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Payne K, Suriyanarayanan H, Brooks J, Mehanna H, Nankivell P, Gendoo D. Exploring the impact of intra-tumoural heterogeneity on liquid biopsy cell-free DNA methylation and copy number in head and neck squamous cell carcinoma. Oral Oncol 2024; 158:107011. [PMID: 39236578 DOI: 10.1016/j.oraloncology.2024.107011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/01/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024]
Abstract
Liquid biopsy profiling is gaining increasing promise towards biomarker-led identification and disease stratification of tumours, particularly for tumours displaying significant intra-tumoural heterogeneity (ITH). For head and neck squamous cell carcinoma (HNSCC), which display high levels of genetic ITH, identification of epigenetic modifications and methylation signatures has shown multiple uses in stratification of HNSCC for prognosis, treatment, and HPV status. In this study, we investigated the potential of liquid biopsy methylomics and genomic copy number to profile HNSCC. We conducted multi-region sampling of tumour core, tumour margin and normal adjacent mucosa, as well as plasma cell-free DNA (cfDNA) across 9 HNSCC patients. Collectively, our work highlights the prevalence of methylomic ITH in HNSCC, and demonstrates the potential of cfDNA methylation as a tool for ITH assessment and serial sampling.
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Affiliation(s)
- Karl Payne
- Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham B15 2TT, United Kingdom.
| | - Harini Suriyanarayanan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jill Brooks
- Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Deena Gendoo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Institute for Interdisciplinary Data Science and AI, University of Birmingham, Birmingham B15 2TT, United Kingdom.
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2
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Idriss S, Hallal M, El-Kurdi A, Zalzali H, El-Rassi I, Ehli EA, Davis CM, Chung PED, Gendoo DMA, Zacksenhaus E, Saab R, Khoueiry P. A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements. Genome Res 2023; 33:269-282. [PMID: 36650051 PMCID: PMC10069464 DOI: 10.1101/gr.277037.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023]
Abstract
Pediatric pineoblastomas (PBs) are rare and aggressive tumors of grade IV histology. Although some oncogenic drivers are characterized, including germline mutations in RB1 and DICER1, the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated genome-wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model of CCND1-driven PB. We identified PB-specific enhancers and super-enhancers, and found that in some cases, the accessible genome dynamics precede transcriptomic changes, a characteristic that is underexplored in tumor progression. During progression of PB, newly acquired open chromatin regions lacking H3K27ac signal become enriched for repressive state elements and harbor motifs of repressor transcription factors like HINFP, GLI2, and YY1. Copy number variant analysis identified deletion events specific to the tumorigenic stage, affecting, among others, the histone gene cluster and Gas1, the growth arrest specific gene. Gene set enrichment analysis and gene expression signatures positioned the model used here close to human PB samples, showing the potential of our findings for exploring new avenues in PB management and therapy. Overall, this study reports the first temporal and in vivo cis-regulatory, expression, and accessibility maps in PB.
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Affiliation(s)
- Salam Idriss
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Mohammad Hallal
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Hasan Zalzali
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Inaam El-Rassi
- Biomedical Engineering Program, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Christel M Davis
- Avera Institute for Human Genetics, Sioux Falls, South Dakota 57108, USA
| | - Philip E D Chung
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, United Kingdom
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Raya Saab
- Department of Pediatric and Adolescent Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.,Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; .,Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
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3
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Rathi KS, Arif S, Koptyra M, Naqvi AS, Taylor DM, Storm PB, Resnick AC, Rokita JL, Raman P. A transcriptome-based classifier to determine molecular subtypes in medulloblastoma. PLoS Comput Biol 2020; 16:e1008263. [PMID: 33119584 PMCID: PMC7654754 DOI: 10.1371/journal.pcbi.1008263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 11/10/2020] [Accepted: 08/16/2020] [Indexed: 11/21/2022] Open
Abstract
Medulloblastoma is a highly heterogeneous pediatric brain tumor with five molecular subtypes, Sonic Hedgehog TP53-mutant, Sonic Hedgehog TP53-wildtype, WNT, Group 3, and Group 4, defined by the World Health Organization. The current mechanism for classification into these molecular subtypes is through the use of immunostaining, methylation, and/or genetics. We surveyed the literature and identified a number of RNA-Seq and microarray datasets in order to develop, train, test, and validate a robust classifier to identify medulloblastoma molecular subtypes through the use of transcriptomic profiling data. We have developed a GPL-3 licensed R package and a Shiny Application to enable users to quickly and robustly classify medulloblastoma samples using transcriptomic data. The classifier utilizes a large composite microarray dataset (15 individual datasets), an individual microarray study, and an RNA-Seq dataset, using gene ratios instead of gene expression measures as features for the model. Discriminating features were identified using the limma R package and samples were classified using an unweighted mean of normalized scores. We utilized two training datasets and applied the classifier in 15 separate datasets. We observed a minimum accuracy of 85.71% in the smallest dataset and a maximum of 100% accuracy in four datasets with an overall median accuracy of 97.8% across the 15 datasets, with the majority of misclassification occurring between the heterogeneous Group 3 and Group 4 subtypes. We anticipate this medulloblastoma transcriptomic subtype classifier will be broadly applicable to the cancer research and clinical communities.
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Affiliation(s)
- Komal S. Rathi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Sherjeel Arif
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ammar S. Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Deanne M. Taylor
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Phillip B. Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Adam C. Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (JLR); (PR)
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (JLR); (PR)
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4
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Chung PED, Gendoo DMA, Ghanbari-Azarnier R, Liu JC, Jiang Z, Tsui J, Wang DY, Xiao X, Li B, Dubuc A, Shih D, Remke M, Ho B, Garzia L, Ben-David Y, Kang SG, Croul S, Haibe-Kains B, Huang A, Taylor MD, Zacksenhaus E. Modeling germline mutations in pineoblastoma uncovers lysosome disruption-based therapy. Nat Commun 2020; 11:1825. [PMID: 32286280 PMCID: PMC7156401 DOI: 10.1038/s41467-020-15585-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/13/2020] [Indexed: 12/19/2022] Open
Abstract
Pineoblastoma is a rare pediatric cancer induced by germline mutations in the tumor suppressors RB1 or DICER1. Presence of leptomeningeal metastases is indicative of poor prognosis. Here we report that inactivation of Rb plus p53 via a WAP-Cre transgene, commonly used to target the mammary gland during pregnancy, induces metastatic pineoblastoma resembling the human disease with 100% penetrance. A stabilizing mutation rather than deletion of p53 accelerates metastatic dissemination. Deletion of Dicer1 plus p53 via WAP-Cre also predisposes to pineoblastoma, albeit with lower penetrance. In silico analysis predicts tricyclic antidepressants such as nortriptyline as potential therapeutics for both pineoblastoma models. Nortriptyline disrupts the lysosome, leading to accumulation of non-functional autophagosome, cathepsin B release and pineoblastoma cell death. Nortriptyline further synergizes with the antineoplastic drug gemcitabine to effectively suppress pineoblastoma in our preclinical models, offering new modality for this lethal childhood malignancy.
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Affiliation(s)
- Philip E D Chung
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Ronak Ghanbari-Azarnier
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada.,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jeff C Liu
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada
| | - Zhe Jiang
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada
| | - Jennifer Tsui
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada
| | - Dong-Yu Wang
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada
| | - Xiao Xiao
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada.,The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou, 550014, China.,State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - Bryan Li
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.,State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - Adrian Dubuc
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - David Shih
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.,Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marc Remke
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ben Ho
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Livia Garzia
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Faculty of Medicine, department of surgery, McGill University, Quebec, Canada
| | - Yaacov Ben-David
- The Key laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, Guizhou, 550014, China.,State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - Seok-Gu Kang
- Neurosurgery, Brain Tumor Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sidney Croul
- Department of Pathology & Laboratory Medicine, Division of Anatomical Pathology, Dalhousie University, Halifax, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Vector Institute, and Ontario Institute For Cancer Research, Toronto, ON, Canada
| | - Annie Huang
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.,State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China
| | - Michael D Taylor
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.,State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550025, China.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eldad Zacksenhaus
- Toronto General Research Institute, University Health Network, 67 College Street, Toronto, ON, M5G 2M1, Canada. .,Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
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5
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Dobson THW, Gopalakrishnan V. Preclinical Models of Pediatric Brain Tumors-Forging Ahead. Bioengineering (Basel) 2018; 5:bioengineering5040081. [PMID: 30279402 PMCID: PMC6315787 DOI: 10.3390/bioengineering5040081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/22/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022] Open
Abstract
Approximately five out of 100,000 children from 0 to 19 years old are diagnosed with a brain tumor. These children are treated with medication designed for adults that are highly toxic to a developing brain. Those that survive are at high risk for a lifetime of limited physical, psychological, and cognitive abilities. Despite much effort, not one drug exists that was designed specifically for pediatric patients. Stagnant government funding and the lack of economic incentives for the pharmaceutical industry greatly limits preclinical research and the development of clinically applicable pediatric brain tumor models. As more data are collected, the recognition of disease sub-groups based on molecular heterogeneity increases the need for designing specific models suitable for predictive drug screening. To overcome these challenges, preclinical approaches will need continual enhancement. In this review, we examine the advantages and shortcomings of in vitro and in vivo preclinical pediatric brain tumor models and explore potential solutions based on past, present, and future strategies for improving their clinical relevancy.
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Affiliation(s)
- Tara H W Dobson
- Department of Pediatrics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Vidya Gopalakrishnan
- Department of Pediatrics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Molecular & Cellular Oncology, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
- Brain Tumor Center, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
- Center for Cancer Epigenetics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.
- Graduate School of Biomedical Sciences UT-Health Science Center, Houston, TX 77030, USA.
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6
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Development of zebrafish medulloblastoma-like PNET model by TALEN-mediated somatic gene inactivation. Oncotarget 2017; 8:55280-55297. [PMID: 28903419 PMCID: PMC5589658 DOI: 10.18632/oncotarget.19424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 07/11/2017] [Indexed: 01/09/2023] Open
Abstract
Genetically engineered animal tumor models have traditionally been generated by the gain of single or multiple oncogenes or the loss of tumor suppressor genes; however, the development of live animal models has been difficult given that cancer phenotypes are generally induced by somatic mutation rather than by germline genetic inactivation. In this study, we developed somatically mutated tumor models using TALEN-mediated somatic gene inactivation of cdkn2a/b or rb1 tumor suppressor genes in zebrafish. One-cell stage injection of cdkn2a/b-TALEN mRNA resulted in malignant peripheral nerve sheath tumors with high frequency (about 39%) and early onset (about 35 weeks of age) in F0 tp53e7/e7 mutant zebrafish. Injection of rb1-TALEN mRNA also led to the formation of brain tumors at high frequency (58%, 31 weeks of age) in F0 tp53e7/e7 mutant zebrafish. Analysis of each tumor induced by somatic inactivation showed that the targeted genes had bi-allelic mutations. Tumors induced by rb1 somatic inactivation were characterized as medulloblastoma-like primitive neuroectodermal tumors based on incidence location, histopathological features, and immunohistochemical tests. In addition, 3' mRNA Quanti-Seq analysis showed differential activation of genes involved in cell cycle, DNA replication, and protein synthesis; especially, genes involved in neuronal development were up-regulated.
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7
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Ivanov DP, Coyle B, Walker DA, Grabowska AM. In vitro models of medulloblastoma: Choosing the right tool for the job. J Biotechnol 2016; 236:10-25. [PMID: 27498314 DOI: 10.1016/j.jbiotec.2016.07.028] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/29/2016] [Indexed: 02/06/2023]
Abstract
The recently-defined four molecular subgroups of medulloblastoma have required updating of our understanding of in vitro models to include molecular classification and risk stratification features from clinical practice. This review seeks to build a more comprehensive picture of the in vitro systems available for modelling medulloblastoma. The subtype classification and molecular characterisation for over 40 medulloblastoma cell-lines has been compiled, making it possible to identify the strengths and weaknesses in current model systems. Less than half (18/44) of established medulloblastoma cell-lines have been subgrouped. The majority of the subgrouped cell-lines (11/18) are Group 3 with MYC-amplification. SHH cell-lines are the next most common (4/18), half of which exhibit TP53 mutation. WNT and Group 4 subgroups, accounting for 50% of patients, remain underrepresented with 1 and 2 cell-lines respectively. In vitro modelling relies not only on incorporating appropriate tumour cells, but also on using systems with the relevant tissue architecture and phenotype as well as normal tissues. Novel ways of improving the clinical relevance of in vitro models are reviewed, focusing on 3D cell culture, extracellular matrix, co-cultures with normal cells and organotypic slices. This paper champions the establishment of a collaborative online-database and linked cell-bank to catalyse preclinical medulloblastoma research.
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Affiliation(s)
- Delyan P Ivanov
- Division of Cancer and Stem Cells, Cancer Biology, University of Nottingham, Nottingham, UK.
| | - Beth Coyle
- Children's Brain Tumour Research Centre, Queens Medical Centre, University of Nottingham, Nottingham, UK.
| | - David A Walker
- Children's Brain Tumour Research Centre, Queens Medical Centre, University of Nottingham, Nottingham, UK.
| | - Anna M Grabowska
- Division of Cancer and Stem Cells, Cancer Biology, University of Nottingham, Nottingham, UK.
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MM2S: personalized diagnosis of medulloblastoma patients and model systems. SOURCE CODE FOR BIOLOGY AND MEDICINE 2016; 11:6. [PMID: 27069505 PMCID: PMC4827218 DOI: 10.1186/s13029-016-0053-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/31/2016] [Indexed: 12/04/2022]
Abstract
Background Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had resulted in improvement of human subtype classification methods, and the parallel development of MB mouse models towards identification of subtype-specific disease origins and signaling pathways. Despite these advances, MB classification schemes remained inadequate for personalized prediction of MB subtypes for individual patient samples and across model systems. To address this issue, we developed the Medullo-Model to Subtypes (MM2S) classifier, a new method enabling classification of individual gene expression profiles from MB samples (patient samples, mouse models, and cell lines) against well-established molecular subtypes [Genomics 106:96-106, 2015]. We demonstrated the accuracy and flexibility of MM2S in the largest meta-analysis of human patients and mouse models to date. Here, we present a new functional package that provides an easy-to-use and fully documented implementation of the MM2S method, with additional functionalities that allow users to obtain graphical and tabular summaries of MB subtype predictions for single samples and across sample replicates. The flexibility of the MM2S package promotes incorporation of MB predictions into large Medulloblastoma-driven analysis pipelines, making this tool suitable for use by researchers. Results The MM2S package is applied in two case studies involving human primary patient samples, as well as sample replicates of the GTML mouse model. We highlight functions that are of use for species-specific MB classification, across individual samples and sample replicates. We emphasize on the range of functions that can be used to derive both singular and meta-centric views of MB predictions, across samples and across MB subtypes. Conclusions Our MM2S package can be used to generate predictions without having to rely on an external web server or additional sources. Our open-source package facilitates and extends the MM2S algorithm in diverse computational and bioinformatics contexts. The package is available on CRAN, at the following URL: https://cran.r-project.org/web/packages/MM2S/, as well as on Github at the following URLs: https://github.com/DGendoo and https://github.com/bhklab. Electronic supplementary material The online version of this article (doi:10.1186/s13029-016-0053-y) contains supplementary material, which is available to authorized users.
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