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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576103. [PMID: 38313282 PMCID: PMC10836086 DOI: 10.1101/2024.01.17.576103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.
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Kong X, Mao Y, Xi F, Li Y, Luo Y, Ma J. Development of a nomogram based on radiomics and semantic features for predicting chromosome 7 gain/chromosome 10 loss in IDH wild-type histologically low-grade gliomas. Front Oncol 2023; 13:1196614. [PMID: 37781185 PMCID: PMC10541227 DOI: 10.3389/fonc.2023.1196614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Purpose To predict chromosome 7 gain and chromosome 10 loss (+7/-10) in IDH wild-type (IDH-wt) histologically low-grade gliomas (LGG) by machine learning models based on MRI radiomics and semantic features. Methods A total of 122 patients diagnosed as IDH-wt histologically LGG were retrospectively included in this study. The patients were randomly divided into a training group and a test group in a ratio of 7:3. The radiomics features were extracted from axial T1WI, T2WI, FLAIR and CET1 sequences, respectively. The distance correlation (DC) and least absolute shrinkage and selection operator (LASSO) were used to select the radiomics signatures. Three machine learning algorithms including neural network (NN), support vector machine (SVM), and linear discriminant analysis (LDA) were used to construct radiomics models. In addition, a nomogram was developed by combining the optimal radiomics signature with clinical risk factors, and the potential clinical utility of the nomogram was evaluated using decision curve analysis. Results The LDA+DC model was identified as the optimal classifier among the six radiomics models. Necrosis was determined as a risk factor for +7/-10 in IDH-wt histologically LGG. The nomogram achieved the best performance, with an AUC of 0.854 and an accuracy of 0.778 in the independent test group. The decision curve of the nomogram confirmed its clinical usefulness in a wide range of thresholds. Conclusion The nomogram combining radiomics and semantic features can predict the +7/-10 status effectively, which may contribute to the risk stratification and individualized treatment planning of patients with IDH-wt histologically LGG.
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Affiliation(s)
- Xin Kong
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Mao
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fengjun Xi
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yan Li
- Department of Radiology, Beijing Fengtai Hospital, Beijing, China
| | - Yuqi Luo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun Ma
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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3
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Tu Z, Wang C, Hu Q, Tao C, Fang Z, Lin L, Lei K, Luo M, Sheng Y, Long X, Li J, Wu L, Huang K, Zhu X. Protein disulfide-isomerase A4 confers glioblastoma angiogenesis promotion capacity and resistance to anti-angiogenic therapy. J Exp Clin Cancer Res 2023; 42:77. [PMID: 36997943 PMCID: PMC10061982 DOI: 10.1186/s13046-023-02640-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 03/31/2023] Open
Abstract
Abstract
Introduction
Increasing evidence has revealed the key activity of protein disulfide isomerase A4 (PDIA4) in the endoplasmic reticulum stress (ERS) response. However, the role of PDIA4 in regulating glioblastoma (GBM)-specific pro-angiogenesis is still unknown.
Methods
The expression and prognostic role of PDIA4 were analyzed using a bioinformatics approach and were validated in 32 clinical samples and follow-up data. RNA-sequencing was used to search for PDIA4-associated biological processes in GBM cells, and proteomic mass spectrum (MS) analysis was used to screen for potential PDIA4 substrates. Western blotting, real-time quantitative polymerase chain reaction (RT-qPCR), and enzyme-linked immunosorbent assays (ELISA) were used to measure the levels of the involved factors. Cell migration and tube formation assays determined the pro-angiogenesis activity of PDIA4 in vitro. An intracranial U87 xenograft GBM animal model was constructed to evaluate the pro-angiogenesis role of PDIA4 in vivo.
Results
Aberrant overexpression of PDIA4 was associated with a poor prognosis in patients with GBM, although PDIA4 could also functionally regulate intrinsic GBM secretion of vascular endothelial growth factor-A (VEGF-A) through its active domains of Cys-X-X-Cys (CXXC) oxidoreductase. Functionally, PDIA4 exhibits pro-angiogenesis activity both in vitro and in vivo, and can be upregulated by ERS through transcriptional regulation of X-box binding protein 1 (XBP1). The XBP1/PDIA4/VEGFA axis partially supports the mechanism underlying GBM cell survival under ER stress. Further, GBM cells with higher expression of PDIA4 showed resistance to antiangiogenic therapy in vivo.
Conclusions
Our findings revealed the pro-angiogenesis role of PDIA4 in GBM progression and its potential impact on GBM survival under a harsh microenvironment. Targeting PDIA4 might help to improve the efficacy of antiangiogenic therapy in patients with GBM.
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von Knebel Doeberitz N, Paech D, Sturm D, Pusch S, Turcan S, Saunthararajah Y. Changing paradigms in oncology: Toward noncytotoxic treatments for advanced gliomas. Int J Cancer 2022; 151:1431-1446. [PMID: 35603902 PMCID: PMC9474618 DOI: 10.1002/ijc.34131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022]
Abstract
Glial-lineage malignancies (gliomas) recurrently mutate and/or delete the master regulators of apoptosis p53 and/or p16/CDKN2A, undermining apoptosis-intending (cytotoxic) treatments. By contrast to disrupted p53/p16, glioma cells are live-wired with the master transcription factor circuits that specify and drive glial lineage fates: these transcription factors activate early-glial and replication programs as expected, but fail in their other usual function of forcing onward glial lineage-maturation-late-glial genes have constitutively "closed" chromatin requiring chromatin-remodeling for activation-glioma-genesis disrupts several epigenetic components needed to perform this work, and simultaneously amplifies repressing epigenetic machinery instead. Pharmacologic inhibition of repressing epigenetic enzymes thus allows activation of late-glial genes and terminates glioma self-replication (self-replication = replication without lineage-maturation), independent of p53/p16/apoptosis. Lineage-specifying master transcription factors therefore contrast with p53/p16 in being enriched in self-replicating glioma cells, reveal a cause-effect relationship between aberrant epigenetic repression of late-lineage programs and malignant self-replication, and point to specific epigenetic targets for noncytotoxic glioma-therapy.
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Affiliation(s)
| | - Daniel Paech
- Division of RadiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Department of NeuroradiologyBonn University HospitalBonnGermany
| | - Dominik Sturm
- Hopp Children's Cancer Center (KiTZ) HeidelbergHeidelbergGermany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK)HeidelbergGermany
- Department of Pediatric Oncology, Hematology & ImmunologyHeidelberg University HospitalHeidelbergGermany
| | - Stefan Pusch
- Department of NeuropathologyInstitute of Pathology, Ruprecht‐Karls‐University HeidelbergHeidelbergGermany
- German Cancer Consortium (DKTK), Clinical Cooperation Unit (CCU) Neuropathology, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Sevin Turcan
- Department of NeurologyHeidelberg University HospitalHeidelbergGermany
| | - Yogen Saunthararajah
- Department of Translational Hematology and Oncology ResearchTaussig Cancer Institute, Cleveland ClinicClevelandOhioUSA
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5
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Intratumor heterogeneity, microenvironment, and mechanisms of drug resistance in glioma recurrence and evolution. Front Med 2021; 15:551-561. [PMID: 33893983 DOI: 10.1007/s11684-020-0760-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
Abstract
Glioma is the most common lethal tumor of the human brain. The median survival of patients with primary World Health Organization grade IV glioma is only 14.6 months. The World Health Organization classification of tumors of the central nervous system categorized gliomas into lower-grade gliomas and glioblastomas. Unlike primary glioblastoma that usually develop de novo in the elderly, secondary glioblastoma enriched with an isocitrate dehydrogenase mutant typically progresses from lower-grade glioma within 5-10 years from the time of diagnosis. Based on various evolutional trajectories brought on by clonal and subclonal alterations, the evolution patterns of glioma vary according to different theories. Some important features distinguish the normal brain from other tissues, e.g., the composition of the microenvironment around the tumor cells, the presence of the blood-brain barrier, and others. The underlying mechanism of glioma recurrence and evolution patterns of glioma are different from those of other types of cancer. Several studies correlated tumor recurrence with tumor heterogeneity and the immune microenvironment. However, the detailed reasons for the progression and recurrence of glioma remain controversial. In this review, we introduce the different mechanisms involved in glioma progression, including tumor heterogeneity, the tumor microenvironment and drug resistance, and their pre-clinical implements in clinical trials. This review aimed to provide new insights into further clinical strategies for the treatment of patients with recurrent and secondary glioma.
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6
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Kısakol B, Sarıhan Ş, Ergün MA, Baysan M. Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels. ACTA ACUST UNITED AC 2021; 45:114-126. [PMID: 33907494 PMCID: PMC8068765 DOI: 10.3906/biy-2008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/03/2021] [Indexed: 11/25/2022]
Abstract
The importance of next generation sequencing (NGS) rises in cancer research as accessing this key technology becomes easier for researchers. The sequence data created by NGS technologies must be processed by various bioinformatics algorithms within a pipeline in order to convert raw data to meaningful information. Mapping and variant calling are the two main steps of these analysis pipelines, and many algorithms are available for these steps. Therefore, detailed benchmarking of these algorithms in different scenarios is crucial for the efficient utilization of sequencing technologies. In this study, we compared the performance of twelve pipelines (three mapping and four variant discovery algorithms) with recommended settings to capture single nucleotide variants. We observed significant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples with overall high specificity and low sensitivity. Additional to the individual evaluation of pipelines, we also constructed and tested the performance of pipeline combinations. In these analyses, we observed that certain pipelines complement each other much better than others and display superior performance than individual pipelines. This suggests that adhering to a single pipeline is not optimal for cancer sequencing analysis and sample heterogeneity should be considered in algorithm optimization.
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Affiliation(s)
- Batuhan Kısakol
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin Ireland
| | - Şahin Sarıhan
- Computer Engineering Department, Faculty of Engineering, Marmara University, İstanbul, Turkey Turkey
| | - Mehmet Arif Ergün
- Computer Engineering Department, Faculty of Computer and Informatics Engineering, İstanbul Technical University,İstanbul Turkey
| | - Mehmet Baysan
- Computer Engineering Department, Faculty of Computer and Informatics Engineering, İstanbul Technical University,İstanbul Turkey
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7
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Galbraith K, Kumar A, Abdullah KG, Walker JM, Adams SH, Prior T, Dimentberg R, Henderson FC, Mirchia K, Sathe AA, Viapiano MS, Chin LS, Corona RJ, Hatanpaa KJ, Snuderl M, Xing C, Brem S, Richardson TE. Molecular Correlates of Long Survival in IDH-Wildtype Glioblastoma Cohorts. J Neuropathol Exp Neurol 2021; 79:843-854. [PMID: 32647886 DOI: 10.1093/jnen/nlaa059] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/29/2020] [Indexed: 02/07/2023] Open
Abstract
IDH-wildtype glioblastoma is a relatively common malignant brain tumor in adults. These patients generally have dismal prognoses, although outliers with long survival have been noted in the literature. Recently, it has been reported that many histologically lower-grade IDH-wildtype astrocytomas have a similar clinical outcome to grade IV tumors, suggesting they may represent early or undersampled glioblastomas. cIMPACT-NOW 3 guidelines now recommend upgrading IDH-wildtype astrocytomas with certain molecular criteria (EGFR amplifications, chromosome 7 gain/10 loss, and/or TERT promoter mutations), establishing the concept of a "molecular grade IV" astrocytoma. In this report, we apply these cIMPACT-NOW 3 criteria to 2 independent glioblastoma cohorts, totaling 393 public database and institutional glioblastoma cases: 89 cases without any of the cIMPACT-NOW 3 criteria (GBM-C0) and 304 cases with one or more criteria (GBM-C1-3). In the GBM-C0 groups, there was a trend toward longer recurrence-free survival (median 12-17 vs 6-10 months), significantly longer overall survival (median 32-41 vs 15-18 months), younger age at initial diagnosis, and lower overall mutation burden compared to the GBM-C1-3 cohorts. These data suggest that while histologic features may not be ideal indicators of patient survival in IDH-wildtype astrocytomas, these 3 molecular features may also be important prognostic factors in IDH-wildtype glioblastoma.
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Affiliation(s)
- Kristyn Galbraith
- From the Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth & Development
| | - Kalil G Abdullah
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas
| | - Jamie M Walker
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas.,Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, Texas
| | - Steven H Adams
- College of Medicine, State University of New York, Upstate Medical University, Syracuse, New York
| | - Timothy Prior
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ryan Dimentberg
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fraser C Henderson
- Department of Neurosurgery, Medical University of South Carolina, Charleston, South Carolina
| | - Kanish Mirchia
- From the Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | | | | | | | - Robert J Corona
- From the Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
| | - Kimmo J Hatanpaa
- State University of New York, Upstate Medical University, Syracuse, New York; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York City, New York
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development.,Department of Bioinformatics and Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Timothy E Richardson
- From the Department of Pathology, State University of New York, Upstate Medical University, Syracuse, New York
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8
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Nicholson JG, Fine HA. Diffuse Glioma Heterogeneity and Its Therapeutic Implications. Cancer Discov 2021; 11:575-590. [PMID: 33558264 DOI: 10.1158/2159-8290.cd-20-1474] [Citation(s) in RCA: 195] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/05/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
Diffuse gliomas represent a heterogeneous group of universally lethal brain tumors characterized by minimally effective genotype-targeted therapies. Recent advances have revealed that a remarkable level of genetic, epigenetic, and environmental heterogeneity exists within each individual glioma. Together, these interconnected layers of intratumoral heterogeneity result in extreme phenotypic heterogeneity at the cellular level, providing for multiple mechanisms of therapeutic resistance and forming a highly adaptable and resilient disease. In this review, we discuss how glioma intratumoral heterogeneity and malignant cellular state plasticity drive resistance to existing therapies and look to a future in which these challenges may be overcome. SIGNIFICANCE: Glioma intratumoral heterogeneity and malignant cell state plasticity represent formidable hurdles to the development of novel targeted therapies. However, the convergence of genotypically diverse glioma cells into a limited set of epigenetically encoded transcriptional cell states may present an opportunity for a novel therapeutic strategy we call "State Selective Lethality." In this approach, cellular states (as opposed to genetic perturbations/mutations) are the subject of therapeutic targeting, and plasticity-mediated resistance is minimized through the design of cell state "trapping agents."
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Affiliation(s)
- James G Nicholson
- Department of Neurology, The Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Howard A Fine
- Department of Neurology, The Meyer Cancer Center, Weill Cornell Medicine, New York, New York.
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9
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Ferreira WAS, Amorim CKN, Burbano RR, Villacis RAR, Marchi FA, Medina TS, Lima MMCD, Oliveira EHCD. Genomic and transcriptomic characterization of the human glioblastoma cell line AHOL1. ACTA ACUST UNITED AC 2021; 54:e9571. [PMID: 33470396 PMCID: PMC7812907 DOI: 10.1590/1414-431x20209571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.
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Affiliation(s)
- W A S Ferreira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil
| | - C K N Amorim
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil
| | - R R Burbano
- Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil.,Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Belém, PA, Brasil.,Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, PA, Brasil
| | - R A R Villacis
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brasil
| | - F A Marchi
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - T S Medina
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - M M C de Lima
- Instituto de Ciências Biológicas, Faculdade de Biomedicina, Universidade Federal do Pará, Belém, PA, Brasil
| | - E H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil.,Instituto de Ciências Exatas e Naturais, Faculdade de Ciências Naturais, Universidade Federal do Pará, Belém, PA, Brasil
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10
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Badr CE, Silver DJ, Siebzehnrubl FA, Deleyrolle LP. Metabolic heterogeneity and adaptability in brain tumors. Cell Mol Life Sci 2020; 77:5101-5119. [PMID: 32506168 PMCID: PMC8272080 DOI: 10.1007/s00018-020-03569-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/18/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
The metabolic complexity and flexibility commonly observed in brain tumors, especially glioblastoma, is fundamental for their development and progression. The ability of tumor cells to modify their genetic landscape and adapt metabolically, subverts therapeutic efficacy, and inevitably instigates therapeutic resistance. To overcome these challenges and develop effective therapeutic strategies targeting essential metabolic processes, it is necessary to identify the mechanisms underlying heterogeneity and define metabolic preferences and liabilities of malignant cells. In this review, we will discuss metabolic diversity in brain cancer and highlight the role of cancer stem cells in regulating metabolic heterogeneity. We will also highlight potential therapeutic modalities targeting metabolic vulnerabilities and examine how intercellular metabolic signaling can shape the tumor microenvironment.
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Affiliation(s)
- Christian E Badr
- Neuro-Oncology Division, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Neuroscience Program, Harvard Medical School, Boston, MA, USA
| | - Daniel J Silver
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Florian A Siebzehnrubl
- European Cancer Stem Cell Research Institute, Cardiff University School of Biosciences, Cardiff, CF24 4HQ, UK
| | - Loic P Deleyrolle
- Lillian S. Wells Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, FL, USA.
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11
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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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12
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Wallenborn M, Xu LX, Kirsten H, Rohani L, Rudolf D, Ahnert P, Schmidt C, Schulz RM, Richter M, Krupp W, Mueller W, Johnson AA, Meixensberger J, Holland H. Molecular analyses of glioblastoma stem-like cells and glioblastoma tissue. PLoS One 2020; 15:e0234986. [PMID: 32634135 PMCID: PMC7340312 DOI: 10.1371/journal.pone.0234986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/05/2020] [Indexed: 01/01/2023] Open
Abstract
Glioblastoma is a common, malignant brain tumor whose disease incidence increases with age. Glioblastoma stem-like cells (GSCs) are thought to contribute to cancer therapy resistance and to be responsible for tumor initiation, maintenance, and recurrence. This study utilizes both SNP array and gene expression profiling to better understand GSCs and their relation to malignant disease. Peripheral blood and primary glioblastoma tumor tissue were obtained from patients, the latter of which was used to generate GSCs as well as a CD133pos./CD15pos. subpopulation. The stem cell features of GSCs were confirmed via the immunofluorescent expression of Nestin, SOX2, and CD133. Both tumor tissue and the isolated primary cells shared unique abnormal genomic characteristics, including a gain of chromosome 7 as well as either a partial or complete loss of chromosome 10. Individual genomic differences were also observed, including the loss of chromosome 4 and segmental uniparental disomy of 9p24.3→p21.3 in GSCs. Gene expression profiling revealed 418 genes upregulated in tumor tissue vs. CD133pos./CD15pos. cells and 44 genes upregulated in CD133pos./CD15pos. cells vs. tumor tissue. Pathway analyses demonstrated that upregulated genes in CD133pos./CD15pos. cells are relevant to cell cycle processes and cancerogenesis. In summary, we detected previously undescribed genomic and gene expression differences when comparing tumor tissue and isolated stem-like subpopulations.
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Affiliation(s)
- Marco Wallenborn
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
- Department of Neurosurgery, University of Leipzig, Leipzig, Germany
| | - Li-Xin Xu
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Leili Rohani
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Daniela Rudolf
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
| | - Christian Schmidt
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
- Clinic of Orthopaedics, Traumatology and Plastic Surgery, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Ronny M. Schulz
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
- Clinic of Orthopaedics, Traumatology and Plastic Surgery, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Mandy Richter
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
| | - Wolfgang Krupp
- Department of Neurosurgery, University of Leipzig, Leipzig, Germany
| | - Wolf Mueller
- Department of Neuropathology, University of Leipzig, Leipzig, Germany
| | - Adiv A. Johnson
- Nikon Instruments, Melville, New York, United States of America
| | | | - Heidrun Holland
- Translational Centre for Regenerative Medicine (TRM) and Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, Leipzig, Germany
- * E-mail:
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13
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de Souza CF, Sabedot TS, Malta TM, Stetson L, Morozova O, Sokolov A, Laird PW, Wiznerowicz M, Iavarone A, Snyder J, deCarvalho A, Sanborn Z, McDonald KL, Friedman WA, Tirapelli D, Poisson L, Mikkelsen T, Carlotti CG, Kalkanis S, Zenklusen J, Salama SR, Barnholtz-Sloan JS, Noushmehr H. A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence. Cell Rep 2019; 23:637-651. [PMID: 29642018 PMCID: PMC8859991 DOI: 10.1016/j.celrep.2018.03.107] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 12/14/2017] [Accepted: 03/23/2018] [Indexed: 01/05/2023] Open
Abstract
Glioma diagnosis is based on histomorphology and grading; however, such classification does not have predictive clinical outcome after glioblastomas have developed. To date, no bona fide biomarkers that significantly translate into a survival benefit to glioblastoma patients have been identified. We previously reported that the IDH mutant G-CIMP-high subtype would be a predecessor to the G-CIMP-low subtype. Here, we performed a comprehensive DNA methylation longitudinal analysis of diffuse gliomas from 77 patients (200 tumors) to enlighten the epigenome-based malignant transformation of initially lower-grade gliomas. Intra-subtype heterogeneity among G-CIMP-high primary tumors allowed us to identify predictive biomarkers for assessing the risk of malignant recurrence at early stages of disease. G-CIMP-low recurrence appeared in 9.5% of all gliomas, and these resembled IDH-wild-type primary glioblastoma. G-CIMP-low recurrence can be characterized by distinct epigenetic changes at candidate functional tissue enhancers with AP-1/SOX binding elements, mesenchymal stem cell-like epigenomic phenotype, and genomic instability. Molecular abnormalities of longitudinal G-CIMP offer possibilities to defy glioblastoma progression.
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Affiliation(s)
- Camila Ferreira de Souza
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Thais S Sabedot
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Lindsay Stetson
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Olena Morozova
- UC Santa Cruz Genomics Institute and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Maciej Wiznerowicz
- Laboratory for Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland; Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; International Institute for Molecular Oncology, Poznan, Poland
| | - Antonio Iavarone
- Department of Pathology and Cell Biology and Neurology Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - James Snyder
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA
| | - Ana deCarvalho
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA
| | | | - Kerrie L McDonald
- Cure Brain Cancer Biomarkers and Translational Research Laboratory, Prince of Wales Clinical School, UNSW, Sydney, NSW, Australia
| | | | - Daniela Tirapelli
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Laila Poisson
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Public Health Sciences, Henry Ford Health System, Detroit, MI 48202, USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA
| | - Carlos G Carlotti
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Steven Kalkanis
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA
| | | | - Sofie R Salama
- UC Santa Cruz Genomics Institute and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, MI 48202, USA; Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
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14
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Jimenez-Pascual A, Hale JS, Kordowski A, Pugh J, Silver DJ, Bayik D, Roversi G, Alban TJ, Rao S, Chen R, McIntyre TM, Colombo G, Taraboletti G, Holmberg KO, Forsberg-Nilsson K, Lathia JD, Siebzehnrubl FA. ADAMDEC1 Maintains a Growth Factor Signaling Loop in Cancer Stem Cells. Cancer Discov 2019; 9:1574-1589. [PMID: 31434712 DOI: 10.1158/2159-8290.cd-18-1308] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 07/02/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023]
Abstract
Glioblastomas (GBM) are lethal brain tumors where poor outcome is attributed to cellular heterogeneity, therapeutic resistance, and a highly infiltrative nature. These characteristics are preferentially linked to GBM cancer stem cells (GSC), but how GSCs maintain their stemness is incompletely understood and the subject of intense investigation. Here, we identify a novel signaling loop that induces and maintains GSCs consisting of an atypical metalloproteinase, ADAMDEC1, secreted by GSCs. ADAMDEC1 rapidly solubilizes FGF2 to stimulate FGFR1 expressed on GSCs. FGFR1 signaling induces upregulation of ZEB1 via ERK1/2 that regulates ADAMDEC1 expression through miR-203, creating a positive feedback loop. Genetic or pharmacologic targeting of components of this axis attenuates self-renewal and tumor growth. These findings reveal a new signaling axis for GSC maintenance and highlight ADAMDEC1 and FGFR1 as potential therapeutic targets in GBM. SIGNIFICANCE: Cancer stem cells (CSC) drive tumor growth in many cancers including GBM. We identified a novel sheddase, ADAMDEC1, which initiates an FGF autocrine loop to promote stemness in CSCs. This loop can be targeted to reduce GBM growth.This article is highlighted in the In This Issue feature, p. 1469.
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Affiliation(s)
- Ana Jimenez-Pascual
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - James S Hale
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio. .,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Anja Kordowski
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - Jamie Pugh
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
| | - Daniel J Silver
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Defne Bayik
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Gustavo Roversi
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Tyler J Alban
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Shilpa Rao
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Rui Chen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Thomas M McIntyre
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia and Institute of Molecular Recognition Chemistry (ICRM-CNR), Milano, Italy
| | | | - Karl O Holmberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Justin D Lathia
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio. .,Case Comprehensive Cancer Center, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic, Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Florian A Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom.
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15
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Chai RC, Li YM, Zhang KN, Chang YZ, Liu YQ, Zhao Z, Wang ZL, Chang YH, Li GZ, Wang KY, Wu F, Wang YZ. RNA processing genes characterize RNA splicing and further stratify lower-grade glioma. JCI Insight 2019; 5:130591. [PMID: 31408440 DOI: 10.1172/jci.insight.130591] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Aberrant expression of RNA processing genes may drive the alterative RNA profile in lower-grade gliomas (LGGs). Thus, we aimed to further stratify LGGs based on the expression of RNA processing genes. METHODS This study included 446 LGGs from The Cancer Genome Atlas (TCGA, training set) and 171 LGGs from the Chinese Glioma Genome Atlas (CGGA, validation set). The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was conducted to develop a risk-signature. The receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to study the prognosis value of the risk-signature. RESULTS Among the tested 784 RNA processing genes, 276 were significantly correlated with the OS of LGGs. Further LASSO Cox regression identified a 19-gene risk-signature, whose risk score was also an independently prognosis factor (P<0.0001, multiplex Cox regression) in the validation dataset. The signature had better prognostic value than the traditional factors "age", "grade" and "WHO 2016 classification" for 3- and 5-year survival both two datasets (AUCs > 85%). Importantly, the risk-signature could further stratify the survival of LGGs in specific subgroups of WHO 2016 classification. Furthermore, alternative splicing events for genes such as EGFR and FGFR were found to be associated with the risk score. mRNA expression levels for genes, which participated in cell proliferation and other processes, were significantly correlated to the risk score. CONCLUSIONS Our results highlight the role of RNA processing genes for further stratifying the survival of patients with LGGs and provide insight into the alternative splicing events underlying this role.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and
| | - Yi-Ming Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yu-Zhou Chang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Zhi-Liang Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yuan-Hao Chang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas, Beijing, China.,China National Clinical Research Center for Neurological Diseases and.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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16
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Chai RC, Wang N, Chang YZ, Zhang KN, Li JJ, Niu JJ, Wu F, Liu YQ, Wang YZ. Systematically profiling the expression of eIF3 subunits in glioma reveals the expression of eIF3i has prognostic value in IDH-mutant lower grade glioma. Cancer Cell Int 2019; 19:155. [PMID: 31171919 PMCID: PMC6549376 DOI: 10.1186/s12935-019-0867-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
Background Abnormal expression of the eukaryotic initiation factor 3 (eIF3) subunits plays critical roles in tumorigenesis and progression, and also has potential prognostic value in cancers. However, the expression and clinical implications of eIF3 subunits in glioma remain unknown. Methods Expression data of eIF3 for patients with gliomas were obtained from the Chinese Glioma Genome Atlas (CGGA) (n = 272) and The Cancer Genome Atlas (TCGA) (n = 595). Cox regression, the receiver operating characteristic (ROC) curves and Kaplan–Meier analysis were used to study the prognostic value. Gene oncology (GO) and gene set enrichment analysis (GSEA) were utilized for functional prediction. Results In both the CGGA and TCGA datasets, the expression levels of eIF3d, eIF3e, eIF3f, eIF3h and eIF3l highly were associated with the IDH mutant status of gliomas. The expression of eIF3b, eIF3i, eIF3k and eIF3m was increased with the tumor grade, and was associated with poorer overall survival [All Hazard ratio (HR) > 1 and P < 0.05]. By contrast, the expression of eIF3a and eIF3l was decreased in higher grade gliomas and was associated with better overall survival (Both HR < 1 and P < 0.05). Importantly, the expression of eIF3i (located on chromosome 1p) and eIF3k (Located on chromosome 19q) were the two highest risk factors in both the CGGA [eIF3i HR = 2.068 (1.425–3.000); eIF3k HR = 1.737 (1.166–2.588)] and TCGA [eIF3i HR = 1.841 (1.642–2.064); eIF3k HR = 1.521 (1.340–1.726)] databases. Among eIF3i, eIF3k alone or in combination, the expression of eIF3i was the more robust in stratifying the survival of glioma in various pathological subgroups. The expression of eIF3i was an independent prognostic factor in IDH-mutant lower grade glioma (LGG) and could also predict the 1p/19q codeletion status of IDH-mutant LGG. Finally, GO and GSEA analysis showed that the elevated expression of eIF3i was significantly correlated with the biological processes of cell proliferation, mRNA processing, translation, T cell receptor signaling, NF-κB signaling and others. Conclusions Our study reveals the expression alterations during glioma progression, and highlights the prognostic value of eIF3i in IDH-mutant LGG. Electronic supplementary material The online version of this article (10.1186/s12935-019-0867-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui-Chao Chai
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,4China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Ning Wang
- 2Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020 China
| | - Yu-Zhou Chang
- 3Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China
| | - Ke-Nan Zhang
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Jing-Jun Li
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Jun-Jie Niu
- Xiang Fen Centers for Disease Control and Prevention, Xiangfen, 041500 Shanxi China
| | - Fan Wu
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yu-Qing Liu
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yong-Zhi Wang
- 1Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,3Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100160 China.,4China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100160 China.,Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
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17
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The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells Int 2019; 2019:2617030. [PMID: 30984267 PMCID: PMC6431486 DOI: 10.1155/2019/2617030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/01/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant human brain tumour, characterized by rapid progression, invasion, intense angiogenesis, high genomic instability, and resistance to therapies. Despite countless experimental researches for new therapeutic strategies and promising clinical trials, the prognosis remains extremely poor, with a mean survival of less than 14 months. GBM aggressive behaviour is due to a subpopulation of tumourigenic stem-like cells, GBM stem cells (GSCs), which hierarchically drive onset, proliferation, and tumour recurrence. The morbidity and mortality of this disease strongly encourage exploring genetic characteristics of GSCs. Here, using array-CGH platform, we investigated genetic and genomic aberration profiles of GBM parent tumour (n = 10) and their primarily derived GSCs. Statistical analysis was performed by using R software and complex heatmap and corrplot packages. Pearson correlation and K-means algorithm were exploited to compare genetic alterations and to group similar genetic profiles in matched pairs of GBM and derived GSCs. We identified, in both GBM and matched GSCs, recurrent copy number alterations, as chromosome 7 polysomy, chromosome 10 monosomy, and chromosome 9p21deletions, which are typical features of primary GBM, essential for gliomagenesis. These observations suggest a condition of strong genomic instability both in GBM as GSCs. Our findings showed the robust similarity between GBM mass and GSCs (Pearson corr.≥0.65) but also highlighted a marked variability among different patients. Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. Furthermore, K-means algorithm identified an impairment of pathways related to the development and progression of cancer, such as angiogenesis, as well as pathways related to the immune system regulation, such as T cell activation. Our data confirmed the preservation of the genomic landscape from tumour tissue to GSCs, supporting the relevance of this cellular model to test in vitro new target therapies for GBM.
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18
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Bunda S, Heir P, Metcalf J, Li ASC, Agnihotri S, Pusch S, Yasin M, Li M, Burrell K, Mansouri S, Singh O, Wilson M, Alamsahebpour A, Nejad R, Choi B, Kim D, von Deimling A, Zadeh G, Aldape K. CIC protein instability contributes to tumorigenesis in glioblastoma. Nat Commun 2019; 10:661. [PMID: 30737375 PMCID: PMC6368580 DOI: 10.1038/s41467-018-08087-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/07/2018] [Indexed: 01/12/2023] Open
Abstract
Capicua (CIC) is a transcriptional repressor that counteracts activation of genes downstream of receptor tyrosine kinase (RTK)/Ras/ERK signaling. It is well-established that tumorigenesis, especially in glioblastoma (GBM), is attributed to hyperactive RTK/Ras/ERK signaling. While CIC is mutated in other tumors, here we show that CIC has a tumor suppressive function in GBM through an alternative mechanism. We find that CIC protein levels are negligible in GBM due to continuous proteasome-mediated degradation, which is mediated by the E3 ligase PJA1 and show that this occurs through binding of CIC to its DNA target and phosphorylation on residue S173. PJA1 knockdown increased CIC stability and extended survival using in-vivo models of GBM. Deletion of the ERK binding site resulted in stabilization of CIC and increased therapeutic efficacy of ERK inhibition in GBM models. Our results provide a rationale to target CIC degradation in Ras/ERK-driven tumors, including GBM, to increase efficacy of ERK inhibitors. Capicua (CIC) is a tumour suppressor in oligodendroglioma. Here, the authors show that ERK activation mediates CIC regulation via ubiquitination and degradation by PJA1 and a degradation resistant form of CIC enhances efficacy of ERK inhibition in glioblastoma.
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Affiliation(s)
- Severa Bunda
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Pardeep Heir
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Julie Metcalf
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Annie Si Cong Li
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Sameer Agnihotri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada.,Department of Neurosurgery, University of Pittsburgh Medical Center, UPMC Presbyterian, Suite B-400, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, D-69120, Germany.,German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology German Cancer Research Center (DKFZ), Heidelberg, D-69120, Germany
| | - Mamatjan Yasin
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Mira Li
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Kelly Burrell
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Sheila Mansouri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Olivia Singh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Mark Wilson
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Amir Alamsahebpour
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Romina Nejad
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Bethany Choi
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - David Kim
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, D-69120, Germany.,German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology German Cancer Research Center (DKFZ), Heidelberg, D-69120, Germany
| | - Gelareh Zadeh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada. .,Division of Neurosurgery, Toronto Western Hospital, Toronto, ON, M5G 2C1, Canada. .,Insititute of Medical Science, University Health Network and University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Kenneth Aldape
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, Toronto, ON, M5G 2C1, Canada. .,Laboratory of Pathology, National Cancer Institute, Bethesda, MD, 20892, USA.
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19
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Waker CA, Lober RM. Brain Tumors of Glial Origin. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1190:281-297. [PMID: 31760651 DOI: 10.1007/978-981-32-9636-7_18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gliomas are a heterogeneous group of tumors with evolving classification based on genotype. Isocitrate dehydrogenase (IDH) mutation is an early event in the formation of some diffuse gliomas, and is the best understood mechanism of their epigenetic dysregulation. Glioblastoma may evolve from lower-grade lesions with IDH mutations, or arise independently from copy number changes in platelet-derived growth factor receptor alpha (PDGFRA) and phosphatase and tensin homolog (PTEN). Several molecular subtypes of glioblastoma arise from a common proneural precursor with a tendency toward transition to a mesenchymal subtype. Following oncogenic transformation, gliomas escape growth arrest through a distinct step of aberrant telomere reverse transcriptase (TERT) expression, or mutations in either alpha thalassemia/mental retardation syndrome (ATRX) or death-domain associated protein (DAXX) genes. Metabolic reprogramming allows gliomas to thrive in harsh microenvironments such as hypoxia, acidity, and nutrient depletion, which contribute to tumor initiation, maintenance, and treatment resistance.
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Affiliation(s)
- Christopher A Waker
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH, USA.,Department of Neurosurgery, Dayton Children's Hospital, One Children's Plaza, Dayton, OH, USA
| | - Robert M Lober
- Department of Neuroscience, Cell Biology and Physiology, Wright State University, Dayton, OH, USA. .,Department of Neurosurgery, Dayton Children's Hospital, One Children's Plaza, Dayton, OH, USA. .,Department of Pediatrics, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA.
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20
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Martinez-Olivera R, Datsi A, Stallkamp M, Köller M, Kohtz I, Pintea B, Gousias K. Silencing of the nucleocytoplasmic shuttling protein karyopherin a2 promotes cell-cycle arrest and apoptosis in glioblastoma multiforme. Oncotarget 2018; 9:33471-33481. [PMID: 30323892 PMCID: PMC6173355 DOI: 10.18632/oncotarget.26033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 08/04/2018] [Indexed: 12/31/2022] Open
Abstract
We have previously shown that the nucleocytoplasmic carrier karyopherin a2 (KPNA2) is overexpressed in glioblastoma multiforme (GBM) whereas its expression is inversely associated with patient prognosis. However, the promoting role of KPNA2 in gliomagenesis is still poorly understood. This study aims to further elucidate this role of KPNA2 in in vitro GBM models. From four different tested GBM cell lines, the U87MG showed the highest proliferation, low adherence and outgrowth in 3D clusters as well as the highest expression of KPNA2, all features conferring greater malignant behaviour. Silencing of KPNA2 via siRNA interference in those cells significantly decreased their proliferative capacity (p = 0.001). We further observed both a significant cell cycle phase arrest (p = 0.040) and the promoting of cellular apoptosis (p = 0.016) as well as a strong trend (p = 0.062) for an inhibition of nuclear import of c-Myc. This study confirms that a higher expression of KPNA2 in GBM is associated with a more malignant phenotype also in in vitro models. While increased expression of KPNA2 promotes proliferation and survival of GBM tumour cells, silencing of KPNA2 conferred a less malignant behaviour. Our results strongly suggest that silencing of KPNA2 may play an important role in modulation of malignant features of GBM cells.
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Affiliation(s)
- Ramon Martinez-Olivera
- Department of Neurosurgery and Neurotraumatology, BG University Hospital Bergmannsheil, 44789 Bochum, Germany
| | - Angeliki Datsi
- Department of Laboratory for Neurosurgical Research, BG University Hospital Bergmannsheil, 44789 Bochum, Germany.,Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Maren Stallkamp
- Department of Laboratory for Neurosurgical Research, BG University Hospital Bergmannsheil, 44789 Bochum, Germany.,Medical School, Rheinische Friedrich-Wilhelms University of Bonn, 53121 Bonn, Germany
| | - Manfred Köller
- Department of Surgical Research, BG University Hospital Bergmannsheil, 44789 Bochum, Germany
| | - Isabelle Kohtz
- Department of Laboratory for Neurosurgical Research, BG University Hospital Bergmannsheil, 44789 Bochum, Germany
| | - Bogdan Pintea
- Department of Neurosurgery and Neurotraumatology, BG University Hospital Bergmannsheil, 44789 Bochum, Germany
| | - Konstantinos Gousias
- Department of Neurosurgery and Neurotraumatology, BG University Hospital Bergmannsheil, 44789 Bochum, Germany.,Department of Laboratory for Neurosurgical Research, BG University Hospital Bergmannsheil, 44789 Bochum, Germany.,Medical School, Rheinische Friedrich-Wilhelms University of Bonn, 53121 Bonn, Germany.,Department of Neurosurgery, University Hospital of Marburg, 35033 Marburg, Germany
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21
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Nguyen HS, Shabani S, Awad AJ, Kaushal M, Doan N. Molecular Markers of Therapy-Resistant Glioblastoma and Potential Strategy to Combat Resistance. Int J Mol Sci 2018; 19:ijms19061765. [PMID: 29899215 PMCID: PMC6032212 DOI: 10.3390/ijms19061765] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant tumor of the central nervous system. With its overall dismal prognosis (the median survival is 14 months), GBMs demonstrate a resounding resilience against all current treatment modalities. The absence of a major progress in the treatment of GBM maybe a result of our poor understanding of both GBM tumor biology and the mechanisms underlying the acquirement of treatment resistance in recurrent GBMs. A comprehensive understanding of these markers is mandatory for the development of treatments against therapy-resistant GBMs. This review also provides an overview of a novel marker called acid ceramidase and its implication in the development of radioresistant GBMs. Multiple signaling pathways were found altered in radioresistant GBMs. Given these global alterations of multiple signaling pathways found in radioresistant GBMs, an effective treatment for radioresistant GBMs may require a cocktail containing multiple agents targeting multiple cancer-inducing pathways in order to have a chance to make a substantial impact on improving the overall GBM survival.
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Affiliation(s)
- Ha S Nguyen
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
- Faculty of Neurosurgery, California Institute of Neuroscience, Thousand Oaks, CA 91360, USA.
| | - Saman Shabani
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Ahmed J Awad
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
- Faculty of Medicine and Health Sciences, An-Najah National University, Nablus 11941, Palestine.
| | - Mayank Kaushal
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Ninh Doan
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
- Department of Neurosurgery, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36688, USA.
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22
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Doan NB, Nguyen HS, Alhajala HS, Jaber B, Al-Gizawiy MM, Ahn EYE, Mueller WM, Chitambar CR, Mirza SP, Schmainda KM. Identification of radiation responsive genes and transcriptome profiling via complete RNA sequencing in a stable radioresistant U87 glioblastoma model. Oncotarget 2018; 9:23532-23542. [PMID: 29805753 PMCID: PMC5955095 DOI: 10.18632/oncotarget.25247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/08/2018] [Indexed: 12/19/2022] Open
Abstract
The absence of major progress in the treatment of glioblastoma (GBM) is partly attributable to our poor understanding of both GBM tumor biology and the acquirement of treatment resistance in recurrent GBMs. Recurrent GBMs are characterized by their resistance to radiation. In this study, we used an established stable U87 radioresistant GBM model and total RNA sequencing to shed light on global mRNA expression changes following irradiation. We identified many genes, the expressions of which were altered in our radioresistant GBM model, that have never before been reported to be associated with the development of radioresistant GBM and should be concertedly further investigated to understand their roles in radioresistance. These genes were enriched in various biological processes such as inflammatory response, cell migration, positive regulation of epithelial to mesenchymal transition, angiogenesis, apoptosis, positive regulation of T-cell migration, positive regulation of macrophage chemotaxis, T-cell antigen processing and presentation, and microglial cell activation involved in immune response genes. These findings furnish crucial information for elucidating the molecular mechanisms associated with radioresistance in GBM. Therapeutically, with the global alterations of multiple biological pathways observed in irradiated GBM cells, an effective GBM therapy may require a cocktail carrying multiple agents targeting multiple implicated pathways in order to have a chance at making a substantial impact on improving the overall GBM survival.
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Affiliation(s)
- Ninh B Doan
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ha S Nguyen
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hisham S Alhajala
- Department of Medicine, Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Basem Jaber
- Faculty of Medicine, University of Damascus, Damascus, Syria
| | - Mona M Al-Gizawiy
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Wade M Mueller
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Christopher R Chitambar
- Department of Medicine, Hematology/Oncology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Shama P Mirza
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee, WI, USA
| | - Kathleen M Schmainda
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, USA.,Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA
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