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Larriba E, de Juan Romero C, García-Martínez A, Quintanar T, Rodríguez-Lescure Á, Soto JL, Saceda M, Martín-Nieto J, Barberá VM. Identification of new targets for glioblastoma therapy based on a DNA expression microarray. Comput Biol Med 2024; 179:108833. [PMID: 38981212 DOI: 10.1016/j.compbiomed.2024.108833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
This study provides a comprehensive perspective on the deregulated pathways and impaired biological functions prevalent in human glioblastoma (GBM). In order to characterize differences in gene expression between individuals diagnosed with GBM and healthy brain tissue, we have designed and manufactured a specific, custom DNA microarray. The results obtained from differential gene expression analysis were validated by RT-qPCR. The datasets obtained from the analysis of common differential expressed genes in our cohort of patients were used to generate protein-protein interaction networks of functionally enriched genes and their biological functions. This network analysis, let us to identify 16 genes that exhibited either up-regulation (CDK4, MYC, FOXM1, FN1, E2F7, HDAC1, TNC, LAMC1, EIF4EBP1 and ITGB3) or down-regulation (PRKACB, MEF2C, CAMK2B, MAPK3, MAP2K1 and PENK) in all GBM patients. Further investigation of these genes and enriched pathways uncovered in this investigation promises to serve as a foundational step in advancing our comprehension of the molecular mechanisms underpinning GBM pathogenesis. Consequently, the present work emphasizes the critical role that the unveiled molecular pathways likely play in shaping innovative therapeutic approaches for GBM management. We finally proposed in this study a list of compounds that target hub of GBM-related genes, some of which are already in clinical use, underscoring the potential of those genes as targets for GBM treatment.
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Affiliation(s)
- Eduardo Larriba
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Camino de Juan Romero
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Avda, Universidad s/n, Ed. Torregaitán, Elche, Spain.
| | - Araceli García-Martínez
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Teresa Quintanar
- Servicio de Oncología Médica. Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Álvaro Rodríguez-Lescure
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Servicio de Oncología Médica. Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; School of Medicine. Universidad Miguel Hernández de Elche. Investigator, Spanish Breast Cancer Research Group (GEICAM), Spain
| | - José Luis Soto
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Miguel Saceda
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Avda, Universidad s/n, Ed. Torregaitán, Elche, Spain
| | - José Martín-Nieto
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain.
| | - Víctor M Barberá
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain.
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Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
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Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
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3
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Lee AV, Nestler KA, Chiappinelli KB. Therapeutic targeting of DNA methylation alterations in cancer. Pharmacol Ther 2024; 258:108640. [PMID: 38570075 DOI: 10.1016/j.pharmthera.2024.108640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
DNA methylation is a critical component of gene regulation and plays an important role in the development of cancer. Hypermethylation of tumor suppressor genes and silencing of DNA repair pathways facilitate uncontrolled cell growth and synergize with oncogenic mutations to perpetuate cancer phenotypes. Additionally, aberrant DNA methylation hinders immune responses crucial for antitumor immunity. Thus, inhibiting dysregulated DNA methylation is a promising cancer therapy. Pharmacologic inhibition of DNA methylation reactivates silenced tumor suppressors and bolster immune responses through induction of viral mimicry. Now, with the advent of immunotherapies and discovery of the immune-modulatory effects of DNA methylation inhibitors, there is great interest in understanding how targeting DNA methylation in combination with other therapies can enhance antitumor immunity. Here, we describe the role of aberrant DNA methylation in cancer and mechanisms by which it promotes tumorigenesis and modulates immune responses. Finally, we review the initial discoveries and ongoing efforts to target DNA methylation as a cancer therapeutic.
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Affiliation(s)
- Abigail V Lee
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Kevin A Nestler
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.
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Liang B, Wang Y, Huang J, Lin S, Mao G, Zhou Z, Yan W, Shan C, Wu H, Etcheverry A, He Y, Liu F, Kang H, Yin A, Zhang S. Genome-wide DNA methylation analysis identifies potent CpG signature for temzolomide response in non-G-CIMP glioblastomas with unmethylated MGMT promoter: MGMT-dependent roles of GPR81. CNS Neurosci Ther 2024; 30:e14465. [PMID: 37830163 PMCID: PMC11017469 DOI: 10.1111/cns.14465] [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: 08/09/2022] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/14/2023] Open
Abstract
PURPOSES To identify potent DNA methylation candidates that could predict response to temozolomide (TMZ) in glioblastomas (GBMs) that do not have glioma-CpGs island methylator phenotype (G-CIMP) but have an unmethylated promoter of O-6-methylguanine-DNA methyltransferase (unMGMT). METHODS The discovery-validation approach was planned incorporating a series of G-CIMP-/unMGMT GBM cohorts with DNA methylation microarray data and clinical information, to construct multi-CpG prediction models. Different bioinformatic and experimental analyses were performed for biological exploration. RESULTS By analyzing discovery sets with radiotherapy (RT) plus TMZ versus RT alone, we identified a panel of 64 TMZ efficacy-related CpGs, from which a 10-CpG risk signature was further constructed. Both the 64-CpG panel and the 10-CpG risk signature were validated showing significant correlations with overall survival of G-CIMP-/unMGMT GBMs when treated with RT/TMZ, rather than RT alone. The 10-CpG risk signature was further observed for aiding TMZ choice by distinguishing differential outcomes to RT/TMZ versus RT within each risk subgroup. Functional studies on GPR81, the gene harboring one of the 10 CpGs, indicated its distinct impacts on TMZ resistance in GBM cells, which may be dependent on the status of MGMT expression. CONCLUSIONS The 64 TMZ efficacy-related CpGs and in particular the 10-CpG risk signature may serve as promising predictive biomarker candidates for guiding optimal usage of TMZ in G-CIMP-/unMGMT GBMs.
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Affiliation(s)
- Bao‐Bao Liang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Yu‐Hong Wang
- The Emergency DepartmentThe Seventh Medical Center of Chinese PLA General HospitalBeijingChina
| | - Jing‐Jing Huang
- Department of Pediatric SurgeryThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Shuai Lin
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Guo‐Chao Mao
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Zhang‐Jian Zhou
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Wan‐Jun Yan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Chang‐You Shan
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Hui‐Zi Wu
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Amandine Etcheverry
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes (IGdR)RennesFrance
| | - Ya‐Long He
- Department of Neurosurgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Fang‐Fang Liu
- Institute of Neurosciences, College of Basic MedicineAir Force Medical UniversityXi'anChina
| | - Hua‐Feng Kang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - An‐An Yin
- Department of Biochemistry and Molecular BiologyAir Force Medical UniversityXi'anChina
- Department of Plastic and Reconstructive Surgery, Xijing HospitalAir Force Medical UniversityXi'anChina
| | - Shu‐Qun Zhang
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
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Chai R, Fang S, Pang B, Liu Y, Wang Y, Zhang W, Jiang T. Molecular pathology and clinical implications of diffuse glioma. Chin Med J (Engl) 2022; 135:2914-2925. [PMID: 36728558 PMCID: PMC10106158 DOI: 10.1097/cm9.0000000000002446] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Indexed: 02/03/2023] Open
Abstract
ABSTRACT The prognosis for diffusely infiltrating gliomas at World Health Organization (WHO) grade 2-4 remains dismal due to their heterogeneity. The rapid development of genome-wide molecular-profiling-associated studies has greatly promoted the accuracy of glioma classification. Thus, the latest version of the WHO classification of the central nervous system tumors published in 2021 has incorporated more molecular biomarkers together with histological features for the diagnosis of gliomas. Advanced usage of molecular pathology in clinical diagnostic practice provides also new opportunities for the therapy of patients with glioma, including surgery, radiotherapy and chemotherapy, targeted therapy, immunotherapy, and more precision clinical trials. Herein, we highlight the updates in the classification of gliomas according to the latest WHO guidelines and summarize the clinically relevant molecular markers by focusing on their applications in clinical practice. We also review the advances in molecular features of gliomas, which can facilitate the development of glioma therapies, thereby discussing the challenges and future directions of molecular pathology toward precision medicine for patients with glioma.
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Affiliation(s)
- Ruichao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Shengyu Fang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yongzhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Research Unit of Accurate Diagnosis, Treatment, and Translational Medicine of Brain Tumors, Chinese Academy of Medical Sciences, Beijing 100070, China
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Soltész B, Pös O, Wlachovska Z, Budis J, Hekel R, Strieskova L, Liptak JB, Krampl W, Styk J, Németh N, Keserű JS, Jenei A, Buglyó G, Klekner Á, Nagy B, Szemes T. Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients. Mol Cell Probes 2022; 66:101875. [PMID: 36379303 DOI: 10.1016/j.mcp.2022.101875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Glioblastoma is the most common malignant tumor of the central nervous system (CNS) in adults. Glioblastoma cells show increased glucose consumption associated with poor prognosis. Since mitochondria play a crucial role in energy metabolism, mutations and copy number changes of mitochondrial DNA may serve as biomarkers. As the brain is difficult to access, analysis of mitochondria directly from the brain tissue represents a challenge. Exosome analysis is an alternative (still poorly explored) approach to investigate molecular changes in CNS tumors. We analyzed brain tissue DNA and plasma-derived exosomal DNA (exoDNA) of 44 glioblastoma patients and 40 control individuals. Quantitative real-time PCR was performed to determine mtDNA copy numbers and the Kruskal-Wallis and Mann-Whitney U test were used for statistical analysis of data. Subsequently, sequencing libraries were prepared and sequenced on the MiSeq platform to identify mtDNA point mutations. Tissue mtDNA copy number was different among controls and patients in multiple comparisons. A similar tendency was detected in exosomes. Based on NGS analysis, several mtDNA point mutations showed slightly different frequencies between cases and controls, but the clinical relevance of these observations is difficult to assess and likely less than that of overall mtDNA copy number changes. Allele frequencies of variants were used to determine the level of heteroplasmy (found to be higher in exo-mtDNA of control individuals). Despite the suggested potential, the use of such biomarkers for the screening and/or diagnosis of glioblastomas is still limited, thus further studies are needed.
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Affiliation(s)
- Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
| | - Zuzana Wlachovska
- Comenius University Science Park, Bratislava, Slovakia; Institute of Informatics, Information Systems and Software Engineering, Faculty of Informatics and Information Technologies, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Rastislav Hekel
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
| | | | - Jana Bozenka Liptak
- Institute of Informatics, Information Systems and Software Engineering, Faculty of Informatics and Information Technologies, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - Werner Krampl
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
| | - Jakub Styk
- Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Nikolett Németh
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Judit Sz Keserű
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Adrienn Jenei
- Department of Neurology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Álmos Klekner
- Department of Neurology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Comenius University Science Park, Bratislava, Slovakia
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia
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Łysiak M, Das J, Malmström A, Söderkvist P. Methylation associated with long- or short-term survival in glioblastoma patients from the Nordic phase 3 trial. Front Genet 2022; 13:934519. [PMID: 36092918 PMCID: PMC9452748 DOI: 10.3389/fgene.2022.934519] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
Patients with glioblastoma (GBM) have a poor outcome, but even among patients receiving the same therapies and with good prognostic factors, one can find those with exceptionally short and long survival. From the Nordic trial, which randomized GBM patients of 60 years or older between two radiotherapy arms (60 Gy or 34 Gy) or temozolomide (TMZ), we selected 59 with good prognostic factors. These selected GBM patients were equally distributed according to treatment and MGMT promoter methylation status but had long or short survival. Methylation profiling with the Illumina Infinium Methylation EPIC BeadChip arrays was performed and utilized for methylation-based CNS tumor classification, and pathway enrichment analysis of differentially methylated CpG sites (DMCs), as well as calculation of epigenetic age acceleration with three different algorithms, to compare the long and short survival groups. Samples identified by the classifier as non-GBM IDH wildtype were excluded. DMCs between long- and short-term survivors were found in patients with methylated MGMT promoter treated with TMZ (123,510), those with unmethylated MGMT treated with 60Gy radiotherapy (4,086), and with methylated MGMT promoter treated with 34Gy radiotherapy (39,649). Long-term survivors with methylated MGMT promoter treated with TMZ exhibited hypermethylation of the Wnt signaling and the platelet activation, signaling, and aggregation pathways. The joint analysis of radiotherapy arms revealed 319 DMCs between long- and short-term survivors with unmethylated MGMT and none for samples with methylated MGMT promoter. An analysis comparing epigenetic age acceleration between patients with long- and short-term survival across all treatment arms showed a decreased epigenetic age acceleration for the latter. We identified DMCs for both TMZ and RT-treated patients and epigenetic age acceleration as a potential prognostic marker, but further systematic analysis of larger patient cohorts is necessary for confirmation of their prognostic and/or predictive properties.
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Affiliation(s)
- Małgorzata Łysiak
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Małgorzata Łysiak, ; Peter Söderkvist,
| | - Jyotirmoy Das
- Bioinformatics Unit (Core Facility), Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Clinical Genomics Linköping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Annika Malmström
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Advanced Home Care, Linköping University, Linköping, Sweden
| | - Peter Söderkvist
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Bioinformatics Unit (Core Facility), Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Clinical Genomics Linköping, SciLife Laboratory, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- *Correspondence: Małgorzata Łysiak, ; Peter Söderkvist,
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Tierling S, Jürgens-Wemheuer WM, Leismann A, Becker-Kettern J, Scherer M, Wrede A, Breuskin D, Urbschat S, Sippl C, Oertel J, Schulz-Schaeffer WJ, Walter J. Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics. Clin Epigenetics 2022; 14:26. [PMID: 35180887 PMCID: PMC8857788 DOI: 10.1186/s13148-022-01244-4] [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: 09/02/2021] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Promoter methylation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) is an acknowledged predictive epigenetic marker in glioblastoma multiforme and anaplastic astrocytoma. Patients with methylated CpGs in the MGMT promoter benefit from treatment with alkylating agents, such as temozolomide, and show an improved overall survival and progression-free interval. A precise determination of MGMT promoter methylation is of importance for diagnostic decisions. We experienced that different methods show partially divergent results in a daily routine. For an integrated neuropathological diagnosis of malignant gliomas, we therefore currently apply a combination of methylation-specific PCR assays and pyrosequencing. Results To better rationalize the variation across assays, we compared these standard techniques and assays to deep bisulfite sequencing results in a cohort of 80 malignant astrocytomas. Our deep analysis covers 49 CpG sites of the expanded MGMT promoter, including exon 1, parts of intron 1 and a region upstream of the transcription start site (TSS). We observed that deep sequencing data are in general in agreement with CpG-specific pyrosequencing, while the most widely used MSP assays published by Esteller et al. (N Engl J Med 343(19):1350–1354, 2000. 10.1056/NEJM200011093431901) and Felsberg et al. (Clin Cancer Res 15(21):6683–6693, 2009. 10.1158/1078-0432.CCR-08-2801) resulted in partially discordant results in 22 tumors (27.5%). Local deep bisulfite sequencing (LDBS) revealed that CpGs located in exon 1 are suited best to discriminate methylated from unmethylated samples. Based on LDBS data, we propose an optimized MSP primer pair with 83% and 85% concordance to pyrosequencing and LDBS data. A hitherto neglected region upstream of the TSS, with an overall higher methylation compared to exon 1 and intron 1 of MGMT, is also able to discriminate the methylation status. Conclusion Our integrated analysis allows to evaluate and redefine co-methylation domains within the MGMT promoter and to rationalize the practical impact on assays used in daily routine diagnostics. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01244-4.
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Affiliation(s)
- Sascha Tierling
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.
| | | | - Alea Leismann
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
| | - Julia Becker-Kettern
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - Michael Scherer
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.,Department of Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain
| | - Arne Wrede
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - David Breuskin
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Steffi Urbschat
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Christoph Sippl
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Joachim Oertel
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | | | - Jörn Walter
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
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Abedalthagafi M, Mobark N, Al-Rashed M, AlHarbi M. Epigenomics and immunotherapeutic advances in pediatric brain tumors. NPJ Precis Oncol 2021; 5:34. [PMID: 33931704 PMCID: PMC8087701 DOI: 10.1038/s41698-021-00173-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Brain tumors are the leading cause of childhood cancer-related deaths. Similar to adult brain tumors, pediatric brain tumors are classified based on histopathological evaluations. However, pediatric brain tumors are often histologically inconsistent with adult brain tumors. Recent research findings from molecular genetic analyses have revealed molecular and genetic changes in pediatric tumors that are necessary for appropriate classification to avoid misdiagnosis, the development of treatment modalities, and the clinical management of tumors. As many of the molecular-based therapies developed from clinical trials on adults are not always effective against pediatric brain tumors, recent advances have improved our understanding of the molecular profiles of pediatric brain tumors and have led to novel epigenetic and immunotherapeutic treatment approaches currently being evaluated in clinical trials. In this review, we focus on primary malignant brain tumors in children and genetic, epigenetic, and molecular characteristics that differentiate them from brain tumors in adults. The comparison of pediatric and adult brain tumors highlights the need for treatments designed specifically for pediatric brain tumors. We also discuss the advancements in novel molecularly targeted drugs and how they are being integrated with standard therapy to improve the classification and outcomes of pediatric brain tumors in the future.
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Affiliation(s)
- Malak Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia.
| | - Nahla Mobark
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
| | - May Al-Rashed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Chair of Medical and Molecular Genetics Research, Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Musa AlHarbi
- Department of Paediatric Oncology Comprehensive Cancer Centre, King Fahad Medical City, Riyadh, Kingdom of Saudi Arabia
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10
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Pan SP, Zheng XL, Zhang N, Lin XM, Li KJ, Xia XF, Zou CL, Zhang WY. A novel nomogram for predicting the risk of epilepsy occurrence after operative in gliomas patients without preoperative epilepsy history. Epilepsy Res 2021; 174:106641. [PMID: 33878595 DOI: 10.1016/j.eplepsyres.2021.106641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Epilepsy is a common complication in glioma patients after undergoing brain tumor surgery combined with chemotherapy and/or radiotherapy. Whether antiepileptic drug prophylaxis could be used in these patients remains an open question. The purpose of this study was to produce a model for predicting the risk of epilepsy occurrence in such patients. METHODS The clinicopathologic data of glioma patients after tumor treatment were reviewed in this study. Univariate and multivariate logistic regression analyses were carried out to analyze the correlation between the clinicopathologic data and the risk of epilepsy occurrence. A nomogram was built according to the multivariate logistic regression model results. RESULTS A total of 219 patients with gliomas were reviewed. Univariate analyses revealed that age, WHO glioma classification, CD34, EGFR, Ki67, MGMT, P53 and VIM were significantly associated with the risk of epilepsy occurrence. Multivariate analyses revealed that age, WHO glioma classification, CD34, EGFR, MGMT, and VIM were predictors of risk of epilepsy occurrence. A nomogram of the risk of epilepsy occurrence was built based on statistically significant variables from the multivariate logistic regression analysis. The c-index of the nomogram was 0.755 (95 % confidence interval (CI), 0.742-0.769). SIGNIFICANCE This nomogram model provides reliable information about the risk of epilepsy occurrence for oncologists and neurological physicians.
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Affiliation(s)
- Si-Pei Pan
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Xiao-Lu Zheng
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Nan Zhang
- Department of Neurology, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Xiao-Min Lin
- Department of Neurology, The People's Hospital of Wencheng, WenZhou, China
| | - Ke-Jie Li
- Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Xiao-Fang Xia
- Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Chang-Lin Zou
- Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China
| | - Wen-Yi Zhang
- Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, WenZhou, China.
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11
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Polano M, Fabbiani E, Adreuzzi E, Cintio FD, Bedon L, Gentilini D, Mongiat M, Ius T, Arcicasa M, Skrap M, Dal Bo M, Toffoli G. A New Epigenetic Model to Stratify Glioma Patients According to Their Immunosuppressive State. Cells 2021; 10:cells10030576. [PMID: 33807997 PMCID: PMC8001235 DOI: 10.3390/cells10030576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 01/02/2023] Open
Abstract
Gliomas are the most common primary neoplasm of the central nervous system. A promising frontier in the definition of glioma prognosis and treatment is represented by epigenetics. Furthermore, in this study, we developed a machine learning classification model based on epigenetic data (CpG probes) to separate patients according to their state of immunosuppression. We considered 573 cases of low-grade glioma (LGG) and glioblastoma (GBM) from The Cancer Genome Atlas (TCGA). First, from gene expression data, we derived a novel binary indicator to flag patients with a favorable immune state. Then, based on previous studies, we selected the genes related to the immune state of tumor microenvironment. After, we improved the selection with a data-driven procedure, based on Boruta. Finally, we tuned, trained, and evaluated both random forest and neural network classifiers on the resulting dataset. We found that a multi-layer perceptron network fed by the 338 probes selected by applying both expert choice and Boruta results in the best performance, achieving an out-of-sample accuracy of 82.8%, a Matthews correlation coefficient of 0.657, and an area under the ROC curve of 0.9. Based on the proposed model, we provided a method to stratify glioma patients according to their epigenomic state.
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Affiliation(s)
- Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Correspondence:
| | - Emanuele Fabbiani
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 27100 Pavia, Italy;
| | - Eva Adreuzzi
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Division of Molecular Oncology, 33081 Aviano, Italy; (E.A.); (M.M.)
| | - Federica Di Cintio
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Luca Bedon
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Davide Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy;
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Maurizio Mongiat
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Division of Molecular Oncology, 33081 Aviano, Italy; (E.A.); (M.M.)
| | - Tamara Ius
- Neurosurgery Unit, Department of Neuroscience, Santa Maria della Misericordia University Hospital, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Mauro Arcicasa
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Department of Radiotherapy, 33081 Aviano, Italy;
| | - Miran Skrap
- Neurosurgery Unit, Department of Neuroscience, Santa Maria della Misericordia University Hospital, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081 Aviano, Italy; (F.D.C.); (L.B.); (M.D.B.); (G.T.)
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12
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Chai R, Li G, Liu Y, Zhang K, Zhao Z, Wu F, Chang Y, Pang B, Li J, Li Y, Jiang T, Wang Y. Predictive value of MGMT promoter methylation on the survival of TMZ treated IDH-mutant glioblastoma. Cancer Biol Med 2021; 18:272-282. [PMID: 33628600 PMCID: PMC7877176 DOI: 10.20892/j.issn.2095-3941.2020.0179] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Objective O6methylguanine-DNA methyltransferase (MGMT) promoter methylation is a biomarker widely used to predict the sensitivity of IDH-wildtype glioblastoma to temozolomide therapy. Given that the IDH status has critical effects on the survival and epigenetic features of glioblastoma, we aimed to assess the role of MGMT promoter methylation in IDH-mutant glioblastoma. Methods This study included 187 IDH-mutant glioblastomas and used 173 IDH-wildtype glioblastomas for comparison. Kaplan-Meier curves and multivariate Cox regression were used to study the predictive effects. Results Compared with IDH-wildtype glioblastomas, IDH-mutant glioblastomas showed significantly higher (P < 0.0001) MGMT promoter methylation. We demonstrated that MGMT promoter methylation status, as determined by a high cutoff value (≥30%) in pyrosequencing, could be used to significantly stratify the survival of 50 IDH-mutant glioblastomas receiving temozolomide therapy (cohort A); this result was validated in another cohort of 25 IDH-mutant glioblastomas (cohort B). The median progression-free survival and median overall survival in cohort A were 9.33 and 13.76 months for unmethylated cases, and 18.37 and 41.61 months for methylated cases, and in cohort B were 6.97 and 9.10 months for unmethylated cases, and 23.40 and 26.40 months for methylated cases. In addition, we confirmed that the MGMT promoter methylation was significantly (P = 0.0001) correlated with longer OS in IDH-mutant patients with GBM, independently of age, gender distribution, tumor type (primary or recurrent/secondary), and the extent of resection. Conclusions MGMT promoter methylation has predictive value in IDH-mutant glioblastoma, but its cutoff value should be higher than that for IDH-wildtype glioblastoma.
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Affiliation(s)
- Ruichao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yuqing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Kenan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yuzhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Jingjun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Yangfang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yongzhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute; Chinese Glioma Genome Atlas Network (CGGA), Capital Medical University, Beijing 100070, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
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13
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Majchrzak‐Celińska A, Dybska E, Barciszewska A. DNA methylation analysis with methylation-sensitive high-resolution melting (MS-HRM) reveals gene panel for glioma characteristics. CNS Neurosci Ther 2020; 26:1303-1314. [PMID: 32783304 PMCID: PMC7702229 DOI: 10.1111/cns.13443] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/07/2020] [Accepted: 07/11/2020] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Local DNA hypermethylation is a potential source of cancer biomarkers. While the evaluation of single gene methylation has limited value, their selected panel may provide better information. AIMS This study aimed to analyze the promoter methylation level in a 7-gene panel in brain tumors and verifies the usefulness of methylation-sensitive high-resolution melting (MS-HRM) for this purpose. METHODS Forty-six glioma samples and one non-neoplastic brain sample were analyzed by MS-HRM in terms of SFRP1, SFRP2, RUNX3, CBLN4, INA, MGMT, and RASSF1A promoter methylation. The results were correlated with patients' clinicopathological features. RESULTS DNA methylation level of all analyzed genes was significantly higher in brain tumor samples as compared to non-neoplastic brain and commercial, unmethylated DNA control. RASSF1A was the most frequently methylated gene, with statistically significant differences depending on the tumor WHO grade. Higher MGMT methylation levels were observed in females, whereas the levels of SFRP1 and INA promoter methylation significantly increased with patients' age. A positive correlation of promoter methylation levels was observed between pairs of genes, for example, CBLN4 and INA or MGMT and RASSF1A. CONCLUSIONS Our 7-gene panel of promoter methylation can be helpful in brain tumor diagnosis or characterization, and MS-HRM is a suitable method for its analysis.
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Affiliation(s)
| | - Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic DiseasesPoznan University of Medical SciencesPoznańPoland
| | - Anna‐Maria Barciszewska
- Intraoperative Imaging UnitChair and Department of Neurosurgery and NeurotraumatologyPoznan University of Medical SciencesPoznańPoland
- Department of Neurosurgery and NeurotraumatologyHeliodor Swiecicki Clinical HospitalPoznańPoland
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14
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Chang YZ, Li GZ, Pang B, Zhang KN, Zhang XH, Wang YZ, Jiang ZL, Chai RC. Transcriptional Characteristics of IDH-Wild Type Glioma Subgroups Highlight the Biological Processes Underlying Heterogeneity of IDH-Wild Type WHO Grade IV Gliomas. Front Cell Dev Biol 2020; 8:580464. [PMID: 33195221 PMCID: PMC7642517 DOI: 10.3389/fcell.2020.580464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Isocitric dehydrogenase (IDH)-wild type diffuse gliomas, which have a poorer prognosis than their IDH-mutant counterparts, are also accompanied with high heterogeneity. Here, we aimed to identify the key biological processes associated with the three groups of IDH-wild type diffuse gliomas in 323 patients. By The Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) update 3 recommendation, the three groups are Group A, diffuse astrocytic glioma, World Health Organization (WHO) grade II/III; Group B, diffuse astrocytic glioma, with one (or more) of the three genetic alterations: TERT promoter mutation, EGFR gene amplification, gain of chromosome 7 combined with loss of chromosome 10, WHO grade IV; and Group C, glioblastoma, WHO grade IV. Consistent with their histologic and genetic molecular features, we successfully identified that biological activities associated with “cell cycle” and “cell mitosis” are significantly elevated in Group B compared with Group A; microenvironment-related hallmarks “angiogenesis” and “hypoxia,” and biological processes of “extracellular matrix,” “immune response,” and “positive regulation of transcriptional activities” were more enriched in Group C than Group B. We also constructed a nine-gene signature from differentially expressed genes among the three groups to further stratify the WHO grade IV gliomas (Groups B and C) whose survival cannot be clearly stratified by current classification systems. This signature was an independent prognosis factor for WHO grade IV gliomas and had better prognostic value than other known factors in both training and validation dataset. In addition, the signature risk score was positively correlated with the amount of infiltrated immune cells, expression of immune checkpoints, and the genes enriched in biological processes of “immune response,” “cell cycle,” and “extracellular matrix.” The bioinformatic analysis results were also validated by immunohistochemistry and patient-derived cell proliferation assay. Overall, our findings revealed the key biological processes underlying the new classifications of IDH-wild type diffuse glioma. Meanwhile, we constructed a signature, which could properly stratify the prognosis, cell proliferation activates, extracellular matrix-mediated biological activities, and immune-microenvironment of IDH-wild type WHO grade IV gliomas.
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Affiliation(s)
- Yu-Zhou Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Bo Pang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Xiao-Hui Zhang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Zhong-Li Jiang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
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15
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Zhang J, Sai K, Wang XL, Ye SQ, Liang LJ, Zhou Y, Chen ZJ, Hu WM, Liu JM. Tim-3 Expression and MGMT Methylation Status Association With Survival in Glioblastoma. Front Pharmacol 2020; 11:584652. [PMID: 33041828 PMCID: PMC7522578 DOI: 10.3389/fphar.2020.584652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND A profound understanding of the molecular landscape of glioblastoma multiforme (GBM) will make it possible to develop better and more intelligent therapies directed toward specific molecular targets and may one day yield better prognostic capabilities. Immune checkpoint molecules have inspired the emergence of immune checkpoint-targeting therapeutic strategies. However, the prognostic significance of the immune checkpoint molecule T cell immunoglobulin mucin-3 (Tim-3) on tumor-infiltrating immune cells (TIICs) and O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status has not yet been fully elucidated. We aimed to develop an MGMT promoter methylation status-associated immune prognostic signature for GBM. PATIENTS AND METHODS A total of 84 patients with newly diagnosed GBM were included in this study. MGMT promoter methylation status was retrospectively analyzed, and the expression level of Tim-3 was investigated using immunohistochemistry (IHC). The correlation between Tim-3 expression combined with MGMT promoter methylation status and prognosis was explored. RESULTS Tim-3 expression varied in GBM patients. Mesenchymal expression of Tim-3 in GBM tissues was present 73.81% (62/84) of patients, and these were subdivided into groups based on low 15.48% (13/84), moderate 7.14% (6/84), or strong expression 51.19% (43/84). Forty-eight patients had tumors that tested positive for MGMT promoter methylation, while the remaining 36 patients tested negative. CONCLUSIONS We profiled the immune status of MGMT promoter methylation in GBM and established a local immune signature for GBM that could independently identify patients with a favorable prognosis, indicating a relationship between prognosis and GBM immune signature. MGMT promoter methylation with lower Tim-3 expression was significantly associated with better survival.
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Affiliation(s)
- Ji Zhang
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ke Sai
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao li Wang
- Department of General Surgery, Shang Jin Nan Fu Hospital of West China Hospital of Sichuan University, Chengdu, China
| | - Sheng quan Ye
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Li jiao Liang
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi Zhou
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhi jie Chen
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wan-Ming Hu
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jian min Liu
- Department of Neurosurgery, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
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16
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Hu Z, Mi Y, Qian H, Guo N, Yan A, Zhang Y, Gao X. A Potential Mechanism of Temozolomide Resistance in Glioma-Ferroptosis. Front Oncol 2020; 10:897. [PMID: 32656078 PMCID: PMC7324762 DOI: 10.3389/fonc.2020.00897] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/07/2020] [Indexed: 01/03/2023] Open
Abstract
Temozolomide (TMZ) is the first-line chemotherapy drug that has been used to treat glioma for over a decade, but the benefits are limited by half of the treated patients who acquired resistance. Studies have shown that glioma TMZ resistance is a complex process with multiple factors, which has not been fully elucidated. Ferroptosis, which is a new type of cell death discovered in recent years, has been reported to play an important role in tumor drug resistance. The present study reviews the relationship between ferroptosis and glioma TMZ resistance, and highlights the role of ferroptosis in glioma TMZ resistance. Finally, the investigators discussed the future orientation for ferroptosis in glioma TMZ resistance, in order to promote the clinical use of ferroptosis induction in glioma treatment.
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Affiliation(s)
- Zhifang Hu
- Shaanxi Key Laboratory of Brain Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, China
| | - Yajing Mi
- Shaanxi Key Laboratory of Brain Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, China
| | - Huiming Qian
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Na Guo
- Shaanxi Key Laboratory of Brain Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, China
| | - Aili Yan
- Shaanxi Key Laboratory of Brain Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, China
| | - Yuelin Zhang
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xingchun Gao
- Shaanxi Key Laboratory of Brain Disorders, School of Basic Medical Science, Xi'an Medical University, Xi'an, China.,Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
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17
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Cao Y, Li X, Kong S, Shang S, Qi Y. CDK4/6 inhibition suppresses tumour growth and enhances the effect of temozolomide in glioma cells. J Cell Mol Med 2020; 24:5135-5145. [PMID: 32277580 PMCID: PMC7205809 DOI: 10.1111/jcmm.15156] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/15/2020] [Accepted: 02/09/2020] [Indexed: 12/20/2022] Open
Abstract
In adults, glioma is the most commonly occurring and invasive brain tumour. For malignant gliomas, the current advanced chemotherapy includes TMZ (temozolomide). However, a sizeable number of gliomas are unyielding to TMZ, hence, giving rise to an urgent need for more efficient treatment choices. Here, we report that cyclin-dependent kinases 4 (CDK4) is expressed at significantly high levels in glioma cell lines and tissues. CDK4 overexpression enhances colony formation and proliferation of glioma cells and extends resistance to inhibition of TMZ-mediated cell proliferation and induction of apoptosis. However, CDK4 knockdown impedes colony formation and cell proliferation, and enhances sensitivity of glioma cells to TMZ. The selective inhibition of CDK4/6 impedes glioma cell proliferation and induces apoptotic induction. The selective inhibitors of CDK4/6 may enhance glioma cell sensitivity to TMZ. We further showed the possible role of RB phosphorylation mediated by CDK4 for its oncogenic function in glioma. The growth of glioma xenografts was inhibited in vivo, through combination treatment, and corresponded to enhanced p-RB levels, reduced staining of Ki-67 and enhanced activation of caspase 3. Therefore, CDK4 inhibition may be a favourable strategy for glioma treatment and overcomes TMZ resistance.
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Affiliation(s)
- Yingxiao Cao
- Department of NeurosurgeryXingtai People’s HospitalXingtaiChina
| | - Xin Li
- Department of NeurosurgeryThe First People's Hospital of ShenyangShenyangChina
| | - Shiqi Kong
- Department of NeurosurgeryXingtai People’s HospitalXingtaiChina
| | - Shuling Shang
- Department of Operating RoomXingtai People’s HospitalXingtaiChina
| | - Yanhui Qi
- Department of Intensive Care UnitXingtai People’s HospitalXingtaiChina
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Zhu X, Xuan Z, Chen J, Li Z, Zheng S, Song P. How DNA methylation affects the Warburg effect. Int J Biol Sci 2020; 16:2029-2041. [PMID: 32549751 PMCID: PMC7294934 DOI: 10.7150/ijbs.45420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
Significant enhancement of the glycolysis pathway is a major feature of tumor cells, even in the presence of abundant oxygen; this enhancement is known as the Warburg effect, and also called aerobic glycolysis. The Warburg effect was discovered nearly a hundred years ago, but its specific mechanism remains difficult to explain. DNA methylation is considered to be a potential trigger for the Warburg effect, as the two processes have many overlapping links during tumorigenesis. Based on a widely recognized potential mechanism of the Warburg effect, we here summarized the relationship between DNA methylation and the Warburg effect with regard to cellular energy metabolism factors, such as glycolysis related enzymes, mitochondrial function, glycolysis bypass pathways, the tumor oxygen sensing pathway and abnormal methylation conditions. We believe that clarifying the relationship between these different mechanisms may further help us understand how DNA methylation works on tumorigenesis and provide new opportunities for cancer therapy.
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Affiliation(s)
- Xingxin Zhu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zefeng Xuan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Jun Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zequn Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Penghong Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
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Liu YQ, Wu F, Li JJ, Li YF, Liu X, Wang Z, Chai RC. Gene Expression Profiling Stratifies IDH-Wildtype Glioblastoma With Distinct Prognoses. Front Oncol 2019; 9:1433. [PMID: 31921684 PMCID: PMC6929203 DOI: 10.3389/fonc.2019.01433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/02/2019] [Indexed: 12/31/2022] Open
Abstract
Objectives: In the present study, we aimed to determine the candidate genes that may function as biomarkers to further distinguish patients with isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM), which are heterogeneous with respect to clinical outcomes. Materials and Methods: We selected 41 candidate genes associated with overall survival (OS) using univariate Cox regression from IDH-wildtype GBM patients based on RNA sequencing (RNAseq) expression data from the Chinese Glioma Genome Atlas (CGGA, n = 105) and The Cancer Genome Atlas (TCGA, n = 139) cohorts. Next, a seven-gene-based risk signature was formulated according to Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm in the CGGA RNAseq database as a training set, while another 525 IDH-wildtype GBM patient TCGA datasets, consisting of RNA sequencing and microarray data, were used for validation. Patient survival in the low- and high-risk groups was calculated using Kaplan-Meier survival curve analysis and the log-rank test. Uni-and multivariate Cox regression analysis was used to assess the prognosis value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were performed for the functional analysis of the seven-gene-based risk signature. Results: We developed a seven-gene-based signature, which allocated each patient to a risk group (low or high). Patients in the high-risk group had dramatically shorter overall survival than their low-risk counterparts in three independent cohorts. Univariate and multivariate analysis showed that the seven-gene signature remained an independent prognostic factor. Moreover, the seven-gene risk signature exhibited a striking prognostic validity, with AUC of 78.4 and 73.9%, which was higher than for traditional “age” (53.7%, 62.4%) and “GBM sub-type” (57.7%, 52.9%) in the CGGA- and TCGA-RNAseq databases, respectively. Subsequent bioinformatics analysis predicted that the seven-gene signature was involved in the inflammatory response, immune response, cell adhesion, and apoptotic process. Conclusions: Our findings indicate that the seven-gene signature could be a potential prognostic biomarker. This study refined the current classification system of IDH-wildtype GBM and may provide a novel perspective for the research and individual therapy of IDH-wildtype GBM.
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Affiliation(s)
- Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Jing-Jun Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Yang-Fang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Xing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
| | - Zheng Wang
- Chinese Glioma Genome Atlas Network, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing, China.,Chinese Glioma Genome Atlas Network, Beijing, China
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