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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Alexiev BA, Vormittag-Nocito ER, Peabody TD, Samet J, Laskin WB. Clear cell chondrosarcoma: a review of clinicopathologic characteristics, differential diagnoses, and patient management. Hum Pathol 2023; 139:126-134. [PMID: 37805864 DOI: 10.1016/j.humpath.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/31/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
Clear cell chondrosarcoma (CCC), an extremely rare primary bone tumor, is currently classified by the World Health Organization as a low-grade malignant cartilaginous neoplasm. Clinically, CCC occurs primarily in males with a peak incidence in the third to fifth decades of life, and occasionally, it presents in skeletally immature patients. Unlike conventional chondrosarcoma, CCC has a predilection for the epiphysis of long bones and often displays radiologic features reminiscent of chondroblastoma. The recommended treatment is wide operative resection. CCC has a local recurrence rate of approximately 30%, and nearly 20% cases metastasize mainly to bone and lung often a decade after surgical intervention. Incomplete excision or curettage is associated with a high rate of recurrence. Histologically, the process is characterized by infiltrative lobules and sheets of round to oval cells with abundant cleared cytoplasm and well-defined cell borders associated with trabecula of osteoid and woven bone, scattered osteoclasts, and foci of conventional low-grade chondrosarcoma in about one-half of cases. Correlation with clinical and radiologic characteristics, such as epiphyseal location and young patient age, assists in establishing a correct diagnosis. Pathologic diagnosis of CCC is complicated by the low diagnostic accuracy of core needle biopsy, overlapping histologic features with other matrix-rich primary bone tumors, and a lack of a specific immunohistochemical and molecular profile. DNA methylation-based profiling classifier (sarcoma classifier) is one recent technologic advancement that may help to confirm the histopathological diagnosis of CCC or indicate the need for thorough reassessment in cases where results contradict previous conventional findings.
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Affiliation(s)
- Borislav A Alexiev
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, IL 60611, USA.
| | - Erica R Vormittag-Nocito
- Department of Pathology, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Chicago, IL 60611, USA
| | - Terrance D Peabody
- Department of Orthopedic Surgery, Northwestern University Feinberg School of Medicine, Northwestern Memorial Hospital, Lavin Family Pavilion, Chicago, IL 60611, USA
| | - Jonathan Samet
- Department of Medical Imaging, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - William B Laskin
- Department of Pathology, Yale-New Haven Hospital, New Haven, CT 06510, USA
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Moss RM, Sorajja N, Mills LJ, Moertel CL, Hoang TT, Spector LG, Largaespada DA, Williams LA. Sex differences in methylation profiles are apparent in medulloblastoma, particularly among SHH tumors. Front Oncol 2023; 13:1113121. [PMID: 37035203 PMCID: PMC10080161 DOI: 10.3389/fonc.2023.1113121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023] Open
Abstract
Background Medulloblastoma, the most common malignant pediatric brain tumor, displays marked sex differences in prevalence of the four main molecular subgroups: SHH, WNT, Group 3 and Group 4. Males are more frequently diagnosed with SHH, Group 3 and 4 tumors, which have worse prognoses than WNT tumors. Little is known about sex differences in methylation profiles within subgroups. Methods Using publicly available methylation data (Illumina HumanMethylation450K array), we compared beta values for males versus females. Differentially methylated positions (DMP) by sex within medulloblastoma subgroups were identified on the autosomes. DMPs were mapped to genes and Reactome pathway analysis was run by subgroup. Kaplan-Meier survival curves (Log-Rank p-values) were assessed for each sex within subgroup. MethylCIBERSORT was used to investigate the tumor microenvironment using deconvolution to estimate the abundances of immune cell types using DNA methylation data. Results There were statistically significant differences in sex by medulloblastoma subgroups (chi-squared p-value=0.00004): Group 3 (n=144; 65% male), Group 4 (n=326; 67% male), SHH (n=223; 57% male) and WNT (n=70; 41% male). Females had worse survival than males for SHH (p-value=0.02). DMPs by sex were identified within subgroups: SHH (n=131), Group 4 (n=29), Group 3 (n=19), and WNT (n=16) and validated in an independent dataset. Unsupervised hierarchical clustering showed that sex-DMPs in SHH did not correlate with other tumor attributes. Ten genes with sex DMPs (RFTN1, C1orf103, FKBP1B, COL25A1, NPDC1, B3GNT1, FOXN3, RNASEH2C, TLE1, and PHF17) were shared across subgroups. Significant pathways (p<0.05) associated with DMPs were identified for SHH (n=22) and Group 4 (n=4) and included signaling pathways for RET proto-oncogene, advanced glycosylation end product receptor, regulation of KIT, neurotrophic receptors, NOTCH, and TGF-β. In SHH, we identified DMPs in four genes (CDK6, COL25A1, MMP16, PRIM2) that encode proteins which are the target of therapies in clinical trials for other cancers. There were few sex differences in immune cell composition within tumor subgroups. Conclusion There are sexually dimorphic methylation profiles for SHH medulloblastoma where survival differences were observed. Sex-specific therapies in medulloblastoma may impact outcomes.
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Affiliation(s)
- Rachel M. Moss
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States
| | - Natali Sorajja
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Macalester College, St. Paul, MN, United States
| | - Lauren J. Mills
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Christopher L. Moertel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Brain Tumor Program, University of Minnesota, Minneapolis, MN, United States
| | - Thanh T. Hoang
- Department of Pediatrics, Division of Hematology-Oncology, Baylor College of Medicine, Houston, TX, United States
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
- Cancer and Hematology Center, Texas Children’s Hospital, Houston, TX, United States
| | - Logan G. Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - David A. Largaespada
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Brain Tumor Program, University of Minnesota, Minneapolis, MN, United States
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Department of Genetics, Cell Biology and Development, University of Minnesota School of Medicine, Minneapolis, MN, United States
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Lindsay A. Williams
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Brain Tumor Program, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Lindsay A. Williams,
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Wenger A, Carén H. Methylation Profiling in Diffuse Gliomas: Diagnostic Value and Considerations. Cancers (Basel) 2022; 14:cancers14225679. [PMID: 36428772 PMCID: PMC9688075 DOI: 10.3390/cancers14225679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Diffuse gliomas cause significant morbidity across all age groups, despite decades of intensive research efforts. Here, we review the differences in diffuse gliomas in adults and children, as well as the World Health Organisation (WHO) 2021 classification of these tumours. We explain how DNA methylation-based classification works and list the methylation-based tumour types and subclasses for adult and paediatric diffuse gliomas. The benefits and utility of methylation-based classification in diffuse gliomas demonstrated to date are described. This entails the identification of novel tumour types/subclasses, patient stratification and targeted treatment/clinical management, and alterations in the clinical diagnosis in favour of the methylation-based over the histopathological diagnosis. Finally, we address several considerations regarding the use of DNA methylation profiling as a diagnostic tool, e.g., the threshold of the classifier, the calibrated score, tumour cell content and intratumour heterogeneity.
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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, 413 90 Gothenburg, Sweden
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90 Gothenburg, Sweden
- Correspondence:
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Machine Learning in the Classification of Pediatric Posterior Fossa Tumors: A Systematic Review. Cancers (Basel) 2022; 14:cancers14225608. [PMID: 36428701 PMCID: PMC9688156 DOI: 10.3390/cancers14225608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/02/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Posterior fossa tumors (PFTs) are a morbid group of central nervous system tumors that most often present in childhood. While early diagnosis is critical to drive appropriate treatment, definitive diagnosis is currently only achievable through invasive tissue collection and histopathological analyses. Machine learning has been investigated as an alternative means of diagnosis. In this systematic review and meta-analysis, we evaluated the primary literature to identify all machine learning algorithms developed to classify and diagnose pediatric PFTs using imaging or molecular data. Methods: Of the 433 primary papers identified in PubMed, EMBASE, and Web of Science, 25 ultimately met the inclusion criteria. The included papers were extracted for algorithm architecture, study parameters, performance, strengths, and limitations. Results: The algorithms exhibited variable performance based on sample size, classifier(s) used, and individual tumor types being investigated. Ependymoma, medulloblastoma, and pilocytic astrocytoma were the most studied tumors with algorithm accuracies ranging from 37.5% to 94.5%. A minority of studies compared the developed algorithm to a trained neuroradiologist, with three imaging-based algorithms yielding superior performance. Common algorithm and study limitations included small sample sizes, uneven representation of individual tumor types, inconsistent performance reporting, and a lack of application in the clinical environment. Conclusions: Artificial intelligence has the potential to improve the speed and accuracy of diagnosis in this field if the right algorithm is applied to the right scenario. Work is needed to standardize outcome reporting and facilitate additional trials to allow for clinical uptake.
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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] [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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McEachron TA, Helman LJ. Recent Advances in Pediatric Cancer Research. Cancer Res 2021; 81:5783-5799. [PMID: 34561271 DOI: 10.1158/0008-5472.can-21-1191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Over the past few years, the field of pediatric cancer has experienced a shift in momentum, and this has led to new and exciting findings that have relevance beyond pediatric malignancies. Here we present the current status of key aspects of pediatric cancer research. We have focused on genetic and epigenetic drivers of disease, cellular origins of different pediatric cancers, disease models, the tumor microenvironment, and cellular immunotherapies.
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Affiliation(s)
| | - Lee J Helman
- Osteosarcoma Institute, Dallas, Texas
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California
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8
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DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker. Clin Epigenetics 2021; 13:176. [PMID: 34538273 PMCID: PMC8451154 DOI: 10.1186/s13148-021-01156-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
Background Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system (CNS) tumors. 5hmC is abundant in the brain, and alterations to 5hmC in adult CNS tumors have been reported. However, traditional approaches to measure DNA methylation do not distinguish between 5-methylcytosine (5mC) and its oxidized counterpart 5hmC, including those used to build CNS tumor DNA methylation classification systems. We measured 5hmC and 5mC epigenome-wide at nucleotide resolution in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using tandem bisulfite and oxidative bisulfite treatments followed by hybridization to the Illumina Methylation EPIC Array that interrogates over 860,000 CpG loci.
Results Linear mixed effects models adjusted for age and sex tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Results from model-based clustering of tumors was used to test the relation of cluster membership with patient survival through multivariable Cox proportional hazards regression. We also assessed the robustness of multiple epigenetic CNS tumor classification methods to 5mC-specific data in both pediatric and adult CNS tumors. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome and tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1. Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence. Our results suggest 5mC-specific data from OxBS-treated samples impacts methylation-based tumor classification systems giving new opportunities for further refinement of classifiers for both pediatric and adult tumors. Conclusions We identified that 5hmC localizes to super-enhancers, and genes commonly implicated in pediatric CNS tumors were differentially hypohydroxymethylated. We demonstrated that distinguishing methylation and hydroxymethylation is critical in identifying tumor-related epigenetic changes. These results have implications for patient prognostication, considerations of epigenetic therapy in CNS tumors, and for emerging molecular neuropathology classification approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01156-9.
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Levy JJ, Chen Y, Azizgolshani N, Petersen CL, Titus AJ, Moen EL, Vaickus LJ, Salas LA, Christensen BC. MethylSPWNet and MethylCapsNet: Biologically Motivated Organization of DNAm Neural Networks, Inspired by Capsule Networks. NPJ Syst Biol Appl 2021; 7:33. [PMID: 34417465 PMCID: PMC8379254 DOI: 10.1038/s41540-021-00193-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) alterations have been heavily implicated in carcinogenesis and the pathophysiology of diseases through upstream regulation of gene expression. DNAm deep-learning approaches are able to capture features associated with aging, cell type, and disease progression, but lack incorporation of prior biological knowledge. Here, we present modular, user-friendly deep-learning methodology and software, MethylCapsNet and MethylSPWNet, that group CpGs into biologically relevant capsules-such as gene promoter context, CpG island relationship, or user-defined groupings-and relate them to diagnostic and prognostic outcomes. We demonstrate these models' utility on 3,897 individuals in the classification of central nervous system (CNS) tumors. MethylCapsNet and MethylSPWNet provide an opportunity to increase DNAm deep-learning analyses' interpretability by enabling a flexible organization of DNAm data into biologically relevant capsules.
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Affiliation(s)
- Joshua J Levy
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA.
| | - Youdinghuan Chen
- Program in Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Curtis L Petersen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
| | - Alexander J Titus
- Department of Life Sciences, University of New Hampshire, Manchester, NH, USA
| | - Erika L Moen
- The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Louis J Vaickus
- Emerging Diagnostic and Investigative Technologies, Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
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Ferreyra Vega S, Olsson Bontell T, Corell A, Smits A, Jakola AS, Carén H. DNA methylation profiling for molecular classification of adult diffuse lower-grade gliomas. Clin Epigenetics 2021; 13:102. [PMID: 33941250 PMCID: PMC8091784 DOI: 10.1186/s13148-021-01085-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation profiling to achieve molecular diagnosis in adult primary diffuse lower-grade glioma (dLGG) according to WHO 2016 classification system. We also evaluated whether methylation profiling could provide improved molecular characterization and identify prognostic differences beyond the classical histological WHO grade together with IDH mutation status and 1p/19q codeletion status. All patients diagnosed with dLGG in the period 2007-2016 from the Västra Götaland region in Sweden were assessed for inclusion in the study. RESULTS A total of 166 dLGG cases were subjected for genome-wide DNA methylation analysis. Of these, 126 (76%) were assigned a defined diagnostic methylation class with a class prediction score ≥ 0.84 and subclass score ≥ 0.50. The assigned methylation classes were highly associated with their IDH mutation status and 1p/19q codeletion status. IDH-wildtype gliomas were further divided into subgroups with distinct molecular features. CONCLUSION The stratification of the patients by methylation profiling was as effective as the integrated WHO 2016 molecular reclassification at predicting the clinical outcome of the patients. Our study shows that DNA methylation profiling is a reliable and robust approach for the classification of dLGG into molecular defined subgroups, providing accurate detection of molecular markers according to WHO 2016 classification.
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Affiliation(s)
- Sandra Ferreyra Vega
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, 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 and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alba Corell
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neurosurgery, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anja Smits
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Neuroscience, Neurology, Uppsala University, Uppsala, 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 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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Abedalthagafi M, Mobark N, Al-Rashed M, AlHarbi M. Epigenomics and immunotherapeutic advances in pediatric brain tumors. NPJ Precis Oncol 2021; 5:34. [PMID: 33931704 PMCID: PMC8087701 DOI: 10.1038/s41698-021-00173-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Brain tumors are the leading cause of childhood cancer-related deaths. Similar to adult brain tumors, pediatric brain tumors are classified based on histopathological evaluations. However, pediatric brain tumors are often histologically inconsistent with adult brain tumors. Recent research findings from molecular genetic analyses have revealed molecular and genetic changes in pediatric tumors that are necessary for appropriate classification to avoid misdiagnosis, the development of treatment modalities, and the clinical management of tumors. As many of the molecular-based therapies developed from clinical trials on adults are not always effective against pediatric brain tumors, recent advances have improved our understanding of the molecular profiles of pediatric brain tumors and have led to novel epigenetic and immunotherapeutic treatment approaches currently being evaluated in clinical trials. In this review, we focus on primary malignant brain tumors in children and genetic, epigenetic, and molecular characteristics that differentiate them from brain tumors in adults. The comparison of pediatric and adult brain tumors highlights the need for treatments designed specifically for pediatric brain tumors. We also discuss the advancements in novel molecularly targeted drugs and how they are being integrated with standard therapy to improve the classification and outcomes of pediatric brain tumors in the future.
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Affiliation(s)
- Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia.
| | - Nahla Mobark
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - May Al-Rashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Chair of Medical and Molecular Genetics Research, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Musa AlHarbi
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
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12
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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: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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13
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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] [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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14
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Weishaupt H, Johansson P, Sundström A, Lubovac-Pilav Z, Olsson B, Nelander S, Swartling FJ. Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes. Bioinformatics 2020; 35:3357-3364. [PMID: 30715209 PMCID: PMC6748729 DOI: 10.1093/bioinformatics/btz066] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 11/28/2018] [Accepted: 01/30/2019] [Indexed: 12/25/2022] Open
Abstract
Motivation Medulloblastoma (MB) is a brain cancer predominantly arising in children. Roughly 70% of patients are cured today, but survivors often suffer from severe sequelae. MB has been extensively studied by molecular profiling, but often in small and scattered cohorts. To improve cure rates and reduce treatment side effects, accurate integration of such data to increase analytical power will be important, if not essential. Results We have integrated 23 transcription datasets, spanning 1350 MB and 291 normal brain samples. To remove batch effects, we combined the Removal of Unwanted Variation (RUV) method with a novel pipeline for determining empirical negative control genes and a panel of metrics to evaluate normalization performance. The documented approach enabled the removal of a majority of batch effects, producing a large-scale, integrative dataset of MB and cerebellar expression data. The proposed strategy will be broadly applicable for accurate integration of data and incorporation of normal reference samples for studies of various diseases. We hope that the integrated dataset will improve current research in the field of MB by allowing more large-scale gene expression analyses. Availability and implementation The RUV-normalized expression data is available through the Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) and can be accessed via the GSE series number GSE124814. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Holger Weishaupt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Patrik Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anders Sundström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Zelmina Lubovac-Pilav
- Division for Biology and Bioinformatics, School of Bioscience, The Systems Biology Research Centre, University of Skövde, Skövde, Sweden
| | - Björn Olsson
- Division for Biology and Bioinformatics, School of Bioscience, The Systems Biology Research Centre, University of Skövde, Skövde, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik J Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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15
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Priesterbach-Ackley LP, Boldt HB, Petersen JK, Bervoets N, Scheie D, Ulhøi BP, Gardberg M, Brännström T, Torp SH, Aronica E, Küsters B, den Dunnen WFA, de Vos FYFL, Wesseling P, de Leng WWJ, Kristensen BW. Brain tumour diagnostics using a DNA methylation-based classifier as a diagnostic support tool. Neuropathol Appl Neurobiol 2020; 46:478-492. [PMID: 32072658 PMCID: PMC7496466 DOI: 10.1111/nan.12610] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 12/28/2022]
Abstract
AIMS Methylation profiling (MP) is increasingly incorporated in the diagnostic process of central nervous system (CNS) tumours at our centres in The Netherlands and Scandinavia. We aimed to identify the benefits and challenges of MP as a support tool for CNS tumour diagnostics. METHODS About 502 CNS tumour samples were analysed using (850 k) MP. Profiles were matched with the DKFZ/Heidelberg CNS Tumour Classifier. For each case, the final pathological diagnosis was compared to the diagnosis before MP. RESULTS In 54.4% (273/502) of all analysed cases, the suggested methylation class (calibrated score ≥0.9) corresponded with the initial pathological diagnosis. The diagnosis of 24.5% of these cases (67/273) was more refined after incorporation of the MP result. In 9.8% of cases (49/502), the MP result led to a new diagnosis, resulting in an altered WHO grade in 71.4% of these cases (35/49). In 1% of cases (5/502), the suggested class based on MP was initially disregarded/interpreted as misleading, but in retrospect, the MP result predicted the right diagnosis for three of these cases. In six cases, the suggested class was interpreted as 'discrepant but noncontributory'. The remaining 33.7% of cases (169/502) had a calibrated score <0.9, including 7.8% (39/502) for which no class indication was given at all (calibrated score <0.3). CONCLUSIONS MP is a powerful tool to confirm and fine-tune the pathological diagnosis of CNS tumours, and to avoid misdiagnoses. However, it is crucial to interpret the results in the context of clinical, radiological, histopathological and other molecular information.
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Affiliation(s)
- L P Priesterbach-Ackley
- Department of Pathology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - H B Boldt
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Research Unit of Pathology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - J K Petersen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Research Unit of Pathology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - N Bervoets
- Department of Pathology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - D Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - B P Ulhøi
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - M Gardberg
- Department of Pathology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
| | - T Brännström
- Department of Pathology, Norrlands University Hospital, Umeå, Sweden
| | - S H Torp
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - E Aronica
- Department of Neuropathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - B Küsters
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - W F A den Dunnen
- Department of Pathology, University Medical Centre Groningen, Groningen, The Netherlands
| | - F Y F L de Vos
- Department of Medical Oncology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - P Wesseling
- Princess Máxima Centre for Paediatric Oncology, Utrecht, The Netherlands.,Department of Pathology, Amsterdam University Medical Centres/VU Medical Centre, Amsterdam, The Netherlands
| | - W W J de Leng
- Department of Pathology, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - B W Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Research Unit of Pathology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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16
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Pickles JC, Stone TJ, Jacques TS. Methylation-based algorithms for diagnosis: experience from neuro-oncology. J Pathol 2020; 250:510-517. [PMID: 32057098 DOI: 10.1002/path.5397] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022]
Abstract
Brain tumours are the most common tumour-related cause of death in young people. Survivors are at risk of significant disability, at least in part related to the effects of treatment. Therefore, there is a need for a precise diagnosis that stratifies patients for the most suitable treatment, matched to the underlying biology of their tumour. Although traditional histopathology has been accurate in predicting treatment responses in many cases, molecular profiling has revealed a remarkable, previously unappreciated, level of biological complexity in the classification of these tumours. Among different molecular technologies, DNA methylation profiling has had the most pronounced impact on brain tumour classification. Furthermore, using machine learning-based algorithms, DNA methylation profiling is changing diagnostic practice. This can be regarded as an exemplar for how molecular pathology can influence diagnostic practice and illustrates some of the unanticipated benefits and risks. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jessica C Pickles
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas J Stone
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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17
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Perez E, Capper D. Invited Review: DNA methylation-based classification of paediatric brain tumours. Neuropathol Appl Neurobiol 2020; 46:28-47. [PMID: 31955441 DOI: 10.1111/nan.12598] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
DNA methylation-based machine learning algorithms represent powerful diagnostic tools that are currently emerging for several fields of tumour classification. For various reasons, paediatric brain tumours have been the main driving forces behind this rapid development and brain tumour classification tools are likely further advanced than in any other field of cancer diagnostics. In this review, we will discuss the main characteristics that were important for this rapid advance, namely the high clinical need for improvement of paediatric brain tumour diagnostics, the robustness of methylated DNA and the consequential possibility to generate high-quality molecular data from archival formalin-fixed paraffin-embedded pathology specimens, the implementation of a single array platform by most laboratories allowing data exchange and data pooling to an unprecedented extent, as well as the high suitability of the data format for machine learning. We will further discuss the four most central output qualities of DNA methylation profiling in a diagnostic setting (tumour classification, tumour sub-classification, copy number analysis and guidance for additional molecular testing) individually for the most frequent types of paediatric brain tumours. Lastly, we will discuss DNA methylation profiling as a tool for the detection of new paediatric brain tumour classes and will give an overview of the rapidly growing family of new tumours identified with the aid of this technique.
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Affiliation(s)
- E Perez
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - D Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
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18
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Xiao GQ, Sherrod AE, Hurth KM. ZBTB16: A new biomarker for primitive neuroectodermal tumor element / Ewing sarcoma. Pathol Res Pract 2019; 215:152536. [PMID: 31326195 DOI: 10.1016/j.prp.2019.152536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/19/2019] [Accepted: 07/12/2019] [Indexed: 10/26/2022]
Abstract
Primitive neuroectodermal tumor (PNET) traditionally encompasses two different classes of tumors with similar morphology - PNET of the peripheral nervous system (pPNET) and PNET of the central nervous system (cPNET). The latter also includes germ cell tumor-derived PNET (gPNET). There are currently no specific markers for gPNET. This study seeks to investigate the expression of ZBTB16 in PNET and other small round blue cell tumors as well as its potential diagnostic utility. Immunohistochemical expression of the ZBTB16 was studied in a total of 27 PNETs (12 pPNETs, 8 cPNETs, 3 primary testicular gPNETs, and 4 metastatic gPNETs) and 38 small round blue cell tumors. Positive expression for ZBTB16 was seen diffusely in 9/12 (75%), moderately in 2/12 (17%) and focally in 1/12 (8%) of pPNETs, diffusely in 3/7 (43%) and moderately in 4/7 (57%) of gPNETs, and diffusely in 2/8 (25%), moderately in 2/8 (25%) and focally in 4/8 (50%) of cPNETs. Whereas, all of the 38 non-PNET small round blue cell tumors were nonreactive. The results suggest that ZBTB16 is a highly sensitive and specific biomarker for both pPNET and gPNET/cPNET. ZBTB16 effectively differentiates PNETs from other small round blue cell tumor mimics, including the two most common germ cell tumor-derived somatic malignancies - rhabdomyosarcoma and nephroblastoma. Of note, compared to the expression of ZBTB16 in pPNET/Ewing sarcoma and gPNET, the expression of ZBTB16 in cPNET was more variable, which appears consistent with the heterogeneity of cPNET. The close proximity of ZBTB16 and FLI-1 genes on chromosome 11q may explain the overexpression of ZBTB16 in PNET, especially in pPNET with t(1122) translocation.
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Affiliation(s)
- Guang-Qian Xiao
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States.
| | - Andy E Sherrod
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States
| | - Kyle M Hurth
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States
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19
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Buus-Gehrig C, Lehrnbecher T, Porto L, Becker M, Freiman T, Mittelbronn M, Bochennek K. Pontine tumor in a neonate: case report and analysis of the current literature. J Neurosurg Pediatr 2019; 23:606-612. [PMID: 30771760 DOI: 10.3171/2018.10.peds18215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/31/2018] [Indexed: 11/06/2022]
Abstract
Tumors of the central nervous system represent the largest group of solid tumors found in pediatric patients. Pilocytic astrocytoma is the most common pediatric glioma, mostly located in the posterior fossa. The majority of brainstem tumors, however, are classified as highly aggressive diffuse intrinsic pontine gliomas (DIPGs) and their prognosis is dismal.The authors report on the case of a neonate in whom MRI and neuropathological assessment were used to diagnose DIPG. Before initiation of the planned chemotherapy, the tumor regressed spontaneously, and the newborn exhibited a normal neurological development. Meanwhile, Illumina Human Methylation450 BeadChip analysis reclassified the tumor as pilocytic astrocytoma of the posterior fossa.In conclusion, the authors advocate not initiating immediate intensive therapy in newborns with brain tumors, even with classical appearance of a DIPG; rather, they would like to encourage a biopsy to define the best individual therapeutic approach and avoid ineffective chemotherapy.
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Affiliation(s)
| | | | | | - Martina Becker
- 1Pediatric Hematology and Oncology, Goethe University; Departments of
| | | | - Michel Mittelbronn
- 4Edinger Institute, Institute of Neurology, Goethe University Frankfurt, Frankfurt am Main, Germany
- 5Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg
- 6NORLUX Neuro-Oncology Laboratory, Luxembourg Institute of Health (LIH)
- 7Laboratoire national de santé (LNS); and
- 8Luxembourg Centre of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Konrad Bochennek
- 1Pediatric Hematology and Oncology, Goethe University; Departments of
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20
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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] [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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21
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Abstract
The characterization of aberrant DNA methylation is emerging as a key part of the study of cancer development and phenotype. The technical advancements and decreasing costs of methods for high-throughput profiling of DNA methylation have brought about a high interest in the use of such methods in disease association studies. Here we discuss the principles for DNA methylation analysis using data from the Infinium DNA methylation BeadChip assays and describe the computational steps and statistical considerations going from processing of the raw array data to analysis of differential methylation. Moreover, we provide detailed guidelines on how to perform tumor subtype classification based on DNA methylation signatures.
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22
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Privacy-Preserving Similar Patient Queries for Combined Biomedical Data. PROCEEDINGS ON PRIVACY ENHANCING TECHNOLOGIES 2018. [DOI: 10.2478/popets-2019-0004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The decreasing costs of molecular profiling have fueled the biomedical research community with a plethora of new types of biomedical data, enabling a breakthrough towards more precise and personalized medicine. Naturally, the increasing availability of data also enables physicians to compare patients’ data and treatments easily and to find similar patients in order to propose the optimal therapy. Such similar patient queries (SPQs) are of utmost importance to medical practice and will be relied upon in future health information exchange systems. While privacy-preserving solutions have been previously studied, those are limited to genomic data, ignoring the different newly available types of biomedical data.
In this paper, we propose new cryptographic techniques for finding similar patients in a privacy-preserving manner with various types of biomedical data, including genomic, epigenomic and transcriptomic data as well as their combination. We design protocols for two of the most common similarity metrics in biomedicine: the Euclidean distance and Pearson correlation coefficient. Moreover, unlike previous approaches, we account for the fact that certain locations contribute differently to a given disease or phenotype by allowing to limit the query to the relevant locations and to assign them different weights. Our protocols are specifically designed to be highly efficient in terms of communication and bandwidth, requiring only one or two rounds of communication and thus enabling scalable parallel queries. We rigorously prove our protocols to be secure based on cryptographic games and instantiate our technique with three of the most important types of biomedical data – namely DNA, microRNA expression, and DNA methylation. Our experimental results show that our protocols can compute a similarity query over a typical number of positions against a database of 1,000 patients in a few seconds. Finally, we propose and formalize strategies to mitigate the threat of malicious users or hospitals.
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23
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Wenger A, Larsson S, Danielsson A, Elbæk KJ, Kettunen P, Tisell M, Sabel M, Lannering B, Nordborg C, Schepke E, Carén H. Stem cell cultures derived from pediatric brain tumors accurately model the originating tumors. Oncotarget 2017; 8:18626-18639. [PMID: 28148893 PMCID: PMC5386635 DOI: 10.18632/oncotarget.14826] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/16/2017] [Indexed: 12/14/2022] Open
Abstract
Brain tumors are the leading cause of cancer-related death in children but high-grade gliomas in children and adolescents have remained a relatively under-investigated disease despite this. A better understanding of the cellular and molecular pathogenesis of the diseases is required in order to improve the outcome for these children. In vitro-cultured primary tumor cells from patients are indispensable tools for this purpose by enabling functional analyses and development of new therapies. However, relevant well-characterized in vitro cultures from pediatric gliomas cultured under serum-free conditions have been lacking. We have therefore established patient-derived in vitro cultures and performed thorough characterization of the cells using large-scale analyses of DNA methylation, copy-number alterations and investigated their stability during prolonged time in culture. We show that the cells were stable during prolonged culture in serum-free stem cell media without apparent alterations in morphology or growth rate. The cells were proliferative, positive for stem cell markers, able to respond to differentiation cues and initiated tumors in zebrafish and mice suggesting that the cells are cancer stem cells or progenitor cells. The cells accurately mirrored the tumor they were derived from in terms of methylation pattern, copy number alterations and DNA mutations. These unique primary in vitro cultures can thus be used as a relevant and robust model system for functional studies on pediatric brain tumors.
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Affiliation(s)
- Anna Wenger
- Department of Pathology, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Susanna Larsson
- Department of Pathology, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Danielsson
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kirstine Juul Elbæk
- Department of Pathology, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Petronella Kettunen
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Magnus Tisell
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 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
| | - Birgitta Lannering
- 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
| | - Claes Nordborg
- Department of Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Elizabeth Schepke
- Department of Pathology, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,The Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Helena Carén
- Department of Pathology, Sahlgrenska Cancer Center, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Abstract
The comprehensive molecular profiling of cancer has resulted in new insights into the biology and classification of numerous tumor types. In the case of primary brain tumors that commonly affect adults, an emerging set of disease-defining biomarker sets is reshaping existing diagnostic entities that had previously been defined on the basis of their microscopic appearance. Substantial progress has been made in this regard for common primary brain tumors in adults, especially diffuse gliomas, where large-scale profiling efforts have led to the incorporation of highly prevalent molecular alterations that promote a biologically based classification as an adjunct to the traditional histopathologic approach. The growing awareness that histologically indistinguishable tumors can be divided into more precise and biologically relevant subgroups has demanded a more global routine approach to biomarker assessment. These considerations have begun to intersect with the decreasing costs and availability of genome-wide analysis tools and, thus, incorporation into routine practice. We review how molecular profiling already has led to an evolution in the classification of brain tumors. In addition, we discuss the likely trajectory of incorporation of global molecular profiling platforms into the routine clinical classification of adult brain tumors.
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Affiliation(s)
- Phedias Diamandis
- Phedias Diamandis and Kenneth D. Aldape, Princess Margaret Cancer Centre; and Kenneth D. Aldape, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- Phedias Diamandis and Kenneth D. Aldape, Princess Margaret Cancer Centre; and Kenneth D. Aldape, University of Toronto, Toronto, Ontario, Canada
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25
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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: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [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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26
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Sandén E, Enríquez Pérez J, Visse E, Kool M, Carén H, Siesjö P, Darabi A. Preoperative systemic levels of VEGFA, IL-7, IL-17A, and TNF-β delineate two distinct groups of children with brain tumors. Pediatr Blood Cancer 2016; 63:2112-2122. [PMID: 27472224 DOI: 10.1002/pbc.26158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Primary brain tumors are the most common solid tumors in children. Increasing evidence demonstrates diverse intratumoral immune signatures, which are tentatively reflected in peripheral blood. PROCEDURE Twenty cytokines were analyzed in preoperative plasma samples from five healthy children and 45 children with brain tumors, using a multiplex platform (MesoScale Discovery V-PLEX® ). Tumor types included medulloblastoma (MB), ependymoma, sarcoma, high-grade glioma, pilocytic astrocytoma, and other low-grade gliomas. RESULTS A panel of four cytokines [VEGFA, interleukin (IL)-7, IL-17A, and tumor necrosis factor (TNF)-β] delineated two distinct patient groups, identified as VEGFAhigh IL-7high IL-17Alow TNF-βlow (Group A) and VEGFAlow IL-7low IL-17Ahigh TNF-βhigh (Group B). Healthy controls and the vast majority of patients with MB were found within Group A, whereas patients with other tumor types were equally distributed between the two groups. Unrelated to A/B affiliation, we detected trends toward increased IL-10 and decreased IL-12/23 and TNF-α in several tumor types. Finally, a small number of patients displayed evidence of enhanced systemic immune activation, including elevated levels of interferon-γ, granulocyte monocyte colony-stimulating factor, IL-6, IL-12/23, and TNF-α. Following tumor resection, cytokine levels in a MB patient approached the levels of healthy controls. CONCLUSIONS We identify common features and individual differences in the systemic immune profiles of children with brain tumors. Overall, patients with MB displayed a uniform cytokine profile, whereas other tumor diagnoses did not predict systemic immunological status in single patients. Future characterization and monitoring of systemic immune responses in children with brain tumors will have important implications for the development and implementation of immunotherapy.
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Affiliation(s)
- Emma Sandén
- Glioma Immunotherapy Group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurosurgery, Lund University, Lund, Sweden.
| | - Julio Enríquez Pérez
- Glioma Immunotherapy Group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurosurgery, Lund University, Lund, Sweden
| | - Edward Visse
- Glioma Immunotherapy Group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurosurgery, Lund University, Lund, Sweden
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ, Heidelberg, Germany
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Peter Siesjö
- Glioma Immunotherapy Group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurosurgery, Lund University, Lund, Sweden.,Department of Clinical Sciences Lund, Neurosurgery, Lund University, Skåne University Hospital, Lund, Sweden
| | - Anna Darabi
- Glioma Immunotherapy Group, Faculty of Medicine, Department of Clinical Sciences Lund, Neurosurgery, Lund University, Lund, Sweden
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27
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Ahamed MT, Danielsson A, Nemes S, Carén H. MethPed: an R package for the identification of pediatric brain tumor subtypes. BMC Bioinformatics 2016; 17:262. [PMID: 27370569 PMCID: PMC4930602 DOI: 10.1186/s12859-016-1144-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/27/2016] [Indexed: 12/29/2022] Open
Abstract
Background DNA methylation profiling of pediatric brain tumors offers a new way of diagnosing and subgrouping these tumors which improves current clinical diagnostics based on histopathology. We have therefore developed the MethPed classifier, which is a multiclass random forest algorithm, based on DNA methylation profiles from many subgroups of pediatric brain tumors. Results We developed an R package that implements the MethPed classifier, making it easily available and accessible. The package can be used for estimating the probability that an unknown sample belongs to each of nine pediatric brain tumor diagnoses/subgroups. Conclusions The MethPed R package efficiently classifies pediatric brain tumors using the developed MethPed classifier. MethPed is available via Bioconductor: http://bioconductor.org/packages/MethPed/
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Affiliation(s)
- Mohammad Tanvir Ahamed
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden
| | - Anna Danielsson
- Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden
| | - Szilárd Nemes
- Swedish Hip Arthroplasty Register, Centre of Registers Västra Götaland, Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, PO Box 425, SE-405 30, Gothenburg, Sweden.
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28
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Sturm D, Orr BA, Toprak UH, Hovestadt V, Jones DTW, Capper D, Sill M, Buchhalter I, Northcott PA, Leis I, Ryzhova M, Koelsche C, Pfaff E, Allen SJ, Balasubramanian G, Worst BC, Pajtler KW, Brabetz S, Johann PD, Sahm F, Reimand J, Mackay A, Carvalho DM, Remke M, Phillips JJ, Perry A, Cowdrey C, Drissi R, Fouladi M, Giangaspero F, Łastowska M, Grajkowska W, Scheurlen W, Pietsch T, Hagel C, Gojo J, Lötsch D, Berger W, Slavc I, Haberler C, Jouvet A, Holm S, Hofer S, Prinz M, Keohane C, Fried I, Mawrin C, Scheie D, Mobley BC, Schniederjan MJ, Santi M, Buccoliero AM, Dahiya S, Kramm CM, von Bueren AO, von Hoff K, Rutkowski S, Herold-Mende C, Frühwald MC, Milde T, Hasselblatt M, Wesseling P, Rößler J, Schüller U, Ebinger M, Schittenhelm J, Frank S, Grobholz R, Vajtai I, Hans V, Schneppenheim R, Zitterbart K, Collins VP, Aronica E, Varlet P, Puget S, Dufour C, Grill J, Figarella-Branger D, Wolter M, Schuhmann MU, Shalaby T, Grotzer M, van Meter T, Monoranu CM, Felsberg J, Reifenberger G, Snuderl M, Forrester LA, Koster J, Versteeg R, Volckmann R, van Sluis P, Wolf S, Mikkelsen T, Gajjar A, Aldape K, Moore AS, Taylor MD, Jones C, Jabado N, Karajannis MA, Eils R, Schlesner M, Lichter P, von Deimling A, Pfister SM, Ellison DW, Korshunov A, Kool M. New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs. Cell 2016; 164:1060-1072. [PMID: 26919435 PMCID: PMC5139621 DOI: 10.1016/j.cell.2016.01.015] [Citation(s) in RCA: 590] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/22/2015] [Accepted: 01/08/2016] [Indexed: 12/11/2022]
Abstract
Primitive neuroectodermal tumors of the central nervous system (CNS-PNETs) are highly aggressive, poorly differentiated embryonal tumors occurring predominantly in young children but also affecting adolescents and adults. Herein, we demonstrate that a significant proportion of institutionally diagnosed CNS-PNETs display molecular profiles indistinguishable from those of various other well-defined CNS tumor entities, facilitating diagnosis and appropriate therapy for patients with these tumors. From the remaining fraction of CNS-PNETs, we identify four new CNS tumor entities, each associated with a recurrent genetic alteration and distinct histopathological and clinical features. These new molecular entities, designated "CNS neuroblastoma with FOXR2 activation (CNS NB-FOXR2)," "CNS Ewing sarcoma family tumor with CIC alteration (CNS EFT-CIC)," "CNS high-grade neuroepithelial tumor with MN1 alteration (CNS HGNET-MN1)," and "CNS high-grade neuroepithelial tumor with BCOR alteration (CNS HGNET-BCOR)," will enable meaningful clinical trials and the development of therapeutic strategies for patients affected by poorly differentiated CNS tumors.
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Affiliation(s)
- Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Brent A. Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Umut H. Toprak
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David T. W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Martin Sill
- Division of Biostatistics, German Cancer Research Center (DKFZ) Heidelberg and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ivo Buchhalter
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Paul A. Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Irina Leis
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marina Ryzhova
- NN Burdenko Neurosurgical Institute, Moscow, 125047 Russia
| | - Christian Koelsche
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Elke Pfaff
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Sariah J. Allen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Gnanaprakash Balasubramanian
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara C. Worst
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Kristian W. Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Sebastian Brabetz
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Pascal D. Johann
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Jüri Reimand
- Ontario Institute for Cancer Research, M5G 0A3, Toronto, ON M5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alan Mackay
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Diana M. Carvalho
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Marc Remke
- Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M4N 1X8, Canada
| | - Joanna J. Phillips
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA
- Neuropathology, Department of Pathology, University of California, San Francisco, CA 94143-0102, USA
- Department of Neurological Surgery, University of California, San Francisco, CA 94143-0112, USA
| | - Arie Perry
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA
- Neuropathology, Department of Pathology, University of California, San Francisco, CA 94143-0102, USA
- Department of Neurological Surgery, University of California, San Francisco, CA 94143-0112, USA
| | - Cynthia Cowdrey
- Brain Tumor Research Center, University of California, San Francisco, CA 94158-9001, USA
| | - Rachid Drissi
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Maryam Fouladi
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Felice Giangaspero
- Department of Radiological, Oncological and Anatomic-Pathological Sciences, Sapienza University of Rome, 00185 Rome, Italy
- IRCCS Neuromed, 86077 Pozzilli, Molise, Italy
| | - Maria Łastowska
- Department of Pathology, Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Wiesława Grajkowska
- Department of Pathology, Children's Memorial Health Institute, 04-730 Warsaw, Poland
| | - Wolfram Scheurlen
- Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, 90419 Nürnberg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical School, 53105 Bonn, Germany
| | - Christian Hagel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Lötsch
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Department of Medicine I, Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Institute of Neurology, Medical University of Vienna, 1097 Vienna, Austria
| | - Anne Jouvet
- Neuro-Oncology and Neuro-Inflammation Team, Inserm U1028, CNRS UMR 5292, University Lyon-1, Neuroscience Center, 69000 Lyon, France, and Centre de Pathologie et de Neuropathologie Est, Hospices Civils de Lyon, 69003 Lyon, France
| | - Stefan Holm
- Department of Women's and Children's Health (KBH), Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Silvia Hofer
- Department of Oncology, Luzerner Kantonsspital, 6000 Luzern 16, Luzern, Switzerland
| | - Marco Prinz
- Institute of Neuropathology, University of Freiburg, Germany & BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany
| | - Catherine Keohane
- Department of Pathology, University College Cork and Cork University Hospital Wilton, Cork, Ireland
| | - Iris Fried
- Department of Pediatric Hematology and Oncology, Hadassah Medical Center, Jerusalem, Israel
| | - Christian Mawrin
- Institute of Neuropathology, University Hospital, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - David Scheie
- Department of Pathology, Copenhagen University Hospital, 2100 København Ø, Denmark
| | - Bret C. Mobley
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J. Schniederjan
- Department of Pathology and Laboratory Administration, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mariarita Santi
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna M. Buccoliero
- Pathology Unit, Anna Meyer Children's University Hospital, 50141 Florence, Italy
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Christof M. Kramm
- Division of Pediatric Hematology and Oncology, Department of Child and Adolescent Health, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - André O. von Bueren
- Division of Pediatric Hematology and Oncology, Department of Child and Adolescent Health, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Katja von Hoff
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christel Herold-Mende
- Department of Neurosurgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | | | - Till Milde
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) Heidelberg, 69120 Heidelberg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, 48149 Münster, Germany
| | - Pieter Wesseling
- Department of Pathology, VU University Medical Center Amsterdam, 1008 MB Amsterdam, The Netherlands
- Department of Pathology, Radboud University Nijmegen Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jochen Rößler
- Department of Pediatric Hematology/Oncology, Center of Pediatrics and Adolescent Medicine, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Ulrich Schüller
- Department of Neuropathology, Ludwig-Maximilians-University, and German Cancer Consortium (DKTK) partner site Munich, 81377 Munich, Germany
| | - Martin Ebinger
- Department of Hematology and Oncology, Children's University Hospital Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Jens Schittenhelm
- Department of Neuropathology, Institute of Pathology and Neuropathology, University of Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Stephan Frank
- Department of Neuropathology, Institute of Pathology, Basel University Hospital, 4031 Basel, Switzerland
| | - Rainer Grobholz
- Department of Pathology, Medical Center Aarau, 5001 Aarau, Switzerland
| | - Istvan Vajtai
- Department of Pathology, University Hospital Bern, 3010 Bern, Switzerland
| | - Volkmar Hans
- Department of Neuropathology, Medical Center Bielefeld, 33617 Bielefeld, Germany
| | - Reinhard Schneppenheim
- Department of Pediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Karel Zitterbart
- Department of Pediatric Oncology, University Hospital Brno and Masaryk University, Faculty of Medicine, 613 00 Brno, Czech Republic
| | - V. Peter Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | - Eleonora Aronica
- Department of Neuropathology, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Pascale Varlet
- Department of Neuropathology, Hôpital Sainte-Anne, 75674, Paris, France
| | - Stephanie Puget
- Pediatric Neurosurgery Department, Necker Enfants Malades Hospital, 75015, Paris, France
| | - Christelle Dufour
- Brain Tumor Program, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris Sud, 94805, Villejuif, France
| | - Jacques Grill
- Brain Tumor Program, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, University Paris Sud, 94805, Villejuif, France
| | - Dominique Figarella-Branger
- Department of Pathology and Neuropathology, la Timone Hospital, AP-HM and UMR911 CR02, Aix-Marseille University, 13385 Marseille, France
| | - Marietta Wolter
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Martin U. Schuhmann
- Department of Neurosurgery, Section of Pediatric Neurosurgery, University Hospital Tübingen, and German Cancer Consortium (DKTK) partner site Tübingen, 72076 Tübingen, Germany
| | - Tarek Shalaby
- Neuro-Oncology Program, Division of Oncology, University Children's Hospital Zurich, 8032 Zürich, Switzerland
| | - Michael Grotzer
- Neuro-Oncology Program, Division of Oncology, University Children's Hospital Zurich, 8032 Zürich, Switzerland
| | | | - Camelia-Maria Monoranu
- Department of Neuropathology, Institute of Pathology, University of Würzburg, and Comprehensive Cancer Center (CCC) Mainfranken, University and University Hospital, 97080 Würzburg, Germany
| | - Jörg Felsberg
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, and German Cancer Consortium (DKTK) partner site Essen/Düsseldorf, 40225 Düsseldorf, Germany
| | - Matija Snuderl
- Department of Pathology, Division of Neuropathology, NYU Langone Medical Center, New York, NY 10016, USA
| | | | - Jan Koster
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Rogier Versteeg
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Richard Volckmann
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Peter van Sluis
- Department of Oncogenomics, AMC, University of Amsterdam, Amsterdam, 1105 AZ, The Netherlands
| | - Stephan Wolf
- Genomics and Proteomics Core Facility, High Throughput Sequencing Unit, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Tom Mikkelsen
- Departments of Neurology and Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Amar Gajjar
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kenneth Aldape
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew S. Moore
- The University of Queensland Diamantina Institute, Translational Research Institute; UQ Child Health Research Centre, The University of Queensland; Queensland Children's Medical Research Institute, Children's Health Queensland Hospital and Health Service; Brisbane, Australia
| | - Michael D. Taylor
- Program in Developmental and Stem Cell Biology, Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON M4N 1X8, Canada
| | - Chris Jones
- Division of Molecular Pathology, The Institute of Cancer Research, SW7 3RP, London, United Kingdom
| | - Nada Jabado
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Matthias A. Karajannis
- Departments of Pediatrics and Otolaryngology, Division of Pediatric Hematology/Oncology, NYU Langone Medical Center and Laura and Isaac Perlmutter Cancer Center, NY 10016, New York, USA
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
- Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Heidelberg Center for Personalized Oncology, DKFZ-HIPO, DKFZ, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David W. Ellison
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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