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Staszkiewicz R, Sobański D, Pulka W, Gładysz D, Gadzieliński M, Strojny D, Grabarek BO. Variances in the Expression Profile of Circadian Clock-Related Genes in Astrocytic Brain Tumors. Cancers (Basel) 2024; 16:2335. [PMID: 39001398 PMCID: PMC11240661 DOI: 10.3390/cancers16132335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
This study explores the role of circadian clock genes in the progression of astrocytic tumors, a prevalent type of brain tumor. The aim was to assess the expression patterns of these genes in relation to the tumor grade. Using microarray analysis, qRT-PCR, and methylation-specific PCR, we examined gene expression, DNA methylation patterns, and microRNA interactions in tumor samples from 60 patients. Our results indicate that the expression of key circadian clock genes, such as clock circadian regulator (CLOCK), protein kinase AMP-activated catalytic subunit alpha 1 (PRKAA1), protein kinase AMP-activated catalytic subunit alpha 2 (PRKAA2), protein kinase AMP-activated non-catalytic subunit beta 1 (PRKAB1), protein kinase AMP-activated non-catalytic subunit beta 2 (PRKAB2), period circadian regulator 1 (PER1), period circadian regulator 2 (PER2) and period circadian regulator 3 (PER3), varies significantly with the tumor grade. Notably, increased CLOCK gene expression and protein levels were observed in higher-grade tumors. DNA methylation analysis revealed that the promoter regions of PER1-3 genes were consistently methylated, suggesting a mechanism for their reduced expression. Our findings also underscore the complex regulatory mechanisms involving miRNAs, such as hsa-miR-106-5p, hsa-miR-20b-5p, and hsa-miR-30d-3p, which impact the expression of circadian clock-related genes. This underscores the importance of circadian clock genes in astrocytic tumor progression and highlights their potential as biomarkers and therapeutic targets. Further research is needed to validate these results and explore their clinical implications.
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Affiliation(s)
- Rafał Staszkiewicz
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
- Department of Neurosurgery, 5th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, 30-901 Cracow, Poland
- Department of Neurosurgery, Faculty of Medicine in Zabrze, Academy of Silesia, 40-555 Katowice, Poland
| | - Dawid Sobański
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
- Department of Neurosurgery, Szpital sw. Rafala in Cracow, 30-693 Cracow, Poland
| | - Wojciech Pulka
- Department of Neurosurgery, Neurotraumatology and Spinal Surgery, Regional Hospital in Elblag, 82-300 Elblag, Poland;
| | - Dorian Gładysz
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
- Department of Neurosurgery, 5th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, 30-901 Cracow, Poland
- Department of Neurosurgery, Faculty of Medicine in Zabrze, Academy of Silesia, 40-555 Katowice, Poland
| | - Marcin Gadzieliński
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
- Department of Neurosurgery, 5th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, 30-901 Cracow, Poland
- Department of Neurosurgery, Faculty of Medicine in Zabrze, Academy of Silesia, 40-555 Katowice, Poland
| | - Damian Strojny
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
- Institute of Health Care, National Academy of Applied Sciences in Przemysl, 37-700 Przemysl, Poland
- New Medical Techniques Specjalist Hospital of St. Family in Rudna Mała, 36-054 Rudna Mala, Poland
| | - Beniamin Oskar Grabarek
- Collegium Medicum, WSB University, 41-300 Dabrowa Gornicza, Poland; (D.S.); (D.G.); (M.G.); (D.S.); (B.O.G.)
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2
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Nurminen R, Afyounian E, Paunu N, Katainen R, Isomäki M, Nurminen A, Scaravilli M, Tolppanen J, Fey V, Kivinen A, Helén P, Välimäki N, Kesseli J, Aaltonen LA, Haapasalo H, Nykter M, Rautajoki KJ. Previously reported CCDC26 risk variant and novel germline variants in GALNT13, AR, and MYO10 associated with familial glioma in Finland. Sci Rep 2024; 14:11562. [PMID: 38773237 PMCID: PMC11109329 DOI: 10.1038/s41598-024-62296-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/15/2024] [Indexed: 05/23/2024] Open
Abstract
Predisposing factors underlying familial aggregation of non-syndromic gliomas are still to be uncovered. Whole-exome sequencing was performed in four Finnish families with brain tumors to identify rare predisposing variants. A total of 417 detected exome variants and 102 previously reported glioma-related variants were further genotyped in 19 Finnish families with brain tumors using targeted sequencing. Rare damaging variants in GALNT13, MYO10 and AR were identified. Two families carried either c.553C>T (R185C) or c.1214T>A (L405Q) on GALNT13. Variant c.553C>T is located on the substrate-binding site of GALNT13. AR c.2180G>T (R727L), which is located on a ligand-binding domain of AR, was detected in two families, one of which also carried a GALNT13 variant. MYO10 c.4448A>G (N1483S) was detected in two families and c.1511C>T (A504V) variant was detected in one family. Both variants are located on functional domains related to MYO10 activity in filopodia formation. In addition, affected cases in six families carried a known glioma risk variant rs55705857 in CCDC26 and low-risk glioma variants. These novel findings indicate polygenic inheritance of familial glioma in Finland and increase our understanding of the genetic contribution to familial glioma susceptibility.
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Affiliation(s)
- Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Niina Paunu
- Department of Oncology, Tampere University Hospital, Tampere, Finland
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mari Isomäki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anssi Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Mauro Scaravilli
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Jenni Tolppanen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Vidal Fey
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Pauli Helén
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Niko Välimäki
- Applied Tumor Genomics Research Program, Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hannu Haapasalo
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories ltd., Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland.
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, Helsinki, Finland.
| | - Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland.
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
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3
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Li W, Chen J, Xiang C, Long Y, Wu K, Li J. The Clinical Relevance and Functional Implications of Thymosin Beta-10 in Glioma. Genet Res (Camb) 2023; 2023:5517445. [PMID: 38026448 PMCID: PMC10653960 DOI: 10.1155/2023/5517445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/02/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Glioma is a highly aggressive form of brain cancer characterized by limited treatment options and poor patient prognosis. In this study, we aimed to elucidate the oncogenic role of thymosin beta-10 (TMSB10) in glioma through comprehensive analyses of patient data from the TCGA and GTEx databases. Our investigation encompassed several key aspects, including the analysis of patients' clinical characteristics, survival analysis, in vitro and in vivo functional experiments, and the exploration of correlations between TMSB10 expression and immune cell infiltration. Our findings revealed a significant upregulation of TMSB10 expression in glioma tissues compared to normal brain tissues, with higher expression levels observed in tumors of advanced histological grades. Moreover, we observed positive correlations between TMSB10 expression and patient age, while no significant association with gender was detected. Additionally, TMSB10 exhibited marked elevation in gliomas with wild-type IDH and noncodeletion of 1p/19q. Survival analysis indicated that high TMSB10 expression was significantly associated with worse overall survival, disease-specific survival, and progression-free survival in glioma patients. Functionally, knockdown of TMSB10 in glioma cells resulted in reduced cellular growth rates and impaired tumor growth in xenograft models. Furthermore, our study revealed intriguing correlations between TMSB10 expression and immune cell infiltration within the tumor microenvironment. Specifically, TMSB10 showed negative associations with plasmacytoid dendritic cells (pDC) and γδ T cells (Tgd), while displaying positive correlations with neutrophils and macrophages. These findings collectively provide valuable insights into the oncogenic properties of TMSB10 in glioma, suggesting its potential as a therapeutic target and a biomarker for patient stratification.
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Affiliation(s)
- Weimin Li
- Department of Neurosurgery, Suining Central Hospital, Suining 629000, China
| | - Jinliang Chen
- Department of Neurosurgery, Suining Central Hospital, Suining 629000, China
| | - Chengwei Xiang
- Department of Neurosurgery, Suining Central Hospital, Suining 629000, China
| | - Yong Long
- Department of Neurosurgery, Suining Central Hospital, Suining 629000, China
| | - Ke Wu
- Department of Neurosurgery, Xichang People's Hospital, Xichang 615000, China
| | - Juan Li
- Department of Pharmacy, Suining Central Hospital, Suining 629000, China
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4
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Bauchet L, Sanson M. Deciphering gliomagenesis from genome-wide association studies. Neuro Oncol 2023; 25:1366-1367. [PMID: 36915962 PMCID: PMC10326471 DOI: 10.1093/neuonc/noad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Indexed: 03/16/2023] Open
Affiliation(s)
- Luc Bauchet
- Department of Neurosurgery, CHU Montpellier, Montpellier, France
- IGF, University of Montpellier, CNRS, INSERM, Montpellier, France
- French Brain Tumor DataBase, Registre des Tumeurs de l’Hérault, ICM, Montpellier, France
| | - Marc Sanson
- AP-HP, Hôpital de la Pitié-Salpêtrière, Service de Neurologie 2, Paris, France
- Sorbonne Université, INSERM Unité 1127, CNRS UMR 7225, Paris Brain Institute, Paris, France
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5
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Tejada Solís S, González Sánchez J, Iglesias Lozano I, Plans Ahicart G, Pérez Núñez A, Meana Carballo L, Gil Salú JL, Fernández Coello A, García Romero JC, Rodríguez de Lope Llorca A, García Duque S, Díez Valle R, Narros Giménez JL, Prat Acín R. Low grade gliomas guide-lines elaborated by the tumor section of Spanish Society of Neurosurgery. NEUROCIRUGIA (ENGLISH EDITION) 2023; 34:139-152. [PMID: 36446721 DOI: 10.1016/j.neucie.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 05/06/2023]
Abstract
Adult low-grade gliomas (Low Grade Gliomas, LGG) are tumors that originate from the glial cells of the brain and whose management involves great controversy, starting from the diagnosis, to the treatment and subsequent follow-up. For this reason, the Tumor Group of the Spanish Society of Neurosurgery (GT-SENEC) has held a consensus meeting, in which the most relevant neurosurgical issues have been discussed, reaching recommendations based on the best scientific evidence. In order to obtain the maximum benefit from these treatments, an individualised assessment of each patient should be made by a multidisciplinary team. Experts in each LGG treatment field have briefly described it based in their experience and the reviewed of the literature. Each area has been summarized and focused on the best published evidence. LGG have been surrounded by treatment controversy, although during the last years more accurate data has been published in order to reach treatment consensus. Neurosurgeons must know treatment options, indications and risks to participate actively in the decision making and to offer the best surgical treatment in every case.
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Affiliation(s)
- Sonia Tejada Solís
- Departamento de Neurocirugía, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain.
| | - Josep González Sánchez
- Departamento de Neurocirugía, Hospital Clínic i Provincial de Barcelona, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Irene Iglesias Lozano
- Departamento de Neurocirugía, Hospital Universitario Puerta del Mar, Cádiz, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Gerard Plans Ahicart
- Departamento de Neurocirugía, Hospital Universitari Bellvitge, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Angel Pérez Núñez
- Departamento de Neurocirugía, Hospital Universitario 12 de Octubre, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Leonor Meana Carballo
- Departamento de Neurocirugía, Centro Médico de Asturias, Oviedo, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Jose Luis Gil Salú
- Departamento de Neurocirugía, Hospital Universitario Puerta del Mar, Cádiz, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Alejandro Fernández Coello
- Departamento de Neurocirugía, Hospital Universitari Bellvitge, Barcelona, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Juan Carlos García Romero
- Departamento de Neurocirugía, Hospital Virgen del Rocío, Sevilla, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Angel Rodríguez de Lope Llorca
- Departamento de Neurocirugía, Hospital Virgen de la Salud, Toledo, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Sara García Duque
- Departamento de Neurocirugía, Hospital Universitario La Fe, Valencia, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Ricardo Díez Valle
- Departamento de Neurocirugía, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Jose Luis Narros Giménez
- Departamento de Neurocirugía, Hospital Virgen del Rocío, Sevilla, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
| | - Ricardo Prat Acín
- Departamento de Neurocirugía, Hospital Universitario La Fe, Valencia, Spain; Departamento de Neurocirugía, Hospital Universitario HM Montepríncipe, Madrid, Spain
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Pang F, He W, Liu X, Zou Z, Wu W, Wang Y, Yang P, Wen B, Jiang J, Teng Y, Yang X, Chen L, Jia Q, Li M, Xu J. Overexpression of PRKCH promotes tumorigenesis in patients with glioma and influences glioma stem cell properties. Pathol Res Pract 2022; 240:154236. [DOI: 10.1016/j.prp.2022.154236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
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7
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Yanchus C, Drucker KL, Kollmeyer TM, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo SB, Ali A, Decker PA, Kosel ML, Panda A, Al-Zahrani KN, Jiang L, Browning JWL, Lowden C, Geuenich M, Hernandez JJ, Gosio JT, Ahmed M, Loganathan SK, Berman J, Trcka D, Michealraj KA, Fortin J, Carson B, Hollingsworth EW, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He HH, Murphy DJ, Wang L, Abyzov A, Dennis JW, Maass PG, Campbell K, Wilson MD, Lachance DH, Wrensch M, Wiencke J, Mak T, Pennacchio LA, Dickel DE, Visel A, Wrana J, Taylor MD, Zadeh G, Dirks P, Eckel-Passow JE, Attisano L, Pombo A, Ida CM, Kvon EZ, Jenkins RB, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022; 378:68-78. [PMID: 36201590 PMCID: PMC9926876 DOI: 10.1126/science.abj2890] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Establishing causal links between inherited polymorphisms and cancer risk is challenging. Here, we focus on the single-nucleotide polymorphism rs55705857, which confers a sixfold greater risk of isocitrate dehydrogenase (IDH)-mutant low-grade glioma (LGG). We reveal that rs55705857 itself is the causal variant and is associated with molecular pathways that drive LGG. Mechanistically, we show that rs55705857 resides within a brain-specific enhancer, where the risk allele disrupts OCT2/4 binding, allowing increased interaction with the Myc promoter and increased Myc expression. Mutating the orthologous mouse rs55705857 locus accelerated tumor development in an Idh1R132H-driven LGG mouse model from 472 to 172 days and increased penetrance from 30% to 75%. Our work reveals mechanisms of the heritable predisposition to lethal glioma in ~40% of LGG patients.
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Affiliation(s)
- Connor Yanchus
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Kristen L. Drucker
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Thomas M. Kollmeyer
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Warren Winick-Ng
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
| | - Minggao Liang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Judy Pawling
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Silvana B. De Lorenzo
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asma Ali
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Paul A. Decker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Matt L. Kosel
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Arijit Panda
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Khalid N. Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lingyan Jiang
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jared W. L. Browning
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Chris Lowden
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Michael Geuenich
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J. Javier Hernandez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jessica T. Gosio
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Sampath Kumar Loganathan
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jacob Berman
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Daniel Trcka
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | | | - Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Brittany Carson
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Parisa Mazrooei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Lily Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Daniel J. Murphy
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, Scotland, UK
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, Scotland, UK
| | - Liguo Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - James W. Dennis
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Philipp G. Maass
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Kieran Campbell
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Wilson
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniel H. Lachance
- Departments of Neurology and Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - John Wiencke
- Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Tak Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Len A. Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Diane E. Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Jeffrey Wrana
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael D. Taylor
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Gelareh Zadeh
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Peter Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ana Pombo
- Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, 13092 Berlin, Germany
- Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
| | - Cristiane M. Ida
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92617, USA
| | - Robert B. Jenkins
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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8
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Association of TP53 rs1042522 C>G Polymorphism with Glioma Risk in Chinese Children. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2712808. [PMID: 35996546 PMCID: PMC9392611 DOI: 10.1155/2022/2712808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022]
Abstract
Glioma is the most common intracranial malignancy. TP53 is a crucial tumor suppressor gene that plays an essential regulatory role in cell growth, apoptosis, and DNA repair. The TP53 rs1042522 C>G polymorphism has been reported to be strongly associated with various tumor risks. To assess the TP53 rs1042522 C>G polymorphism with glioma risk in Chinese children, we determined the genotypes of the TP53 rs1042522 C>G polymorphism in 171 glioma patients and 228 cancer-free controls by Taqman assay. We assessed the association of the polymorphism with glioma risk using odds ratio (OR) and 95% confidence interval (CI) generated by logistic regression models. We also performed stratified analyses by age, gender, tumor subtypes, and clinical stages, but no significant association was detected between TP53 rs1042522 C>G polymorphism and childhood glioma risk. These results suggest that the TP53 rs1042522 C>G polymorphism is not associated with glioma risk in Chinese children. Subsequent studies with a larger sample size are needed to validate our results.
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Karabacak M, Ozkara BB, Mordag S, Bisdas S. Deep learning for prediction of isocitrate dehydrogenase mutation in gliomas: a critical approach, systematic review and meta-analysis of the diagnostic test performance using a Bayesian approach. Quant Imaging Med Surg 2022; 12:4033-4046. [PMID: 35919062 PMCID: PMC9338374 DOI: 10.21037/qims-22-34] [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: 01/13/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
Background Conventionally, identifying isocitrate dehydrogenase (IDH) mutation in gliomas is based on histopathological analysis of tissue specimens acquired via stereotactic biopsy or definitive resection. Accurate pre-treatment prediction of IDH mutation status using magnetic resonance imaging (MRI) can guide clinical decision-making. We aim to evaluate the diagnostic performance of deep learning (DL) to determine IDH mutation status in gliomas. Methods A systematic search of Cochrane Library, Web of Science, Medline, and Scopus was conducted to identify relevant publications until August 1, 2021. Articles were included if all the following criteria were met: (I) patients with histopathologically confirmed World Health Organization (WHO) grade II, III, or IV gliomas; (II) histopathological examination with the IDH mutation; (III) DL was used to predict the IDH mutation status; (IV) sufficient data for reconstruction of confusion matrices in terms of the diagnostic performance of the DL algorithms; and (V) original research articles. Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) and Checklist for Artificial Intelligence in Medical Imaging (CLAIM) was used to assess the studies' quality. Bayes theorem was utilized to calculate the posttest probability. Results Four studies with a total of 1,295 patients were included. In the training set, the pooled sensitivity, specificity, and area under the summary receiver operating characteristic (SROC) curve were 93.9%, 90.9% and 0.958, respectively. In the validation set, the pooled sensitivity, specificity, and area under the SROC curve were 90.8%, 85.5% and 0.939, respectively. With a known pretest probability of 80.2%, the Bayes theorem yielded a posttest probability of 97.6% and 96.0% for a positive test and 27.0% and 30.6% for a negative test for training sets and validation sets, respectively. Discussion This is the first meta-analysis that summarizes the diagnostic performance of DL in predicting IDH mutation status in gliomas via the Bayes theorem. DL algorithms demonstrate excellent diagnostic performance in predicting IDH mutation in gliomas. Radiomic features associated with IDH mutation, and its underlying pathophysiology extracted from advanced MRI may improve prediction probability. However, more studies are required to optimize and increase its reliability. Limitations include obtaining some data via email and lack of training and test sets statistics.
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Affiliation(s)
- Mert Karabacak
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpasa, Istanbul, Turkey
| | - Burak Berksu Ozkara
- Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Cerrahpasa, Istanbul, Turkey
| | - Seren Mordag
- Faculty of Medicine, Hacettepe University, Sihhiye, Ankara, Turkey
| | - Sotirios Bisdas
- Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, UK
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10
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Tewari S, Tom MC, Park DYJ, Wei W, Chao ST, Yu JS, Suh JH, Kilic S, Peereboom DM, Stevens GHJ, Lathia JD, Prayson R, Barnett GH, Angelov L, Mohammadi AM, Ahluwalia MS, Murphy ES. Sex-Specific Differences in Low Grade Glioma Presentation and Outcome. Int J Radiat Oncol Biol Phys 2022; 114:283-292. [PMID: 35667529 DOI: 10.1016/j.ijrobp.2022.05.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 05/02/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE In addition to established prognostic factors in low-grade glioma (LGG), studies suggest a sexual dimorphism with male sex portending worse prognosis. Our objective was to identify the impact of sex on presentation and outcomes in LGG. METHODS We conducted a retrospective cohort study of adults (aged ≥ 18 years) diagnosed with LGG (WHO 2016 grade 2 glioma). Patients with IDH wildtype tumors were excluded. Patients were matched between male and female sex by age, treatment, and surgery via propensity score matching. Patient, tumor, and treatment characteristics were analyzed by sex. Endpoints included overall survival (OS), next intervention free survival (NIFS), progression free survival (PFS), and malignant transformation free survival (MTFS). Kaplan Meier analyses and Cox proportional hazards regression multivariable analysis (MVA) with backwards elimination was completed. RESULTS Of the 532 patients identified, 258 (48%) were male. Males were more likely to present with seizure (69.38% vs. 56.57%, p = 0.002), but no other statistically significant differences between sexes at presentation were identified. 5-year OS was higher in females at 87% (95% CI 83%-91%) versus 78% (95% CI 73-84%) in males (p=0.0045). NIFS was significantly higher in female patients at 68% (95% CI 62-74%) versus 57% (95% CI 51%-64%) in males (p = 0.009). On MVA, female sex was independently associated with improved OS (HR 1.54, 95% CI 1.16-2.05; p= 0.002), NIFS (HR 1.42, 95% CI 1.42; p= 0.004), and MTFS (HR 1.62, 95% CI 1.24-2.12; p= 0.0004). In patients with molecularly defined LGG (IDH and 1p19q status) (n = 291), female sex remained independently associated with improved OS (HR 1.79, 95% CI 1.16-2.77; p = 0.008) and NIFS (HR 1.45, 95% CI 1.07-1.96; p = 0.016). CONCLUSIONS In this study, female sex was independently associated with improved outcomes. These findings support intrinsic sex-specific differences in LGG behavior, justifying further studies to optimize management and therapeutics based on sex.
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Affiliation(s)
- Surabhi Tewari
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
| | - Martin C Tom
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL
| | - Deborah Y J Park
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
| | - Wei Wei
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Samuel T Chao
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Jennifer S Yu
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - John H Suh
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Sarah Kilic
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - David M Peereboom
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Glen H J Stevens
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH
| | - Justin D Lathia
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Richard Prayson
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Gene H Barnett
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Neurological Surgery, Neurological Institute, Cleveland Clinic, Cleveland, OH
| | - Lilyana Angelov
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Neurological Surgery, Neurological Institute, Cleveland Clinic, Cleveland, OH
| | - Alireza M Mohammadi
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Neurological Surgery, Neurological Institute, Cleveland Clinic, Cleveland, OH
| | - Manmeet S Ahluwalia
- Department of Solid Tumor Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL
| | - Erin S Murphy
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH; Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH; Department of Anatomic Pathology, Cleveland Clinic, Cleveland, OH.
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11
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Zhang G, Li Y, Li N, Shen LF, Li Z. Functional implications of aging-related lncRNAs for predicting prognosis and immune status in glioma patients. Aging (Albany NY) 2022; 14:2348-2366. [PMID: 35273128 PMCID: PMC8954967 DOI: 10.18632/aging.203944] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/01/2022] [Indexed: 11/25/2022]
Abstract
This study is aimed to establish a new glioma prognosis model by integrating the aging-related lncRNA expression profiles and clinical parameters of glioma patients enrolled in the Chinese Glioma Genome Atlas and The Cancer Genome Atlas. The aging-related lncRNAs were explored using Pearson correlation analysis (|R|> 0.6, P < 0.001), and the prognostic signature in glioma patients was screened using univariate cox regression and least absolute shrinkage/selection operator regression. Based on the fifteen lncRNAs screened out, we divided the glioma patients into three subtypes, and developed a prognostic model. Kaplan-Meier survival curve analysis showed that low-risk patients survived longer time than high-risk patients. Principal component analysis indicated that the signature of aging-related lncRNAs was clearly distinct between the high- and low-risk groups. We also found the fifteen lncRNAs were closely correlated with 119 genes by establishing a co-expression network. Kyoto Encyclopedia of Genes and Genomes analysis displayed that the high- and low-risk groups were enriched in different functions and pathways. Different missense mutations were observed in the two groups, and the most frequent variant types were single nucleotide polymorphism. This study demonstrates that the novel aging-related lncRNAs signature has an important prognosis prediction ability and may contribute to individualized treatment for glioma.
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Affiliation(s)
- Guangying Zhang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China
| | - Yanyan Li
- Department of Nursing, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China
| | - Liang-Fang Shen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan Province 410008, PR China
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12
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Francis SS, Ostrom QT, Cote DJ, Smith TR, Claus E, Barnholtz-Sloan JS. The Epidemiology of Central Nervous System Tumors. Hematol Oncol Clin North Am 2022; 36:23-42. [PMID: 34801162 DOI: 10.1016/j.hoc.2021.08.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This article reviews the current epidemiology of central nervous system tumors. Population-level basic epidemiology, nationally and internationally, and current understanding of germline genetic risk are discussed, with a focus on known and well-studied risk factors related to the etiology of central nervous system tumors.
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Affiliation(s)
- Stephen S Francis
- Department of Neurological Surgery, Division of Neuro and Molecular Epidemiology, University of California San Francisco School of Medicine, 1450 3rd Street, HD442, San Francisco, CA 94158, USA.
| | - Quinn T Ostrom
- Department of Neurosurgery, Duke University School of Medicine, 571 Research Drive, MSRB-1, Rm 442, Durham, NC 27710, USA
| | - David J Cote
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, 1200 N State Street, Suite 3300, Los Angeles, CA 90033, USA
| | - Timothy R Smith
- Department of Neurosurgery, Computational Neuroscience Outcomes Center, Brigham and Women's Hospital, Harvard Medical School, 60 Fenwood Avenue, Boston, MA 02115, USA
| | - Elizabeth Claus
- Department of Neurosurgery, Yale University, Yale School of Public Health, Brigham and Women's Hospital, 60 College Street, New Haven, CT 06510, USA
| | - Jill S Barnholtz-Sloan
- Center for Biomedical Informatics and Information Technology, Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), NCI Shady Grove, 9609 Medical Center Dr, Rockville, MD 20850, USA
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13
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Yang Z, Ling F, Ruan S, Hu J, Tang M, Sun X, Long W. Clinical and Prognostic Implications of 1p/19q, IDH, BRAF, MGMT Promoter, and TERT Promoter Alterations, and Expression of Ki-67 and p53 in Human Gliomas. Cancer Manag Res 2021; 13:8755-8765. [PMID: 34849029 PMCID: PMC8627377 DOI: 10.2147/cmar.s336213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background and Objective Genetic alterations, including IDH, BRAF, and TERT promoter mutations (IDH-mu, BRAF-mu, TERTp-mu, respectively), 1p/19q co-deletion (1p/19q-codel), and MGMT promoter methylation (MGMTp-M), are correlated with glioma tumor development. Therefore, these genetic alterations could serve as biomarkers for the diagnosis, prognosis, and classification of gliomas, combined with the immunohistochemical markers Ki-67 and p53. However, the correlation between these alterations and the expression of Ki-67 and p53 is poorly understood. Methods We analyzed the prevalence and prognosis of these five alterations, as well as Ki-67 and p53 expression, in 103 primary grade II–IV gliomas via fluorescence qPCR, Sanger sequencing, fluorescence in situ hybridization, and immunohistochemistry. Results In the 103 cases, MGMTp-M was the most common alteration (70.9%), followed by TERTp-mu (58.3%), IDH-mu (46.6%), 1p/19q-codel (34.0%), and BRAF-mu (5.8%). No cases showed quintuple-positive alterations, but 26 cases (25.2%) showed quadruple-positive alterations (IDH-mu/TERTp-mu/MGMTp-M/1p/19q-codel). The percentage of TERTp-mu and 1p/19q-codel cases decreased with p53 expression, and the percentage of IDH-mu and 1p/19q-codel cases decreased with Ki-67 expression. IDH-mu, MGMTp-M, and 1p/19q-codel were positive factors for survival rates in glioma patients, while TERTp-mu, p53, and Ki-67 positivity were negative factors. Old age, histological grade IV, IDH-mu, 1p/19q-codel, Ki-67+, and p53+/Ki-67+ were significantly correlated with overall survival (OS). However, only p53+/Ki-67+ was an independent prognostic factor for OS in the multivariate Cox-model analysis. Conclusion IDH-mu only and quadruple-positivity were associated with good OS in glioma patients, while TERTp-mu only, TERTp-mu/MGMTp-M and p53+/Ki-67+ were associated with poor prognosis. Combining these genomic alterations and Ki-67/p53 expression should have clinical value in gliomas.
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Affiliation(s)
- Zixi Yang
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Feng Ling
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Sibei Ruan
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Jiajia Hu
- School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Mingxi Tang
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xingwang Sun
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Wenbo Long
- Pathology Department of the First Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
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14
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Abstract
PURPOSE OF REVIEW Brain and other central nervous system (CNS) tumors, while rare, cause significant morbidity and mortality across all ages. This article summarizes the current state of the knowledge on the epidemiology of brain and other CNS tumors. RECENT FINDINGS For childhood and adolescent brain and other CNS tumors, high birth weight, non-chromosomal structural birth defects and higher socioeconomic position were shown to be risk factors. For adults, increased leukocyte telomere length, proportion of European ancestry, higher socioeconomic position, and HLA haplotypes increase risk of malignant brain tumors, while immune factors decrease risk. Although no risk factor accounting for a large proportion of brain and other CNS tumors has been discovered, the use of high throughput "omics" approaches and improved detection/measurement of environmental exposures will help us refine our current understanding of these factors and discover novel risk factors for this disease.
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Affiliation(s)
- Quinn T Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Stephen S Francis
- Department of Neurological Surgery, Division of Neuro and Molecular Epidemiology, University of California, San Francisco, CA, USA
| | - Jill S Barnholtz-Sloan
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, and Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, MD, USA.
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15
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Saunders CN, Kinnersley B, Culliford R, Cornish AJ, Law PJ, Houlston RS. Relationship between genetically determined telomere length and glioma risk. Neuro Oncol 2021; 24:171-181. [PMID: 34477880 PMCID: PMC8804896 DOI: 10.1093/neuonc/noab208] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Telomere maintenance is increasingly recognized as being fundamental to glioma oncogenesis with longer leukocyte telomere length (LTL) reported to increase risk of glioma. To gain further insight into the relationship between telomere genetics and risk of glioma, we conducted several complementary analyses, using genome-wide association studies data on LTL (78 592 individuals) and glioma (12 488 cases and 18 169 controls). Methods We performed both classical and summary Mendelian randomization (SMR), coupled with heterogeneity in dependent instruments tests, at genome-wide significant LTL loci to examine if an association was mediated by the same causal variant in glioma. To prioritize genes underscoring glioma-LTL associations, we analyzed gene expression and DNA methylation data. Results Genetically increased LTL was significantly associated with increased glioma risk, random-effects inverse variance weighted ORs per 1 SD unit increase in the putative risk factor (odds ratio [OR]SD) 4.79 (95% confidence interval: 2.11-10.85; P = 1.76 × 10−4). SMR confirmed the previously reported LTL associations at 3q26.2 (TERC; PSMR = 1.33 × 10−5), 5p15.33 (TERT; PSMR = 9.80 × 10−27), 10q24.33 (STN1 alias OBFC1; PSMR = 4.31 × 10−5), and 20q13.3 (STMN3/RTEL1; PSMR = 2.47 × 10−4) glioma risk loci. Our analysis implicates variation at 1q42.12 (PSMR = 1.55 × 10−2), 6p21.3 (PSMR = 9.76 × 10−3), 6p22.2 (PSMR = 5.45 × 10−3), 7q31.33 (PSMR = 6.52 × 10−3), and 11q22.3 (PSMR = 8.89 × 10−4) as risk factors for glioma risk. While complicated by patterns of linkage disequilibrium, genetic variation involving PARP1, PRRC2A, CARMIL1, POT1, and ATM-NPAT1 was implicated in the etiology of glioma. Conclusions These observations extend the role of telomere-related genes in the development of glioma.
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Affiliation(s)
- Charlie N Saunders
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London SW7 3RP, UK
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16
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Association of Circadian Clock Gene Expression with Glioma Tumor Microenvironment and Patient Survival. Cancers (Basel) 2021; 13:cancers13112756. [PMID: 34199348 PMCID: PMC8199552 DOI: 10.3390/cancers13112756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/29/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Gliomas are the most common type of malignant primary brain tumors and are classified according to the cell of origin and genetic features, which can help predict the prognosis and treatment sensitivity. Improving the prognosis remains a challenge; however, chronobiology is a promising field for future works, as circadian clock genes are linked to the tumor biology and outcomes in multiple cancers, including glioma. Here, we examined the relationship of circadian clock genes, IDH mutational status, and prognosis in glioma patients by using unsupervised clustering of the expression of 13 clock genes. We further explored the expression of the clock genes across the tumor regions and cell subpopulations, highlighting the importance of the tumor microenvironment in researching circadian rhythms in cancer. Our research is important for understanding how best to target circadian rhythms to improve patient outcomes in neuro-oncology. Abstract Circadian clock genes have been linked to clinical outcomes in cancer, including gliomas. However, these studies have not accounted for established markers that predict the prognosis, including mutations in Isocitrate Dehydrogenase (IDH), which characterize the majority of lower-grade gliomas and secondary high-grade gliomas. To demonstrate the connection between circadian clock genes and glioma outcomes while accounting for the IDH mutational status, we analyzed multiple publicly available gene expression datasets. The unsupervised clustering of 13 clock gene transcriptomic signatures from The Cancer Genome Atlas showed distinct molecular subtypes representing different disease states and showed the differential prognosis of these groups by a Kaplan–Meier analysis. Further analyses of these groups showed that a low period (PER) gene expression was associated with the negative prognosis and enrichment of the immune signaling pathways. These findings prompted the exploration of the relationship between the microenvironment and clock genes in additional datasets. Circadian clock gene expression was found to be differentially expressed across the anatomical tumor location and cell type. Thus, the circadian clock expression is a potential predictive biomarker in glioma, and further mechanistic studies to elucidate the connections between the circadian clock and microenvironment are warranted.
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17
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Manjunath M, Yan J, Youn Y, Drucker KL, Kollmeyer TM, McKinney AM, Zazubovich V, Zhang Y, Costello JF, Eckel-Passow J, Selvin PR, Jenkins RB, Song JS. Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. Neuro Oncol 2021; 23:638-649. [PMID: 33130899 DOI: 10.1093/neuonc/noaa248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals' risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown. METHODS We hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. We assessed their potential regulatory role via in silico TF binding sequence perturbations, convolutional neural network trained on TF binding data, and simulated annealing-based interpretation methods. RESULTS We built an interactive website (http://education.knoweng.org/alg3/) summarizing the functional footprinting of 280 variants in 25 LGG GWAS regions, providing rich information for further computational and experimental scrutiny. We identified as case studies PHLDB1 and SLC25A26 as candidate target genes of rs12803321 and rs11706832, respectively, and predicted the GWAS variant rs648044 to be the causal SNP modulating ZBTB16, a known tumor suppressor in multiple cancers. We showed that rs648044 likely perturbed the binding affinity of the TF MAFF, as supported by RNA interference and in vitro MAFF binding experiments. CONCLUSIONS The identified candidate (causal SNP, target gene, TF) triplets and the accompanying resource will help accelerate our understanding of the molecular mechanisms underlying genetic risk factors for gliomas.
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Affiliation(s)
- Mohith Manjunath
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jialu Yan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kristen L Drucker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew M McKinney
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal, Québec, Canada
| | - Yi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | | | - Paul R Selvin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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18
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Eckel-Passow JE, Drucker KL, Kollmeyer TM, Kosel ML, Decker PA, Molinaro AM, Rice T, Praska CE, Clark L, Caron A, Abyzov A, Batzler A, Song JS, Pekmezci M, Hansen HM, McCoy LS, Bracci PM, Wiemels J, Wiencke JK, Francis S, Burns TC, Giannini C, Lachance DH, Wrensch M, Jenkins RB. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro Oncol 2021; 22:1602-1613. [PMID: 32386320 DOI: 10.1093/neuonc/noaa117] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Twenty-five germline variants are associated with adult diffuse glioma, and some of these variants have been shown to be associated with particular subtypes of glioma. We hypothesized that additional germline variants could be identified if a genome-wide association study (GWAS) were performed by molecular subtype. METHODS A total of 1320 glioma cases and 1889 controls were used in the discovery set and 799 glioma cases and 808 controls in the validation set. Glioma cases were classified into molecular subtypes based on combinations of isocitrate dehydrogenase (IDH) mutation, telomerase reverse transcriptase (TERT) promoter mutation, and 1p/19q codeletion. Logistic regression was applied to the discovery and validation sets to test for associations of variants with each of the subtypes. A meta-analysis was subsequently performed using a genome-wide P-value threshold of 5 × 10-8. RESULTS Nine variants in or near D-2-hydroxyglutarate dehydrogenase (D2HGDH) on chromosome 2 were genome-wide significant in IDH-mutated glioma (most significant was rs5839764, meta P = 2.82 × 10-10). Further stratifying by 1p/19q codeletion status, one variant in D2HGDH was genome-wide significant in IDH-mutated non-codeleted glioma (rs1106639, meta P = 4.96 × 10-8). Further stratifying by TERT mutation, one variant near FAM20C (family with sequence similarity 20, member C) on chromosome 7 was genome-wide significant in gliomas that have IDH mutation, TERT mutation, and 1p/19q codeletion (rs111976262, meta P = 9.56 × 10-9). Thirty-six variants in or near GMEB2 on chromosome 20 near regulator of telomere elongation helicase 1 (RTEL1) were genome-wide significant in IDH wild-type glioma (most significant was rs4809313, meta P = 2.60 × 10-10). CONCLUSIONS Performing a GWAS by molecular subtype identified 2 new regions and a candidate independent region near RTEL1, which were associated with specific glioma molecular subtypes.
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Affiliation(s)
| | - Kristen L Drucker
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Matt L Kosel
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Paul A Decker
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California
| | - Corinne E Praska
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lauren Clark
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Alissa Caron
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Alexej Abyzov
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Anthony Batzler
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Jun S Song
- Department of Physics, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California
| | - Lucie S McCoy
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California
| | - Paige M Bracci
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Joseph Wiemels
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Stephen Francis
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Terry C Burns
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Daniel H Lachance
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.,Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California.,Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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19
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Ali MW, Patro CPK, Zhu JJ, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lau C, Lai RK, Casey G. A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes. Hum Mutat 2020; 42:77-88. [PMID: 33169458 PMCID: PMC7839675 DOI: 10.1002/humu.24134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
Genome‐wide association studies (GWAS) have identified single‐nucleotide polymorphisms (SNPs) associated with glioma risk on 20q13.33, but the biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 20q13.33 impacted the activity of an enhancer, leading to an altered expression of nearby genes. To identify candidate functional SNPs, we identified all SNPs in linkage disequilibrium with the risk‐associated SNP rs2297440 that mapped to putative enhancers. Putative enhancers containing candidate functional SNPs were tested for allele‐specific effects in luciferase enhancer activity assays against glioblastoma multiforme (GBM) cell lines. An enhancer containing SNP rs3761124 exhibited allele‐specific effects on activity. Deletion of this enhancer by CRISPR‐Cas9 editing in GBM cell lines correlated with an altered expression of multiple genes, including STMN3, RTEL1, RTEL1‐TNFRSF6B, GMEB2, and SRMS. Expression quantitative trait loci (eQTL) analyses using nondiseased brain samples, isocitrate dehydrogenase 1 (IDH1) wild‐type glioma, and neurodevelopmental tissues showed STMN3 to be a consistent significant eQTL with rs3761124. RTEL1 and GMEB2 were also significant eQTLs in the context of early CNS development and/or in IDH1 wild‐type glioma. We provide evidence that rs3761124 is a functional variant on 20q13.33 related to glioma/GBM risk that modulates the expression of STMN3 and potentially other genes across diverse cellular contexts.
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Affiliation(s)
- Mourad Wagdy Ali
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - C Pawan K Patro
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Christopher H Dampier
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Sarah J Plummer
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Cem Kuscu
- Department of Surgery, James D. Eason Transplant Research Institute, University of Tennessee, Memphis, Tennessee, USA
| | - Mazhar Adli
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, Illinois, USA
| | - Ching Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
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20
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Poetsch L, Bronnimann C, Loiseau H, Frénel JS, Siegfried A, Seizeur R, Gauchotte G, Cappellen D, Carpentier C, Figarella-Branger D, Eimer S, Meyronet D, Ducray F. Characteristics of IDH-mutant gliomas with non-canonical IDH mutation. J Neurooncol 2020; 151:279-286. [PMID: 33205355 DOI: 10.1007/s11060-020-03662-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/09/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND Approximately 10% of IDH-mutant gliomas harbour non-canonical IDH mutations (non-p.R132H IDH1 and IDH2 mutations). OBJECTIVE The aim of this study was to analyse the characteristics of non-canonical IDH-mutant gliomas. MATERIALS AND METHODS We retrospectively analysed the characteristics of 166 patients with non-canonical IDH mutant gliomas and compared them to those of 155 consecutive patients with IDH1 p.R132H mutant gliomas. RESULTS The median age at diagnosis was 38 years in patients with non-canonical IDH mutant gliomas and 43 years in glioma patients with IDH1 p.R132H-mutant tumours. Family history of cancer was more frequent among glioma patients harbouring non-canonical IDH mutations than in patients with IDH1 p.R132H mutations (22.2% vs 5.1%; P < 0.05). Tumours were predominantly localised in the frontal lobe regardless of the type of IDH mutation. Compared to IDH1 p.R132H-mutant gliomas, tumours with non-canonical IDH mutations were more frequently found in the infratentorial region (5.5% vs 0%; P < 0.05) and were often multicentric (4.8% vs 0.9%; P < 0.05). Compared to IDH1 P.R132H-mutant gliomas, tumours with non-canonical IDH1 mutations were more frequently astrocytomas (65.6% vs 43%, P < 0.05), while those with IDH2 mutations were more frequently oligodendrogliomas (85% vs 48.3%; P < 0.05). The median overall survival was similar in patients with IDH1 p.R132H-mutant gliomas and patients with non-canonical IDH-mutant gliomas. CONCLUSION Gliomas with non-canonical IDH mutations have distinct radiological and histological characteristics. The presence of such tumours seems to be associated with genetic predisposition to cancer development.
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Affiliation(s)
- L Poetsch
- Service d'Oncologie Médicale, CHU de Bordeaux- Hôpital Saint André, 33000, Bordeaux, France
| | - C Bronnimann
- Service d'Oncologie Médicale, CHU de Bordeaux- Hôpital Saint André, 33000, Bordeaux, France.
| | - H Loiseau
- Service de Neurochirurgie B, CHU de Bordeaux - Hôpital Pellegrin, 33076, Bordeaux, France.,EA 7435 - IMOTION (Imagerie moléculaire et thérapies innovantes en oncologie) Université de Bordeaux, 33076, Bordeaux, France
| | - J S Frénel
- Institut de Cancérologie de l'Ouest, Centre René Gauducheau, 44800, Saint Herblain, France
| | - A Siegfried
- Service de Pathologie, Institut Universitaire du Cancer de Toulouse Oncopole, Toulouse, France
| | - R Seizeur
- Service de Neurochirurgie, Hôpital de la Cavale Blanche, CHRU de Brest, Université de Brest, Brest, France
| | - G Gauchotte
- Service d'Anatomie et Cytologie Pathologiques, CRB BB-0033-00035, CHRU de Nancy, INSERM U1256, Université de Lorraine, 54500, Vandœuvre-lès-Nancy, France
| | - D Cappellen
- U1035 Inserm - Biothérapie des Maladies Génétiques, Inflammatoires et Cancers (BMGIC), Univ. Bordeaux, 33076, Bordeaux, France.,Service de Biologie des Tumeurs, CHU de Bordeaux - Hôpital du Haut Lévêque, 33604, Pessac, France
| | - C Carpentier
- AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle Epiniere, ICM, 75013, Paris, France
| | - D Figarella-Branger
- Aix-Marseille Univ, APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Marseille, France
| | - S Eimer
- Service de Pathologie, CHU de Bordeaux, Hôpital Pellegrin, 33076, Bordeaux, France
| | - D Meyronet
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Cancer Cell Plasticity department, Université Claude Bernard Lyon 1, Lyon, France.,Neuro-oncology Department, Hospices Civils de Lyon, Lyon, France
| | - F Ducray
- Centre de Recherche en Cancérologie de Lyon, INSERM U1052, CNRS UMR 5286, Cancer Cell Plasticity department, Université Claude Bernard Lyon 1, Lyon, France.,Neuro-oncology Department, Hospices Civils de Lyon, Lyon, France
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21
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Peng H, Huo J, Li B, Cui Y, Zhang H, Zhang L, Ma L. Predicting Isocitrate Dehydrogenase (IDH) Mutation Status in Gliomas Using Multiparameter MRI Radiomics Features. J Magn Reson Imaging 2020; 53:1399-1407. [PMID: 33179832 DOI: 10.1002/jmri.27434] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Accurate and noninvasive detection of isocitrate dehydrogenase (IDH, including IDH1 and IDH2) status is clinically meaningful for molecular stratification of glioma, but remains challenging. PURPOSE To establish a model for classifying IDH status in gliomas based on multiparametric MRI. STUDY TYPE Retrospective, radiomics. POPULATION In all, 105 consecutive cases of grade II-IV glioma with 50 IDH1 or IDH2 mutant (IDHm) and 55 IDH wildtype (IDHw) were separated into a training cohort (n = 73) and a test cohort (n = 32). FIELD STRENGTH/SEQUENCE Contrast-enhanced T1 -weighted (CE-T1 W), T2 -weighted (T2 W), and arterial spin labeling (ASL) images were acquired at 3.0T. ASSESSMENT Two doctors manually labeled the volume of interest (VOI) on CE-T1 W, then T2 W and ASL were coregistered to CE-T1 W. A total of 851 radiomics features were extracted on each VOI of three sequences. From the training cohort, all radiomics features with age and gender were processed by the Mann-Whitney U-test, Pearson test, and least absolute shrinkage and selection operator to obtain optimal feature groups to train support vector machine models. The accuracy and area under curve (AUC) of all models for classifying the IDH status were calculated on the test cohort. Two subtasks were performed to verify the efficiency of texture features and the Pearson test in IDH status classification, respectively. STATISTICAL TESTS The permutation test with Bonferroni correction; chi-square test. RESULTS The accuracy and AUC of the classifier, which combines the features of all three sequences, achieved 0.823 and 0.770 (P < 0.05), respectively. The best model established by texture features only had an AUC of 0.819 and an accuracy of 0.761. The best model established without the Pearson test got an AUC of 0.747 and an accuracy of 0.719. DATA CONCLUSION IDH genotypes of glioma can be identified by radiomics features from multiparameter MRI. The Pearson test improved the performance of the IDH classification models. LEVEL OF EVIDENCE 4 TECHNICAL EFFICACY STAGE: 1.
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Affiliation(s)
- Hong Peng
- Medical School of Chinese PLA, Beijing, China.,Department of Radiology, The 1st Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Jiaohua Huo
- School of Computer Science and Engineering, Xidian University, Xi'an, China
| | - Bo Li
- Department of Radiology, Xiangtan Central Hospital, Xiangtan, China
| | - Yuanyuan Cui
- Medical School of Chinese PLA, Beijing, China.,Department of Radiology, The 1st Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hao Zhang
- Medical School of Chinese PLA, Beijing, China.,Department of Radiology, The 1st Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Liang Zhang
- School of Computer Science and Engineering, Xidian University, Xi'an, China
| | - Lin Ma
- Medical School of Chinese PLA, Beijing, China.,Department of Radiology, The 1st Medical Centre, Chinese PLA General Hospital, Beijing, China
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22
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Long Q, Hua Y, He L, Zhang C, Sui S, Li Y, Qiu H, Tian T, An X, Luo G, Yan Y, Zhao A, Shi D, Xie F, Chen M, Zheng F, Deng W. Poly(U) binding splicing factor 60 promotes renal cell carcinoma growth by transcriptionally upregulating telomerase reverse transcriptase. Int J Biol Sci 2020; 16:3002-3017. [PMID: 33061812 PMCID: PMC7545719 DOI: 10.7150/ijbs.45115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Abnormal transcriptional upregulation of telomerase reverse transcriptase (TERT) plays a dominant role in telomerase activation in various cancers. TERT promoter mutations (TPMs) have been identified as a key mechanism in TERT upregulation. However, the mechanism of TERT upregulation in cancers with low frequency of TPMs are not fully elucidated so far. Methods: The expression of PUF60 and TERT was detected by real-time PCR, western blot and immunohistochemistry. TERT promoter binding proteins were identified by streptavidin-agarose pulldown assay and mass spectrum (MS) analysis. The role of PUF60/TERT in renal cancer was evaluated on cell growth in vitro and in vivo. Results: In this study, we identify the regulation mechanism of TERT in renal cell carcinoma (RCC) cells which have rare TPMs but exert significant upregulation of TERT. We found that TERT was highly expressed in RCC tumor tissues, and elevated TERT expression was associated with poor prognosis for patients. We also detected the relatively rare TPM status in both RCC tumor tissues and RCC cell lines. Mechanistically, PUF60, a RNA binding protein, was identified as a novel TERT regulator which bound to the TERT and transcriptionally upregulated TERT expression in RCC cells. The in vitro and in vivo experiments also demonstrated that PUF60 could promote RCC cell growth through activation of TERT expression in a TPM status independent way. Furthermore, we showed that there was a strong correlation of the expression of PUF60 and TERT in RCC tumor tissues and RCC cell lines, and the patients with high expression of PUF60 and TERT had significantly shorter survival. Conclusions: Collectively, these results indicated that PUF60 transcriptionally upregulated TERT expression to promote RCC growth and progression in a TPM status independent way, suggesting that the PUF60/TERT signaling pathway may serve as potential prognostic biomarkers and therapeutic targets for RCC.
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Affiliation(s)
- Qian Long
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yijun Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Liru He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Changlin Zhang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Silei Sui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Huijuan Qiu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Tian Tian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Xin An
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Guangyu Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yue Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Anshi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Dingbo Shi
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fangyun Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fufu Zheng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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23
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Wen PY, Weller M, Lee EQ, Alexander BM, Barnholtz-Sloan JS, Barthel FP, Batchelor TT, Bindra RS, Chang SM, Chiocca EA, Cloughesy TF, DeGroot JF, Galanis E, Gilbert MR, Hegi ME, Horbinski C, Huang RY, Lassman AB, Le Rhun E, Lim M, Mehta MP, Mellinghoff IK, Minniti G, Nathanson D, Platten M, Preusser M, Roth P, Sanson M, Schiff D, Short SC, Taphoorn MJB, Tonn JC, Tsang J, Verhaak RGW, von Deimling A, Wick W, Zadeh G, Reardon DA, Aldape KD, van den Bent MJ. Glioblastoma in adults: a Society for Neuro-Oncology (SNO) and European Society of Neuro-Oncology (EANO) consensus review on current management and future directions. Neuro Oncol 2020; 22:1073-1113. [PMID: 32328653 PMCID: PMC7594557 DOI: 10.1093/neuonc/noaa106] [Citation(s) in RCA: 538] [Impact Index Per Article: 134.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Glioblastomas are the most common form of malignant primary brain tumor and an important cause of morbidity and mortality. In recent years there have been important advances in understanding the molecular pathogenesis and biology of these tumors, but this has not translated into significantly improved outcomes for patients. In this consensus review from the Society for Neuro-Oncology (SNO) and the European Association of Neuro-Oncology (EANO), the current management of isocitrate dehydrogenase wildtype (IDHwt) glioblastomas will be discussed. In addition, novel therapies such as targeted molecular therapies, agents targeting DNA damage response and metabolism, immunotherapies, and viral therapies will be reviewed, as well as the current challenges and future directions for research.
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Affiliation(s)
- Patrick Y Wen
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Weller
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Eudocia Quant Lee
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Brian M Alexander
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jill S Barnholtz-Sloan
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio, USA
| | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Tracy T Batchelor
- Department of Neurology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School
| | - Ranjit S Bindra
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Susan M Chang
- University of California San Francisco, San Francisco, California, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Timothy F Cloughesy
- David Geffen School of Medicine, Department of Neurology, University of California Los Angeles, Los Angeles, California, USA
| | - John F DeGroot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Monika E Hegi
- Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raymond Y Huang
- Division of Neuroradiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew B Lassman
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, NewYork-Presbyterian Hospital/Columbia University Irving Medical Center, New York, New York, USA
| | - Emilie Le Rhun
- University of Lille, Inserm, Neuro-oncology, General and Stereotaxic Neurosurgery service, University Hospital of Lille, Lille, France; Breast Cancer Department, Oscar Lambret Center, Lille, France and Department of Neurology & Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Lim
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Ingo K Mellinghoff
- Department of Neurology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Giuseppe Minniti
- Radiation Oncology Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - David Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, USA
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, MCTN, Heidelberg University, Heidelberg, Germany
| | - Matthias Preusser
- Division of Oncology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Patrick Roth
- Department of Neurology and Brain Tumor Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière – Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David Schiff
- University of Virginia School of Medicine, Division of Neuro-Oncology, Department of Neurology, University of Virginia, Charlottesville, Virginia, USA
| | - Susan C Short
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Martin J B Taphoorn
- Department of Neurology, Medical Center Haaglanden, The Hague and Department of Neurology, Leiden University Medical Center, the Netherlands
| | | | - Jonathan Tsang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Andreas von Deimling
- Neuropathology and Clinical Cooperation Unit Neuropathology, University Heidelberg and German Cancer Center, Heidelberg, Germany
| | - Wolfgang Wick
- Department of Neurology and Neuro-oncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Gelareh Zadeh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, Canada
| | - David A Reardon
- Dana-Farber Cancer Institute, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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PART1 and hsa-miR-429-Mediated SHCBP1 Expression Is an Independent Predictor of Poor Prognosis in Glioma Patients. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1767056. [PMID: 32351983 PMCID: PMC7174919 DOI: 10.1155/2020/1767056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
Gliomas are the most common primary brain tumors. Because of their high degree of malignancy, patient survival rates are unsatisfactory. Therefore, exploring glioma biomarkers will play a key role in early diagnosis, guiding treatment, and monitoring the prognosis of gliomas. We found two lncRNAs, six miRNAs, and nine mRNAs that were differentially expressed by analyzing genomic data of glioma patients. The diagnostic value of mRNA expression levels in gliomas was determined by receiver operating characteristic (ROC) curve analysis. Among the nine mRNAs, the area under the ROC curve values of only CEP55 and SHCBP1 were >0.7, specifically 0.834 and 0.816, respectively. Additionally, CEP55 and SHCBP1 were highly expressed in glioma specimens and showed increased expression according to the glioma grade, and outcomes of high expression patients were poor. CEP55 was enriched in the cell cycle, DNA replication, mismatch repair, and P53 signaling pathway. SHCBP1 was enriched in the cell cycle, DNA replication, ECM receptor interaction, and P53 signaling pathway. Age, grade, IDH status, chromosome 19/20 cogain, and SHCBP1 were independent factors for prognosis. Our findings suggest the PART1-hsa-miR-429-SHCBP1 regulatory network plays an important role in gliomas.
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Dahlin AM, Wibom C, Andersson U, Bybjerg-Grauholm J, Deltour I, Hougaard DM, Scheurer ME, Lau CC, McKean-Cowdin R, Kennedy RJ, Hung LT, Yee J, Margol AS, Barrington-Trimis J, Gauderman WJ, Feychting M, Schüz J, Röösli M, Kjaerheim K, Januszkiewicz-Lewandowska D, Fichna M, Nowak J, Searles Nielsen S, Asgharzadeh S, Mirabello L, Hjalmars U, Melin B. A genome-wide association study on medulloblastoma. J Neurooncol 2020; 147:309-315. [PMID: 32056145 PMCID: PMC7136185 DOI: 10.1007/s11060-020-03424-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/03/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Medulloblastoma is a malignant embryonal tumor of the cerebellum that occurs predominantly in children. To find germline genetic variants associated with medulloblastoma risk, we conducted a genome-wide association study (GWAS) including 244 medulloblastoma cases and 247 control subjects from Sweden and Denmark. METHODS Genotyping was performed using Illumina BeadChips, and untyped variants were imputed using IMPUTE2. RESULTS Fifty-nine variants in 11 loci were associated with increased medulloblastoma risk (p < 1 × 10-5), but none were statistically significant after adjusting for multiple testing (p < 5 × 10-8). Thirteen of these variants were genotyped, whereas 46 were imputed. Genotyped variants were further investigated in a validation study comprising 249 medulloblastoma cases and 629 control subjects. In the validation study, rs78021424 (18p11.23, PTPRM) was associated with medulloblastoma risk with OR in the same direction as in the discovery cohort (ORT = 1.59, pvalidation = 0.02). We also selected seven medulloblastoma predisposition genes for investigation using a candidate gene approach: APC, BRCA2, PALB2, PTCH1, SUFU, TP53, and GPR161. The strongest evidence for association was found for rs201458864 (PALB2, ORT = 3.76, p = 3.2 × 10-4) and rs79036813 (PTCH1, ORA = 0.42, p = 2.6 × 10-3). CONCLUSION The results of this study, including a novel potential medulloblastoma risk loci at 18p11.23, are suggestive but need further validation in independent cohorts.
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Affiliation(s)
- Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Jonas Bybjerg-Grauholm
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Isabelle Deltour
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
- Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - David M Hougaard
- Danish Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Ching C Lau
- Department of Pediatrics, Section of Hematology-Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Roberta McKean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rebekah J Kennedy
- Children's Center for Cancer and Blood Diseases, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Long T Hung
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Janis Yee
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Ashley S Margol
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jessica Barrington-Trimis
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Maria Feychting
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer, Lyon, France
| | - Martin Röösli
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Danuta Januszkiewicz-Lewandowska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Pediatric Oncology, Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Jerzy Nowak
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Susan Searles Nielsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Neurology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Shahab Asgharzadeh
- Department of Pediatrics, Section of Hematology-Oncology, Children's Hospital Los Angeles and The Saban Research Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Saban Research Institute at Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
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The Genetic Architecture of Gliomagenesis-Genetic Risk Variants Linked to Specific Molecular Subtypes. Cancers (Basel) 2019; 11:cancers11122001. [PMID: 31842352 PMCID: PMC6966482 DOI: 10.3390/cancers11122001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies have identified 25 germline genetic loci that increase the risk of glioma. The somatic tumor molecular alterations, including IDH-mutation status and 1p/19q co-deletion, have been included into the WHO 2016 classification system for glioma. To investigate how the germline genetic risk variants correlate with the somatic molecular subtypes put forward by WHO, we performed a meta-analysis that combined findings from 330 Swedish cases and 876 controls with two other recent studies. In total, 5,103 cases and 10,915 controls were included. Three categories of associations were found. First, variants in TERT and TP53 were associated with increased risk of all glioma subtypes. Second, variants in CDKN2B-AS1, EGFR, and RTEL1 were associated with IDH-wildtype glioma. Third, variants in CCDC26 (the 8q24 locus), C2orf80 (close to IDH), LRIG1, PHLDB1, ETFA, MAML2 and ZBTB16 were associated with IDH-mutant glioma. We therefore propose three etiopathological pathways in gliomagenesis based on germline variants for future guidance of diagnosis and potential functional targets for therapies. Future prospective clinical trials of patients with suspicion of glioma diagnoses, using the genetic variants as biomarkers, are necessary to disentangle how strongly they can predict glioma diagnosis.
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Goyal A, Yolcu YU, Goyal A, Kerezoudis P, Brown DA, Graffeo CS, Goncalves S, Burns TC, Parney IF. The T2-FLAIR–mismatch sign as an imaging biomarker for IDH and 1p/19q status in diffuse low-grade gliomas: a systematic review with a Bayesian approach to evaluation of diagnostic test performance. Neurosurg Focus 2019; 47:E13. [DOI: 10.3171/2019.9.focus19660] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/19/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVEWith the revised WHO 2016 classification of brain tumors, there has been increasing interest in imaging biomarkers to predict molecular status and improve the yield of genetic testing for diffuse low-grade gliomas (LGGs). The T2-FLAIR–mismatch sign has been suggested to be a highly specific radiographic marker of isocitrate dehydrogenase (IDH) gene mutation and 1p/19q codeletion status in diffuse LGGs. The presence of T2-FLAIR mismatch indicates a T2-hyperintense lesion that is hypointense on FLAIR with the exception of a hyperintense rim.METHODSIn accordance with PRISMA guidelines, we performed a systematic review of the Ovid Medline, Embase, Scopus, and Cochrane databases for reports of studies evaluating the diagnostic performance of T2-FLAIR mismatch in predicting the IDH and 1p/19q codeletion status in diffuse LGGs. Results were combined into a 2 × 2 format, and the following diagnostic performance parameters were calculated: sensitivity, specificity, positive predictive value, negative predictive value, and positive (LR+) and negative (LR−) likelihood ratios. In addition, we utilized Bayes theorem to calculate posttest probabilities as a function of known pretest probabilities from previous genome-wide association studies and the calculated LRs. Calculations were performed for 1) IDH mutation with 1p/19q codeletion (IDHmut-Codel), 2) IDH mutation without 1p/19q codeletion (IDHmut-Noncodel), 3) IDH mutation overall, and 4) 1p/19q codeletion overall. The QUADAS-2 (revised Quality Assessment of Diagnostic Accuracy Studies) tool was utilized for critical appraisal of included studies.RESULTSA total of 4 studies were included, with inclusion of 2 separate cohorts from a study reporting testing and validation (n = 746). From pooled analysis of all cohorts, the following values were obtained for each molecular profile—IDHmut-Codel: sensitivity 30%, specificity 73%, LR+ 1.1, LR− 1.0; IDHmut-Noncodel: sensitivity 33.7%, specificity 98.5%, LR+ 22.5, LR− 0.7; IDH: sensitivity 32%, specificity 100%, LR+ 32.1, LR− 0.7; 1p/19q codeletion: sensitivity 0%, specificity 54%, LR+ 0.01, LR− 1.9. Bayes theorem was used to calculate the following posttest probabilities after a positive and negative result, respectively—IDHmut-Codel: 32.2% and 29.4%; IDHmut-Noncodel: 95% and 40%; IDH: 99.2% and 73.5%; 1p/19q codeletion: 0.4% and 35.1%.CONCLUSIONSThe T2-FLAIR–mismatch sign was an insensitive but highly specific marker of IDH mutation and IDHmut-Noncodel profile, although significant exceptions may exist to this finding. Tumors with a positive sign may still be IDHwt or 1p/19q codeleted. These findings support the utility of T2-FLAIR mismatch as an imaging-based biomarker for positive selection of patients with IDH-mutant gliomas.
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Affiliation(s)
- Anshit Goyal
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
| | - Yagiz U. Yolcu
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
| | - Aakshit Goyal
- 2Department of Neuroradiology, George Washington University Hospital, Washington, DC
| | | | - Desmond A. Brown
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
| | | | - Sandy Goncalves
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
| | - Terence C. Burns
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
| | - Ian F. Parney
- 1Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota; and
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Ostrom QT, Fahmideh MA, Cote DJ, Muskens IS, Schraw JM, Scheurer ME, Bondy ML. Risk factors for childhood and adult primary brain tumors. Neuro Oncol 2019; 21:1357-1375. [PMID: 31301133 PMCID: PMC6827837 DOI: 10.1093/neuonc/noz123] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Primary brain tumors account for ~1% of new cancer cases and ~2% of cancer deaths in the United States; however, they are the most commonly occurring solid tumors in children. These tumors are very heterogeneous and can be broadly classified into malignant and benign (or non-malignant), and specific histologies vary in frequency by age, sex, and race/ethnicity. Epidemiological studies have explored numerous potential risk factors, and thus far the only validated associations for brain tumors are ionizing radiation (which increases risk in both adults and children) and history of allergies (which decreases risk in adults). Studies of genetic risk factors have identified 32 germline variants associated with increased risk for these tumors in adults (25 in glioma, 2 in meningioma, 3 in pituitary adenoma, and 2 in primary CNS lymphoma), and further studies are currently under way for other histologic subtypes, as well as for various childhood brain tumors. While identifying risk factors for these tumors is difficult due to their rarity, many existing datasets can be leveraged for future discoveries in multi-institutional collaborations. Many institutions are continuing to develop large clinical databases including pre-diagnostic risk factor data, and developments in molecular characterization of tumor subtypes continue to allow for investigation of more refined phenotypes. Key Point 1. Brain tumors are a heterogeneous group of tumors that vary significantly in incidence by age, sex, and race/ethnicity.2. The only well-validated risk factors for brain tumors are ionizing radiation (which increases risk in adults and children) and history of allergies (which decreases risk).3. Genome-wide association studies have identified 32 histology-specific inherited genetic variants associated with increased risk of these tumors.
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Affiliation(s)
- Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Maral Adel Fahmideh
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine, Solna, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - David J Cote
- Channing Division of Network Medicine, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Computational Neuroscience Outcomes Center, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ivo S Muskens
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jeremy M Schraw
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
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Molinaro AM, Taylor JW, Wiencke JK, Wrensch MR. Genetic and molecular epidemiology of adult diffuse glioma. Nat Rev Neurol 2019; 15:405-417. [PMID: 31227792 PMCID: PMC7286557 DOI: 10.1038/s41582-019-0220-2] [Citation(s) in RCA: 397] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/24/2022]
Abstract
The WHO 2007 glioma classification system (based primarily on tumour histology) resulted in considerable interobserver variability and substantial variation in patient survival within grades. Furthermore, few risk factors for glioma were known. Discoveries over the past decade have deepened our understanding of the molecular alterations underlying glioma and have led to the identification of numerous genetic risk factors. The advances in molecular characterization of glioma have reframed our understanding of its biology and led to the development of a new classification system for glioma. The WHO 2016 classification system comprises five glioma subtypes, categorized by both tumour morphology and molecular genetic information, which led to reduced misclassification and improved consistency of outcomes within glioma subtypes. To date, 25 risk loci for glioma have been identified and several rare inherited mutations that might cause glioma in some families have been discovered. This Review focuses on the two dominant trends in glioma science: the characterization of diagnostic and prognostic tumour markers and the identification of genetic and other risk factors. An overview of the many challenges still facing glioma researchers is also included.
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Affiliation(s)
- Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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Abstract
PURPOSE OF REVIEW This review summarizes recent advances in the molecular classification of adult gliomas. RECENT FINDINGS According to the 2016 WHO classification, five main molecular subgroups of adult diffuse gliomas can be distinguished based on the 1p/19q codeletion, isocitrate dehydrogenase (IDH), and histone H3.3 mutation status. In the future, this classification may be further refined based on the integration of additional biomarkers, in particular CDKN2A/B homozygous deletion in IDH-mutant astrocytomas, TERT promoter mutations, EGFR amplification, chromosome 7 gain and chromosome 10 loss in IDH-wildtype astrocytomas, and FGFR1 mutations in midline gliomas. Histone H3.3 G34R/V defines a distinct subgroup of hemispheric IDH-wildtype high-grade gliomas occurring in young patients and FGFR gene fusions characterize a subgroup of IDH-wildtype glioblastomas that could benefit from specific treatment approaches. RNA sequencing may identify targetable gene fusions in circumscribed gliomas lacking classical BRAF alterations. In chordoid gliomas, recurrent PRKCA mutations could serve as a new diagnostic marker. Among comprehensive molecular analysis methods, DNA methylation profiling appears as a particularly powerful approach to identify new molecular subgroups of gliomas and to classify difficult cases. SUMMARY The classification of adult gliomas may be improved by the integration of additional biomarkers and/or by comprehensive molecular analysis, in particular DNA methylation profiling. The most relevant approach, however, remains to be established.
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Ostrom Q, Bondy ML, Huse JT. Integrating germline and somatic genomic analysis to probe etiological mechanism in malignant glioma. Oncotarget 2019; 10:3086-3087. [PMID: 31139320 PMCID: PMC6517101 DOI: 10.18632/oncotarget.26897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/16/2019] [Indexed: 11/25/2022] Open
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Eckel-Passow JE, Decker PA, Kosel ML, Kollmeyer TM, Molinaro AM, Rice T, Caron AA, Drucker KL, Praska CE, Pekmezci M, Hansen HM, McCoy LS, Bracci PM, Erickson BJ, Lucchinetti CF, Wiemels JL, Wiencke JK, Bondy ML, Melin B, Burns TC, Giannini C, Lachance DH, Wrensch MR, Jenkins RB. Using germline variants to estimate glioma and subtype risks. Neuro Oncol 2019; 21:451-461. [PMID: 30624711 PMCID: PMC6422428 DOI: 10.1093/neuonc/noz009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Twenty-five single nucleotide polymorphisms (SNPs) are associated with adult diffuse glioma risk. We hypothesized that the inclusion of these 25 SNPs with age at diagnosis and sex could estimate risk of glioma as well as identify glioma subtypes. METHODS Case-control design and multinomial logistic regression were used to develop models to estimate the risk of glioma development while accounting for histologic and molecular subtypes. Case-case design and logistic regression were used to develop models to predict isocitrate dehydrogenase (IDH) mutation status. A total of 1273 glioma cases and 443 controls from Mayo Clinic were used in the discovery set, and 852 glioma cases and 231 controls from UCSF were used in the validation set. All samples were genotyped using a custom Illumina OncoArray. RESULTS Patients in the highest 5% of the risk score had more than a 14-fold increase in relative risk of developing an IDH mutant glioma. Large differences in lifetime absolute risk were observed at the extremes of the risk score percentile. For both IDH mutant 1p/19q non-codeleted glioma and IDH mutant 1p/19q codeleted glioma, the lifetime risk increased from almost null to 2.3% and almost null to 1.7%, respectively. The SNP-based model that predicted IDH mutation status had a validation concordance index of 0.85. CONCLUSIONS These results suggest that germline genotyping can provide new tools for the initial management of newly discovered brain lesions. Given the low lifetime risk of glioma, risk scores will not be useful for population screening; however, they may be useful in certain clinically defined high-risk groups.
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Affiliation(s)
| | - Paul A Decker
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Matt L Kosel
- Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | - Terri Rice
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Alissa A Caron
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kristen L Drucker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Corinne E Praska
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Melike Pekmezci
- Department of Pathology, UCSF, San Francisco, California, USA
| | - Helen M Hansen
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Lucie S McCoy
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
| | | | | | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, California, USA
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Institute of Human Genetics, UCSF, San Francisco, California, USA
| | - Melissa L Bondy
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Terry C Burns
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Daniel H Lachance
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Institute of Human Genetics, UCSF, San Francisco, California, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Scheie D, Kufaishi HHA, Broholm H, Lund EL, de Stricker K, Melchior LC, Grauslund M. Biomarkers in tumors of the central nervous system - a review. APMIS 2019; 127:265-287. [PMID: 30740783 DOI: 10.1111/apm.12916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Until recently, diagnostics of brain tumors were almost solely based on morphology and immunohistochemical stainings for relatively unspecific lineage markers. Although certain molecular markers have been known for longer than a decade (combined loss of chromosome 1p and 19q in oligodendrogliomas), molecular biomarkers were not included in the WHO scheme until 2016. Now, the classification of diffuse gliomas rests on an integration of morphology and molecular results. Also, for many other central nervous system tumor entities, specific diagnostic, prognostic and predictive biomarkers have been detected and continue to emerge. Previously, we considered brain tumors with similar histology to represent a single disease entity. We now realize that histologically identical tumors might show alterations in different molecular pathways, and often represent separate diseases with different natural history and response to treatment. Hence, knowledge about specific biomarkers is of great importance for individualized treatment and follow-up. In this paper we review the biomarkers that we currently use in the diagnostic work-up of brain tumors.
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Affiliation(s)
- David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | - Helle Broholm
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Eva Løbner Lund
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | - Morten Grauslund
- Department of Genetics and Pathology, Laboratory Medicine, Lund, Sweden
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Atkins I, Kinnersley B, Ostrom QT, Labreche K, Il'yasova D, Armstrong GN, Eckel-Passow JE, Schoemaker MJ, Nöthen MM, Barnholtz-Sloan JS, Swerdlow AJ, Simon M, Rajaraman P, Chanock SJ, Shildkraut J, Bernstein JL, Hoffmann P, Jöckel KH, Lai RK, Claus EB, Olson SH, Johansen C, Wrensch MR, Melin B, Jenkins RB, Sanson M, Bondy ML, Houlston RS. Transcriptome-Wide Association Study Identifies New Candidate Susceptibility Genes for Glioma. Cancer Res 2019; 79:2065-2071. [PMID: 30709929 DOI: 10.1158/0008-5472.can-18-2888] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/20/2018] [Accepted: 01/24/2019] [Indexed: 11/16/2022]
Abstract
Genome-wide association studies (GWAS) have so far identified 25 loci associated with glioma risk, with most showing specificity for either glioblastoma (GBM) or non-GBM tumors. The majority of these GWAS susceptibility variants reside in noncoding regions and the causal genes underlying the associations are largely unknown. Here we performed a transcriptome-wide association study to search for novel risk loci and candidate causal genes at known GWAS loci using Genotype-Tissue Expression Project (GTEx) data to predict cis-predicted gene expression in relation to GBM and non-GBM risk in conjunction with GWAS summary statistics on 12,488 glioma cases (6,183 GBM and 5,820 non-GBM) and 18,169 controls. Imposing a Bonferroni-corrected significance level of P < 5.69 × 10-6, we identified 31 genes, including GALNT6 at 12q13.33, as a candidate novel risk locus for GBM (mean Z = 4.43; P = 5.68 × 10-6). GALNT6 resides at least 55 Mb away from any previously identified glioma risk variant, while all other 30 significantly associated genes were located within 1 Mb of known GWAS-identified loci and were not significant after conditioning on the known GWAS-identified variants. These data identify a novel locus (GALNT6 at 12q13.33) and 30 genes at 12 known glioma risk loci associated with glioma risk, providing further insights into glioma tumorigenesis. SIGNIFICANCE: This study identifies new genes associated with glioma risk, increasing understanding of how these tumors develop.
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Affiliation(s)
- Isabelle Atkins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom.
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio.,Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Karim Labreche
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Dora Il'yasova
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, Georgia.,Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina
| | - Georgina N Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Markus M Nöthen
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom.,Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Matthias Simon
- Department of Neurosurgery, University of Bonn Medical Center, Bonn, Germany
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Joellen Shildkraut
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Per Hoffmann
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut.,Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christoffer Johansen
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark.,Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, California.,Institute of Human Genetics, University of California, San Francisco, California
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota
| | - Marc Sanson
- Sorbonne Universités UPMC Univ Paris 06, INSERM CNRS, U1127, UMR 7225, ICM, Paris, France.,AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Neurologie 2-Mazarin, Paris, France
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom.,Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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Kinnersley B, Sud A, Coker EA, Tym JE, Di Micco P, Al-Lazikani B, Houlston RS. Leveraging Human Genetics to Guide Cancer Drug Development. JCO Clin Cancer Inform 2018; 2:1-11. [PMID: 30652614 PMCID: PMC6874034 DOI: 10.1200/cci.18.00077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
PURPOSE The high attrition rate of cancer drug development programs is a barrier to realizing the promise of precision oncology. We have examined whether the genetic insights from genome-wide association studies of cancer can guide drug development and repurposing in oncology. MATERIALS AND METHODS Across 37 cancers, we identified 955 genetic risk variants from the National Human Genome Research Institute-European Bioinformatics Institute genome-wide association study catalog. We linked these variants to target genes using strategies that were based on linkage disequilibrium, DNA three-dimensional structure, and integration of predicted gene function and expression. With the use of the Informa Pharmaprojects database, we identified genes that are targets of unique drugs and assessed the level of enrichment that would be afforded by incorporation of genetic information in preclinical and phase II studies. For targets not under development, we implemented machine learning approaches to assess druggability. RESULTS For all preclinical targets incorporating genetic information, a 2.00-fold enrichment of a drug being successfully approved could be achieved (95% CI, 1.14- to 3.48-fold; P = .02). For phase II targets, a 2.75-fold enrichment could be achieved (95% CI, 1.42- to 5.35-fold; P < .001). Application of genetic information suggests potential repurposing of 15 approved nononcology drugs. CONCLUSION The findings illustrate the value of using insights from the genetics of inherited cancer susceptibility discovery projects as part of a data-driven strategy to inform drug discovery. Support for cancer germline genetic information for prospective targets is available online from the Institute of Cancer Research.
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Affiliation(s)
- Ben Kinnersley
- All authors: The Institute of Cancer Research, London, United Kingdom
| | - Amit Sud
- All authors: The Institute of Cancer Research, London, United Kingdom
| | | | - Joseph E. Tym
- All authors: The Institute of Cancer Research, London, United Kingdom
| | - Patrizio Di Micco
- All authors: The Institute of Cancer Research, London, United Kingdom
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Picca A, Berzero G, Di Stefano AL, Sanson M. The clinical use of IDH1 and IDH2 mutations in gliomas. Expert Rev Mol Diagn 2018; 18:1041-1051. [PMID: 30427756 DOI: 10.1080/14737159.2018.1548935] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Mutations in the genes isocitrate dehydrogenase (IDH) 1 and 2 have been reported in a limited number of tumors. In gliomas, IDH mutations are primarily detected in WHO grade II-III tumors and represent a major biomarker with diagnostic, prognostic, and predictive implications. The recent development of IDH inhibitors and vaccines suggests that the IDH mutation is also an appealing target for therapy. Areas covered: This review focuses on the role of IDH mutations in diffuse gliomas. Besides discussing their role in gliomagenesis, we will emphasize the role of IDH mutations in clinical practice as a diagnostic, prognostic and predictive biomarker, and as a potential therapeutic target. Noninvasive detection of the IDH mutation by means of liquid biopsy and MR spectroscopy will also be discussed. Expert commentary: While IDH mutation is a consolidated diagnostic and prognostic biomarker in clinical practice, its role in oncogenesis is far from being elucidated, and there are several pending issues. The routine use of noninvasive techniques for detection and monitoring of the IDH status remains challenging. Although the IDH mutation is a very early alteration in gliomagenesis, it may then be omitted during tumor progression. This observation has important implications when designing targeted clinical trials.
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Affiliation(s)
- Alberto Picca
- a Neuroscience Consortium , University of Pavia , Pavia , Italy
| | - Giulia Berzero
- b Neuroncology Unit , IRCCS Mondino Foundation , Pavia , Italy.,c Biomedical Sciences , University of Pavia , Pavia , Italy
| | - Anna Luisa Di Stefano
- d Sorbonne Universités , Paris , France.,e Department of Neurology , Foch Hospital , Suresnes, Paris , France
| | - Marc Sanson
- d Sorbonne Universités , Paris , France.,f Service de Neurologie 2 , AP-HP, Hôpital de la Pitié-Salpêtrière , Paris , France
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Duffau H. Diffuse low-grade glioma, oncological outcome and quality of life: a surgical perspective. Curr Opin Oncol 2018; 30:383-389. [DOI: 10.1097/cco.0000000000000483] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pellerino A, Franchino F, Soffietti R, Rudà R. Overview on current treatment standards in high-grade gliomas. THE QUARTERLY JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING : OFFICIAL PUBLICATION OF THE ITALIAN ASSOCIATION OF NUCLEAR MEDICINE (AIMN) [AND] THE INTERNATIONAL ASSOCIATION OF RADIOPHARMACOLOGY (IAR), [AND] SECTION OF THE SOCIETY OF RADIOPHARMACEUTICAL CHEMISTRY AND BIOLOGY 2018; 62:225-238. [PMID: 29696949 DOI: 10.23736/s1824-4785.18.03096-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High-grade gliomas (HGGs) are the most common primary tumors of the central nervous system, which include anaplastic gliomas (grade III) and glioblastomas (GBM, grade IV). Surgery is the mainstay of treatment in HGGs in order to achieve a histological and molecular characterization, as well as relieve neurological symptoms and improve seizure control. Combinations of some molecular factors, such as IDH 1-2 mutations, 1p/19q codeletion and MGMT methylation status, allow to classify different subtypes of gliomas and identify patients with different outcome. The SOC in HGGs consists in a combination of radiotherapy and chemotherapy with alkylating agents. Despite this therapeutic approach, tumor recurrence occurs in HGGs, and new surgical debulking, reirradiation or second-line chemotherapy are needed. Considering the poor results in terms of survival, several clinical trials have explored the efficacy and tolerability of antiangiogenic agents, targeted therapies against epidermal growth factor receptor (EGFR) and different immunotherapeutic approaches in recurrent and newly-diagnosed GBM, including immune checkpoint inhibitors (ICIs), and cell- or peptide-based vaccination with unsatisfactory results in term of disease control. In this review we describe the major updates in molecular biology of HGGs according to 2016 WHO Classification, the current management in newly-diagnosed and recurrent GBM and grade III gliomas, and the results of the most relevant clinical trials on targeted agents and immunotherapy.
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Affiliation(s)
- Alessia Pellerino
- Department of Neuro-Oncology, University and City of Health and Science Hospital, Turin, Italy -
| | - Federica Franchino
- Department of Neuro-Oncology, University and City of Health and Science Hospital, Turin, Italy
| | - Riccardo Soffietti
- Department of Neuro-Oncology, University and City of Health and Science Hospital, Turin, Italy
| | - Roberta Rudà
- Department of Neuro-Oncology, University and City of Health and Science Hospital, Turin, Italy
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