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Wilcock DM, Goold E, Zuromski LM, Davidson C, Mao Q, Sirohi D. EGFR/CEP7 high polysomy is separate and distinct from EGFR amplification in glioblastoma as determined by fluorescence in situ hybridization. J Neuropathol Exp Neurol 2024; 83:338-344. [PMID: 38605523 PMCID: PMC11029461 DOI: 10.1093/jnen/nlae028] [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] [Indexed: 04/13/2024] Open
Abstract
EGFR amplification in gliomas is commonly defined by an EGFR/CEP7 ratio of ≥2. In testing performed at a major reference laboratory, a small subset of patients had ≥5 copies of both EGFR and CEP7 yet were not amplified by the EGFR/CEP7 ratio and were designated high polysomy cases. To determine whether these tumors are more closely related to traditionally defined EGFR-amplified or nonamplified gliomas, a retrospective search identified 22 out of 1143 (1.9%) gliomas with an average of ≥5 copies/cell of EGFR and CEP7 with an EGFR/CEP7 ratio of <2 displaying high polysomy. Of these cases, 4 had insufficient clinicopathologic data to include in additional analysis, 15 were glioblastomas, 2 were IDH-mutant astrocytomas, and 1 was a high-grade glial neoplasm, NOS. Next-generation sequencing available on 3 cases demonstrated one with a TERT promoter mutation, TP53 mutations in all cases, and no EGFR mutations or amplifications, which most closely matched the nonamplified cases. The median overall survival times were 42.86, 66.07, and 41.14 weeks for amplified, highly polysomic, and nonamplified, respectively, and were not significantly different (p = 0.3410). High chromosome 7 polysomic gliomas are rare but our data suggest that they may be biologically similar to nonamplified gliomas.
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Affiliation(s)
- Diane M Wilcock
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Eric Goold
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Lauren M Zuromski
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Christian Davidson
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Qinwen Mao
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
| | - Deepika Sirohi
- Institute for Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, Utah, USA
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2
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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576103. [PMID: 38313282 PMCID: PMC10836086 DOI: 10.1101/2024.01.17.576103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.
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3
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Saviuk M, Sleptsova E, Redkin T, Turubanova V. Unexplained Causes of Glioma-Associated Epilepsies: A Review of Theories and an Area for Research. Cancers (Basel) 2023; 15:5539. [PMID: 38067243 PMCID: PMC10705208 DOI: 10.3390/cancers15235539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/25/2023] Open
Abstract
Approximately 30% of glioma patients are able to survive beyond one year postdiagnosis. And this short time is often overshadowed by glioma-associated epilepsy. This condition severely impairs the patient's quality of life and causes great suffering. The genetic, molecular and cellular mechanisms underlying tumour development and epileptogenesis remain incompletely understood, leading to numerous unanswered questions. The various types of gliomas, namely glioblastoma, astrocytoma and oligodendroglioma, demonstrate distinct seizure susceptibility and disease progression patterns. Patterns have been identified in the presence of IDH mutations and epilepsy, with tumour location in cortical regions, particularly the frontal lobe, showing a more frequent association with seizures. Altered expression of TP53, MGMT and VIM is frequently detected in tumour cells from individuals with epilepsy associated with glioma. However, understanding the pathogenesis of these modifications poses a challenge. Moreover, hypoxic effects induced by glioma and associated with the HIF-1a factor may have a significant impact on epileptogenesis, potentially resulting in epileptiform activity within neuronal networks. We additionally hypothesise about how the tumour may affect the functioning of neuronal ion channels and contribute to disruptions in the blood-brain barrier resulting in spontaneous depolarisations.
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Affiliation(s)
- Mariia Saviuk
- Institute of Neurosciences, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603022 Nizhny Novgorod, Russia; (M.S.); (E.S.); (T.R.)
- Cell Death Investigation and Therapy Laboratory, Anatomy and Embryology Unit, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Ekaterina Sleptsova
- Institute of Neurosciences, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603022 Nizhny Novgorod, Russia; (M.S.); (E.S.); (T.R.)
| | - Tikhon Redkin
- Institute of Neurosciences, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603022 Nizhny Novgorod, Russia; (M.S.); (E.S.); (T.R.)
| | - Victoria Turubanova
- Institute of Neurosciences, National Research Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., 603022 Nizhny Novgorod, Russia; (M.S.); (E.S.); (T.R.)
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Feng J, Hsu PF, Esteva E, Labella R, Wang Y, Khodadadi-Jamayran A, Pucella J, Liu CZ, Arbini AA, Tsirigos A, Kousteni S, Reizis B. Haplodeficiency of the 9p21 tumor suppressor locus causes myeloid disorders driven by the bone marrow microenvironment. Blood 2023; 142:460-476. [PMID: 37267505 DOI: 10.1182/blood.2022018512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023] Open
Abstract
The chromosome 9p21 locus comprises several tumor suppressor genes including MTAP, CDKN2A, and CDKN2B, and its homo- or heterozygous deletion is associated with reduced survival in multiple cancer types. We report that mice with germ line monoallelic deletion or induced biallelic deletion of the 9p21-syntenic locus (9p21s) developed a fatal myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN)-like disease associated with aberrant trabecular bone formation and/or fibrosis in the bone marrow (BM). Reciprocal BM transfers and conditional targeting of 9p21s suggested that the disease originates in the BM stroma. Single-cell analysis of 9p21s-deficient BM stroma revealed the expansion of chondrocyte and osteogenic precursors, reflected in increased osteogenic differentiation in vitro. It also showed reduced expression of factors maintaining hematopoietic stem/progenitor cells, including Cxcl12. Accordingly, 9p21s-deficient mice showed reduced levels of circulating Cxcl12 and concomitant upregulation of the profibrotic chemokine Cxcl13 and the osteogenesis- and fibrosis-related multifunctional glycoprotein osteopontin/Spp1. Our study highlights the potential of mutations in the BM microenvironment to drive MDS/MPN-like disease.
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Affiliation(s)
- Jue Feng
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Pei-Feng Hsu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Eduardo Esteva
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Rossella Labella
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- Edward P. Evans Center for Myelodysplastic Syndromes, Columbia University Medical Center, New York, NY
| | - Yueyang Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Alireza Khodadadi-Jamayran
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY
| | - Joseph Pucella
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Cynthia Z Liu
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Arnaldo A Arbini
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, NY
| | - Stavroula Kousteni
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University Medical Center, New York, NY
- Edward P. Evans Center for Myelodysplastic Syndromes, Columbia University Medical Center, New York, NY
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Boris Reizis
- Department of Pathology, New York University Grossman School of Medicine, New York, NY
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Forecasting Molecular Features in IDH-Wildtype Gliomas: The State of the Art of Radiomics Applied to Neurosurgery. Cancers (Basel) 2023; 15:cancers15030940. [PMID: 36765898 PMCID: PMC9913449 DOI: 10.3390/cancers15030940] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The fifth edition of the WHO Classification of Tumors of the Central Nervous System (CNS), published in 2021, marks a step forward the future diagnostic approach to these neoplasms. Alongside this, radiomics has experienced rapid evolution over the last several years, allowing us to correlate tumor imaging heterogeneity with a wide range of tumor molecular and subcellular features. Radiomics is a translational field focused on decoding conventional imaging data to extrapolate the molecular and prognostic features of tumors such as gliomas. We herein analyze the state-of-the-art of radiomics applied to glioblastoma, with the goal to estimate its current clinical impact and potential perspectives in relation to well-rounded patient management, including the end-of-life stage. METHODS A literature review was performed on the PubMed, MEDLINE and Scopus databases using the following search items: "radiomics and glioma", "radiomics and glioblastoma", "radiomics and glioma and IDH", "radiomics and glioma and TERT promoter", "radiomics and glioma and EGFR", "radiomics and glioma and chromosome". RESULTS A total of 719 articles were screened. Further quantitative and qualitative analysis allowed us to finally include 11 papers. This analysis shows that radiomics is rapidly evolving towards a reliable tool. CONCLUSIONS Further studies are necessary to adjust radiomics' potential to the newest molecular requirements pointed out by the 2021 WHO classification of CNS tumors. At a glance, its application in the clinical routine could be beneficial to achieve a timely diagnosis, especially for those patients not eligible for surgery and/or adjuvant therapies but still deserving palliative and supportive care.
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Bader JM, Deigendesch N, Misch M, Mann M, Koch A, Meissner F. Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status. Cell Rep Med 2022; 4:100877. [PMID: 36584682 PMCID: PMC9873829 DOI: 10.1016/j.xcrm.2022.100877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/15/2022] [Accepted: 12/07/2022] [Indexed: 12/30/2022]
Abstract
High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.
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Affiliation(s)
- Jakob Maximilian Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nikolaus Deigendesch
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Martin Misch
- Department of Neurosurgery, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Arend Koch
- Department of Neuropathology, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany.
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Systems Immunology and Proteomics, Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany.
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7
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Bae T, Wang Y, Vaccarino FM, Abyzov A. Somatic genomic mosaicism in the brain during aging: Scratching the surface. Clin Transl Med 2022; 12:e1138. [PMID: 36495113 PMCID: PMC9736788 DOI: 10.1002/ctm2.1138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health SciencesCenter for Individualized Medicine, Mayo ClinicRochesterMinnesotaUSA
| | - Yifan Wang
- Department of Quantitative Health SciencesCenter for Individualized Medicine, Mayo ClinicRochesterMinnesotaUSA
| | - Flora M Vaccarino
- Child Study CenterYale UniversityNew HavenConnecticutUSA
- Department of NeuroscienceYale UniversityNew HavenConnecticutUSA
| | - Alexej Abyzov
- Department of Quantitative Health SciencesCenter for Individualized Medicine, Mayo ClinicRochesterMinnesotaUSA
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8
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Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022; 377:511-517. [PMID: 35901164 PMCID: PMC9420557 DOI: 10.1126/science.abm6222] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.
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Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | - Caroline Dias
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yasmine Chahine
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rosalinda C. Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham Al, 35294
| | - Anita Huttner
- Department of Pathology, Yale University, New Haven, CT 06520
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
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Guarnaccia M, Guarnaccia L, La Cognata V, Navone SE, Campanella R, Ampollini A, Locatelli M, Miozzo M, Marfia G, Cavallaro S. A Targeted Next-Generation Sequencing Panel to Genotype Gliomas. LIFE (BASEL, SWITZERLAND) 2022; 12:life12070956. [PMID: 35888045 PMCID: PMC9320073 DOI: 10.3390/life12070956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/12/2022]
Abstract
Gliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, we developed and validated a targeted next-generation sequencing (NGS) approach to analyze variants or chromosomal aberrations correlated with tumorigenesis and response to treatment in gliomas. Our targeted NGS analysis covered 13 glioma-related genes (ACVR1, ATRX, BRAF, CDKN2A, EGFR, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, P53, PDGFRA, PTEN), a 125 bp region of the TERT promoter, and 54 single nucleotide polymorphisms (SNPs) along chromosomes 1 and 19 for reliable assessment of their copy number alterations (CNAs). Our targeted NGS approach provided a portrait of gliomas’ molecular heterogeneity with high accuracy, specificity, and sensitivity in a single workflow, enabling the detection of variants associated with unfavorable outcomes, disease progression, and drug resistance. These preliminary results support its use in routine diagnostic neuropathology.
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Affiliation(s)
- Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Laura Guarnaccia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Department of Clinical Sciences and Community Health, University of Milan, Via Festa del Perdono 7, 20122 Milan, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
| | - Stefania Elena Navone
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Rolando Campanella
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Antonella Ampollini
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
| | - Marco Locatelli
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- “Aldo Ravelli” Research Center, Via Antonio di Rudinì 8, 20142 Milan, Italy
- Department of Medical-Surgical Physiopathology and Transplantation, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Monica Miozzo
- Department of Health Sciences, University of Milan, 20122 Milan, Italy;
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milan, Italy
| | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; (L.G.); (S.E.N.); (R.C.); (A.A.); (M.L.); (G.M.)
- Clinical Pathology Unit, Aerospace Medicine Institute “A. Mosso”, Italian Air Force, Viale dell’Aviazione 1, 20138 Milan, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, Italy; (M.G.); (V.L.C.)
- Correspondence: ; Tel.: +39-09-57338128
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10
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Vilar JB, Christmann M, Tomicic MT. Alterations in Molecular Profiles Affecting Glioblastoma Resistance to Radiochemotherapy: Where Does the Good Go? Cancers (Basel) 2022; 14:cancers14102416. [PMID: 35626024 PMCID: PMC9139489 DOI: 10.3390/cancers14102416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Glioblastoma is a type of brain cancer that remains incurable. Despite multiple past and ongoing preclinical studies and clinical trials, involving adjuvants to the conventional therapy and based on molecular targeting, no relevant benefit for patients’ survival has been achieved so far. The current first-line treatment regimen is based on ionizing radiation and the monoalkylating compound, temozolomide, and has been administered for more than 15 years. Glioblastoma is extremely resistant to most agents due to a mutational background that elicits quick response to insults and adapts to microenvironmental and metabolic changes. Here, we present the most recent evidence concerning the molecular features and their alterations governing pathways involved in GBM response to the standard radio-chemotherapy and discuss how they collaborate with acquired GBM’s resistance. Abstract Glioblastoma multiforme (GBM) is a brain tumor characterized by high heterogeneity, diffuse infiltration, aggressiveness, and formation of recurrences. Patients with this kind of tumor suffer from cognitive, emotional, and behavioral problems, beyond exhibiting dismal survival rates. Current treatment comprises surgery, radiotherapy, and chemotherapy with the methylating agent, temozolomide (TMZ). GBMs harbor intrinsic mutations involving major pathways that elicit the cells to evade cell death, adapt to the genotoxic stress, and regrow. Ionizing radiation and TMZ induce, for the most part, DNA damage repair, autophagy, stemness, and senescence, whereas only a small fraction of GBM cells undergoes treatment-induced apoptosis. Particularly upon TMZ exposure, most of the GBM cells undergo cellular senescence. Increased DNA repair attenuates the agent-induced cytotoxicity; autophagy functions as a pro-survival mechanism, protecting the cells from damage and facilitating the cells to have energy to grow. Stemness grants the cells capacity to repopulate the tumor, and senescence triggers an inflammatory microenvironment favorable to transformation. Here, we highlight this mutational background and its interference with the response to the standard radiochemotherapy. We discuss the most relevant and recent evidence obtained from the studies revealing the molecular mechanisms that lead these cells to be resistant and indicate some future perspectives on combating this incurable tumor.
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11
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Calabrese E, Rudie JD, Rauschecker AM, Villanueva-Meyer JE, Clarke JL, Solomon DA, Cha S. Combining radiomics and deep convolutional neural network features from preoperative MRI for predicting clinically relevant genetic biomarkers in glioblastoma. Neurooncol Adv 2022; 4:vdac060. [PMID: 35611269 PMCID: PMC9122791 DOI: 10.1093/noajnl/vdac060] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Glioblastoma is the most common primary brain malignancy, yet treatment options are limited, and prognosis remains guarded. Individualized tumor genetic assessment has become important for accurate prognosis and for guiding emerging targeted therapies. However, challenges remain for widespread tumor genetic testing due to costs and the need for tissue sampling. The aim of this study is to evaluate a novel artificial intelligence method for predicting clinically relevant genetic biomarkers from preoperative brain MRI in patients with glioblastoma.
Methods
We retrospectively analyzed preoperative MRI data from 400 patients with glioblastoma and grade 4 astrocytoma, IDH mutant who underwent resection and genetic testing. Nine genetic biomarkers were assessed: hotspot mutations of IDH1 or TERT promoter, pathogenic mutations of TP53, PTEN, ATRX, or CDKN2A/B, MGMT promoter methylation, EGFR amplification, and combined aneuploidy of chromosomes 7 & 10. Models were developed to predict biomarker status from MRI data using radiomics features, convolutional neural network (CNN) features, and a combination of both.
Results
Combined model performance was good for IDH1 and TERT promoter hotspot mutations, pathogenic mutations of ATRX and CDKN2A/B, and combined aneuploidy of chromosomes 7 & 10, with receiver operating characteristic area under the curve (ROC AUC) > 0.85 and was fair for all other tested biomarkers with ROC AUC > 0.7. Combined model performance was statistically superior to individual radiomics and CNN feature models for prediction chromosome 7 & 10 aneuploidy, MGMT promoter methylation, and PTEN loss.
Conclusions
Combining radiomics and CNN features from preoperative MRI yields improved non-invasive genetic biomarker prediction performance in patients with grade 4 diffuse gliomas.
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Affiliation(s)
- Evan Calabrese
- Department of Radiology and Biomedical Imaging, University of California at San Francisco, San Francisco, California, USA
- Center for Intelligent Imaging, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey D Rudie
- Department of Radiology and Biomedical Imaging, University of California at San Francisco, San Francisco, California, USA
| | - Andreas M Rauschecker
- Department of Radiology and Biomedical Imaging, University of California at San Francisco, San Francisco, California, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California at San Francisco, San Francisco, California, USA
- Center for Intelligent Imaging, University of California San Francisco, San Francisco, California, USA
| | - Jennifer L Clarke
- Division of Neuro-Oncology, Department of Neurology and Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
- Clinical Cancer Genomics Laboratory, University of California San Francisco, San Francisco, California, USA
| | - Soonmee Cha
- Department of Radiology and Biomedical Imaging, University of California at San Francisco, San Francisco, California, USA
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12
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Wolter M, Felsberg J, Malzkorn B, Kaulich K, Reifenberger G. Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas. Acta Neuropathol Commun 2022; 10:42. [PMID: 35361262 PMCID: PMC8973808 DOI: 10.1186/s40478-022-01335-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2022] [Indexed: 11/10/2022] Open
Abstract
Classification of gliomas involves the combination of histological features with molecular biomarkers to establish an integrated histomolecular diagnosis. Here, we report on the application and validation of a set of molecular assays for glioma diagnostics based on digital PCR technology using the QX200™ Droplet Digital™ PCR (ddPCR) system. The investigated ddPCR-based assays enable the detection of diagnostically relevant glioma-associated mutations in the IDH1, IDH2, H3-3A, BRAF, and PRKCA genes, as well as in the TERT promoter. In addition, ddPCR-based assays assessing diagnostically relevant copy number alterations were studied, including 1p/19q codeletion, gain of chromosome 7 and loss of chromosome 10 (+ 7/-10), EGFR amplification, duplication of the BRAF locus, and CDKN2A homozygous deletion. Results obtained by ddPCR were validated by other methods, including immunohistochemistry, Sanger sequencing, pyrosequencing, microsatellite analyses for loss of heterozygosity, as well as real-time PCR- or microarray-based copy number assays. Particular strengths of the ddPCR approach are (1) its high analytical sensitivity allowing for reliable detection of mutations even with low mutant allele frequencies, (2) its quantitative determination of mutant allele frequencies and copy number changes, and (3) its rapid generation of results within a single day. Thus, in line with other recent studies our findings support ddPCR analysis as a valuable approach for molecular glioma diagnostics in a fast, quantitative and highly sensitive manner.
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13
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Fu X, Lei H, Tao Y, Heselmeyer-Haddad K, Torres I, Dean M, Ried T, Schwartz R. Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers. J Comput Biol 2021; 28:1035-1051. [PMID: 34612714 DOI: 10.1089/cmb.2021.0255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aneuploidy and whole genome duplication (WGD) events are common features of cancers associated with poor outcomes, but the ways they influence trajectories of clonal evolution are poorly understood. Phylogenetic methods for reconstructing clonal evolution from genomic data have proven a powerful tool for understanding how clonal evolution occurs in the process of cancer progression, but extant methods so far have limited the ability to resolve tumor evolution via ploidy changes. This limitation exists in part because single-cell DNA-sequencing (scSeq), which has been crucial to developing detailed profiles of clonal evolution, has difficulty in resolving ploidy changes and WGD. Multiplex interphase fluorescence in situ hybridization (miFISH) provides a more unambiguous signal of single-cell ploidy changes but it is limited to profiling small numbers of single markers. Here, we develop a joint clustering method to combine these two data sources with the goal of better resolving ploidy changes in tumor evolution. We develop a probabilistic framework to maximize the probability of latent variables given the pre-clustered datasets, which we optimize via Markov chain Monte Carlo sampling combined with linear regression. We validate the method by using simulated data derived from a glioblastoma (GBM) case profiled by both scSeq and miFISH. We further apply the method to two GBM cases with scSeq and miFISH data by reconstructing a phylogenetic tree from the joint clustering results, demonstrating their synergistic value in understanding how focal copy number changes and WGD events can collectively contribute to tumor progression.
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Affiliation(s)
- Xuecong Fu
- Department of Biological Sciences, and Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Haoyun Lei
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Yifeng Tao
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Schwartz
- Department of Biological Sciences, and Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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14
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Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R. Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinformatics 2021; 37:4704-4711. [PMID: 34289030 PMCID: PMC8665747 DOI: 10.1093/bioinformatics/btab504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Computational reconstruction of clonal evolution in cancers has become a crucial tool for understanding how tumors initiate and progress and how this process varies across patients. The field still struggles, however, with special challenges of applying phylogenetic methods to cancers, such as the prevalence and importance of copy number alteration (CNA) and structural variation (SV) events in tumor evolution, which are difficult to profile accurately by prevailing sequencing methods in such a way that subsequent reconstruction by phylogenetic inference algorithms is accurate. RESULTS In the present work, we develop computational methods to combine sequencing with multiplex interphase fluorescence in situ hybridization (miFISH) to exploit the complementary advantages of each technology in inferring accurate models of clonal CNA evolution accounting for both focal changes and aneuploidy at whole-genome scales. By integrating such information in an integer linear programming (ILP) framework, we demonstrate on simulated data that incorporation of FISH data substantially improves accurate inference of focal CNA and ploidy changes in clonal evolution from deconvolving bulk sequence data. Analysis of real glioblastoma data for which FISH, bulk sequence, and single cell sequence are all available confirms the power of FISH to enhance accurate reconstruction of clonal copy number evolution in conjunction with bulk and optionally single-cell sequence data. AVAILABILITY Source code is available on Github at https://github.com/CMUSchwartzLab/FISH_deconvolution.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - E Michael Gertz
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xuecong Fu
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Yifeng Tao
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Irianna Torres
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guibo Li
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Liqin Xu
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Soltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Yong Hou
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Kui Wu
- Department of Biology, University of Copenhagen, Copenhagen, 1599, Denmark
| | - Xulian Shi
- Shenzhen Luohu People's Hospital, Shenzhen, 518000, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, MD, 20814, USA
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Russell Schwartz
- Computational Biology Dept, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Dept. of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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15
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Zeng C, Wang J, Li M, Wang H, Lou F, Cao S, Lu C. Comprehensive Molecular Characterization of Chinese Patients with Glioma by Extensive Next-Generation Sequencing Panel Analysis. Cancer Manag Res 2021; 13:3573-3588. [PMID: 33953611 PMCID: PMC8092857 DOI: 10.2147/cmar.s291681] [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: 11/25/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background Tremendous efforts have been made to explore biomarkers for classifying and grading glioma. However, the majority of the current understanding is based on public databases that might not accurately reflect the Asian population. Here, we investigated the genetic landscape of Chinese glioma patients using a validated multigene next-generation sequencing (NGS) panel to provide a strong rationale for the future classification and prognosis of glioma in this population. Methods We analyzed 83 samples, consisting of 71 initial treatments and 12 recurrent surgical tumors, from 81 Chinese patients with gliomas by performing multigene NGS with an Acornmed panel targeting 808 cancer-related hotspot genes, including genes related to glioma (hotspots, selected exons or complete coding sequences) and full-length SNPs located on chromosomes 1 and 19. Results A total of 76 (91.57%) glioma samples had at least one somatic mutation. The most commonly mutated genes were TP53, TERT, IDH1, PTEN, ATRX, and EGFR. Approximately one-third of cases exhibited more than one copy number variation. Of note, this study identified the amplification of genes, such as EGFR and PDGFRA, which were significantly associated with glioblastoma but had not been previously used for clinical classification (P<0.05). Significant differences in genomic profiles between different pathological subtypes and WHO grade were observed. Compared to the MSKCC database primarily comprised of Caucasians, H3F3A mutations and MET amplifications exhibited higher mutation rates, whereas TERT mutations and EGFR and CDKN2A/B copy number variations presented a lower mutation rate in Chinese patients with glioma (P<0.05). Conclusion Our multigene NGS in the simultaneous evaluation of multiple relevant markers revealed several novel genetic alterations in Chinese patients with glioma. NGS-based molecular analysis is a reliable and effective method for diagnosing brain tumors, assisting clinicians in evaluating additional potential therapeutic options, such as targeted therapy, for glioma patients in different racial/ethnic groups.
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Affiliation(s)
- Chun Zeng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, People's Republic of China.,China National Clinical Research Center for Neurological Diseases, Beijing, People's Republic of China
| | - Jing Wang
- Department of Neurosurgery, Peking University International Hospital, Beijing, People's Republic of China
| | - Mingwei Li
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Feng Lou
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd, Beijing, People's Republic of China
| | - Changyu Lu
- Department of Neurosurgery, Peking University International Hospital, Beijing, People's Republic of China
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16
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Zhang H, Cui B, Zhou Y, Wang X, Wu W, Wang Z, Dai Z, Cheng Q, Yang K. B2M overexpression correlates with malignancy and immune signatures in human gliomas. Sci Rep 2021; 11:5045. [PMID: 33658560 PMCID: PMC7930032 DOI: 10.1038/s41598-021-84465-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/17/2021] [Indexed: 12/11/2022] Open
Abstract
Because of the limited treatment strategy of gliomas, the key of diagnosis and treatment is finding new molecular biomarkers. Here, we explored the potential of β2-microglobulin (B2M) to serve as a hopeful candidate for immunotherapy or diagnostic biomarker in gliomas. The genomic profiles, clinical characteristics, and immune signatures were analyzed based on TCGA and CGGA databases. We carried out the whole statistical analyses using R project. High B2M expression correlated with worse prognosis. Somatic mutations of gliomas with high B2M expression are associated with PTEN deletion and EGFR amplification. Isocitrate dehydrogenase (IDH) mutations accounted for 82% in gliomas with low B2M expression. In addition, B2M positively correlated with ESTIMATE scores, interacted with infiltrating immune and stromal cell types. B2M also suppressed anti-tumor immunity through immune related processes. Meanwhile, B2M was associated with immune checkpoint molecules and inflammatory activities. Finally, functional annotation of the identified B2M related genes verified that B2M was a potential candidate for immunotherapy. We confirmed that B2M played a critical role in tumor progression, patient prognosis and immunotherapy of gliomas.
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Biqi Cui
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Yulai Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Xinxing Wang
- Department of Orthopedics, The Third Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Kui Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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17
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Bobach IS, Stougaard M. SNP-based detection of allelic imbalance: A novel approach for identifying KIAA1549-BRAF fusion in pilocytic astrocytoma using DNA sequencing. Exp Mol Pathol 2021; 120:104621. [PMID: 33626378 DOI: 10.1016/j.yexmp.2021.104621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 11/19/2022]
Abstract
Pilocytic astrocytoma (PA) is the most common glioma subtype found in children, and it is a non-malignant tumor type. The majority of PAs is caused by an approximately 2 Mb tandem duplication within 7q34 which creates an in-frame KIAA1549-BRAF fusion gene. The kinase domain of BRAF is fused to the N-terminal of KIAA1549, whereby BRAF is constitutively activated. We here present a novel approach for identifying KIAA1549-BRAF fusion based on single nucleotide polymorphism (SNP) analysis and next generation sequencing (NGS). Highly polymorphic SNPs in the duplicated area and in adjacent areas were selected and a custom targeted amplicon based NGS panel was designed. The panel was tested on DNA extracted from formalin fixed and paraffin embedded tissue from a retrospective cohort, consisting of biopsies from patients with PA, anaplastic astrocytoma, oligodendroglioma and glioblastoma as well as two non-tumor biopsies. The panel could distinguish chromosome 7 gain from BRAF fusion and correctly identified 8/9 PA samples with KIAA1549-BRAF fusion confirmed by RNA sequencing. The one biopsy where no fusion was detected was fresh frozen and from the RNA sequencing expected to have very low tumor content. No allelic imbalance was detected in either oligodendroglioma or in the non-tumor biopsies.
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Affiliation(s)
- Ida Schwartz Bobach
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Pathology, Aarhus University Hospital, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Denmark; Department of Pathology, Aarhus University Hospital, Denmark.
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18
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Ardizzone A, Scuderi SA, Giuffrida D, Colarossi C, Puglisi C, Campolo M, Cuzzocrea S, Esposito E, Paterniti I. Role of Fibroblast Growth Factors Receptors (FGFRs) in Brain Tumors, Focus on Astrocytoma and Glioblastoma. Cancers (Basel) 2020; 12:E3825. [PMID: 33352931 PMCID: PMC7766440 DOI: 10.3390/cancers12123825] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Despite pharmacological treatments and surgical practice options, the mortality rate of astrocytomas and glioblastomas remains high, thus representing a medical emergency for which it is necessary to find new therapeutic strategies. Fibroblast growth factors (FGFs) act through their associated receptors (FGFRs), a family of tyrosine kinase receptors consisting of four members (FGFR1-4), regulators of tissue development and repair. In particular, FGFRs play an important role in cell proliferation, survival, and migration, as well as angiogenesis, thus their gene alteration is certainly related to the development of the most common diseases, including cancer. FGFRs are subjected to multiple somatic aberrations such as chromosomal amplification of FGFR1; mutations and multiple dysregulations of FGFR2; and mutations, translocations, and significant amplifications of FGFR3 and FGFR4 that correlate to oncogenesis process. Therefore, the in-depth study of these receptor systems could help to understand the etiology of both astrocytoma and glioblastoma so as to achieve notable advances in more effective target therapies. Furthermore, the discovery of FGFR inhibitors revealed how these biological compounds improve the neoplastic condition by demonstrating efficacy and safety. On this basis, this review focuses on the role and involvement of FGFRs in brain tumors such as astrocytoma and glioblastoma.
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Affiliation(s)
- Alessio Ardizzone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
| | - Sarah A. Scuderi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
| | - Dario Giuffrida
- Istituto Oncologico del Mediterraneo, Via Penninazzo 7, 95029 Viagrande (CT), Italy; (D.G.); (C.C.)
| | - Cristina Colarossi
- Istituto Oncologico del Mediterraneo, Via Penninazzo 7, 95029 Viagrande (CT), Italy; (D.G.); (C.C.)
| | - Caterina Puglisi
- IOM Ricerca Srl, Via Penninazzo 11, 95029 Viagrande (CT), Italy;
| | - Michela Campolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (A.A.); (S.A.S.); (M.C.); (S.C.); (E.E.)
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19
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Identification of New Genetic Clusters in Glioblastoma Multiforme: EGFR Status and ADD3 Losses Influence Prognosis. Cells 2020; 9:cells9112429. [PMID: 33172155 PMCID: PMC7694764 DOI: 10.3390/cells9112429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma multiforme (GB) is one of the most aggressive tumors. Despite continuous efforts to improve its clinical management, there is still no strategy to avoid a rapid and fatal outcome. EGFR amplification is the most characteristic alteration of these tumors. Although effective therapy against it has not yet been found in GB, it may be central to classifying patients. We investigated somatic-copy number alterations (SCNA) by multiplex ligation-dependent probe amplification in a series of 137 GB, together with the detection of EGFRvIII and FISH analysis for EGFR amplification. Publicly available data from 604 patients were used as a validation cohort. We found statistical associations between EGFR amplification and/or EGFRvIII, and SCNA in CDKN2A, MSH6, MTAP and ADD3. Interestingly, we found that both EGFRvIII and losses on ADD3 were independent markers of bad prognosis (p = 0.028 and 0.014, respectively). Finally, we got an unsupervised hierarchical classification that differentiated three clusters of patients based on their genetic alterations. It offered a landscape of EGFR co-alterations that may improve the comprehension of the mechanisms underlying GB aggressiveness. Our findings can help in defining different genetic profiles, which is necessary to develop new and different approaches in the management of our patients.
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20
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Parney IF, Gustafson MP, Solseth M, Bulur P, Peterson TE, Smadbeck JB, Johnson SH, Murphy SJ, Vasmatzis G, Dietz AB. Novel strategy for manufacturing autologous dendritic cell/allogeneic tumor lysate vaccines for glioblastoma. Neurooncol Adv 2020; 2:vdaa105. [PMID: 33134920 PMCID: PMC7592424 DOI: 10.1093/noajnl/vdaa105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Glioblastoma, the most common primary malignant brain tumor, is nearly universally fatal by 5 years. Dendritic cell vaccines are promising but often limited clinically by antigen choice, dendritic cell potency, and/or manufacturing yield. We optimized vaccine manufacture, generating potent mature autologous dendritic cells pulsed with allogeneic glioblastoma lysates. Methods Platelet lysate-based supplement was used to establish human glioblastoma cell lines. Phenotype and genotype were assessed. An improved culture technique to generate mature dendritic cells from glioblastoma patients’ monocytes was developed. The ability of T cells stimulated with autologous dendritic cells pulsed with allogeneic glioblastoma cell lysate to kill HLA-A2-matched glioblastoma cells was assessed. Results Glioblastoma cell lines established with platelet lysate supplement grew faster and expressed more stem-like markers than lines grown in neural stem cell media or in the presence of serum. They expressed a variety of glioma-associated antigens and had genomic abnormalities characteristic of glioblastoma stable up to 15 doublings. Unlike standard culture techniques, our optimized technique produced high levels of mature dendritic cells from glioblastoma patients’ monocytes. Autologous T cells stimulated with mature dendritic cells pulsed with allogeneic glioblastoma cell line lysate briskly killed HLA-A2-matched glioblastoma cells. Conclusions Our glioblastoma culture method provides a renewable source for a broad spectrum glioblastoma neoantigens while our dendritic cell culture technique results in more mature dendritic cells in glioblastoma patients than standard techniques. This broadly applicable strategy could be easily integrated into patient care.
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Affiliation(s)
- Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
- Corresponding Author: Ian F. Parney, MD, PhD or Allan B. Dietz, PhD, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, USA ( or )
| | | | - Mary Solseth
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Peggy Bulur
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy E Peterson
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - James B Smadbeck
- Division of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen J Murphy
- Division of Genetics and Bioinformatics, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Allan B Dietz
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Transfusion Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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21
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Campanella R, Guarnaccia L, Caroli M, Zarino B, Carrabba G, La Verde N, Gaudino C, Rampini A, Luzzi S, Riboni L, Locatelli M, Navone SE, Marfia G. Personalized and translational approach for malignant brain tumors in the era of precision medicine: the strategic contribution of an experienced neurosurgery laboratory in a modern neurosurgery and neuro-oncology department. J Neurol Sci 2020; 417:117083. [PMID: 32784071 DOI: 10.1016/j.jns.2020.117083] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022]
Abstract
Personalized medicine (PM) aims to optimize patient management, taking into account the individual traits of each patient. The main purpose of PM is to obtain the best response, improving health care and lowering costs. Extending traditional approaches, PM introduces novel patient-specific paradigms from diagnosis to treatment, with greater precision. In neuro-oncology, the concept of PM is well established. Indeed, every neurosurgical intervention for brain tumors has always been highly personalized. In recent years, PM has been introduced in neuro-oncology also to design and prescribe specific therapies for the patient and the patient's tumor. The huge advances in basic and translational research in the fields of genetics, molecular and cellular biology, transcriptomics, proteomics, and metabolomics have led to the introduction of PM into clinical practice. The identification of a patient's individual variation map may allow to design selected therapeutic protocols that ensure successful outcomes and minimize harmful side effects. Thus, clinicians can switch from the "one-size-fits-all" approach to PM, ensuring better patient care and high safety margin. Here, we review emerging trends and the current literature about the development of PM in neuro-oncology, considering the positive impact of innovative advanced researches conducted by a neurosurgical laboratory.
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Affiliation(s)
- Rolando Campanella
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Guarnaccia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Manuela Caroli
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Barbara Zarino
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giorgio Carrabba
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Chiara Gaudino
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela Rampini
- Neurosurgery Unit, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Sabino Luzzi
- Neurosurgery Unit, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Neurosurgery Unit, Department of Surgical Sciences, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Laura Riboni
- Department of Medical Biotechnology and Translational Medicine, LITA-Segrate, University of Milan, Milan, Italy
| | - Marco Locatelli
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Aldo Ravelli" Research Center, Milan, Italy; Department of Medical-Surgical Physiopathology and Transplantation, University of Milan, Milan, Italy
| | - Stefania Elena Navone
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Aldo Ravelli" Research Center, Milan, Italy.
| | - Giovanni Marfia
- Laboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Aldo Ravelli" Research Center, Milan, Italy; Clinical Pathology Unit, Istituto di Medicina Aerospaziale "A. Moosso", Aeronautica Militare, Milan, Italy
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22
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Calabrese E, Villanueva-Meyer JE, Cha S. A fully automated artificial intelligence method for non-invasive, imaging-based identification of genetic alterations in glioblastomas. Sci Rep 2020; 10:11852. [PMID: 32678261 PMCID: PMC7366666 DOI: 10.1038/s41598-020-68857-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/29/2020] [Indexed: 02/02/2023] Open
Abstract
Glioblastoma is the most common malignant brain parenchymal tumor yet remains challenging to treat. The current standard of care-resection and chemoradiation-is limited in part due to the genetic heterogeneity of glioblastoma. Previous studies have identified several tumor genetic biomarkers that are frequently present in glioblastoma and can alter clinical management. Currently, genetic biomarker status is confirmed with tissue sampling, which is costly and only available after tumor resection or biopsy. The purpose of this study was to evaluate a fully automated artificial intelligence approach for predicting the status of several common glioblastoma genetic biomarkers on preoperative MRI. We retrospectively analyzed multisequence preoperative brain MRI from 199 adult patients with glioblastoma who subsequently underwent tumor resection and genetic testing. Radiomics features extracted from fully automated deep learning-based tumor segmentations were used to predict nine common glioblastoma genetic biomarkers with random forest regression. The proposed fully automated method was useful for predicting IDH mutations (sensitivity = 0.93, specificity = 0.88), ATRX mutations (sensitivity = 0.94, specificity = 0.92), chromosome 7/10 aneuploidies (sensitivity = 0.90, specificity = 0.88), and CDKN2 family mutations (sensitivity = 0.76, specificity = 0.86).
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Affiliation(s)
- Evan Calabrese
- Department of Radiology and Biomedical Imaging, University of California At San Francisco, 350 Parnassus Ave, Suite 307H, San Francisco, CA, 94143-0628, USA.
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California At San Francisco, 350 Parnassus Ave, Suite 307H, San Francisco, CA, 94143-0628, USA
| | - Soonmee Cha
- Department of Radiology and Biomedical Imaging, University of California At San Francisco, 350 Parnassus Ave, Suite 307H, San Francisco, CA, 94143-0628, USA
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23
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Lyakhova I, Piatkova M, Gulaia V, Romanishin A, Shmelev M, Bryukhovetskiy A, Sharma A, Sharma HS, Khotimchenko R, Bryukhovetskiy I. Alkaloids of fascaplysin are promising chemotherapeutic agents for the treatment of glioblastoma: Review. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 151:299-324. [PMID: 32448613 DOI: 10.1016/bs.irn.2020.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glioblastoma is one of the most aggressive human brain tumors. Even following all the modern protocols of complex treatment, the median patient survival typically does not exceed 15 months. This review analyzes the main reasons for glioblastoma resistance to therapy, as well as attempts at categorizing the main approaches to increasing chemotherapy efficiency. Special emphasis is placed on the specific group of compounds, known as marine alkaloids and their synthetic derivatives exerting a general antitumor effect on glioblastoma cells. The unique mechanisms of marine alkaloid influence on the tumor cells prompt considering them as a promising basis for creating new chemotherapeutic agents for glioblastoma treatment.
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Affiliation(s)
- Irina Lyakhova
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Mariia Piatkova
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Laboratory of Biomedical Cell Technologies, Department of Medical Biology and Biotechnology, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Aleksandr Romanishin
- Laboratory of Biomedical Cell Technologies, Department of Medical Biology and Biotechnology, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Mikhail Shmelev
- Laboratory of Biomedical Cell Technologies, Department of Medical Biology and Biotechnology, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Andrey Bryukhovetskiy
- NeuroVita Clinic of Interventional and Restorative Neurology and Therapy, Moscow, Russia
| | - Aruna Sharma
- International Experimental Central Nervous System Injury & Repair (IECNSIR), Department of Surgical Sciences, Anesthesiology & Intensive Care Medicine, University Hospital, Uppsala University, S-75185 Uppsala, Sweden
| | - Hari Shanker Sharma
- International Experimental Central Nervous System Injury & Repair (IECNSIR), Department of Surgical Sciences, Anesthesiology & Intensive Care Medicine, University Hospital, Uppsala University, S-75185 Uppsala, Sweden
| | - Rodion Khotimchenko
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; Laboratory of Pharmacology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Igor Bryukhovetskiy
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia; Laboratory of Pharmacology, National Scientific Center of Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia.
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24
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Lei H, Lyu B, Gertz EM, Schäffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R. Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. J Comput Biol 2020; 27:565-598. [PMID: 32181683 DOI: 10.1089/cmb.2019.0302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Characterizing intratumor heterogeneity (ITH) is crucial to understanding cancer development, but it is hampered by limits of available data sources. Bulk DNA sequencing is the most common technology to assess ITH, but involves the analysis of a mixture of many genetically distinct cells in each sample, which must then be computationally deconvolved. Single-cell sequencing is a promising alternative, but its limitations-for example, high noise, difficulty scaling to large populations, technical artifacts, and large data sets-have so far made it impractical for studying cohorts of sufficient size to identify statistically robust features of tumor evolution. We have developed strategies for deconvolution and tumor phylogenetics combining limited amounts of bulk and single-cell data to gain some advantages of single-cell resolution with much lower cost, with specific focus on deconvolving genomic copy number data. We developed a mixed membership model for clonal deconvolution via non-negative matrix factorization balancing deconvolution quality with similarity to single-cell samples via an associated efficient coordinate descent algorithm. We then improve on that algorithm by integrating deconvolution with clonal phylogeny inference, using a mixed integer linear programming model to incorporate a minimum evolution phylogenetic tree cost in the problem objective. We demonstrate the effectiveness of these methods on semisimulated data of known ground truth, showing improved deconvolution accuracy relative to bulk data alone.
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Affiliation(s)
- Haoyun Lei
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Bochuan Lyu
- Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, Indiana
| | - E Michael Gertz
- National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, Maryland.,Cancer Data Science Laboratory, National Cancer Institute, U.S. National Institutes of Health, Bethesda, Maryland
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, U.S. National Institutes of Health, Bethesda, Maryland.,Cancer Data Science Laboratory, National Cancer Institute, U.S. National Institutes of Health, Bethesda, Maryland
| | | | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology & Genetics, National Cancer Institute, U.S. National Institutes of Health, Gaithersburg, Maryland
| | - Russell Schwartz
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
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25
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The Role of Rho GTPases in Motility and Invasion of Glioblastoma Cells. Anal Cell Pathol (Amst) 2020; 2020:9274016. [PMID: 32089990 PMCID: PMC7013281 DOI: 10.1155/2020/9274016] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 12/27/2022] Open
Abstract
Astrocytomas are primary malignant brain tumors that originate from astrocytes. Grade IV astrocytoma or glioblastoma is a highly invasive tumor that occur within the brain parenchyma. The Rho family of small GTPases, which includes Rac1, Cdc42, and RhoA, is an important family whose members are key regulators of the invasion and migration of glioblastoma cells. In this review, we describe the role played by the Rho family of GTPases in the regulation of the invasion and migration of glioblastoma cells. Specifically, we focus on the role played by RhoA, Rac1, RhoG, and Cdc42 in cell migration through rearrangement of actin cytoskeleton, cell adhesion, and invasion. Finally, we highlight the importance of potentially targeting Rho GTPases in the treatment of glioblastoma.
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26
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Dissecting Molecular Features of Gliomas: Genetic Loci and Validated Biomarkers. Int J Mol Sci 2020; 21:ijms21020685. [PMID: 31968687 PMCID: PMC7014190 DOI: 10.3390/ijms21020685] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, several studies focused on the genetics of gliomas. This allowed identifying several germline loci that contribute to individual risk for tumor development, as well as various somatic mutations that are key for disease classification. Unfortunately, none of the germline loci clearly confers increased risk per se. Contrariwise, somatic mutations identified within the glioma tissue define tumor genotype, thus representing valid diagnostic and prognostic markers. Thus, genetic features can be used in glioma classification and guided therapy. Such copious genomic variabilities are screened routinely in glioma diagnosis. In detail, Sanger sequencing or pyrosequencing, fluorescence in-situ hybridization, and microsatellite analyses were added to immunohistochemistry as diagnostic markers. Recently, Next Generation Sequencing was set-up as an all-in-one diagnostic tool aimed at detecting both DNA copy number variations and mutations in gliomas. This approach is widely used also to detect circulating tumor DNA within cerebrospinal fluid from patients affected by primary brain tumors. Such an approach is providing an alternative cost-effective strategy to genotype all gliomas, which allows avoiding surgical tissue collection and repeated tumor biopsies. This review summarizes available molecular features that represent solid tools for the genetic diagnosis of gliomas at present or in the next future.
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27
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Cilibrasi C, Guzzi A, Bazzoni R, Riva G, Cadamuro M, Hochegger H, Bentivegna A. A Ploidy Increase Promotes Sensitivity of Glioma Stem Cells to Aurora Kinases Inhibition. JOURNAL OF ONCOLOGY 2019; 2019:9014045. [PMID: 31531022 PMCID: PMC6720056 DOI: 10.1155/2019/9014045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/09/2019] [Accepted: 06/24/2019] [Indexed: 12/02/2022]
Abstract
Glioma stem cells account for glioblastoma relapse and resistance to conventional therapies, and protein kinases, involved in the regulation of the mitotic machinery (i.e., Aurora kinases), have recently emerged as attractive therapeutic targets. In this study, we investigated the effect of Aurora kinases inhibition in five glioma stem cell lines isolated from glioblastoma patients. As expected, cell lines responded to the loss of Aurora kinases with cytokinesis failure and mitotic exit without cell division. Surprisingly, this resulted in a proliferative arrest in only two of the five cell lines. These sensitive cell lines entered a senescent/autophagic state following aberrant mitotic exit, while the non-sensitive cell lines continued to proliferate. This senescence response did not correlate with TP53 mutation status but only occurred in the cell lines with the highest chromosome content. Repeated rounds of Aurora kinases inhibition caused a gradual increase in chromosome content in the resistant cell lines and eventually caused a similar senescence response and proliferative arrest. Our results suggest that a ploidy threshold is the main determinant of Aurora kinases sensitivity in TP53 mutant glioma stem cells. Thus, ploidy could be used as a biomarker for treating glioma patients with Aurora kinases inhibitors.
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Affiliation(s)
- Chiara Cilibrasi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Ph.D. Program in Neuroscience, University of Milano-Bicocca, 20900 Monza, Italy
- NeuroMI, Milan Center of Neuroscience, University of Milano-Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, 20900 Monza, Italy
| | - Andrèe Guzzi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Riccardo Bazzoni
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- NeuroMI, Milan Center of Neuroscience, University of Milano-Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, 20900 Monza, Italy
| | - Gabriele Riva
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- NeuroMI, Milan Center of Neuroscience, University of Milano-Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, 20900 Monza, Italy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Massimiliano Cadamuro
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- International Center for Digestive Health (ICDH), University of Milano-Bicocca, 20900 Monza, Italy
| | - Helfrid Hochegger
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Angela Bentivegna
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- NeuroMI, Milan Center of Neuroscience, University of Milano-Bicocca, Dept. of Neurology and Neuroscience, San Gerardo Hospital, 20900 Monza, Italy
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28
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Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis. Int J Genomics 2019; 2019:1287671. [PMID: 31093489 PMCID: PMC6481143 DOI: 10.1155/2019/1287671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/26/2022] Open
Abstract
Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes. The results of this initial analysis were extended and validated in a set of 89 paired normal mucosa and CRC samples. We found that 14% of genes showed ASE in one or more cell lines and identified allelic switching of the potential cell survival genes DLX5, GRB10, and SVOPL on chromosome 7, whereby the most abundantly expressed allele in the normal tissue is the lowest expressed allele in the tumor and vice versa. We established that this allelic switch does not result from loss of imprinting. The allelic switching of SVOPL may be a result of transcriptional downregulation, while the exact mechanisms resulting in the allelic switching of DLX5 and GRB10 remain to be elucidated. In conclusion, our results show that profound changes take place in allelic transcriptional regulation during the tumorigenesis of CRC.
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29
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Wood MD, Halfpenny AM, Moore SR. Applications of molecular neuro-oncology - a review of diffuse glioma integrated diagnosis and emerging molecular entities. Diagn Pathol 2019; 14:29. [PMID: 30967140 PMCID: PMC6457044 DOI: 10.1186/s13000-019-0802-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/12/2019] [Indexed: 11/10/2022] Open
Abstract
Insights into the molecular underpinnings of primary central nervous system tumors have radically changed the approach to tumor diagnosis and classification. Diagnostic emphasis has shifted from the morphology of a tumor under the microscope to an integrated approach based on morphologic and molecular features, including gene mutations, chromosomal copy number alterations, and gene rearrangements. In 2016, the World Health Organization provided guidelines for making an integrated diagnosis that incorporates both morphologic and molecular features in a subset of brain tumors. The integrated diagnosis now applies to infiltrating gliomas, a category that includes diffusely infiltrating astrocytoma grades II, III, and IV, and oligodendroglioma, grades II and III, thereby encompassing the most common primary intra-axial central nervous system tumors. Other neoplasms such as medulloblastoma, embryonal tumor with multilayered rosettes, certain supratentorial ependymomas, and atypical teratoid/rhabdoid tumor are also eligible for integrated diagnosis, which can sometimes be aided by characteristic immunohistochemical markers. Since 2016, advances in molecular neuro-oncology have resulted in periodic updates and clarifications to the integrated diagnostic approach. These advances reflect expanding knowledge on the molecular pathology of brain tumors, but raise a challenge in rapidly incorporating new molecular findings into diagnostic practice. This review provides a background on the molecular characteristics of primary brain tumors, emphasizing the molecular basis for classification of infiltrating gliomas, the most common entities that are eligible for an integrated diagnosis. We then discuss entities within the diffuse gliomas that do not receive an integrated diagnosis by WHO 2016 criteria, but have distinctive molecular features that are important to recognize because their clinical behavior can influence clinical management and prognosis. Particular attention is given to the histone H3 G34R/G34V mutant astrocytomas, an entity to consider when faced with an infiltrating glioma in the cerebral hemisphere of children and young adults, and to the group of histologically lower grade diffuse astrocytic gliomas with molecular features of glioblastoma, an important category of tumors to recognize due to their aggressive clinical behavior.
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Affiliation(s)
- Matthew D Wood
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA.
| | - Aaron M Halfpenny
- OHSU Department of Pathology, Division of Anatomic Pathology, Section of Neuropathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, L-113, Portland, OR, 97213, USA
| | - Stephen R Moore
- Knight Diagnostic Laboratories and Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, 97239, USA
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30
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The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells Int 2019; 2019:2617030. [PMID: 30984267 PMCID: PMC6431486 DOI: 10.1155/2019/2617030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/01/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant human brain tumour, characterized by rapid progression, invasion, intense angiogenesis, high genomic instability, and resistance to therapies. Despite countless experimental researches for new therapeutic strategies and promising clinical trials, the prognosis remains extremely poor, with a mean survival of less than 14 months. GBM aggressive behaviour is due to a subpopulation of tumourigenic stem-like cells, GBM stem cells (GSCs), which hierarchically drive onset, proliferation, and tumour recurrence. The morbidity and mortality of this disease strongly encourage exploring genetic characteristics of GSCs. Here, using array-CGH platform, we investigated genetic and genomic aberration profiles of GBM parent tumour (n = 10) and their primarily derived GSCs. Statistical analysis was performed by using R software and complex heatmap and corrplot packages. Pearson correlation and K-means algorithm were exploited to compare genetic alterations and to group similar genetic profiles in matched pairs of GBM and derived GSCs. We identified, in both GBM and matched GSCs, recurrent copy number alterations, as chromosome 7 polysomy, chromosome 10 monosomy, and chromosome 9p21deletions, which are typical features of primary GBM, essential for gliomagenesis. These observations suggest a condition of strong genomic instability both in GBM as GSCs. Our findings showed the robust similarity between GBM mass and GSCs (Pearson corr.≥0.65) but also highlighted a marked variability among different patients. Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. Furthermore, K-means algorithm identified an impairment of pathways related to the development and progression of cancer, such as angiogenesis, as well as pathways related to the immune system regulation, such as T cell activation. Our data confirmed the preservation of the genomic landscape from tumour tissue to GSCs, supporting the relevance of this cellular model to test in vitro new target therapies for GBM.
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31
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Romo CG, Palsgrove DN, Sivakumar A, Elledge CR, Kleinberg LR, Chaichana KL, Gocke CD, Rodriguez FJ, Holdhoff M. Widely metastatic IDH1-mutant glioblastoma with oligodendroglial features and atypical molecular findings: a case report and review of current challenges in molecular diagnostics. Diagn Pathol 2019; 14:16. [PMID: 30738431 PMCID: PMC6368694 DOI: 10.1186/s13000-019-0793-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/01/2019] [Indexed: 01/06/2023] Open
Abstract
Background Gliomas with 1p/19q-codeletion as well as mutation of isocitrate dehydrogenase (IDH) 1 are typically characterized as oligodendrogliomas with comparatively good response to treatment with radiation and chemotherapy. Case presentation We present the case of a 28-year-old man with an IDH1 and TP53 mutant high grade glioma with abnormalities in chromosomes 1 and 19 suggestive of anaplastic oligodendroglioma that rapidly progressed to widespread metastatic disease. Biopsy of a liver lesion confirmed metastasis of the patient’s known brain primary and chemotherapy with temozolomide was initiated. The patient’s rapidly growing tumor burden with fulminant liver failure and tumor lysis led to multisystem failure of which the patient died. Further molecular testing illustrated features more consistent with glioblastoma: multiple large chromosomal aberrations including loss of whole chromosome 1 and 2q; gain/amplification of MYCN, MET, and CDK4; loss of CDKN2A/B; and an ATRX mutation. Conclusion This case illustrates the importance of higher level molecular diagnostic testing for patients with particularly aggressive disease progression that is not concordant with standard prognoses. Additional data on cases with atypical alterations of 1p and 19q are needed to better understand the distinct biology of these cancers so that appropriate therapies can be developed. Electronic supplementary material The online version of this article (10.1186/s13000-019-0793-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carlos G Romo
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA
| | - Doreen N Palsgrove
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Ananyaa Sivakumar
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA
| | - Christen R Elledge
- Department of Radiation Oncology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Lawrence R Kleinberg
- Department of Radiation Oncology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Kaisorn L Chaichana
- Department of Neurosurgery, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Fausto J Rodriguez
- Department of Pathology, Johns Hopkins University of Medicine, Baltimore, MD, USA
| | - Matthias Holdhoff
- Brain Cancer Program, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 1550 Orleans Street, 1M16, Baltimore, MD, 21287, USA.
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32
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Gulaia V, Kumeiko V, Shved N, Cicinskas E, Rybtsov S, Ruzov A, Kagansky A. Molecular Mechanisms Governing the Stem Cell's Fate in Brain Cancer: Factors of Stemness and Quiescence. Front Cell Neurosci 2018; 12:388. [PMID: 30510501 PMCID: PMC6252330 DOI: 10.3389/fncel.2018.00388] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Cellular quiescence is a reversible, non-cycling state controlled by epigenetic, transcriptional and niche-associated molecular factors. Quiescence is a condition where molecular signaling pathways maintain the poised cell-cycle state whilst enabling rapid cell cycle re-entry. To achieve therapeutic breakthroughs in oncology it is crucial to decipher these molecular mechanisms employed by the cancerous milieu to control, maintain and gear stem cells towards re-activation. Cancer stem-like cells (CSCs) have been extensively studied in most malignancies, including glioma. Here, the aberrant niche activities skew the quiescence/activation equilibrium, leading to rapid tumor relapse after surgery and/or chemotherapy. Unraveling quiescence mechanisms promises to afford prevention of (often multiple) relapses, a key problem in current glioma treatment. This review article covers the current knowledge regarding normal and aberrant cellular quiescence control whilst also exploring how different molecular mechanisms and properties of the neighboring cells can influence the molecular processes behind glioma stem cell quiescence.
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Affiliation(s)
- Valeriia Gulaia
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Nikita Shved
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Eduardas Cicinskas
- Department of Cellular Biology and Genetics, School of Natural Sciences, Far Eastern Federal University, Vladivostok, Russia
- Laboratory of Pharmacology and Bioassays, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Stanislav Rybtsov
- Institute for Stem Cell Research, Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, SCRM Bioquarter, Scotland, United Kingdom
| | - Alexey Ruzov
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), Division of Cancer and Stem Cells, School of Medicine, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Alexander Kagansky
- Centre for Genomic and Regenerative Medicine, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
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Jain KK. A Critical Overview of Targeted Therapies for Glioblastoma. Front Oncol 2018; 8:419. [PMID: 30374421 PMCID: PMC6196260 DOI: 10.3389/fonc.2018.00419] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/10/2018] [Indexed: 01/07/2023] Open
Abstract
Over the past century, treatment of malignant tumors of the brain has remained a challenge. Refinements in neurosurgical techniques, discovery of powerful chemotherapeutic agents, advances in radiotherapy, applications of biotechnology, and improvements in methods of targeted delivery have led to some extension of length of survival of glioblastoma patients. Refinements in surgery are mentioned because most of the patients with glioblastoma undergo surgery and many of the other innovative therapies are combined with surgery. However, cure of glioblastoma has remained elusive because it requires complete destruction of the tumor. Radical surgical ablation is not possible in the brain and even a small residual tumor leads to rapid recurrence that eventually kills the patient. Blood-brain barrier (BBB) comprising brain endothelial cells lining the cerebral microvasculature, limits delivery of drugs to the brain. Even though opening of the BBB in tumor core occurs locally, BBB limits systemic chemotherapy especially at the tumor periphery, where tumor cells invade normal brain structure comprising intact BBB. Comprehensive approaches are necessary to gain maximally from promising targeted therapies. Common methods used for critical evaluation of targeted therapies for glioblastoma include: (1) novel methods for targeted delivery of chemotherapy; (2) strategies for delivery through BBB and blood-tumor barriers; (3) innovations in radiotherapy for selective destruction of tumor; (4) techniques for local destruction of tumor; (5) tumor growth inhibitors; (6) immunotherapy; and (7) cell/gene therapies. Suggestions for improvements in glioblastoma therapy include: (1) controlled targeted delivery of anticancer therapy to glioblastoma through the BBB using nanoparticles and monoclonal antibodies; (2) direct introduction of genetically modified bacteria that selectively destroy cancer cells but spare the normal brain into the remaining tumor after resection; (3) use of better animal models for preclinical testing; and (4) personalized/precision medicine approaches to therapy in clinical trials and translation into practice of neurosurgery and neurooncology. Advances in these techniques suggest optimism for the future management of glioblastoma.
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González-Tablas M, Crespo I, Vital AL, Otero Á, Nieto AB, Sousa P, Patino-Alonso MC, Corchete LA, Tão H, Rebelo O, Barbosa M, Almeida MR, Guedes AF, Lopes MC, French PJ, Orfao A, Tabernero MD. Prognostic stratification of adult primary glioblastoma multiforme patients based on their tumor gene amplification profiles. Oncotarget 2018; 9:28083-28102. [PMID: 29963263 PMCID: PMC6021328 DOI: 10.18632/oncotarget.25562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/14/2018] [Indexed: 01/08/2023] Open
Abstract
Several classification systems have been proposed to address genomic heterogeneity of glioblastoma multiforme, but they either showed limited prognostic value and/or are difficult to implement in routine diagnostics. Here we propose a prognostic stratification model for these primary tumors based on tumor gene amplification profiles, that might be easily implemented in routine diagnostics, and potentially improve the patients management. Gene amplification profiles were prospectively evaluated in 80 primary glioblastoma multiforme tumors using single-nucleotide polymorphism arrays and the results obtained validated in publicly available data from 267/347 cases. Gene amplification was detected in 45% of patients, and chromosome 7p11.2 including the EGFR gene, was the most frequently amplified chromosomal region – either alone (18%) or in combination with amplification of DNA sequences in other chromosomal regions (10% of cases). Other frequently amplified DNA sequences included regions in chromosomes 12q(10%), 4q12(7%) and 1q32.1(4%). Based on their gene amplification profiles, glioblastomas were subdivided into: i) tumors with no gene amplification (55%); ii) tumors with chromosome 7p/EGFR gene amplification (with or without amplification of other chromosomal regions) (38%); and iii) glioblastoma multiforme with a single (11%) or multiple (6%) amplified DNA sequences in chromosomal regions other than chromosome 7p. From the prognostic point of view, these amplification profiles showed a significant impact on overall survival of glioblastoma multiforme patients (p>0.001). Based on these gene amplification profiles, a risk-stratification scoring system was built for prognostic stratification of glioblastoma which might be easily implemented in routine diagnostics, and potentially contribute to improved patient management.
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Affiliation(s)
- María González-Tablas
- Centre for Cancer Research (CIC IBMCC-CSIC/USAL), Department of Medicine, CIBERONC, University of Salamanca, Salamanca, Spain
| | - Inês Crespo
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Luísa Vital
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Álvaro Otero
- Servicio de Neurocirugía, Hospital Universitario e Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
| | - Ana Belén Nieto
- Department of Statistics, University of Salamanca, Salamanca, Spain
| | - Pablo Sousa
- Servicio de Neurocirugía, Hospital Universitario e Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
| | | | - Luis Antonio Corchete
- Departamento de Hematología, Hospital Universitario, IBSAL, IBMCC (USAL-CSIC), Salamanca, Spain
| | - Hermínio Tão
- Neurosurgery Service, University Hospital of Coimbra, Coimbra, Portugal
| | - Olinda Rebelo
- Neuropathology Laboratory, Neurology Service, University Hospital of Coimbra, Coimbra, Portugal
| | - Marcos Barbosa
- Neurosurgery Service, University Hospital of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | - Ana Filipa Guedes
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - María Celeste Lopes
- Centre for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Pim J French
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Alberto Orfao
- Centre for Cancer Research (CIC IBMCC-CSIC/USAL), Department of Medicine, CIBERONC, University of Salamanca, Salamanca, Spain.,Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
| | - María Dolores Tabernero
- Centre for Cancer Research (CIC IBMCC-CSIC/USAL), Department of Medicine, CIBERONC, University of Salamanca, Salamanca, Spain.,Instituto Biosanitario de Salamanca (IBSAL), Salamanca, Spain
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Deng G, Yang J, Zhang Q, Xiao ZX, Cai H. MethCNA: a database for integrating genomic and epigenomic data in human cancer. BMC Genomics 2018; 19:138. [PMID: 29433427 PMCID: PMC5810021 DOI: 10.1186/s12864-018-4525-0] [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: 10/26/2017] [Accepted: 02/05/2018] [Indexed: 12/23/2022] Open
Abstract
Background The integration of DNA methylation and copy number alteration data promises to provide valuable insight into the underlying molecular mechanisms responsible for cancer initiation and progression. However, the generation and processing of these datasets are costly and time-consuming if carried out separately. The Illumina Infinium HumanMethylation450 BeadChip, initially designed for the evaluation of DNA methylation levels, allows copy number variant calling using bioinformatics tools. Results A substantial amount of Infinium HumanMethylation450 data across various cancer types has been accumulated in recent years and is a valuable resource for large-scale data analysis. Here we present MethCNA, a comprehensive database for genomic and epigenomic data integration in human cancer. In the current release, MethCNA contains about 10,000 tumor samples representing 37 cancer types. All raw array data were collected from The Cancer Genome Atlas and NCBI Gene Expression Omnibus database and analyzed using a pipeline that integrated multiple computational resources and tools. The normalized copy number aberration data and DNA methylation alterations were obtained. We provide a user-friendly web-interface for data mining and visualization. Conclusions The Illumina Infinium HumanMethylation450 BeadChip enables the interrogation and integration of both genomic and epigenomic data from exactly the same DNA specimen, and thus can aid in distinguishing driver from passenger mutations in cancer. We expect MethCNA will enable researchers to explore DNA methylation and copy number alteration patterns, identify key oncogenic drivers in cancer, and assist in the development of targeted therapies. MethCNA is publicly available online at http://cgma.scu.edu.cn/MethCNA. Electronic supplementary material The online version of this article (10.1186/s12864-018-4525-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaofeng Deng
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Qing Zhang
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou, Jiangsu, 221002, China.,Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221002, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
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Cell biology of glioblastoma multiforme: from basic science to diagnosis and treatment. Med Oncol 2018; 35:27. [PMID: 29387965 DOI: 10.1007/s12032-018-1083-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 01/09/2018] [Indexed: 12/20/2022]
Abstract
First described in the 1800s, glioblastoma multiforme (GBM), a class IV neoplasm with astrocytic differentiation, as per the revised 2016 World Health Organization classification of tumors of the central nervous system (CNS) is the most common malignant tumor of the CNS. GBM has an extremely wide set of alterations, both genetic and epigenetic, which yield a great number of mutation subgroups, some of which have an established role in independent patient survival and treatment response. All of those components not only represent a closed cycle but are also relevant to the tumor biological behavior and resistance to treatment as they form the pathobiological behavior and clinical course. The presence of different triggering mutations on the background of the presence of key mutations in the GBM stem cells (GBMsc) further separates GBM as primary arising de novo from neural stem cell precursors developing into GBMsc and secondary, by means of aggregated mutations. Some of the change in cellular biology in GBM can be observed via light microscope as they form the cellular and tissue hallmarks of the condition. Changes in genetic information, resulting in alteration, suppression and expression of genes compared to their physiological levels in healthy astrocytes lead to not only cellular, but also extracellular matrix reorganization. These changes result in a multiform number of micromorphological and purely immunological/biochemical forms. Therefore, in the twenty-first century the term multiforme, previously outcast from nomenclatures, has gained new popularity on the background of genotypic diversity in this neoplastic entry.
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Song L, Bhuvaneshwar K, Wang Y, Feng Y, Shih IM, Madhavan S, Gusev Y. CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data. Cancer Inform 2017; 16:1176935117746637. [PMID: 29343938 PMCID: PMC5761903 DOI: 10.1177/1176935117746637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/26/2017] [Indexed: 01/10/2023] Open
Abstract
The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control groups), which is a typical use case in translational research. The differentially changed cytobands or chromosomes can then be linked to genes located in the affected genomic regions, as well as pathways. This enables in-depth systems biology-based network analysis and assessment of the impact of CNA on various biological processes or clinical outcomes. This package was successfully applied to analysis of DNA copy number data in colorectal cancer as a part of multi-omics integrative study as well as for analysis of several other cancer types. The source code, along with an end-to-end tutorial, and example data are freely available in Bioconductor at http://bioconductor.org/packages/CINdex/.
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Affiliation(s)
- Lei Song
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yue Wang
- The Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Yuanjian Feng
- The Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA
| | - Ie-Ming Shih
- Department of Gynecology and Obstetrics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
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38
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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Contribution of 1p, 19q, 9p and 10q Automated Analysis by FISH to the Diagnosis and Prognosis of Oligodendroglial Tumors According to WHO 2016 Guidelines. PLoS One 2016; 11:e0168728. [PMID: 28030632 PMCID: PMC5193469 DOI: 10.1371/journal.pone.0168728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023] Open
Abstract
Objective To study the feasibility and the diagnostic and prognostic interest of automated analysis of 1p, 19q, 9p and 10q status by FISH technique in oligodendroglial tumors. Methods We analyzed a retrospective series of 33 consecutive gliomas with oligodendroglial histology (originally diagnosed as 24 oligodendrogliomas and 9 oligoastrocytomas). For all cases, automated FISH analysis of 1p, 19q, 9p and 10q status were performed and compared to clinical and histological data, ATRX, IDH1R132H and alpha-internexin status (studied by immunohistochemistry) and overall survival (OS). Manual analysis of 9p and 10q status were also performed and compared to automated analysis to verify the concordance of the two methods. Results The 33 gliomas were reclassified into 13 low-grade oligodendrogliomas (OII), 10 anaplastic oligodendrogliomas (OIII), 3 diffuse astrocytomas (AII), 3 anaplastic astrocytomas (AIII) and 4 glioblastomas (GBM) according to the WHO 2016 histological criteria. The 1p and/or 19q imbalanced status were restricted to astrocytomas with no correlation to their grade or their OS. Chromosome 9p deletion was restricted to OIII (70%) and GBM (100%) and was correlated with a shorter OS in the total cohort (p = 0.0007), the oligodendroglioma cohort (p = 0.03) and the astrocytoma cohort (p = 0.001). Concordance between 9p manual and automated analysis was satisfactory (81%, κ = 0.69). Chromosome 10q deletion was restricted to GBMs (50%) and was correlated with a poor OS in both the total cohort (p = 0.003) and the astrocytoma (AS) cohort (p = 0.04). Concordance between manual and automated analysis was satisfactory (79%, κ = 0.62). Conclusion Automated analysis of 1p, 19q, 9p and 10q status by FISH is a reliable technique which allows for refined classification of oligodendroglial tumors. 1p and/or 19q imbalanced status is evidence of astrocytic differentiation. 9p deletion is found in high grade oligodendrogliomas and astrocytomas with a poor OS. 10q is related to GBM status and a poor OS.
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Bhuvaneshwar K, Belouali A, Singh V, Johnson RM, Song L, Alaoui A, Harris MA, Clarke R, Weiner LM, Gusev Y, Madhavan S. G-DOC Plus - an integrative bioinformatics platform for precision medicine. BMC Bioinformatics 2016; 17:193. [PMID: 27130330 PMCID: PMC4851789 DOI: 10.1186/s12859-016-1010-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/04/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. RESULTS G-DOC Plus currently holds data from over 10,000 patients selected from private and public resources including Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the recently added datasets from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT), caArray studies of lung and colon cancer, ImmPort and the 1000 genomes data sets. The system allows researchers to explore clinical-omic data one sample at a time, as a cohort of samples; or at the level of population, providing the user with a comprehensive view of the data. G-DOC Plus tools have been leveraged in cancer and non-cancer studies for hypothesis generation and validation; biomarker discovery and multi-omics analysis, to explore somatic mutations and cancer MRI images; as well as for training and graduate education in bioinformatics, data and computational sciences. Several of these use cases are described in this paper to demonstrate its multifaceted usability. CONCLUSION G-DOC Plus can be used to support a variety of user groups in multiple domains to enable hypothesis generation for precision medicine research. The long-term vision of G-DOC Plus is to extend this translational bioinformatics platform to stay current with emerging omics technologies and analysis methods to continue supporting novel hypothesis generation, analysis and validation for integrative biomedical research. By integrating several aspects of the disease and exposing various data elements, such as outpatient lab workup, pathology, radiology, current treatments, molecular signatures and expected outcomes over a web interface, G-DOC Plus will continue to strengthen precision medicine research. G-DOC Plus is available at: https://gdoc.georgetown.edu .
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Affiliation(s)
- Krithika Bhuvaneshwar
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Anas Belouali
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Varun Singh
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Robert M. Johnson
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Lei Song
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Adil Alaoui
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Michael A. Harris
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
| | - Robert Clarke
- />Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC USA
| | - Louis M. Weiner
- />Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC USA
| | - Yuriy Gusev
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
- />Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC USA
| | - Subha Madhavan
- />Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC USA
- />Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC USA
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Roth JJ, Fierst TM, Waanders AJ, Yimei L, Biegel JA, Santi M. Whole Chromosome 7 Gain Predicts Higher Risk of Recurrence in Pediatric Pilocytic Astrocytomas Independently From KIAA1549-BRAF Fusion Status. J Neuropathol Exp Neurol 2016; 75:306-15. [PMID: 26945035 DOI: 10.1093/jnen/nlw001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The most frequent genetic alteration identified in pediatric pilocytic astrocytomas and pilomyxoid variant is the KIAA1549-BRAF fusion, which typically results from a 2.0 Mb tandem duplication in chromosome band 7q34. Less frequent abnormalities include fusion genes,BRAF, FGFR, KRAS, and NF1 point mutations, and whole chromosome gains. To correlate genetic alterations with clinical course data, we retrospectively analyzed the tumors with pilocytic and pilomyxoid histology of a cohort of 116 pediatric patients, aged 5 months to 23 years. Gross total resection was associated with a decreased risk of recurrence (p = 0.001), supporting previous findings that complete tumor excision correlates with long-term and disease-free survival. We found no significant association between recurrence rate and the presence of the KIAA1549-BRAF fusion or BRAF mutation (p = 0.167). Interestingly, gain of whole chromosome 7 (WC7) was associated with a 4.7-fold increased risk of tumor recurrence, even after adjusting for surgical status (p = 0.025), and other genetic alterations. Using fluorescence in situ hybridization, we demonstrated that when WC7 gain accompanies the KIAA1549-BRAF fusion, the fusion likely arises first. This study highlights the utility of genetic studies for risk assessment of pilocytic and pilomyxoid astrocytomas, which may impact treatment selections.
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Affiliation(s)
- Jacquelyn J Roth
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB)
| | - Tamara M Fierst
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB)
| | - Angela J Waanders
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB)
| | - Li Yimei
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB)
| | - Jaclyn A Biegel
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB)
| | - Mariarita Santi
- From the Department of Pediatrics (JJR, AJW), Department of Pathology and Laboratory Medicine (MS), and Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (AJW); Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania (JJR); Department of Bio- statistics and Epidemiology, Perelman School of Medicine at the Univer- sity of Pennsylvania, Philadelphia, Pennsylvania (LY); Department of Neurosurgery, Temple University School of Medicine, Philadelphia, Pennsylvania (TMF); Department of Pathology and Laboratory Medicine, Children s Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California (JAB).
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Makale M, Kesari S. Cell Phones and Glioma Risk: An Update. Neurooncol Pract 2015. [DOI: 10.1093/nop/npv045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cohen A, Sato M, Aldape K, Mason CC, Alfaro-Munoz K, Heathcock L, South ST, Abegglen LM, Schiffman JD, Colman H. DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status. Acta Neuropathol Commun 2015; 3:34. [PMID: 26091668 PMCID: PMC4474351 DOI: 10.1186/s40478-015-0213-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/21/2022] Open
Abstract
Introduction Isocitrate dehydrogenase (IDH) mutation status and grade define subgroups of diffuse gliomas differing based on age, tumor location, presentation, and prognosis. While some biologic differences between IDH mutated (IDHmut) and wild-type (IDHwt) gliomas are clear, the distinct alterations associated with progression of the two subtypes to glioblastoma (GBM, Grade IV) have not been well described. We analyzed copy number alterations (CNAs) across grades (Grade II–III and GBM) in both IDHmut and IDHwt infiltrating gliomas using molecular inversion probe arrays. Results Ninety four patient samples were divided into four groups: Grade II–III IDHwt (n = 17), Grade II–III IDHmut (n = 28), GBM IDHwt (n = 25), and GBM IDHmut (n = 24). We validated prior observations that IDHwt GBM have a high frequency of chromosome 7 gain (including EGFR) and chromosome 10 loss (including PTEN) compared with IDHmut GBM. Hierarchical clustering of IDHmut gliomas demonstrated distinct CNA patterns distinguishing lower grade gliomas versus GBM. However, similar hierarchical clustering of IDHwt gliomas demonstrated no CNA distinction between lower grade glioma and GBM. Functional analyses showed that IDHwt gliomas had more chromosome gains in regions containing receptor tyrosine kinase pathways. In contrast, IDHmut gliomas more commonly demonstrated amplification of cyclins and cyclin dependent kinase genes. One of the most common alterations associated with transformation of lower grade to GBM IDHmut gliomas was the loss of chromosomal regions surrounding PTEN. IDHmut GBM tumors demonstrated significantly higher levels of overall CNAs compared to lower grade IDHmut tumors and all grades of IDHwt tumors, and IDHmut GBMs also demonstrated significant increase in incidence of chromothripsis. Conclusions Taken together, these analyses demonstrate distinct molecular ontogeny between IDHwt and IDHmut gliomas. Our data also support the novel findings that malignant progression of IDHmut gliomas to GBM involves increased genomic instability and genomic catastrophe, while IDHwt lower grade tumors are virtually identical to GBMs at the level of DNA copy number alterations. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0213-3) contains supplementary material, which is available to authorized users.
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Crespo I, Vital AL, Gonzalez-Tablas M, Patino MDC, Otero A, Lopes MC, de Oliveira C, Domingues P, Orfao A, Tabernero MD. Molecular and Genomic Alterations in Glioblastoma Multiforme. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1820-33. [PMID: 25976245 DOI: 10.1016/j.ajpath.2015.02.023] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 01/16/2015] [Accepted: 02/09/2015] [Indexed: 12/19/2022]
Abstract
In recent years, important advances have been achieved in the understanding of the molecular biology of glioblastoma multiforme (GBM); thus, complex genetic alterations and genomic profiles, which recurrently involve multiple signaling pathways, have been defined, leading to the first molecular/genetic classification of the disease. In this regard, different genetic alterations and genetic pathways appear to distinguish primary (eg, EGFR amplification) versus secondary (eg, IDH1/2 or TP53 mutation) GBM. Such genetic alterations target distinct combinations of the growth factor receptor-ras signaling pathways, as well as the phosphatidylinositol 3-kinase/phosphatase and tensin homolog/AKT, retinoblastoma/cyclin-dependent kinase (CDK) N2A-p16(INK4A), and TP53/mouse double minute (MDM) 2/MDM4/CDKN2A-p14(ARF) pathways, in cells that present features associated with key stages of normal neurogenesis and (normal) central nervous system cell types. This translates into well-defined genomic profiles that have been recently classified by The Cancer Genome Atlas Consortium into four subtypes: classic, mesenchymal, proneural, and neural GBM. Herein, we review the most relevant genetic alterations of primary versus secondary GBM, the specific signaling pathways involved, and the overall genomic profile of this genetically heterogeneous group of malignant tumors.
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Affiliation(s)
- Ines Crespo
- Centre for Neurosciences and Cell Biology, Faculties of Pharmacy and Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Louisa Vital
- Centre for Neurosciences and Cell Biology, Faculties of Pharmacy and Medicine, University of Coimbra, Coimbra, Portugal
| | - María Gonzalez-Tablas
- Department of Medicine, Centre for Cancer Research (Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer; Centro Superior de Investigaciones Científicas/Universidad de Salamanca; Instituto de Investigación Biomédica de Salamanca), University of Salamanca, Salamanca, Spain
| | | | - Alvaro Otero
- Neurosurgery Service, University Hospital of Salamanca, Salamanca, Spain; Biomedical Research Institute of Salamanca, Salamanca, Spain
| | - María Celeste Lopes
- Centre for Neurosciences and Cell Biology, Faculties of Pharmacy and Medicine, University of Coimbra, Coimbra, Portugal
| | - Catarina de Oliveira
- Centre for Neurosciences and Cell Biology, Faculties of Pharmacy and Medicine, University of Coimbra, Coimbra, Portugal
| | - Patricia Domingues
- Centre for Neurosciences and Cell Biology, Faculties of Pharmacy and Medicine, University of Coimbra, Coimbra, Portugal; Department of Medicine, Centre for Cancer Research (Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer; Centro Superior de Investigaciones Científicas/Universidad de Salamanca; Instituto de Investigación Biomédica de Salamanca), University of Salamanca, Salamanca, Spain; Biomedical Research Institute of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine, Centre for Cancer Research (Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer; Centro Superior de Investigaciones Científicas/Universidad de Salamanca; Instituto de Investigación Biomédica de Salamanca), University of Salamanca, Salamanca, Spain; Biomedical Research Institute of Salamanca, Salamanca, Spain
| | - Maria Dolores Tabernero
- Department of Medicine, Centre for Cancer Research (Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer; Centro Superior de Investigaciones Científicas/Universidad de Salamanca; Instituto de Investigación Biomédica de Salamanca), University of Salamanca, Salamanca, Spain; Biomedical Research Institute of Salamanca, Salamanca, Spain; Institute of Health Science Studies of Castilla and León Research Laboratory, University Hospital of Salamanca, Salamanca, Spain.
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Vyazunova I, Maklakova VI, Berman S, De I, Steffen MD, Hong W, Lincoln H, Morrissy AS, Taylor MD, Akagi K, Brennan CW, Rodriguez FJ, Collier LS. Sleeping Beauty mouse models identify candidate genes involved in gliomagenesis. PLoS One 2014; 9:e113489. [PMID: 25423036 PMCID: PMC4244117 DOI: 10.1371/journal.pone.0113489] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/27/2014] [Indexed: 01/01/2023] Open
Abstract
Genomic studies of human high-grade gliomas have discovered known and candidate tumor drivers. Studies in both cell culture and mouse models have complemented these approaches and have identified additional genes and processes important for gliomagenesis. Previously, we found that mobilization of Sleeping Beauty transposons in mice ubiquitously throughout the body from the Rosa26 locus led to gliomagenesis with low penetrance. Here we report the characterization of mice in which transposons are mobilized in the Glial Fibrillary Acidic Protein (GFAP) compartment. Glioma formation in these mice did not occur on an otherwise wild-type genetic background, but rare gliomas were observed when mobilization occurred in a p19Arf heterozygous background. Through cloning insertions from additional gliomas generated by transposon mobilization in the Rosa26 compartment, several candidate glioma genes were identified. Comparisons to genetic, epigenetic and mRNA expression data from human gliomas implicates several of these genes as tumor suppressor genes and oncogenes in human glioblastoma.
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Affiliation(s)
- Irina Vyazunova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Vilena I. Maklakova
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Samuel Berman
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Ishani De
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Megan D. Steffen
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Won Hong
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - Hayley Lincoln
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
| | - A. Sorana Morrissy
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Keiko Akagi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, United States of America
| | - Cameron W. Brennan
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Fausto J. Rodriguez
- Department of Pathology, Division of Neuropathology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Lara S. Collier
- School of Pharmacy and University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Madison, WI, United States of America
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Codispoti KET, Mosier S, Ramsey R, Lin MT, Rodriguez FJ. Genetic and pathologic evolution of early secondary gliosarcoma. Brain Tumor Pathol 2013; 31:40-6. [PMID: 23324827 DOI: 10.1007/s10014-012-0132-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 12/23/2012] [Indexed: 12/18/2022]
Abstract
Gliosarcoma is a subset of glioblastoma with glial and mesenchymal components. True secondary gliosarcomas (i.e. progressing from lower-grade precursors) in the absence of radiation therapy are very rare. We report the unique case of a 61-year-old male who developed a fibrillary astrocytoma (WHO grade II). In the absence of adjuvant therapy the tumor recurred 3 years later as a gliosarcoma comprising an infiltrating glial component and a curious, early high-grade sarcomatous component surrounding intratumoral vessels. DNA was extracted from formalin fixed paraffin-embedded tissues from the precursor low-grade glioma and from the glioma and sarcomatous components at progression. Samples were hybridized separately to a 300 k Illumina SNP array. IDH1(R132H) mutant protein immunohistochemistry was positive in all tissue components. Alterations identified in all samples included dup(1)(q21q41), del(1)(q41qter), del(2)(q31.1), del(2)(q36.3qter), del(4)(q35.1qter), dup(7)(q22.2q36.3), del(7)(q36.3qter), del(9)(p21.3pter), dup(10)(p13pter), del(10)(q26.13q26.3), dup(17) (q12qter), and copy neutral LOH(20)(p11.23p11.21). The recurrent tumor had additional alterations, including del(3)(p21.31q13.31), del(18)(q21.2qter), and a homozygous del(9)(p21.3)(CDKN2A locus) and the sarcoma component had, in addition, del(4)(p14pter), del(6)(q12qter), del(11)(q24.3qter), and del(16)(p11.2pter). In conclusion, unique copy number alterations were identified during tumor progression from a low-grade glioma to gliosarcoma. A subset of alterations developed specifically in the sarcomatous component.
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Amplified and homozygously deleted genes in glioblastoma: impact on gene expression levels. PLoS One 2012; 7:e46088. [PMID: 23029397 PMCID: PMC3460955 DOI: 10.1371/journal.pone.0046088] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/27/2012] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) displays multiple amplicons and homozygous deletions that involve relevant pathogenic genes and other genes whose role remains unknown. METHODOLOGY Single-nucleotide polymorphism (SNP)-arrays were used to determine the frequency of recurrent amplicons and homozygous deletions in GBM (n = 46), and to evaluate the impact of copy number alterations (CNA) on mRNA levels of the genes involved. PRINCIPAL FINDINGS Recurrent amplicons were detected for chromosomes 7 (50%), 12 (22%), 1 (11%), 4 (9%), 11 (4%), and 17 (4%), whereas homozygous deletions involved chromosomes 9p21 (52%) and 10q (22%). Most genes that displayed a high correlation between DNA CNA and mRNA levels were coded in the amplified chromosomes. For some amplicons the impact of DNA CNA on mRNA expression was restricted to a single gene (e.g., EGFR at 7p11.2), while for others it involved multiple genes (e.g., 11 and 5 genes at 12q14.1-q15 and 4q12, respectively). Despite homozygous del(9p21) and del(10q23.31) included multiple genes, association between these DNA CNA and RNA expression was restricted to the MTAP gene. CONCLUSIONS Overall, our results showed a high frequency of amplicons and homozygous deletions in GBM with variable impact on the expression of the genes involved, and they contributed to the identification of other potentially relevant genes.
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