101
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Lathia JD. Drak, Drak, Goose: A New Signaling Axis in Glioblastoma. Cancer Res 2019; 79:1036-1037. [PMID: 30877099 DOI: 10.1158/0008-5472.can-19-0229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022]
Abstract
While many molecular alterations in glioblastoma (GBM), the most common primary malignant brain tumor, have been defined, the intricate signaling networks associated with these alterations that represent actionable therapeutic targets are less well established. Chen and colleagues leverage a Drosophila GBM model to identify a conserved signaling axis downstream of the EGFR and PI3K that involves the death-associated protein kinase (Drak), a cytoplasmic serine/threonine kinase orthologous to the human kinase STK17A. Functional studies revealed that targeting this signaling axis attenuated mitosis and cytokinesis, providing a new pathway for therapeutic development in GBM.See related article by Chen et al., p. 1085.
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Affiliation(s)
- Justin D Lathia
- Cleveland Clinic Lerner Research Institute, Cleveland, Ohio.
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102
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Zanders ED, Svensson F, Bailey DS. Therapy for glioblastoma: is it working? Drug Discov Today 2019; 24:1193-1201. [PMID: 30878561 DOI: 10.1016/j.drudis.2019.03.008] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/06/2019] [Accepted: 03/08/2019] [Indexed: 12/21/2022]
Abstract
Glioblastoma (GBM) remains one of the most intransigent of cancers, with a median overall survival of only 15 months after diagnosis. Drug treatments have largely proven ineffective; it is thought that this is related to the heterogeneous nature and plasticity of GBM-initiating stem cell lineages. Although many combination drug therapies are being positioned to address tumour heterogeneity, the most promising therapeutic approaches for GBM to date appear to be those targeting GBM by vaccination or antibody- and cell-based immunotherapy. We review the most recent clinical trials for GBM and discuss the role of adaptive clinical trials in developing personalised treatment strategies to address intra- and inter-tumoral heterogeneity.
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Affiliation(s)
- Edward D Zanders
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK
| | - Fredrik Svensson
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK
| | - David S Bailey
- IOTA Pharmaceuticals Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 0WS, UK.
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103
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O'Loughlin TA, Gilbert LA. Functional Genomics for Cancer Research: Applications In Vivo and In Vitro. ANNUAL REVIEW OF CANCER BIOLOGY 2019. [DOI: 10.1146/annurev-cancerbio-030518-055742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional genomics holds great promise for the dissection of cancer biology. The elucidation of genetic cooperation and molecular details that govern oncogenesis, metastasis, and response to therapy is made possible by robust technologies for perturbing gene function coupled to quantitative analysis of cancer phenotypes resulting from genetic or epigenetic perturbations. Multiplexed genetic perturbations enable the dissection of cooperative genetic lesions as well as the identification of synthetic lethal gene pairs that hold particular promise for constructing innovative cancer therapies. Lastly, functional genomics strategies enable the highly multiplexed in vivo analysis of genes that govern tumorigenesis as well as of the complex multicellular biology of a tumor, such as immune response and metastasis phenotypes. In this review, we discuss both historical and emerging functional genomics approaches and their impact on the cancer research landscape.
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Affiliation(s)
- Thomas A. O'Loughlin
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
| | - Luke A. Gilbert
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
- Innovative Genomics Institute, University of California, San Francisco, California 94158, USA
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104
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Wei M, Ma R, Huang S, Liao Y, Ding Y, Li Z, Guo Q, Tan R, Zhang L, Zhao L. Oroxylin A increases the sensitivity of temozolomide on glioma cells by hypoxia-inducible factor 1α/hedgehog pathway under hypoxia. J Cell Physiol 2019; 234:17392-17404. [PMID: 30790292 DOI: 10.1002/jcp.28361] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Microenvironmental hypoxia-mediated drug resistance is responsible for the failure of cancer therapy. To date, the role of the hedgehog pathway in resistance to temozolomide (TMZ) under hypoxia has not been investigated. In this study, we discovered that the increasing hypoxia-inducible factor 1α (HIF-1α) activated the hedgehog pathway in hypoxic microenvironment by promoting autocrine secretion of sonic hedgehog protein (Shh), and then upregulating transfer of Gli1 to the nucleus, finally contributed to TMZ resistance in glioma cells. Oroxylin A (C16H12O5), a bioactive flavonoid, could induce HIF-1α degradation via prolyl-hydroxylases-VHL signaling pathway, resulting in the inactivation of the hedgehog. Besides, oroxylin A increased the expression of Sufu, which is a negative regulator of Gli1. By this mechanism, oroxylin A sensitized TMZ on glioma cells. U251 intracranial transplantation model and GL261 xenograft model were used to confirm the reversal effects of oroxylin A in vivo. In conclusion, our results demonstrated that HIF-1α/hedgehog pathway conferred TMZ resistance under hypoxia, and oroxylin A was capable of increasing the sensitivity of TMZ on glioma cells in vitro and in vivo by inhibiting HIF-1α/hedgehog pathway and depressing the activation of Gli1 directly.
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Affiliation(s)
- Mian Wei
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Rong Ma
- Department of Anesthesiology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Shaoliang Huang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Yan Liao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Youxiang Ding
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Zhaohe Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Qinglong Guo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
| | - Renxiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Xianlin, Nanjing, China
| | - Lulu Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education, Department of Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Zhao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Tongjiaxiang, Nanjing, China
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105
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Mining-Guided Machine Learning Analyses Revealed the Latest Trends in Neuro-Oncology. Cancers (Basel) 2019; 11:cancers11020178. [PMID: 30717468 PMCID: PMC6406908 DOI: 10.3390/cancers11020178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 01/26/2023] Open
Abstract
In conducting medical research, a system which can objectively predict the future trends of the given research field is awaited. This study aims to establish a novel and versatile algorithm that predicts the latest trends in neuro-oncology. Seventy-nine neuro-oncological research fields were selected with computational sorting methods such as text-mining analyses. Thirty journals that represent the recent trends in neuro-oncology were also selected. As a novel concept, the annual impact (AI) of each year was calculated for each journal and field (number of articles published in the journal × impact factor of the journal). The AI index (AII) for the year was defined as the sum of the AIs of the 30 journals. The AII trends of the 79 fields from 2008 to 2017 were subjected to machine learning predicting analyses. The accuracy of the predictions was validated using actual past data. With this algorithm, the latest trends in neuro-oncology were predicted. As a result, the linear prediction model achieved relatively good accuracy. The predicted hottest fields in recent neuro-oncology included some interesting emerging fields such as microenvironment and anti-mitosis. This algorithm may be an effective and versatile tool for prediction of future trends in a particular medical field.
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106
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Jia B, Liu W, Gu J, Wang J, Lv W, Zhang W, Hao Q, Pang Z, Mu N, Zhang W, Guo Q. MiR-7-5p suppresses stemness and enhances temozolomide sensitivity of drug-resistant glioblastoma cells by targeting Yin Yang 1. Exp Cell Res 2018; 375:73-81. [PMID: 30586549 DOI: 10.1016/j.yexcr.2018.12.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 12/27/2022]
Abstract
Glioblastoma multiforme (GBM) is the most malignant tumor of the central nervous system, and chemoresistance blunts the effect of temozolomide (TMZ) in the treatment of GBM. Clarifying the underlying mechanism of chemoresistance might yield novel strategies to improve the patients' response to chemotherapeutics. Mounting evidence indicates that microRNAs (miRNAs) are involved in chemoresistance and tumorigenesis. At present, miR-7-5p has been recognized as a tumor suppressor involved in multiple cancers. However, the biological effects of miR-7-5p in TMZ resistance have not been illuminated. In this study, we used RNA sequencing and high-throughput screening techniques, which revealed that miR-7-5p is significantly downregulated in TMZ resistant LN229 cells (LN229/TMZ-R) compared to control cells (LN229), and low miR-7-5p expression was correlated with recurrence in GBM patients. Ectopic overexpression of miR-7-5p sensitized LN229/TMZ-R cells to TMZ and suppressed the stemness of glioblastoma stem cells (GSCs). Further experiments demonstrated that miR-7-5p exerts its role by directly targeting the 3'-untranslated region of Yin Yang 1 (YY1). Our findings suggest that combinational use of miR-7-5p and TMZ might be a promising therapeutic strategy to increase the long-term drug response in GBM patients.
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Affiliation(s)
- Bo Jia
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Wei Liu
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Jintao Gu
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Jiancai Wang
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Weifeng Lv
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Wangqian Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Qiang Hao
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Zhijun Pang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China
| | - Nan Mu
- Department of Pathophysiology, School of Basic Medicine, Fourth Military Medical University, Xi'an 710032, China.
| | - Wei Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi'an 710032, China.
| | - Qingdong Guo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
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107
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Falchetti ML, D'Alessandris QG, Pacioni S, Buccarelli M, Morgante L, Giannetti S, Lulli V, Martini M, Larocca LM, Vakana E, Stancato L, Ricci-Vitiani L, Pallini R. Glioblastoma endothelium drives bevacizumab-induced infiltrative growth via modulation of PLXDC1. Int J Cancer 2018; 144:1331-1344. [PMID: 30414187 PMCID: PMC6590500 DOI: 10.1002/ijc.31983] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/10/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022]
Abstract
Bevacizumab, a VEGF‐targeting monoclonal antibody, may trigger an infiltrative growth pattern in glioblastoma. We investigated this pattern using both a human specimen and rat models. In the human specimen, a substantial fraction of infiltrating tumor cells were located along perivascular spaces in close relationship with endothelial cells. Brain xenografts of U87MG cells treated with bevacizumab were smaller than controls (p = 0.0055; Student t‐test), however, bands of tumor cells spread through the brain farther than controls (p < 0.001; Student t‐test). Infiltrating tumor Cells exhibited tropism for vascular structures and propensity to form tubules and niches with endothelial cells. Molecularly, bevacizumab triggered an epithelial to mesenchymal transition with over‐expression of the receptor Plexin Domain Containing 1 (PLXDC1). These results were validated using brain xenografts of patient‐derived glioma stem‐like cells. Enforced expression of PLXDC1 in U87MG cells promoted brain infiltration along perivascular spaces. Importantly, PLXDC1 inhibition prevented perivascular infiltration and significantly increased the survival of bevacizumab‐treated rats. Our study indicates that bevacizumab‐induced brain infiltration is driven by vascular endothelium and depends on PLXDC1 activation of tumor cells. What's new? Bevacizumab, a VEGF‐targeting monoclonal antibody, has been observed to trigger an infiltrative growth pattern in glioblastoma as an escape mechanism. The mechanisms underlying this gliomatosis‐like growth pattern, however, remain unclear. Here, the authors found that the infiltrative growth pattern occurs mostly along perivascular spaces and relies on the over‐expression of PLXDC1 by tumor cells and on the restoration of the endothelial component of blood brain barrier. Altogether, the data show that the brain infiltration induced by bevacizumab is mainly driven by the vascular endothelium. Importantly, inhibition of PLXDC1 prevents bevacizumab‐induced infiltrative growth, resulting in significant increase of survival.
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Affiliation(s)
| | - Quintino Giorgio D'Alessandris
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Simone Pacioni
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Liliana Morgante
- Institute of Anatomy and Cell Biology, Universitá Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Giannetti
- Institute of Anatomy and Cell Biology, Universitá Cattolica del Sacro Cuore, Rome, Italy
| | - Valentina Lulli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Maurizio Martini
- Pathology, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luigi Maria Larocca
- Pathology, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Eliza Vakana
- Discovery Research, Eli Lilly and Company, Indianapolis, IN
| | - Louis Stancato
- Discovery Research, Eli Lilly and Company, Indianapolis, IN
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Pallini
- Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, Rome, Italy
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108
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Shergalis A, Bankhead A, Luesakul U, Muangsin N, Neamati N. Current Challenges and Opportunities in Treating Glioblastoma. Pharmacol Rev 2018; 70:412-445. [PMID: 29669750 PMCID: PMC5907910 DOI: 10.1124/pr.117.014944] [Citation(s) in RCA: 495] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma multiforme (GBM), the most common and aggressive primary brain tumor, has a high mortality rate despite extensive efforts to develop new treatments. GBM exhibits both intra- and intertumor heterogeneity, lending to resistance and eventual tumor recurrence. Large-scale genomic and proteomic analysis of GBM tumors has uncovered potential drug targets. Effective and “druggable” targets must be validated to embark on a robust medicinal chemistry campaign culminating in the discovery of clinical candidates. Here, we review recent developments in GBM drug discovery and delivery. To identify GBM drug targets, we performed extensive bioinformatics analysis using data from The Cancer Genome Atlas project. We discovered 20 genes, BOC, CLEC4GP1, ELOVL6, EREG, ESR2, FDCSP, FURIN, FUT8-AS1, GZMB, IRX3, LITAF, NDEL1, NKX3-1, PODNL1, PTPRN, QSOX1, SEMA4F, TH, VEGFC, and C20orf166AS1 that are overexpressed in a subpopulation of GBM patients and correlate with poor survival outcomes. Importantly, nine of these genes exhibit higher expression in GBM versus low-grade glioma and may be involved in disease progression. In this review, we discuss these proteins in the context of GBM disease progression. We also conducted computational multi-parameter optimization to assess the blood-brain barrier (BBB) permeability of small molecules in clinical trials for GBM treatment. Drug delivery in the context of GBM is particularly challenging because the BBB hinders small molecule transport. Therefore, we discuss novel drug delivery methods, including nanoparticles and prodrugs. Given the aggressive nature of GBM and the complexity of targeting the central nervous system, effective treatment options are a major unmet medical need. Identification and validation of biomarkers and drug targets associated with GBM disease progression present an exciting opportunity to improve treatment of this devastating disease.
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Affiliation(s)
- Andrea Shergalis
- Department of Medicinal Chemistry, College of Pharmacy, North Campus Research Complex, Ann Arbor, Michigan (A.S., U.L., N.N.); Biostatistics Department and School of Public Health, University of Michigan, Ann Arbor, Michigan (A.B.); and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand (U.L., N.M.)
| | - Armand Bankhead
- Department of Medicinal Chemistry, College of Pharmacy, North Campus Research Complex, Ann Arbor, Michigan (A.S., U.L., N.N.); Biostatistics Department and School of Public Health, University of Michigan, Ann Arbor, Michigan (A.B.); and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand (U.L., N.M.)
| | - Urarika Luesakul
- Department of Medicinal Chemistry, College of Pharmacy, North Campus Research Complex, Ann Arbor, Michigan (A.S., U.L., N.N.); Biostatistics Department and School of Public Health, University of Michigan, Ann Arbor, Michigan (A.B.); and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand (U.L., N.M.)
| | - Nongnuj Muangsin
- Department of Medicinal Chemistry, College of Pharmacy, North Campus Research Complex, Ann Arbor, Michigan (A.S., U.L., N.N.); Biostatistics Department and School of Public Health, University of Michigan, Ann Arbor, Michigan (A.B.); and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand (U.L., N.M.)
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, North Campus Research Complex, Ann Arbor, Michigan (A.S., U.L., N.N.); Biostatistics Department and School of Public Health, University of Michigan, Ann Arbor, Michigan (A.B.); and Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand (U.L., N.M.)
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109
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Sharma P, Lioutas A, Fernandez-Fuentes N, Quilez J, Carbonell-Caballero J, Wright RHG, Di Vona C, Le Dily F, Schüller R, Eick D, Oliva B, Beato M. Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription. Mol Cell 2018; 73:84-96.e7. [PMID: 30472187 DOI: 10.1016/j.molcel.2018.10.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/21/2022]
Abstract
The post-translational modification of key residues at the C-terminal domain of RNA polymerase II (RNAP2-CTD) coordinates transcription, splicing, and RNA processing by modulating its capacity to act as a landing platform for a variety of protein complexes. Here, we identify a new modification at the CTD, the deimination of arginine and its conversion to citrulline by peptidyl arginine deiminase 2 (PADI2), an enzyme that has been associated with several diseases, including cancer. We show that, among PADI family members, only PADI2 citrullinates R1810 (Cit1810) at repeat 31 of the CTD. Depletion of PADI2 or loss of R1810 results in accumulation of RNAP2 at transcription start sites, reduced gene expression, and inhibition of cell proliferation. Cit1810 is needed for interaction with the P-TEFb (positive transcription elongation factor b) kinase complex and for its recruitment to chromatin. In this way, CTD-Cit1810 favors RNAP2 pause release and efficient transcription in breast cancer cells.
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Affiliation(s)
- Priyanka Sharma
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Antonios Lioutas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Narcis Fernandez-Fuentes
- IBERS, Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth SY23 3EB, UK
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - José Carbonell-Caballero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roni H G Wright
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Chiara Di Vona
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Schüller
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Baldomero Oliva
- Universitat Pompeu Fabra (UPF), Barcelona, Spain; Structural Bioinformatics Laboratory (GRIB-IMIM), Department of Experimental and Health Sciences, Barcelona 08003, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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110
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Meng W, Wang J, Wang B, Liu F, Li M, Zhao Y, Zhang C, Li Q, Chen J, Zhang L, Tang Y, Ma J. CDK7 inhibition is a novel therapeutic strategy against GBM both in vitro and in vivo. Cancer Manag Res 2018; 10:5747-5758. [PMID: 30532595 PMCID: PMC6245350 DOI: 10.2147/cmar.s183696] [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] [Indexed: 12/15/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) remains to be one of the top lethal cancer types for adult to date. Current GBM therapies suffer greatly from the highly heterogeneous and adaptable nature of GBM cells, indicating an urgent need of alternative therapeutic options. In this study, we focused on identifying novel epigenetic targeted strategy against GBM. Methods A collection of epigenetic modulating small molecules were subjected to anti-GBM screening and the inhibitory effect of identified agent was validated both in vitro and in vivo. Genetic targeting approaches were also used to verify the on-target inhibitory effect of identified agent. Furthermore, the inhibitory mechanism of identified agent was investigated by integrative analyses of drug-treated GBM cells and GBM tumor databases. Results The covalent CDK7 inhibitor THZ1 was one of the top hits in our screening and its anti-GBM activity was confirmed both in vitro and in vivo. CDK7 inhibition through CRISPR-Cas9 or RNA interference also markedly disrupted GBM cell growth. Furthermore, analyses of multiple GBM tumor databases consistently revealed that CDK7 expression was significantly elevated in GBM compared with normal brain tissues and lower grade gliomas. Higher CDK7 expression was correlated with worse prognosis for both glioma and GBM. Mechanistically, THZ1 treatment led to considerable disruption of global gene transcription in GBM cells, preferentially targeting those associated with super-enhancers (SEs). We also showed that THZ1 sensitive and SE-related genes had important roles for GBM growth. Conclusion Our study shows that targeting SE-associated transcription addiction by CDK7 inhibition could be an effective therapeutic strategy against GBM.
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Affiliation(s)
- Wei Meng
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Jiajia Wang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Baocheng Wang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Fang Liu
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China,
| | - Meng Li
- Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China,
| | - Yang Zhao
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Chenran Zhang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Qifeng Li
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
| | - Juxiang Chen
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Liye Zhang
- Zhang's Laboratory, School of Life Science and Technology, Shanghai Tech University, Shanghai, People's Republic of China
| | - Yujie Tang
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, , .,Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China,
| | - Jie Ma
- Department of Pediatric Neurosurgery, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China, ,
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111
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Gaviraghi M, Vivori C, Pareja Sanchez Y, Invernizzi F, Cattaneo A, Santoliquido BM, Frenquelli M, Segalla S, Bachi A, Doglioni C, Pelechano V, Cittaro D, Tonon G. Tumor suppressor PNRC1 blocks rRNA maturation by recruiting the decapping complex to the nucleolus. EMBO J 2018; 37:embj.201899179. [PMID: 30373810 DOI: 10.15252/embj.201899179] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022] Open
Abstract
Focal deletions occur frequently in the cancer genome. However, the putative tumor-suppressive genes residing within these regions have been difficult to pinpoint. To robustly identify these genes, we implemented a computational approach based on non-negative matrix factorization, NMF, and interrogated the TCGA dataset. This analysis revealed a metagene signature including a small subset of genes showing pervasive hemizygous deletions, reduced expression in cancer patient samples, and nucleolar function. Amid the genes belonging to this signature, we have identified PNRC1, a nuclear receptor coactivator. We found that PNRC1 interacts with the cytoplasmic DCP1α/DCP2 decapping machinery and hauls it inside the nucleolus. PNRC1-dependent nucleolar translocation of the decapping complex is associated with a decrease in the 5'-capped U3 and U8 snoRNA fractions, hampering ribosomal RNA maturation. As a result, PNRC1 ablates the enhanced proliferation triggered by established oncogenes such as RAS and MYC These observations uncover a previously undescribed mechanism of tumor suppression, whereby the cytoplasmic decapping machinery is hauled within nucleoli, tightly regulating ribosomal RNA maturation.
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Affiliation(s)
- Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Claudia Vivori
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Yerma Pareja Sanchez
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Francesca Invernizzi
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Cattaneo
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Benedetta Maria Santoliquido
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Michela Frenquelli
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Angela Bachi
- Functional Proteomics Program, Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Vicent Pelechano
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy .,Center for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
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112
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Abstract
Cyclin-dependent kinase 9 (CDK9) is critical for RNA Polymerase II (Pol II) transcription initiation, elongation, and termination in several key biological processes including development, differentiation, and cell fate responses. A broad range of diseases are characterized by CDK9 malfunction, illustrating its importance in maintaining transcriptional homeostasis in basal- and signal-regulated conditions. Here we provide a historical recount of CDK9 discovery and the current models suggesting CDK9 is a central hub necessary for proper execution of different steps in the transcription cycle. Finally, we discuss the current therapeutic strategies to treat CDK9 malfunction in several disease states. Abbreviations: CDK: Cyclin-dependent kinase; Pol II: RNA Polymerase II; PIC: Pre-initiation Complex; TFIIH: Transcription Factor-II H; snoRNA: small nucleolar RNA; CycT: CyclinT1/T2; P-TEFb: Positive Transcription Elongation Factor Complex; snRNP: small nuclear ribonucleo-protein; HEXIM: Hexamethylene Bis-acetamide-inducible Protein 1/2; LARP7: La-related Protein 7; MePCE: Methylphosphate Capping Enzyme; HIV: human immunodeficiency virus; TAT: trans-activator of transcription; TAR: Trans-activation response element; Hsp70: Heat Shock Protein 70; Hsp90/Cdc37: Hsp90- Hsp90 co-chaperone Cdc37; DSIF: DRB Sensitivity Inducing Factor; NELF: Negative Elongation Factor; CPSF: cleavage and polyadenylation-specific factor; CSTF: cleavage-stimulatory factor; eRNA: enhancer RNA; BRD4: Bromodomain-containing protein 4; JMJD6: Jumonji C-domain-containing protein 6; SEC: Super Elongation Complex; ELL: eleven-nineteen Lys-rich leukemia; ENL: eleven-nineteen leukemia; MLL: mixed lineage leukemia; BEC: BRD4-containing Elongation Complex; SEC-L2/L3: SEC-like complexes; KAP1: Kruppel-associated box-protein 1; KEC: KAP1-7SK Elongation Complex; DRB: Dichloro-1-ß-D-Ribofuranosylbenzimidazole; H2Bub1: H2B mono-ubiquitination; KM: KM05382; PP1: Protein Phosphatase 1; CDK9i: CDK9 inhibitor; SHAPE: Selective 2'-hydroxyl acylation analyzed by primer extension; TE: Typical enhancer; SE : Super enhancer.
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Affiliation(s)
- Curtis W Bacon
- a Biological Chemistry Graduate Program , The University of Texas Southwestern Medical Center , Dallas, TX , USA
| | - Iván D'Orso
- b Department of Microbiology , The University of Texas Southwestern Medical Center , Dallas , TX , USA
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113
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Gargiulo G. Next-Generation in vivo Modeling of Human Cancers. Front Oncol 2018; 8:429. [PMID: 30364119 PMCID: PMC6192385 DOI: 10.3389/fonc.2018.00429] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Animal models of human cancers played a major role in our current understanding of tumor biology. In pre-clinical oncology, animal models empowered drug target and biomarker discovery and validation. In turn, this resulted in improved care for cancer patients. In the quest for understanding and treating a diverse spectrum of cancer types, technological breakthroughs in genetic engineering and single cell "omics" offer tremendous potential to enhance the informative value of pre-clinical models. Here, I review the state-of-the-art in modeling human cancers with focus on animal models for human malignant gliomas. The review highlights the use of glioma models in dissecting mechanisms of tumor initiation, in the retrospective identification of tumor cell-of-origin, in understanding tumor heterogeneity and in testing the potential of immuno-oncology. I build on the deep review of glioma models as a basis for a more general discussion of the potential ways in which transformative technologies may shape the next-generation of pre-clinical models. I argue that refining animal models along the proposed lines will benefit the success rate of translation for pre-clinical research in oncology.
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Affiliation(s)
- Gaetano Gargiulo
- Molecular Oncology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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114
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Li D, Chi G, Chen Z, Jin X. MicroRNA-1225-5p behaves as a tumor suppressor in human glioblastoma via targeting of IRS1. Onco Targets Ther 2018; 11:6339-6350. [PMID: 30319274 PMCID: PMC6167988 DOI: 10.2147/ott.s178001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) play an important role in cancer initiation, progression, and metastasis by directly regulating their target genes. Materials and methods In this study, we observed that the miR-1225-5p expression level in glioblastoma tissues was significantly lower as compared with that in normal brain tissues, and its low expression was significantly associated with histopathological grade and poor patient prognosis. Results Through establishing a miR-1225-5p overexpression glioblastoma cell line, we found that ectopic overexpression of miR-1225-5p inhibited the proliferation, migration, and invasion of glioblastoma cells in vitro. Moreover, the growth of a glioblastoma xenograft tumor was attenuated by overexpression of miR-1225-5p. Further integrative studies suggested that the insulin receptor substrate 1 (IRS1) was a direct functional target of miR-1225-5p in glioblastoma, and the mRNA and protein levels of IRS1 in six human glioblastoma cell lines (A172, SW1783, U87, LN-229, SW1088, and T98G) were significantly higher as compared with normal human astrocytes. Conclusion These results suggest that miR-1225-5p may be a novel candidate for glioblastoma therapy.
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Affiliation(s)
- Dongyuan Li
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, People's Republic of China,
| | - Guonan Chi
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, People's Republic of China,
| | - Zhuo Chen
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, People's Republic of China,
| | - Xingyi Jin
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, People's Republic of China,
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115
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Mair R, Wright AJ, Ros S, Hu DE, Booth T, Kreis F, Rao J, Watts C, Brindle KM. Metabolic Imaging Detects Low Levels of Glycolytic Activity That Vary with Levels of c-Myc Expression in Patient-Derived Xenograft Models of Glioblastoma. Cancer Res 2018; 78:5408-5418. [PMID: 30054337 DOI: 10.1158/0008-5472.can-18-0759] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/06/2018] [Accepted: 07/23/2018] [Indexed: 11/16/2022]
Abstract
13C MRI of hyperpolarized [1-13C]pyruvate metabolism has been used in oncology to detect disease, investigate disease progression, and monitor response to treatment with a view to guiding treatment in individual patients. This technique has translated to the clinic with initial studies in prostate cancer. Here, we use the technique to investigate its potential uses in patients with glioblastoma (GB). We assessed the metabolism of hyperpolarized [1-13C]pyruvate in an orthotopically implanted cell line model (U87) of GB and in patient-derived tumors, where these were produced by orthotopic implantation of cells derived from different patients. Lactate labeling was higher in the U87 tumor when compared with patient-derived tumors, which displayed intertumoral heterogeneity, reflecting the intra- and intertumoral heterogeneity in the patients' tumors from which they were derived. Labeling in some patient-derived tumors could be observed before their appearance in morphologic images, whereas in other tumors it was not significantly greater than the surrounding brain. Increased lactate labeling in tumors correlated with c-Myc-driven expression of hexokinase 2, lactate dehydrogenase A, and the monocarboxylate transporters and was accompanied by increased radioresistance. Because c-Myc expression correlates with glioma grade, this study demonstrates that imaging with hyperpolarized [1-13C]pyruvate could be used clinically with patients with GB to determine disease prognosis, to detect early responses to drugs that modulate c-Myc expression, and to select tumors, and regions of tumors for increased radiotherapy dose.Significance: Metabolic imaging with hyperpolarized [1-13C]pyruvate detects low levels of c-Myc-driven glycolysis in patient-derived glioblastoma models, which, when translated to the clinic, could be used to detect occult disease, determine disease prognosis, and target radiotherapy. Cancer Res; 78(18); 5408-18. ©2018 AACR.
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Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Alan J Wright
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Susana Ros
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - De-En Hu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Tom Booth
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Felix Kreis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Jyotsna Rao
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Colin Watts
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge United Kingdom
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116
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Liu Y, Long YH, Wang SQ, Zhang YY, Li YF, Mi JS, Yu CH, Li DY, Zhang JH, Zhang XJ. JMJD6 regulates histone H2A.X phosphorylation and promotes autophagy in triple-negative breast cancer cells via a novel tyrosine kinase activity. Oncogene 2018; 38:980-997. [PMID: 30185813 DOI: 10.1038/s41388-018-0466-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/04/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
Overexpression of Jumonji domain-containing 6 (JMJD6) has been reported to be associated with more aggressive breast cancer characteristics. However, the precise role of JMJD6 in breast cancer development remains unclear. Here, we demonstrate that JMJD6 has intrinsic tyrosine kinase activity and can utilize ATP and GTP as phosphate donors to phosphorylate Y39 of histone H2A.X (H2A.XY39ph). High JMJD6 levels promoted autophagy in triple negative breast cancer (TNBC) cells by regulating the expression of autophagy-related genes. The JMJD6-H2A.XY39ph axis promoted TNBC cell growth via the autophagy pathway. We show that combined inhibition of JMJD6 kinase activity and autophagy efficiently decreases TNBC growth. Together, these findings suggest an effective strategy for TNBC treatment.
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Affiliation(s)
- Yan Liu
- College of Life Science, North China University of Science and Technology, Tangshan, China.,Cancer Institute, Tangshan People's Hospital, Tangshan, China
| | - Yue-Hong Long
- College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Shu-Qing Wang
- Hospital of North China University of Science and Technology, Tangshan, China.
| | - Yuan-Yue Zhang
- College of Life Science, North China University of Science and Technology, Tangshan, China.,Cancer Institute, Tangshan People's Hospital, Tangshan, China
| | - Yu-Feng Li
- Cancer Institute, Tangshan People's Hospital, Tangshan, China
| | | | | | - De-Yan Li
- People's Hospital of Zunhua, Zunhua, China
| | - Jing-Hua Zhang
- Cancer Institute, Tangshan People's Hospital, Tangshan, China.
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117
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Schuster A, Erasimus H, Fritah S, Nazarov PV, van Dyck E, Niclou SP, Golebiewska A. RNAi/CRISPR Screens: from a Pool to a Valid Hit. Trends Biotechnol 2018; 37:38-55. [PMID: 30177380 DOI: 10.1016/j.tibtech.2018.08.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/09/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
Abstract
High-throughput genetic screens interfering with gene expression are invaluable tools to identify gene function and phenotype-to-genotype interactions. Implementing such screens in the laboratory is challenging, and the choice between currently available technologies based on RNAi and CRISPR/Cas9 (CRISPR-associated protein 9) is not trivial. Identifying reliable candidate hits requires a streamlined experimental setup adjusted to the specific biological question. Here, we provide a critical assessment of the various RNAi/CRISPR approaches to pooled screens and discuss their advantages and pitfalls. We specify a set of best practices for key parameters enabling a reproducible screen and provide a detailed overview of analysis methods and repositories for identifying the best candidate gene hits.
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Affiliation(s)
- Anne Schuster
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Hélène Erasimus
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Petr V Nazarov
- Genomics and Proteomics Research Unit, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Eric van Dyck
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; KG Jebsen Brain Tumour Research Center, Department of Biomedicine, University of Bergen, Bergen, Norway; Co-senior authors.
| | - Anna Golebiewska
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg; Co-senior authors.
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118
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Yuan Z, Zhao L, Zhang Y, Li S, Pan B, Hua L, Wang Z, Ye C, Lu J, Yu R, Liu H. Inhibition of glioma growth by a GOLPH3 siRNA-loaded cationic liposomes. J Neurooncol 2018; 140:249-260. [PMID: 30105446 DOI: 10.1007/s11060-018-2966-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/01/2018] [Indexed: 11/26/2022]
Abstract
PURPOSE GOLPH3 has been shown to be involved in glioma proliferation. In this study, we aimed to demonstrate that GOLPH3 can serve as a target for glioma gene therapy. METHODS During the experiment, cationic liposomes with angiopep-2 (A2-CL) were used to deliver siGOLPH3 crossing the blood-brain barrier and reaching the glioma. RESULTS At the cellular level, the A2-CL/siGOLPH3 could silence GOLPH3 and then effectively inhibited the proliferation of cells. In vivo experiments, using U87-GFP-Luci-bearing BALB/c mouse models, we demonstrated that A2-CL could deliver GOLPH3-siRNA specifically to glioma and effectively inhibit glioma growth. CONCLUSIONS This study shows that GOLPH3 has great potential as a target for the gene therapy of glioma and is of great value in precise medical applications.
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Affiliation(s)
- Zixuan Yuan
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Liang Zhao
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Yafei Zhang
- General Hospital of Xuzhou Mining Group, Xuzhou, Jiangsu, People's Republic of China
| | - Shun Li
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Bomin Pan
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Lei Hua
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Zhen Wang
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Chengkun Ye
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China
| | - Jun Lu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu, People's Republic of China.
| | - Rutong Yu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China.
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China.
| | - Hongmei Liu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, 221002, Jiangsu, People's Republic of China.
- Brain Hospital, Affiliated Hospital of Xuzhou Medical University, 99 West Huai-hai Road, Xuzhou, 221002, Jiangsu, People's Republic of China.
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119
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de Ruiter JR, Wessels LFA, Jonkers J. Mouse models in the era of large human tumour sequencing studies. Open Biol 2018; 8:180080. [PMID: 30111589 PMCID: PMC6119864 DOI: 10.1098/rsob.180080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/13/2018] [Indexed: 12/16/2022] Open
Abstract
Cancer is a complex disease in which cells progressively accumulate mutations disrupting their cellular processes. A fraction of these mutations drive tumourigenesis by affecting oncogenes or tumour suppressor genes, but many mutations are passengers with no clear contribution to tumour development. The advancement of DNA and RNA sequencing technologies has enabled in-depth analysis of thousands of human tumours from various tissues to perform systematic characterization of their (epi)genomes and transcriptomes in order to identify (epi)genetic changes associated with cancer. Combined with considerable progress in algorithmic development, this expansion in scale has resulted in the identification of many cancer-associated mutations, genes and pathways that are considered to be potential drivers of tumour development. However, it remains challenging to systematically identify drivers affected by complex genomic rearrangements and drivers residing in non-coding regions of the genome or in complex amplicons or deletions of copy-number driven tumours. Furthermore, functional characterization is challenging in the human context due to the lack of genetically tractable experimental model systems in which the effects of mutations can be studied in the context of their tumour microenvironment. In this respect, mouse models of human cancer provide unique opportunities for pinpointing novel driver genes and their detailed characterization. In this review, we provide an overview of approaches for complementing human studies with data from mouse models. We also discuss state-of-the-art technological developments for cancer gene discovery and validation in mice.
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Affiliation(s)
- J R de Ruiter
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of EEMCS, Delft University of Technology, Delft, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - J Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
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120
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Hubler Z, Allimuthu D, Bederman I, Elitt MS, Madhavan M, Allan KC, Shick HE, Garrison E, T Karl M, Factor DC, Nevin ZS, Sax JL, Thompson MA, Fedorov Y, Jin J, Wilson WK, Giera M, Bracher F, Miller RH, Tesar PJ, Adams DJ. Accumulation of 8,9-unsaturated sterols drives oligodendrocyte formation and remyelination. Nature 2018; 560:372-376. [PMID: 30046109 PMCID: PMC6423962 DOI: 10.1038/s41586-018-0360-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 05/03/2018] [Indexed: 01/08/2023]
Abstract
Regeneration of myelin is mediated by oligodendrocyte progenitor cells (OPCs), an abundant stem cell population in the CNS and the principal source of new myelinating oligodendrocytes. Loss of myelin-producing oligodendrocytes in the central nervous system (CNS) underlies a number of neurological diseases, including multiple sclerosis (MS) and diverse genetic diseases1–3. Using high throughput chemical screening approaches, we and others have identified small molecules that stimulate oligodendrocyte formation from OPCs and functionally enhance remyelination in vivo4–10. Here we show a broad range of these pro-myelinating small molecules function not through their canonical targets but by directly inhibiting CYP51 (cytochrome P450, family 51), TM7SF2, or EBP (emopamil binding protein), a narrow range of enzymes within the cholesterol biosynthesis pathway. Subsequent accumulation of the 8,9-unsaturated sterol substrates of these enzymes is a key mechanistic node that promotes oligodendrocyte formation, as 8,9-unsaturated sterols are effective when supplied to OPCs in purified form while analogous sterols lacking this structural feature have no effect. Collectively, our results define a unifying sterol-based mechanism-of-action for most known small-molecule enhancers of oligodendrocyte formation and highlight specific targets to propel the development of optimal remyelinating therapeutics.
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Affiliation(s)
- Zita Hubler
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Dharmaraja Allimuthu
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ilya Bederman
- Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Matthew S Elitt
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Mayur Madhavan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - H Elizabeth Shick
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Eric Garrison
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Molly T Karl
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary S Nevin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Joel L Sax
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Matthew A Thompson
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yuriy Fedorov
- Small Molecule Drug Development Core, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jing Jin
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Franz Bracher
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians University of Munich, Munich, Germany
| | - Robert H Miller
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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121
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Berry C. The failure of rodent carcinogenesis as a model for Man. Toxicol Res (Camb) 2018; 7:553-557. [PMID: 30090605 PMCID: PMC6062156 DOI: 10.1039/c7tx00283a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/14/2017] [Indexed: 11/21/2022] Open
Abstract
Recent advances in our understanding of the process of carcinogenesis in Man have required revision of our thinking about the classical initiation/promotion sequence; understanding must now encompass the roles of both genetic and epigenetic change, realisation of the importance of the variable genetic backgrounds of the tumour bearers in any group and an understanding of the importance of random genetic events over time. The behavior of tumours, once established, is more complex than has been thought. Current views of the processes involved are not modelled in toxicity testing programmes.
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Affiliation(s)
- Colin Berry
- Queen Mary , London , Mile End Rd , London E1 4NS , UK .
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122
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Sarvestani SK, Signs SA, Lefebvre V, Mack S, Ni Y, Morton A, Chan ER, Li X, Fox P, Ting A, Kalady MF, Cruise M, Ashburn J, Stiene J, Lai W, Liska D, Xiang S, Huang EH. Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids. Oncotarget 2018; 9:28717-28730. [PMID: 29983891 PMCID: PMC6033374 DOI: 10.18632/oncotarget.25617] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/24/2018] [Indexed: 02/07/2023] Open
Abstract
Ulcerative colitis (UC) is a prevalent form of inflammatory bowel disease (IBD) whose pathogenic mechanisms remain unclear. Elucidating these mechanisms is important to reduce UC symptoms and to prevent UC progression into colitis-associated colon cancer (CAC). Our goal was to develop and validate faithful, human-derived, UC models and analyze them at histologic, transcriptomic and epigenetic levels to allow mechanistic studies of UC and CAC pathogenesis. We generated patient-derived primary-organoid cultures from UC and non-IBD colonic epithelium. We phenotyped them histologically and used next-generation-sequencing approaches to profile whole transcriptomes and epigenomes of organoids and primary tissues. Tissue organization and expression of mucin 2 (MUC2) and lysozyme (LYZ) demonstrated histologic faithfulness of organoids to healthy and diseased colonic epithelium. Transcriptomic analyses showed increased expression of inflammatory pathways in UC patient-derived organoids and tissues. Profiling for active enhancers using the H3K27ac histone modification revealed UC-derived organoid enrichment for pathways indicative of gastrointestinal cancer, including S100 calcium-binding protein P (S100P), and revealed novel markers for GI cancer, including both LYZ and neuropeptide S receptor 1 (NPSR1). Immunolocalization showed increased levels of LYZ, S100P, and NPSR1 proteins in UC and CAC. In conclusion, primary colonic organoid cultures from UC and non-IBD patients can be established that faithfully represent diseased or normal colonic states. These models reveal precancerous molecular pathways that are already activated in UC. The findings demonstrate the suitability of primary organoids for dissecting UC and CAC pathogenic mechanisms and suggest new targets for therapeutic intervention.
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Affiliation(s)
- Samaneh K Sarvestani
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Steven A Signs
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Veronique Lefebvre
- Department of Cell and Molecular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stephen Mack
- Department of Pediatrics Baylor College of Medicine, Houston, Texas, USA
| | - Ying Ni
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Andrew Morton
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ernest R Chan
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiaoxia Li
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paul Fox
- Department of Cell and Molecular Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Angela Ting
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Matthew F Kalady
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Michael Cruise
- Department of Pathology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jean Ashburn
- Department of Surgery, Wake Forest School of Medicine, Salem, North Carolina, USA
| | - Jennifer Stiene
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Wei Lai
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - David Liska
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shao Xiang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emina H Huang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio, USA
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123
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Zapata L, Pich O, Serrano L, Kondrashov FA, Ossowski S, Schaefer MH. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biol 2018; 19:67. [PMID: 29855388 PMCID: PMC5984361 DOI: 10.1186/s13059-018-1434-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments. Electronic supplementary material The online version of this article (10.1186/s13059-018-1434-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Zapata
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Oriol Pich
- Evolutionary Genomics Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Luis Serrano
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Fyodor A Kondrashov
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Stephan Ossowski
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
| | - Martin H Schaefer
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
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124
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Mikheev AM, Mikheeva SA, Severs LJ, Funk CC, Huang L, McFaline-Figueroa JL, Schwensen J, Trapnell C, Price ND, Wong S, Rostomily RC. Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma. Mol Oncol 2018; 12:1188-1202. [PMID: 29754406 PMCID: PMC6026950 DOI: 10.1002/1878-0261.12320] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022] Open
Abstract
TWIST1 (TW) is a bHLH transcription factor (TF) and master regulator of the epithelial-to-mesenchymal transition (EMT). In vitro, TW promotes mesenchymal change, invasion, and self-renewal in glioblastoma (GBM) cells. However, the potential therapeutic relevance of TW has not been established through loss-of-function studies in human GBM cell xenograft models. The effects of TW loss of function (gene editing and knockdown) on inhibition of tumorigenicity of U87MG and GBM4 glioma stem cells were tested in orthotopic xenograft models and conditional knockdown in established flank xenograft tumors. RNAseq and the analysis of tumors investigated putative TW-associated mechanisms. Multiple bioinformatic tools revealed significant alteration of ECM, membrane receptors, signaling transduction kinases, and cytoskeleton dynamics leading to identification of PI3K/AKT signaling. We experimentally show alteration of AKT activity and periostin (POSTN) expression in vivo and/or in vitro. For the first time, we show that effect of TW knockout inhibits AKT activity in U87MG cells in vivo independent of PTEN mutation. The clinical relevance of TW and candidate mechanisms was established by analysis of the TCGA and ENCODE databases. TW expression was associated with decreased patient survival and LASSO regression analysis identified POSTN as one of top targets of TW in human GBM. While we previously demonstrated the role of TW in promoting EMT and invasion of glioma cells, these studies provide direct experimental evidence supporting protumorigenic role of TW independent of invasion in vivo and the therapeutic relevance of targeting TW in human GBM. Further, the role of TW driving POSTN expression and AKT signaling suggests actionable targets, which could be leveraged to mitigate the oncogenic effects of TW in GBM.
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Affiliation(s)
- Andrei M Mikheev
- Department of Neurosurgery, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Department of Neurosurgery and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Svetlana A Mikheeva
- Department of Neurosurgery, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Department of Neurosurgery and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Liza J Severs
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | - Lei Huang
- Department of Systems Medicine& Bioengineering, Houston Methodist Hospital and Research Institute, Weil Cornell Medical College, Houston, TX, USA
| | | | - Jeanette Schwensen
- Department of Neurosurgery and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Stephen Wong
- Department of Systems Medicine& Bioengineering, Houston Methodist Hospital and Research Institute, Weil Cornell Medical College, Houston, TX, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Houston Methodist Hospital and Research Institute, Houston, TX, USA.,Department of Neurosurgery and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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125
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Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science 2018; 360:660-663. [PMID: 29748285 PMCID: PMC6414061 DOI: 10.1126/science.aaf2666] [Citation(s) in RCA: 337] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.
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Affiliation(s)
- Ralph B Puchalski
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nameeta Shah
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA.
- Mazumdar Shaw Center for Translational Research, Bangalore 560099, India
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Steve R Nomura
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jae-Guen Yoon
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Michael Lankerovich
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Suvro Datta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xu Feng
- Radia Inc., Lynnwood, WA 98036, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Parvinder Hothi
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kevin Joines
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hwahyung Lee
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chantal Murthy
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zack Riley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Andrew Sodt
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Don Marsh
- White Marsh Forests, Seattle, WA 98119, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Neurological Surgery, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allan Jones
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Haley R Gittleman
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | - Megha S Uppin
- Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, India
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | | | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael E Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
- Department of Pathology, Columbia University, New York, NY 10032, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Charles Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Greg D Foltz
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
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126
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A functional genomic screen in vivo identifies CEACAM5 as a clinically relevant driver of breast cancer metastasis. NPJ Breast Cancer 2018; 4:9. [PMID: 29736411 PMCID: PMC5928229 DOI: 10.1038/s41523-018-0062-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022] Open
Abstract
Tumor cells disseminate early in tumor development making metastasis-prevention strategies difficult. Identifying proteins that promote the outgrowth of disseminated tumor cells may provide opportunities for novel therapeutic strategies. Despite multiple studies demonstrating that the mesenchymal-to-epithelial transition (MET) is critical for metastatic colonization, key regulators that initiate this transition remain unknown. We serially passaged lung metastases from a primary triple negative breast cancer xenograft to the mammary fat pads of recipient mice to enrich for gene expression changes that drive metastasis. An unbiased transcriptomic signature of potential metastatic drivers was generated, and a high throughput gain-of-function screen was performed in vivo to validate candidates. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a metastatic driver. CEACAM5 overproduction enriched for an epithelial gene expression pattern and facilitated tumor outgrowth at metastatic sites. Tissues from patients with metastatic breast cancer confirmed elevated levels of CEACAM5 in lung metastases relative to breast tumors, and an inverse correlation between CEACAM5 and the mesenchymal marker vimentin was demonstrated. Thus, CEACAM5 facilitates tumor outgrowth at metastatic sites by promoting MET, warranting its investigation as a therapeutic target and biomarker of aggressiveness in breast cancer. A screen for drivers of metastasis has revealed a key protein involved in the spread of breast cancer into lung tissues. A US research team led by Helen Piwnica-Worms from the University of Texas MD Anderson Cancer Center in Houston enriched cells for genes involved in metastasis by engrafting mice with breast tumor biopsies taken from women with metastatic triple negative breast cancer and then metastases of these mice to mammary fat pads of recipient mice. The researchers pinpointed the gene encoding CEACAM5—a protein known to play a role in cell invasion and spread—as a key promoter of the cellular transition associated with metastasis. Tissues samples from patients confirmed that CEACAM5 levels were elevated in metastatic lung tumors relative to primary breast tumors. The protein provides a potential therapeutic target for drug development and candidate biomarker for patient stratification.
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127
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Sun L, Yang S, Chi G, Jin X. Hsp90 inhibitor NMS-E973 exerts the anticancer effect against glioblastoma via induction of PUMA-mediated apoptosis. Onco Targets Ther 2018; 11:1583-1593. [PMID: 29593424 PMCID: PMC5865573 DOI: 10.2147/ott.s160813] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glioblastoma is one of the most aggressive and common malignancies of the central nervous system in humans. Owing to the correlation of high Hsp90 expression with prognosis and clinical pathology features of diverse types of cancer, targeting Hsp90 with small-molecule inhibitors has become a promising anticancer strategy. PURPOSE In this study, we aimed to explore the possibility of anticancer effect of NMS-E973 in giloblastoma and elucidate the mechanism. METHODS Cell based MTT assay and colony formation assay were used to detect cell viability. Apoptosis was analyzed by nuclear staining with Hoechst 33258 and Annexin V/propidium iodide staining followed by flow cytometry. Western-blot and RT-PCR were used to detect gene expression. Xenograft assay was used to explore the anticancer effect of NMS-E973 in vivo. RESULTS We found that NMS-E973 induces apoptosis and inhibits cell growth in glioblastoma cells in cell culture and xenograft models. As a proapoptotic Bcl-2 member, PUMA was induced by NMS-E973 in a p53-dependent manner in glioblastoma in cell culture, thereby inducing apoptosis in glioblastoma cells. Furthermore, PUMA was induced by NMS-E973 treatment in xenograft tumors, and deficiency in PUMA significantly suppressed the antitumor effects of NMS-E973. CONCLUSION Our study suggests that PUMA-mediated apoptosis is important for the therapeutic responses of NMS-E973. Induction of PUMA might be a potential biomarker for predicting NMS-E973 responses.
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Affiliation(s)
- Libo Sun
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changhun, Jilin, People’s Republic of China
| | - Shoujun Yang
- Department of Rehabilitation, China-Japan Union Hospital of Jilin University, Changhun, Jilin, People’s Republic of China
| | - Guonan Chi
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changhun, Jilin, People’s Republic of China
| | - Xingyi Jin
- First Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changhun, Jilin, People’s Republic of China
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128
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An Z, Aksoy O, Zheng T, Fan QW, Weiss WA. Epidermal growth factor receptor and EGFRvIII in glioblastoma: signaling pathways and targeted therapies. Oncogene 2018; 37:1561-1575. [PMID: 29321659 PMCID: PMC5860944 DOI: 10.1038/s41388-017-0045-7] [Citation(s) in RCA: 351] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 01/05/2023]
Abstract
Amplification of epidermal growth factor receptor (EGFR) and its active mutant EGFRvIII occurs frequently in glioblastoma (GBM). While EGFR and EGFRvIII play critical roles in pathogenesis, targeted therapy with EGFR-tyrosine kinase inhibitors (TKIs) or antibodies has only shown limited efficacy in patients. Here we discuss signaling pathways mediated by EGFR/EGFRvIII, current therapeutics, and novel strategies to target EGFR/EGFRvIII-amplified GBM.
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Affiliation(s)
- Zhenyi An
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Ozlem Aksoy
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Tina Zheng
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Qi-Wen Fan
- Department of Neurology, University of California, San Francisco, CA, USA
| | - William A Weiss
- Department of Neurology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.
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129
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Staberg M, Rasmussen RD, Michaelsen SR, Pedersen H, Jensen KE, Villingshøj M, Skjoth-Rasmussen J, Brennum J, Vitting-Seerup K, Poulsen HS, Hamerlik P. Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone demethylase KDM2B. Mol Oncol 2018; 12:406-420. [PMID: 29360266 PMCID: PMC5830623 DOI: 10.1002/1878-0261.12174] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) ranks among the most lethal cancers, with current therapies offering only palliation. Inter‐ and intrapatient heterogeneity is a hallmark of GBM, with epigenetically distinct cancer stem‐like cells (CSCs) at the apex. Targeting GSCs remains a challenging task because of their unique biology, resemblance to normal neural stem/progenitor cells, and resistance to standard cytotoxic therapy. Here, we find that the chromatin regulator, JmjC domain histone H3K36me2/me1 demethylase KDM2B, is highly expressed in glioblastoma surgical specimens compared to normal brain. Targeting KDM2B function genetically or pharmacologically impaired the survival of patient‐derived primary glioblastoma cells through the induction of DNA damage and apoptosis, sensitizing them to chemotherapy. KDM2B loss decreased the GSC pool, which was potentiated by coadministration of chemotherapy. Collectively, our results demonstrate KDM2B is crucial for glioblastoma maintenance, with inhibition causing loss of GSC survival, genomic stability, and chemoresistance.
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Affiliation(s)
- Mikkel Staberg
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Signe Regner Michaelsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark.,Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Henriette Pedersen
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Mette Villingshøj
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | | | - Jannick Brennum
- Department of Neurosurgery, Copenhagen University Hospital, Denmark
| | | | - Hans Skovgaard Poulsen
- Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
| | - Petra Hamerlik
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
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130
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Giuliano CJ, Lin A, Smith JC, Palladino AC, Sheltzer JM. MELK expression correlates with tumor mitotic activity but is not required for cancer growth. eLife 2018; 7:32838. [PMID: 29417930 PMCID: PMC5805410 DOI: 10.7554/elife.32838] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/10/2018] [Indexed: 12/22/2022] Open
Abstract
The Maternal Embryonic Leucine Zipper Kinase (MELK) has been identified as a promising therapeutic target in multiple cancer types. MELK over-expression is associated with aggressive disease, and MELK has been implicated in numerous cancer-related processes, including chemotherapy resistance, stem cell renewal, and tumor growth. Previously, we established that triple-negative breast cancer cell lines harboring CRISPR/Cas9-induced null mutations in MELK proliferate at wild-type levels in vitro (Lin et al., 2017). Here, we generate several additional knockout clones of MELK and demonstrate that across cancer types, cells lacking MELK exhibit wild-type growth in vitro, under environmental stress, in the presence of cytotoxic chemotherapies, and in vivo. By combining our MELK-knockout clones with a recently described, highly specific MELK inhibitor, we further demonstrate that the acute inhibition of MELK results in no specific anti-proliferative phenotype. Analysis of gene expression data from cohorts of cancer patients identifies MELK expression as a correlate of tumor mitotic activity, explaining its association with poor clinical prognosis. In total, our results demonstrate the power of CRISPR/Cas9-based genetic approaches to investigate cancer drug targets, and call into question the rationale for treating patients with anti-MELK monotherapies.
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Affiliation(s)
| | - Ann Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | | | - Ann C Palladino
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Jason M Sheltzer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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131
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Mazzarella L, Curigliano G. A new approach to assess drug sensitivity in cells for novel drug discovery. Expert Opin Drug Discov 2018; 13:339-346. [PMID: 29415581 DOI: 10.1080/17460441.2018.1437136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION There is a pressing need to improve strategies to select candidate drugs early on in the drug development pipeline, especially in oncology, as the efficiency of new drug approval has steadily declined these past years. Traditional methods of drug screening have relied on low-cost assays on cancer cell lines growing on plastic dishes. Recent massive-scale screens have generated big data amenable for sophisticated computational modeling and integration with clinical data. However, 2D culturing has several intrinsic limitations and novel methodologies have been devised for culturing in three dimensions, to include cells from the tumor immune microenvironment. These major improvements are bringing in vitro systems even closer to a physiological, more clinically relevant state. Areas covered: In this article, the authors review the literature on methodologies for early-phase drug screening, focusing on in vitro systems and analyzing both novel experimental and statistical approaches. The article does not cover the expanding literature on in vivo systems. Expert opinion: The popularity of three-dimensional systems is exploding, driven by the development of 'organoid' derivation technology in 2009. These assays are growing in sophistication to accommodate the increasing need by modern oncology to develop drugs that target the microenvironment.
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Affiliation(s)
- Luca Mazzarella
- a Division of Early Drug Development , European Institute of Oncology , Milano , Italy
| | - Giuseppe Curigliano
- a Division of Early Drug Development , European Institute of Oncology , Milano , Italy.,b Department of Oncology and Hemato-Oncology , University of Milano , Milano , Italy
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132
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Adams FF, Hoffmann T, Zuber J, Heckl D, Schambach A, Schwarzer A. Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries. Hum Gene Ther Methods 2018; 29:16-29. [PMID: 29325442 DOI: 10.1089/hgtb.2017.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.
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Affiliation(s)
- Felix F Adams
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Thomas Hoffmann
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Johannes Zuber
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Heckl
- 3 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,4 Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adrian Schwarzer
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,5 Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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133
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Liu X, Wu X, Wang Y, Li Y, Chen X, Yang W, Jiang L. CD47 Promotes Human Glioblastoma Invasion Through Activation of the PI3K/Akt Pathway. Oncol Res 2018; 27:415-422. [PMID: 29321087 PMCID: PMC7848455 DOI: 10.3727/096504018x15155538502359] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cluster of differentiation 47 (CD47) overexpression is common in various malignancies. This study investigated whether CD47 promotes human glioblastoma invasion and, if so, the underlying mechanisms involved. CD47 expression was found to be stronger in tissues of patients with glioblastoma and in various cancer cell lines than in normal controls. CD47 downregulation via siRNA suppressed invasion in vitro, whereas CD47 overexpression through plasmid transfection exerted the opposite effect. However, overexpression or knocking down of CD47 had no effect on cell proliferation. Moreover, CD47 expression was related to Akt phosphorylation at the cellular molecular level. Suppression of Akt with a specific inhibitor impaired the invasion ability of CD47-overexpressing cells, indicating that stimulation of the PI3K/Akt pathway served as the downstream regulator of CD47-triggered invasion. These results suggest that CD47 might be a useful predictor of poor prognosis and metastasis and a potential target for treating glioblastomas.
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Affiliation(s)
- Xuejian Liu
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
| | - Xia Wu
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
| | - Yanming Wang
- Department of Radiotherapy, Jinan Military Region General Hospital, Jinan, Shandong, P.R. China
| | - Yuhua Li
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
| | - Xiangli Chen
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
| | - Wenchuan Yang
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
| | - Lihua Jiang
- Department of Oncology, Linyi Third People's Hospital, Linyi, Shandong, P.R. China
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Merino J, Florez JC. Precision medicine in diabetes: an opportunity for clinical translation. Ann N Y Acad Sci 2018; 1411:140-152. [PMID: 29377200 PMCID: PMC6686889 DOI: 10.1111/nyas.13588] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
Metabolic disorders present a public health challenge of staggering proportions. In diabetes, there is an urgent need to better understand disease heterogeneity, clinical trajectories, and related comorbidities. A pressing and timely question is whether we are ready for precision medicine in diabetes. Some biological insights that have emerged during the last decade have already been used to direct clinical decision making, especially in monogenic forms of diabetes. However, much work is necessary to integrate high-dimensional explorations into complex disease architectures, less penetrant biological alterations, and broader phenotypes, such as type 2 diabetes. In addition, for precision medicine to take hold in diabetes, reproducibility, interpretability, and actionability remain key guiding objectives. In this review, we examine how mounting data sets generated during the last decade to understand biological variability are now inspiring new venues to clarify diabetes nosology and ultimately translate findings into more effective prevention and treatment strategies.
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Affiliation(s)
- Jordi Merino
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jose C. Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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135
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Sulaiman A, Wang L. Bridging the divide: preclinical research discrepancies between triple-negative breast cancer cell lines and patient tumors. Oncotarget 2017; 8:113269-113281. [PMID: 29348905 PMCID: PMC5762590 DOI: 10.18632/oncotarget.22916] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most refractory subtype of breast cancer and disproportionately accounts for the majority of breast cancer related deaths. Effective treatment of this disease remains an unmet medical need. Over the past several decades, TNBC cell lines have been used as the foundation for drug development and disease modeling. However, ever-mounting research demonstrates striking differences between cell lines and clinical TNBC tumors, disconnecting bench research and actual clinical responses. In this review, we discuss the limitations of cell lines and the importance of using patients' tumors for translational research, and highlight the usage of patient-derived xenograft (PDXs) models that have emerged as a clinically relevant platform for preclinical studies. PDX tumors possess tumor heterogeneity with similar cellular, molecular, genetic and epigenetic properties akin to those found within patients' tumors. Moreover, PDX and clinical tumors possess abnormal vasculature with higher blood vessel permeability, a feature that is not always demonstrated in in vivo cell line xenografts. Development of clinically relevant, novel drug-nanoparticles capable of accumulating in PDX tumors through the enhanced permeability and retention effect in tumor vasculature may lead to new and effective TNBC treatments.
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Affiliation(s)
- Andrew Sulaiman
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
- China-Canada Centre of Research for Digestive Diseases, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
- China-Canada Centre of Research for Digestive Diseases, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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Mucignat-Caretta C, Denaro L, D'Avella D, Caretta A. Protein Kinase A Distribution Differentiates Human Glioblastoma from Brain Tissue. Cancers (Basel) 2017; 10:cancers10010002. [PMID: 29267253 PMCID: PMC5789352 DOI: 10.3390/cancers10010002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 12/17/2022] Open
Abstract
Brain tumor glioblastoma has no clear molecular signature and there is no effective therapy. In rodents, the intracellular distribution of the cyclic AMP (cAMP)-dependent protein kinase (Protein kinase A, PKA) R2Alpha subunit was previously shown to differentiate tumor cells from healthy brain cells. Now, we aim to validate this observation in human tumors. The distribution of regulatory (R1 and R2) and catalytic subunits of PKA was examined via immunohistochemistry and Western blot in primary cell cultures and biopsies from 11 glioblastoma patients. Data were compared with information obtained from 17 other different tumor samples. The R1 subunit was clearly detectable only in some samples. The catalytic subunit was variably distributed in the different tumors. Similar to rodent tumors, all human glioblastoma specimens showed perinuclear R2 distribution in the Golgi area, while it was undetectable outside the tumor. To test the effect of targeting PKA as a therapeutic strategy, the intracellular cyclic AMP concentration was modulated with different agents in four human glioblastoma cell lines. A significant increase in cell death was detected after increasing cAMP levels or modulating PKA activity. These data raise the possibility of targeting the PKA intracellular pathway for the development of diagnostic and/or therapeutic tools for human glioblastoma.
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Affiliation(s)
- Carla Mucignat-Caretta
- Department of Molecular Medicine, University of Padova, Padova 35131, Italy.
- Biostructures and Biosystems National Institute, Rome 00136, Italy.
| | - Luca Denaro
- Department of Neuroscience, University of Padova, Padova 35131, Italy.
| | - Domenico D'Avella
- Department of Neuroscience, University of Padova, Padova 35131, Italy.
| | - Antonio Caretta
- Biostructures and Biosystems National Institute, Rome 00136, Italy.
- Department of Food and Drug, University of Parma, Parma 43121, Italy.
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137
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NFAT1-regulated IL6 signalling contributes to aggressive phenotypes of glioma. Cell Commun Signal 2017; 15:54. [PMID: 29258522 PMCID: PMC5735798 DOI: 10.1186/s12964-017-0210-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
Background We previously demonstrated that the local immune status correlated with the glioma prognosis. Interleukin-6 (IL6) was identified as an important local immune-related risk marker related to unfavourable prognosis. In this study, we further investigated the role and regulation of IL6 signalling in glioma. Methods The expression and prognostic value of IL6 and the IL6 receptor (IL6R) were explored in The Cancer Genome Atlas (TCGA) and REMBRANDT databases and clinical samples. Functional effects of genetic knockdown and overexpression of IL6R or IL6 stimulation were examined in vitro and in tumours in vivo. The effects of the nuclear factor of activated T cells-1 (NFAT1) on the promoter activities of IL6R and IL6 were also examined. Results High IL6- and IL6R-expression were significantly associated with mesenchymal subtype and IDH-wildtype gliomas, and were predictors of poor survival. Knockdown of IL6R decreased cell proliferation, invasion and neurosphere formation in vitro, and inhibited tumorigenesis in vivo. IL6R overexpression or IL6 stimulation enhanced the invasion and growth of glioma cells. TCGA database searching revealed that IL6- and IL6R-expression were correlated with that of NFAT1. In glioma cells, NFAT1 enhanced the promoter activities of IL6R and IL6, and upregulated the expression of both IL6R and IL6. Conclusion NFAT1-regulated IL6 signalling contributes to aggressive phenotypes of gliomas, emphasizing the role of immunomodulatory factors in glioma malignant progression. Electronic supplementary material The online version of this article (10.1186/s12964-017-0210-1) contains supplementary material, which is available to authorized users.
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139
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Gusyatiner O, Hegi ME. Glioma epigenetics: From subclassification to novel treatment options. Semin Cancer Biol 2017; 51:50-58. [PMID: 29170066 DOI: 10.1016/j.semcancer.2017.11.010] [Citation(s) in RCA: 321] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 12/26/2022]
Abstract
Gliomas are the most common malignant primary brain tumors, of which glioblastoma is the most malignant form (WHO grade IV), and notorious for treatment resistance. Over the last decade mutations in epigenetic regulator genes have been identified as key drivers of subtypes of gliomas with distinct clinical features. Most characteristic are mutations in IDH1 or IDH2 in lower grade gliomas, and histone 3 mutations in pediatric high grade gliomas that are also associated with characteristic DNA methylation patterns. Furthermore, in adult glioblastoma patients epigenetic silencing of the DNA repair gene MGMT by promoter methylation is predictive for benefit from alkylating agent therapy. These epigenetic alterations are used as biomarkers and play a central role for classification of gliomas (WHO 2016) and treatment decisions. Here we review the pivotal role of epigenetic alterations in the etiology and biology of gliomas. We summarize the complex interactions between "driver" mutations, DNA methylation, histone post-translational modifications, and overall chromatin organization, and how they inform current efforts of testing epigenetic compounds and combinations in preclinical and clinical studies.
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Affiliation(s)
- Olga Gusyatiner
- Laboratory of Brain Tumor Biology and Genetics, Neuroscience Research Center and Service of Neurosurgery, Lausanne University Hospital, 1066 Epalinges, Switzerland
| | - Monika E Hegi
- Laboratory of Brain Tumor Biology and Genetics, Neuroscience Research Center and Service of Neurosurgery, Lausanne University Hospital, 1066 Epalinges, Switzerland.
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140
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Abstract
In this issue of Cancer Cell, Pathania et al. report sporadic childhood histone K27M mutant malignant glioma mouse models that faithfully recapitulate the human tumor phenotypes. Beyond emphasizing the importance of correct timing in mouse modeling of cancer, these models will facilitate research to effectively treat this lethal childhood cancer.
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Affiliation(s)
- Vijay Ramaswamy
- Division of Haematology/Oncology, Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON, Canada.
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