abstract
This chapter discusses analysis and interpretation of large-scale Illumina DNA methylation microarray data, used in the context of cancer studies. We outline commonly used normalization procedures and list issues to consider regarding data preprocessing. Focusing on software packages for R, we describe methods for finding features in the methylation data that are of importance for generating and testing hypotheses in cancer research, like differentially methylated positions or regions and global methylation trends.
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Affiliation(s)
- Teresia Kling
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Department of Pathology and Genetics, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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16
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Wenger A, Ferreyra Vega S, Kling T, Olsson Bontell T, Jakola AS, Carén H. OS3.4 Intra-tumour DNA methylation heterogeneity in glioblastoma. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.023] [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: 11/14/2022] Open
Affiliation(s)
- A Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - T Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - T Olsson Bontell
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - A S Jakola
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - H Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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17
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Wenger A, Larsson S, Dósa S, Sabel M, Kling T, Carén H. PCLN-03. ORTHOTOPIC TRANSPLANTATION OF PAEDIATRIC GLIOMA STEM CELLS IN MICE MIRRORS THE CLINICAL COURSE OF THE PATIENT. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.572] [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: 11/14/2022] Open
Affiliation(s)
- Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susanna Larsson
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sándor Dósa
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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18
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Heiland DH, Ferrarese R, Claus R, Dai F, Masilamani AP, Kling E, Weyerbrock A, Kling T, Nelander S, Carro MS. c-Jun-N-terminal phosphorylation regulates DNMT1 expression and genome wide methylation in gliomas. Oncotarget 2018; 8:6940-6954. [PMID: 28036297 PMCID: PMC5351681 DOI: 10.18632/oncotarget.14330] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 06/11/2016] [Accepted: 12/15/2016] [Indexed: 12/19/2022] Open
Abstract
High-grade gliomas (HGG) are the most common brain tumors, with an average survival time of 14 months. A glioma-CpG island methylator phenotype (G-CIMP), associated with better clinical outcome, has been described in low and high-grade gliomas. Mutation of IDH1 is known to drive the G-CIMP status. In some cases, however, the hypermethylation phenotype is independent of IDH1 mutation, suggesting the involvement of other mechanisms. Here, we demonstrate that DNMT1 expression is higher in low-grade gliomas compared to glioblastomas and correlates with phosphorylated c-Jun. We show that phospho-c-Jun binds to the DNMT1 promoter and causes DNA hypermethylation. Phospho-c-Jun activation by Anisomycin treatment in primary glioblastoma-derived cells attenuates the aggressive features of mesenchymal glioblastomas and leads to promoter methylation and downregulation of key mesenchymal genes (CD44, MMP9 and CHI3L1). Our findings suggest that phospho-c-Jun activates an important regulatory mechanism to control DNMT1 expression and regulate global DNA methylation in Glioblastoma.
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Affiliation(s)
- Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roberto Ferrarese
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rainer Claus
- Department of Hematology, Oncology, and Stem Cell Transplantation, University of Freiburg Medical Center, Freiburg, Germany
| | - Fangping Dai
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anie P Masilamani
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva Kling
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Teresia Kling
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology and Science for Life Laboratories, University of Uppsala, Uppsala, Sweden
| | - Maria S Carro
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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19
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Tűzesi Á, Kling T, Wenger A, Lunavat TR, Jang SC, Rydenhag B, Lötvall J, Pollard SM, Danielsson A, Carén H. Pediatric brain tumor cells release exosomes with a miRNA repertoire that differs from exosomes secreted by normal cells. Oncotarget 2017; 8:90164-90175. [PMID: 29163818 PMCID: PMC5685739 DOI: 10.18632/oncotarget.21621] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 07/28/2016] [Accepted: 08/19/2017] [Indexed: 12/13/2022] Open
Abstract
High-grade gliomas (HGGs) are very aggressive brain tumors with a cancer stem cell component. Cells, including cancer stem cells, release vesicles called exosomes which contain small non-coding RNAs such as microRNAs (miRNAs). These are thought to play an important role in cell-cell communication. However, we have limited knowledge of the types of exosomal miRNAs released by pediatric HGG stem cells; a prerequisite for exploring their potential roles in HGG biology. Here we isolated exosomes released by pediatric glioma stem cells (GSCs) and compared their repertoire of miRNAs to genetically normal neural stem cells (NSCs) exosomes, as well as their respective cellular miRNA content. Whereas cellular miRNAs are similar, we find that the exosomal miRNA profiles differ between normal and tumor cells, and identify several differentially expressed miRNAs. Of particular interest is miR-1290 and miR-1246, which have previously been linked to 'stemness' and invasion in other cancers. We demonstrate that GSC-secreted exosomes influence the gene expression of receiving NSCs, particularly targeting genes with a role in cell fate and tumorigenesis. Thus, our study shows that GSCs and NSCs have similar cellular miRNA profiles, yet differ significantly in the repertoire of exosomal miRNAs and these could influence malignant features of HGG.
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Affiliation(s)
- Ágota Tűzesi
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Taral R. Lunavat
- Krefting Research Center, Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - Su Chul Jang
- Krefting Research Center, Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - Bertil Rydenhag
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lötvall
- Krefting Research Center, Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | - Steven M. Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, UK
| | - Anna Danielsson
- Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Kling T, Wenger A, Beck S, Carén H. Validation of the MethylationEPIC BeadChip for fresh-frozen and formalin-fixed paraffin-embedded tumours. Clin Epigenetics 2017; 9:33. [PMID: 28392843 PMCID: PMC5379646 DOI: 10.1186/s13148-017-0333-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [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: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 02/01/2023] Open
Abstract
DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression, and its involvement in the pathogenesis of cancer and several diseases upon aberrations in methylation. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumours. We also performed analysis on the EPIC array with paired FF and FFPE samples to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array. The Pearson correlation of β values for common probes on the 450K and EPIC array was high for both FF (mean: 0.992) and FFPE (mean: 0.984) samples. The β values generated from the EPIC array for FFPE samples correlated well with the paired FF tumours, but varied between 0.901 and 0.987. We did note that sample pairs with lower correlation had less bimodal density distributions of β values and displayed higher noise in the copy number alteration plots (generated from the methylation array data) in the FFPE sample. Both REPLI-g and the Infinium restoration for FFPE samples performed well on the EPIC array and generated equivalent correlation scores to the paired FF sample.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 405 30, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 405 30, Gothenburg, Sweden
| | - Stephan Beck
- Department of Cancer Biology, UCL Cancer Institute, University College London, London, UK
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 425, 405 30, Gothenburg, Sweden
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Kling T, Ferrarese R, Ó hAilín D, Johansson P, Heiland DH, Dai F, Vasilikos I, Weyerbrock A, Jörnsten R, Carro MS, Nelander S. Integrative Modeling Reveals Annexin A2-mediated Epigenetic Control of Mesenchymal Glioblastoma. EBioMedicine 2016; 12:72-85. [PMID: 27667176 PMCID: PMC5078587 DOI: 10.1016/j.ebiom.2016.08.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 12/02/2022] Open
Abstract
Glioblastomas are characterized by transcriptionally distinct subtypes, but despite possible clinical relevance, their regulation remains poorly understood. The commonly used molecular classification systems for GBM all identify a subtype with high expression of mesenchymal marker transcripts, strongly associated with invasive growth. We used a comprehensive data-driven network modeling technique (augmented sparse inverse covariance selection, aSICS) to define separate genomic, epigenetic, and transcriptional regulators of glioblastoma subtypes. Our model identified Annexin A2 (ANXA2) as a novel methylation-controlled positive regulator of the mesenchymal subtype. Subsequent evaluation in two independent cohorts established ANXA2 expression as a prognostic factor that is dependent on ANXA2 promoter methylation. ANXA2 knockdown in primary glioblastoma stem cell-like cultures suppressed known mesenchymal master regulators, and abrogated cell proliferation and invasion. Our results place ANXA2 at the apex of a regulatory cascade that determines glioblastoma mesenchymal transformation and validate aSICS as a general methodology to uncover regulators of cancer subtypes. Glioblastoma, a form of brain cancer, is characterised by distinct molecular subtypes: proneural, classical and mesenchymal. We used a comprehensive data-driven strategy, aSICS, to elucidate the cellular mechanisms behind the subtypes. Epigenetic control of Annexin A2 (ANXA2) was predicted and confirmed to determine the invasive mesenchymal subtype.
Most cancers have distinct and clinically relevant transcriptional subtypes, but the underlying cellular mechanism behind such subtypes is often hard to resolve. We show that joint analysis across several layers of genomics data can uncover subtype regulators with good accuracy. Our method is applied to the brain cancer glioblastoma multiforme (GBM), revealing that the invasive mesenchymal subtype is driven by epigenetic modulation of the expression of Annexin A2 (ANXA2). Our analysis adds significantly to our understanding of brain cancer subtypes and open for new potential treatment options. The proposed computational technique can be applied to other cancers as well.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Roberto Ferrarese
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Darren Ó hAilín
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, Schnzlestrasse 1, University of Freiburg, D-79104 Freiburg, Germany
| | - Patrik Johansson
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Fangping Dai
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Ioannis Vasilikos
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Astrid Weyerbrock
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Rebecka Jörnsten
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Maria Stella Carro
- Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Sven Nelander
- Dept of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden.
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Kling T, Johansson P, Sanchez J, Marinescu VD, Jornsten R, Nelander S. Abstract B2-35: Efficient exploration of multi-cancer networks by generalized covariance selection and interactive web content. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-35] [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
Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools for network construction and interpretation are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as the Cancer Genome Atlas (TCGA). Here, we describe a novel strategy to construct and analyze integrative network models heterogeneous data from multiple cancers. First, we introduce a generalization of sparse inverse covariance selection (SICS) designed to integrate genetic, epigenetic and transcriptional data from multiple cancers into a comparative network. The algorithm is shown to be statistically robust, effective at detecting direct pathway links in data from The Cancer Genome Atlas (TCGA), and uses a new strategy involving non-informative priors to balance different cancers and data types. Second, we propose to rationalize the interpretation of the derived networks by a new and publicly accessible tool (cancerlandscapes.org), in which derived models are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model of genetic, epigenetic and transcriptional data for eight TCGA cancers, using data from 3900 patients. The derived model rediscovered known mechanisms and contained interesting predictions. Possible applications include the prediction of regulatory relationships between genes in particular cancers, comparison of network modules in across multiple forms of cancer, and identification of drug targets in relation to network structure.
Citation Format: Teresia Kling, Patrik Johansson, Jose Sanchez, Voichita D. Marinescu, Rebecka Jornsten, Sven Nelander. Efficient exploration of multi-cancer networks by generalized covariance selection and interactive web content. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-35.
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Affiliation(s)
| | | | - Jose Sanchez
- 2Chalmers University of Technology, Gothenburg, Sweden
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Kling T, Johansson P, Sanchez J, Marinescu VD, Jörnsten R, Nelander S. Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. Nucleic Acids Res 2015; 43:e98. [PMID: 25953855 PMCID: PMC4551906 DOI: 10.1093/nar/gkv413] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 11/17/2014] [Accepted: 04/17/2015] [Indexed: 12/25/2022] Open
Abstract
Statistical network modeling techniques are increasingly important tools to analyze cancer genomics data. However, current tools and resources are not designed to work across multiple diagnoses and technical platforms, thus limiting their applicability to comprehensive pan-cancer datasets such as The Cancer Genome Atlas (TCGA). To address this, we describe a new data driven modeling method, based on generalized Sparse Inverse Covariance Selection (SICS). The method integrates genetic, epigenetic and transcriptional data from multiple cancers, to define links that are present in multiple cancers, a subset of cancers, or a single cancer. It is shown to be statistically robust and effective at detecting direct pathway links in data from TCGA. To facilitate interpretation of the results, we introduce a publicly accessible tool (cancerlandscapes.org), in which the derived networks are explored as interactive web content, linked to several pathway and pharmacological databases. To evaluate the performance of the method, we constructed a model for eight TCGA cancers, using data from 3900 patients. The model rediscovered known mechanisms and contained interesting predictions. Possible applications include prediction of regulatory relationships, comparison of network modules across multiple forms of cancer and identification of drug targets.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Cancer Center and Dept of Molecular and Clinical Medicine, University of Gothenburg, Box 425, SE-405 30 Gothenburg, Sweden
| | - Patrik Johansson
- Department of Immunology, Genetics and Pathology (IGP) and Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden
| | - José Sanchez
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Voichita D Marinescu
- Department of Immunology, Genetics and Pathology (IGP) and Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology (IGP) and Science for Life Laboratory, Uppsala University, Rudbecklaboratoriet, SE-751 85 Uppsala, Sweden
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Geller T, Prakash V, Batanian J, Guzman M, Duncavage E, Gershon T, Crowther A, Wu J, Liu H, Fang F, Davis I, Tripolitsioti D, Ma M, Kumar K, Grahlert J, Egli K, Fiaschetti G, Shalaby T, Grotzer M, Baumgartner M, Braoudaki M, Lambrou GI, Giannikou K, Millionis V, Papadodima SA, Settas N, Sfakianos G, Stefanaki K, Kattamis A, Spiliopoulou CA, Tzortzatou-Stathopoulou F, Kanavakis E, Gholamin S, Mitra S, Feroze A, Zhang M, Esparza R, Kahn S, Richard C, Achrol A, Volkmer A, Liu J, Volkmer J, Majeti R, Weissman I, Cheshier S, Bhatia K, Brown N, Teague J, Lo P, Challis J, Beshay V, Sullivan M, Mechinaud F, Hansford J, Arifin MZ, Dahlan RH, Sobana M, Saputra P, Tisell MT, Danielsson A, Caren H, Bhardwaj R, Chakravadhanula M, Hampton C, Ozals V, Georges J, Decker W, Kodibagkar V, Nguyen A, Legrain M, Gaub MP, Pencreach E, Chenard MP, Guenot D, Entz-Werle N, Kanemura Y, Ichimura K, Shofuda T, Nishikawa R, Yamasaki M, Shibui S, Arai H, Xia J, Brian A, Prins R, Pennell C, Moertel C, Olin M, Bie L, Zhang X, Liu H, Olsson M, Kling T, Nelander S, Biassoni V, Bongarzone I, Verderio P, Massimino M, Magni R, Pizzamiglio S, Ciniselli C, Taverna E, De Bortoli M, Luchini A, Liotta L, Barzano E, Spreafico F, Visse E, Sanden E, Darabi A, Siesjo P, Jackson S, Cohen K, Lin D, Burger P, Rodriguez F, Yao X, Liucheng R, Qin L, Na T, Meilin W, Zhengdong Z, Yongjun F, Pfeifer S, Nister M, de Stahl TD, Basmaci E, Orphanidou-Vlachou E, Brundler MA, Sun Y, Davies N, Wilson M, Pan X, Arvanitis T, Grundy R, Peet A, Eden C, Ju B, Phoenix T, Nimmervoll B, Tong Y, Ellison D, Lessman C, Taylor M, Gilbertson R, Folgiero V, del Bufalo F, Carai A, Cefalo MG, Citti A, Rutella S, Locatelli F, Mastronuzzi A, Maher O, Khatua S, Zaky W, Lourdusamy A, Meijer L, Layfield R, Grundy R, Jones DTW, Capper D, Sill M, Hovestadt V, Schweizer L, Lichter P, Zagzag D, Karajannis MA, Aldape KD, Korshunov A, von Deimling A, Pfister S, Chakrabarty A, Feltbower R, Sheridon E, Hassan H, Shires M, Picton S, Hatziagapiou K, Braoudaki M, Lambrou GI, Tsorteki F, Tzortzatou-Stathopoulou F, Bethanis K, Gemou-Engesaeth V, Chi SN, Bandopadhayay P, Janeway K, Pinches N, Malkin H, Kieran MW, Manley PE, Green A, Goumnerova L, Ramkissoon S, Harris MH, Ligon KL, Kahlert U, Suarez M, Maciaczyk J, Bar E, Eberhart C, Kenchappa R, Krishnan N, Forsyth P, McKenzie B, Pisklakova A, McFadden G, Kenchappa R, Forsyth P, Pan W, Rodriguez L, Glod J, Levy JM, Thompson J, Griesinger A, Amani V, Donson A, Birks D, Morgan M, Handler M, Foreman N, Thorburn A, Lulla RR, Laskowski J, Fangusaro J, DiPatri AJ, Alden T, Tomita T, Vanin EF, Goldman S, Soares MB, Remke M, Ramaswamy V, Wang X, Jorgensen F, Morrissy AS, Marra M, Packer R, Bouffet E, Pfister S, Jabado N, Taylor M, Cole B, Rudzinski E, Anderson M, Bloom K, Lee A, Leary S, Leprivier G, Remke M, Rotblat B, Agnihotri S, Kool M, Derry B, Pfister S, Taylor MD, Sorensen PH, Dobson T, Busschers E, Taylor H, Hatcher R, Fangusaro J, Lulla R, Goldman S, Rajaram V, Das C, Gopalakrishnan V. TUMOUR BIOLOGY. Neuro Oncol 2014; 16:i137-i145. [PMCID: PMC4046298 DOI: 10.1093/neuonc/nou082] [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: 07/22/2023] Open
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Schmidt L, Kling T, Monsefi N, Olsson M, Hansson C, Baskaran S, Lundgren B, Martens U, Häggblad M, Westermark B, Forsberg Nilsson K, Uhrbom L, Karlsson-Lindahl L, Gerlee P, Nelander S. Comparative drug pair screening across multiple glioblastoma cell lines reveals novel drug-drug interactions. Neuro Oncol 2013; 15:1469-78. [PMID: 24101737 DOI: 10.1093/neuonc/not111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most aggressive brain tumor in adults, and despite state-of-the-art treatment, survival remains poor and novel therapeutics are sorely needed. The aim of the present study was to identify new synergistic drug pairs for GBM. In addition, we aimed to explore differences in drug-drug interactions across multiple GBM-derived cell cultures and predict such differences by use of transcriptional biomarkers. METHODS We performed a screen in which we quantified drug-drug interactions for 465 drug pairs in each of the 5 GBM cell lines U87MG, U343MG, U373MG, A172, and T98G. Selected interactions were further tested using isobole-based analysis and validated in 5 glioma-initiating cell cultures. Furthermore, drug interactions were predicted using microarray-based transcriptional profiling in combination with statistical modeling. RESULTS Of the 5 × 465 drug pairs, we could define a subset of drug pairs with strong interaction in both standard cell lines and glioma-initiating cell cultures. In particular, a subset of pairs involving the pharmaceutical compounds rimcazole, sertraline, pterostilbene, and gefitinib showed a strong interaction in a majority of the cell cultures tested. Statistical modeling of microarray and interaction data using sparse canonical correlation analysis revealed several predictive biomarkers, which we propose could be of importance in regulating drug pair responses. CONCLUSION We identify novel candidate drug pairs for GBM and suggest possibilities to prospectively use transcriptional biomarkers to predict drug interactions in individual cases.
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Affiliation(s)
- Linnéa Schmidt
- Corresponding Author: Sven Nelander, PhD, Immunology, Genetics and Pathology (IGP), Uppsala University; and Science for Life Laboratory, SE-751 85 Uppsala, Sweden..
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Gerlee P, Schmidt L, Monsefi N, Kling T, Jörnsten R, Nelander S. Searching for synergies: matrix algebraic approaches for efficient pair screening. PLoS One 2013; 8:e68598. [PMID: 23935877 PMCID: PMC3723843 DOI: 10.1371/journal.pone.0068598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 12/15/2012] [Accepted: 05/31/2013] [Indexed: 11/21/2022] Open
Abstract
Functionally interacting perturbations, such as synergistic drugs pairs or synthetic lethal gene pairs, are of key interest in both pharmacology and functional genomics. However, to find such pairs by traditional screening methods is both time consuming and costly. We present a novel computational-experimental framework for efficient identification of synergistic target pairs, applicable for screening of systems with sizes on the order of current drug, small RNA or SGA (Synthetic Genetic Array) libraries (>1000 targets). This framework exploits the fact that the response of a drug pair in a given system, or a pair of genes' propensity to interact functionally, can be partly predicted by computational means from (i) a small set of experimentally determined target pairs, and (ii) pre-existing data (e.g. gene ontology, PPI) on the similarities between targets. Predictions are obtained by a novel matrix algebraic technique, based on cyclical projections onto convex sets. We demonstrate the efficiency of the proposed method using drug-drug interaction data from seven cancer cell lines and gene-gene interaction data from yeast SGA screens. Our protocol increases the rate of synergism discovery significantly over traditional screening, by up to 7-fold. Our method is easy to implement and could be applied to accelerate pair screening for both animal and microbial systems.
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Affiliation(s)
- Philip Gerlee
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
| | - Linnéa Schmidt
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Naser Monsefi
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
| | - Sven Nelander
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Persson M, Andrén Y, Moskaluk CA, Frierson HF, Cooke SL, Futreal PA, Kling T, Nelander S, Nordkvist A, Persson F, Stenman G. Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in head and neck adenoid cystic carcinoma. Genes Chromosomes Cancer 2012; 51:805-17. [PMID: 22505352 DOI: 10.1002/gcc.21965] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 03/29/2012] [Indexed: 12/17/2022] Open
Abstract
Adenoid cystic carcinoma (ACC) of the head and neck is a malignant tumor with poor long-term prognosis. Besides the recently identified MYB-NFIB fusion oncogene generated by a t(6;9) translocation, little is known about other genetic alterations in ACC. Using high-resolution, array-based comparative genomic hybridization, and massively paired-end sequencing, we explored genomic alterations in 40 frozen ACCs. Eighty-six percent of the tumors expressed MYB-NFIB fusion transcripts and 97% overexpressed MYB mRNA, indicating that MYB activation is a hallmark of ACC. Thirty-five recurrent copy number alterations (CNAs) were detected, including losses involving 12q, 6q, 9p, 11q, 14q, 1p, and 5q and gains involving 1q, 9p, and 22q. Grade III tumors had on average a significantly higher number of CNAs/tumor compared to Grade I and II tumors (P = 0.007). Losses of 1p, 6q, and 15q were associated with high-grade tumors, whereas losses of 14q were exclusively seen in Grade I tumors. The t(6;9) rearrangements were associated with a complex pattern of breakpoints, deletions, insertions, inversions, and for 9p also gains. Analyses of fusion-negative ACCs using high-resolution arrays and massively paired-end sequencing revealed that MYB may also be deregulated by other mechanisms in addition to gene fusion. Our studies also identified several down-regulated candidate tumor suppressor genes (CTNNBIP1, CASP9, PRDM2, and SFN) in 1p36.33-p35.3 that may be of clinical significance in high-grade tumors. Further, studies of these and other potential target genes may lead to the identification of novel driver genes in ACC.
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Affiliation(s)
- Marta Persson
- Sahlgrenska Cancer Center, Department of Pathology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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Jörnsten R, Abenius T, Kling T, Schmidt L, Johansson E, Nordling TEM, Nordlander B, Sander C, Gennemark P, Funa K, Nilsson B, Lindahl L, Nelander S. Network modeling of the transcriptional effects of copy number aberrations in glioblastoma. Mol Syst Biol 2011; 7:486. [PMID: 21525872 PMCID: PMC3101951 DOI: 10.1038/msb.2011.17] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [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: 11/30/2010] [Accepted: 03/21/2011] [Indexed: 12/25/2022] Open
Abstract
DNA copy number aberrations (CNAs) are a hallmark of cancer genomes. However, little is known about how such changes affect global gene expression. We develop a modeling framework, EPoC (Endogenous Perturbation analysis of Cancer), to (1) detect disease-driving CNAs and their effect on target mRNA expression, and to (2) stratify cancer patients into long- and short-term survivors. Our method constructs causal network models of gene expression by combining genome-wide DNA- and RNA-level data. Prognostic scores are obtained from a singular value decomposition of the networks. By applying EPoC to glioblastoma data from The Cancer Genome Atlas consortium, we demonstrate that the resulting network models contain known disease-relevant hub genes, reveal interesting candidate hubs, and uncover predictors of patient survival. Targeted validations in four glioblastoma cell lines support selected predictions, and implicate the p53-interacting protein Necdin in suppressing glioblastoma cell growth. We conclude that large-scale network modeling of the effects of CNAs on gene expression may provide insights into the biology of human cancer. Free software in MATLAB and R is provided.
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Affiliation(s)
- Rebecka Jörnsten
- Mathematical Sciences, University of Gothenburg and Chalmers University of Technology, Gothenburg, Sweden
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Tjassing H, Kling T, Janssens P, van Gorp J, Bramall J, Bowman A. Home care business opportunities in Europe. Caring 1998; 17:50-1, 53-5, 57. [PMID: 10185401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The demand for home care services will continue to grow exponentially around the world. This demand is being driven by demographics, technology, and personal choice. Providers of home care have a great deal to teach and learn from each other. The opportunities for collaboration and joint ventures are great now and will continue to increase with the passing of time. This article has been extracted from a 1996 panel discussion at the International Home Care Forum held in Nashville, Tennessee.
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Kling T, Shung KK, Thieme GA. Reverberation reduction in ultrasonic B-mode images via dual frequency image subtraction. IEEE Trans Med Imaging 1993; 12:792-802. [PMID: 18218475 DOI: 10.1109/42.251131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The authors demonstrate the feasibility of an approach, dual-frequency subtraction imaging, for suppressing artifacts produced by reverberation of strong echoes among specular reflectors. This method is based upon the principle that specularly reflected echoes from flat boundaries are frequency-independent whereas the diffusely scattered echoes from small scatterers are frequency-dependent. The approach was assessed on phantoms including one consisting of two parallel plastic plates between layers of foam sponges using a prototype experimental system. Preliminary results show that this method is superior to simple thresholding techniques or signal compression and holds great promise for suppressing reverberation artifacts in ultrasonic images.
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Affiliation(s)
- T Kling
- Pennsylvania State Univ., University Park, PA
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