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Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
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Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
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2
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Wu M, Wang T, Ji N, Lu T, Yuan R, Wu L, Zhang J, Li M, Cao P, Zhao J, Li G, Li J, Li Y, Tang Y, Gao Z, Wang X, Cheng W, Ge M, Cui G, Li R, Wu A, You Y, Zhang W, Wang Q, Chen J. Multi-omics and pharmacological characterization of patient-derived glioma cell lines. Nat Commun 2024; 15:6740. [PMID: 39112531 PMCID: PMC11306361 DOI: 10.1038/s41467-024-51214-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Glioblastoma (GBM) is the most common brain tumor and remains incurable. Primary GBM cultures are widely used tools for drug screening, but there is a lack of genomic and pharmacological characterization for these primary GBM cultures. Here, we collect 50 patient-derived glioma cell (PDGC) lines and characterize them by whole genome sequencing, RNA sequencing, and drug response screening. We identify three molecular subtypes among PDGCs: mesenchymal (MES), proneural (PN), and oxidative phosphorylation (OXPHOS). Drug response profiling reveals that PN subtype PDGCs are sensitive to tyrosine kinase inhibitors, whereas OXPHOS subtype PDGCs are sensitive to histone deacetylase inhibitors, oxidative phosphorylation inhibitors, and HMG-CoA reductase inhibitors. PN and OXPHOS subtype PDGCs stably form tumors in vivo upon intracranial transplantation into immunodeficient mice, whereas most MES subtype PDGCs fail to form tumors in vivo. In addition, PDGCs cultured by serum-free medium, especially long-passage PDGCs, carry MYC/MYCN amplification, which is rare in GBM patients. Our study provides a valuable resource for understanding primary glioma cell cultures and clinical translation and highlights the problems of serum-free PDGC culture systems that cannot be ignored.
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Affiliation(s)
- Min Wu
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, China
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Tingting Wang
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Changping Laboratory, Beijing, China
- Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ting Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ran Yuan
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, China
| | - Lingxiang Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Junxia Zhang
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mengyuan Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
- Changping Laboratory, Beijing, China
| | - Penghui Cao
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiarui Zhao
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Guanzhang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jianyu Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Li
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yujie Tang
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengliang Gao
- Fundamental Research Center, Shanghai YangZhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), School of Medicine, Tongji University, Shanghai, China
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), School of Medicine, Shanghai University, Nantong, China
- Department of Anesthesiology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Xiuxing Wang
- National Health Commission Key Laboratory of Antibody Techniques, Department of Cell Biology, Jiangsu Provincial Key Laboratory of Human Functional Genomics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Wen Cheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ming Ge
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Gang Cui
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Rui Li
- Department of Neurosurgery, China-Japan Friendship Hospital, No. 2 Yinghua East Road, Chaoyang District, Beijing, China
| | - Anhua Wu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yongping You
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Wei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.
- Institute for Brain Tumors, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
- The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Jian Chen
- Chinese Institute for Brain Research, Beijing, Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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3
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Yap CX, Vo DD, Heffel MG, Bhattacharya A, Wen C, Yang Y, Kemper KE, Zeng J, Zheng Z, Zhu Z, Hannon E, Vellame DS, Franklin A, Caggiano C, Wamsley B, Geschwind DH, Zaitlen N, Gusev A, Pasaniuc B, Mill J, Luo C, Gandal MJ. Brain cell-type shifts in Alzheimer's disease, autism, and schizophrenia interrogated using methylomics and genetics. SCIENCE ADVANCES 2024; 10:eadn7655. [PMID: 38781333 PMCID: PMC11114225 DOI: 10.1126/sciadv.adn7655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/14/2024] [Indexed: 05/25/2024]
Abstract
Few neuropsychiatric disorders have replicable biomarkers, prompting high-resolution and large-scale molecular studies. However, we still lack consensus on a more foundational question: whether quantitative shifts in cell types-the functional unit of life-contribute to neuropsychiatric disorders. Leveraging advances in human brain single-cell methylomics, we deconvolve seven major cell types using bulk DNA methylation profiling across 1270 postmortem brains, including from individuals diagnosed with Alzheimer's disease, schizophrenia, and autism. We observe and replicate cell-type compositional shifts for Alzheimer's disease (endothelial cell loss), autism (increased microglia), and schizophrenia (decreased oligodendrocytes), and find age- and sex-related changes. Multiple layers of evidence indicate that endothelial cell loss contributes to Alzheimer's disease, with comparable effect size to APOE genotype among older people. Genome-wide association identified five genetic loci related to cell-type composition, involving plausible genes for the neurovascular unit (P2RX5 and TRPV3) and excitatory neurons (DPY30 and MEMO1). These results implicate specific cell-type shifts in the pathophysiology of neuropsychiatric disorders.
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Affiliation(s)
- Chloe X. Yap
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel D. Vo
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children’s Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew G. Heffel
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute for Data Science in Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cindy Wen
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuanhao Yang
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Zhihong Zhu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- The National Centre for Register-based Research, Aarhus University, Denmark
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alice Franklin
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Christa Caggiano
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Brie Wamsley
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H. Geschwind
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Noah Zaitlen
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
- Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J. Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children’s Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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4
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Wu H, Yang Z, Chang C, Wang Z, Zhang D, Guo Q, Zhao B. A novel disulfide death-related genes prognostic signature identifies the role of IPO4 in glioma progression. Cancer Cell Int 2024; 24:168. [PMID: 38734657 PMCID: PMC11088110 DOI: 10.1186/s12935-024-03358-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/06/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND "Disulfide death," a form of cellular demise, is triggered by the abnormal accumulation of intracellular disulfides under conditions of glucose deprivation. However, its role in the prognosis of glioma remains undetermined. Therefore, the main objective of this study is to establish prognostic signature based on disulfide death-related genes (DDRGs) and to provide new solutions in choosing the effective treatment of glioma. METHODS The RNA transcriptome, clinical information, and mutation data of glioma samples were sourced from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), while normal samples were obtained from the Genotype-Tissue Expression (GTEx). DDRGs were compiled from previous studies and selected through differential analysis and univariate Cox regression analysis. The molecular subtypes were determined through consensus clustering analysis. Further, LASSO analysis was employed to select characteristic genes, and subsequently, a risk model comprising seven DDRGs was constructed based on multivariable Cox analysis. Kaplan-Meier survival curves were employed to assess survival differences between high and low-risk groups. Additionally, functional analyses (GO, KEGG, GSEA) were conducted to explore the potential biological functions and signaling pathways of genes associated with the model. The study also explored immune checkpoint (ICP) genes, immune cell infiltration levels, and immune stromal scores. Finally, the effect of Importin-4(IPO4) on glioma has been further confirmed through RT-qPCR, Western blot, and cell functional experiments. RESULTS 7 genes associated with disulfide death were obtained and two subgroups of patients with different prognosis and clinical characteristics were identified. Risk signature was subsequently developed and proved to serve as an prognostic predictor. Notably, the high-risk group exhibited an immunosuppressive microenvironment characterized by a high concentration of M2 macrophages and regulatory T cells (Tregs). In contrast, the low-risk group showed lower half-maximal inhibitory concentration (IC50) values. Therefore, patients in the high-risk group may benefit more from immunotherapy, while patients in the low-risk group may benefit more from chemotherapy. In addition, in vitro experiments have shown that inhibition of the expression of IPO4 leads to a significant reduction in the proliferation, migration, and invasion of glioma cells. CONCLUSION This study identified two glioma subtypes and constructed a prognostic signature based on DDRGs. The signature has the potential to optimize the selection of patients for immune- and chemotherapy and provided a potential therapeutic target for glioma.
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Affiliation(s)
- HaoYuan Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiHao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ChenXi Chang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - ZhiWei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - DeRan Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - QingGuo Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China.
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Feng L, Chen X, Sheng G, Li Y, Li Y, Zhang Y, Yao K, Wu Z, Zhang R, Kiboku T, Kawasaki A, Horimoto K, Tang Y, Sun M, Han F, Chen D. Synthesis and Bioevaluation of 3-(Arylmethylene)indole Derivatives: Discovery of a Novel ALK Modulator with Antiglioblastoma Activities. J Med Chem 2023; 66:14609-14622. [PMID: 37861443 DOI: 10.1021/acs.jmedchem.3c01090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Glioblastoma is the most common brain tumor, with high recurrence and low survival rates. An integrative bioinformatics analysis demonstrated that anaplastic lymphoma kinase (ALK) is a promising therapeutic target for glioblastoma. We designed and synthesized a series of 3-(arylmethylene)indole derivatives, which were further evaluated for antiproliferative activity using glioma cell lines. Among them, compound 4a significantly inhibited the viability of glioblastoma cells. With favorable pharmacokinetic characteristics and blood-brain barrier permeability, 4a improved the survival rate and inhibited the growth of orthotopic glioblastoma. The Phospho-Totum system revealed that ALK was a potential target for the antiglioblastoma activity of 4a. Further experiments indicated that 4a might be a novel ALK modulator, which interacted with the extracellular ligand-binding domain of ALK, thus selectively induced ERK-mediated autophagy and apoptosis. Our findings provide an alternative ALK-based targeting strategy and a new drug candidate for glioblastoma therapy.
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Affiliation(s)
- Lili Feng
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Xiang Chen
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Gang Sheng
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yingchun Li
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yingying Li
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yixuan Zhang
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215001, China
| | - Kun Yao
- Laboratory of Medicinal Chemical Biology, Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215006, China
| | - Zhouyue Wu
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Rong Zhang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | | | | | - Katsuhisa Horimoto
- Socium Inc., Tokyo 1350064, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 1350064, Japan
| | - Yamin Tang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Meiling Sun
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Feng Han
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215001, China
- Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Dongyin Chen
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, China, International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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6
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Sun YM, Zhang YM, Shi HL, Yang S, Zhao YL, Liu HJ, Li C, Liu HL, Yang JP, Song J, Sun GZ, Yang JK. Enhancer-driven transcription of MCM8 by E2F4 promotes ATR pathway activation and glioma stem cell characteristics. Hereditas 2023; 160:29. [PMID: 37349788 DOI: 10.1186/s41065-023-00292-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Glioma stem cells (GSCs) are responsible for glioma recurrence and drug resistance, yet the mechanisms underlying their maintenance remains unclear. This study aimed to identify enhancer-controlled genes involved in GSCs maintenance and elucidate the mechanisms underlying their regulation. METHODS We analyzed RNA-seq data and H3K27ac ChIP-seq data from GSE119776 to identify differentially expressed genes and enhancers, respectively. Gene Ontology analysis was performed for functional enrichment. Transcription factors were predicted using the Toolkit for Cistrome Data Browser. Prognostic analysis and gene expression correlation was conducted using the Chinese Glioma Genome Atlas (CGGA) data. Two GSC cell lines, GSC-A172 and GSC-U138MG, were isolated from A172 and U138MG cell lines. qRT-PCR was used to detect gene transcription levels. ChIP-qPCR was used to detect H3K27ac of enhancers, and binding of E2F4 to target gene enhancers. Western blot was used to analyze protein levels of p-ATR and γH2AX. Sphere formation, limiting dilution and cell growth assays were used to analyze GSCs growth and self-renewal. RESULTS We found that upregulated genes in GSCs were associated with ataxia-telangiectasia-mutated-and-Rad3-related kinase (ATR) pathway activation, and that seven enhancer-controlled genes related to ATR pathway activation (LIN9, MCM8, CEP72, POLA1, DBF4, NDE1, and CDKN2C) were identified. Expression of these genes corresponded to poor prognosis in glioma patients. E2F4 was identified as a transcription factor that regulates enhancer-controlled genes related to the ATR pathway activation, with MCM8 having the highest hazard ratio among genes positively correlated with E2F4 expression. E2F4 bound to MCM8 enhancers to promote its transcription. Overexpression of MCM8 partially restored the inhibition of GSCs self-renewal, cell growth, and the ATR pathway activation caused by E2F4 knockdown. CONCLUSION Our study demonstrated that E2F4-mediated enhancer activation of MCM8 promotes the ATR pathway activation and GSCs characteristics. These findings offer promising targets for the development of new therapies for gliomas.
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Affiliation(s)
- Yu-Meng Sun
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Yi-Meng Zhang
- Medical Department, The First Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Hai-Liang Shi
- Department of Neurosurgery, Hebei General Hospital, Shijiazhuang, 050000, Hebei, China
| | - Song Yang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Yin-Long Zhao
- Department of Anesthesiology and Intensive Care, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Hong-Jiang Liu
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Chen Li
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Hong-Lei Liu
- Department of Neurosurgery, Shijiazhuang Third Hospital, Shijiazhuang, 050011, Hebei, China
| | - Ji-Peng Yang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Jian Song
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Guo-Zhu Sun
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China
| | - Jian-Kai Yang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, China.
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7
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Jain S, Rick JW, Joshi RS, Beniwal A, Spatz J, Gill S, Chang ACC, Choudhary N, Nguyen AT, Sudhir S, Chalif EJ, Chen JS, Chandra A, Haddad AF, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, Costello JF, Diaz A, Heiland DH, Aghi MK. Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects. J Clin Invest 2023; 133:e147087. [PMID: 36856115 PMCID: PMC9974099 DOI: 10.1172/jci147087] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/12/2023] [Indexed: 03/02/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) were presumed absent in glioblastoma given the lack of brain fibroblasts. Serial trypsinization of glioblastoma specimens yielded cells with CAF morphology and single-cell transcriptomic profiles based on their lack of copy number variations (CNVs) and elevated individual cell CAF probability scores derived from the expression of 9 CAF markers and absence of 5 markers from non-CAF stromal cells sharing features with CAFs. Cells without CNVs and with high CAF probability scores were identified in single-cell RNA-Seq of 12 patient glioblastomas. Pseudotime reconstruction revealed that immature CAFs evolved into subtypes, with mature CAFs expressing actin alpha 2, smooth muscle (ACTA2). Spatial transcriptomics from 16 patient glioblastomas confirmed CAF proximity to mesenchymal glioblastoma stem cells (GSCs), endothelial cells, and M2 macrophages. CAFs were chemotactically attracted to GSCs, and CAFs enriched GSCs. We created a resource of inferred crosstalk by mapping expression of receptors to their cognate ligands, identifying PDGF and TGF-β as mediators of GSC effects on CAFs and osteopontin and HGF as mediators of CAF-induced GSC enrichment. CAFs induced M2 macrophage polarization by producing the extra domain A (EDA) fibronectin variant that binds macrophage TLR4. Supplementing GSC-derived xenografts with CAFs enhanced in vivo tumor growth. These findings are among the first to identify glioblastoma CAFs and their GSC interactions, making them an intriguing target.
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Affiliation(s)
- Saket Jain
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jonathan W. Rick
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Angad Beniwal
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jordan Spatz
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sabraj Gill
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Nikita Choudhary
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Alan T. Nguyen
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sweta Sudhir
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Eric J. Chalif
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jia-Shu Chen
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Ankush Chandra
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Harsh Wadhwa
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sumedh S. Shah
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Serah Choi
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Josie L. Hayes
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Lin Wang
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Garima Yagnik
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Aaron Diaz
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Manish K. Aghi
- Department of Neurosurgery, UCSF, San Francisco, California, USA
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8
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Nikitin PV, Musina GR, Polozov VN, Goreiko DN, Krasnovsky VM, Werkenbark L, Kjelin M, Timashev PS. Development of Glioblastoma from Stem Cells to a Full-Fledged Tumor. Turk Patoloji Derg 2023; 39:117-132. [PMID: 35876685 PMCID: PMC10518198 DOI: 10.5146/tjpath.2022.01582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE IDH wild-type glioblastomas (GBM) are one of the most malignant and complex tumors for treatment. The urgent question of new therapeutic and diagnostic tools searching should be resolved based on cellular and molecular pathogenesis mechanisms, which remain insufficiently studied. In this study, we aimed to investigate GBM pathogenesis. MATERIAL AND METHOD /b > Using the isolation of different GBM cell populations and the cell cultures, animal models, and molecular genetic methods, we tried to clarify the picture of GBM pathogenesis by constructing a projection from different glioma stem cells types to an integral neoplasm. RESULTS We have shown a potential transformation pathway for both glioma stem cells and four definitive cell populations during gliomagenesis. Moreover, we have characterized each population, taking into account its place in the pathogenetic continuum, with a description of the most fundamental molecular and functional properties. CONCLUSION Finally, we have formed a complex holistic concept of the pathogenetic evolution of GBM at the cell-population level by integrating our results with the data of the world literature.
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Affiliation(s)
| | | | | | | | | | | | | | - Piotr Sergeevich Timashev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Moscow, Russia; World-Class Research Center “Digital biodesign and personalized healthcare,” Sechenov First Moscow State Medical University, Moscow, Russia
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9
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Li Z, Song Y, Zhang J. lncRNA PDCD4-AS1 Promotes the Progression of Glioma by Regulating miR-30b-3p/METTL7B Signaling. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:3492480. [PMID: 37151605 PMCID: PMC10162875 DOI: 10.1155/2023/3492480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/29/2022] [Indexed: 05/09/2023]
Abstract
Background Gliomas are the most common and most malignant primary tumors of the adult central nervous system, but their etiology and pathogenesis remain unclear. This study was aimed at investigating the expression and function of lncRNA PDCD4-AS1 in glioma and elucidating the mechanism by which PDCD4-AS1 regulates the biological features of glioma. Method The expression of PDCD4-AS1 was determined by bioinformatic analysis and qRT-PCR assay. PDCD4-AS1 was knocked down in glioma cells using siRNA transfection. The functional analysis of cells was conducted using CCK-8 proliferation, cell migration, and invasion assays, as well as cell cycle analysis. An in vivo tumorigenesis assay was performed to investigate the role of PDCD4-AS1 knockdown in glioma tumor growth. We performed bioinformatic analysis, RNA pull-down, and luciferase reporter assays to investigate the downstream targets of PDCD4-AS1. A rescue experiment was then performed to confirm the regulating mechanism. Results PDCD4-AS1 was found to be significantly upregulated in glioma patients' tumor tissues and cell lines. The silencing of PDCD4-AS1 inhibited glioma cell proliferation, invasion, migration, and induced cell cycle arrest. In vivo experiments showed that silencing PDCD4-AS1 inhibited glioma tumor growth. An investigation of the underlying mechanism suggested that PDCD4-AS1 positively regulated METTL7B expression by sponging miR-30b-3. Both the knockdown of miR-30b-3p and the overexpression of METTL7B could, respectively, reverse the malignant phenotype of cells affected by silencing PDCD4-AS1. Conclusion These results demonstrate that PDCD4-AS1 exerted an oncogenic role by regulating the miR-30b-3p/METTL7B axis.
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Affiliation(s)
- Zuowei Li
- Shandong University of Traditional Chinese Medicine, Jinan 250011, China
- Department of Encephalopathy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250011, China
| | - Yelin Song
- Department of Cardiovascular Medicine, Qingdao Hospital of Traditional Chinese Medicine, Qingdao 266011, China
| | - Jimei Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250011, China
- The 960th Hospital of the PLA Joint Logistics Support Force (Tai'an), Tai'an 271099, China
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10
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McCornack C, Woodiwiss T, Hardi A, Yano H, Kim AH. The function of histone methylation and acetylation regulators in GBM pathophysiology. Front Oncol 2023; 13:1144184. [PMID: 37205197 PMCID: PMC10185819 DOI: 10.3389/fonc.2023.1144184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023] Open
Abstract
Glioblastoma (GBM) is the most common and lethal primary brain malignancy and is characterized by a high degree of intra and intertumor cellular heterogeneity, a starkly immunosuppressive tumor microenvironment, and nearly universal recurrence. The application of various genomic approaches has allowed us to understand the core molecular signatures, transcriptional states, and DNA methylation patterns that define GBM. Histone posttranslational modifications (PTMs) have been shown to influence oncogenesis in a variety of malignancies, including other forms of glioma, yet comparatively less effort has been placed on understanding the transcriptional impact and regulation of histone PTMs in the context of GBM. In this review we discuss work that investigates the role of histone acetylating and methylating enzymes in GBM pathogenesis, as well as the effects of targeted inhibition of these enzymes. We then synthesize broader genomic and epigenomic approaches to understand the influence of histone PTMs on chromatin architecture and transcription within GBM and finally, explore the limitations of current research in this field before proposing future directions for this area of research.
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Affiliation(s)
- Colin McCornack
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, United States
| | - Timothy Woodiwiss
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa, IA, United States
| | - Angela Hardi
- Bernard Becker Medical Library, Washington University School of Medicine, St. Louis, MO, United States
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, United States
- The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, United States
- *Correspondence: Albert H. Kim,
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11
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Hersh AM, Gaitsch H, Alomari S, Lubelski D, Tyler BM. Molecular Pathways and Genomic Landscape of Glioblastoma Stem Cells: Opportunities for Targeted Therapy. Cancers (Basel) 2022; 14:3743. [PMID: 35954407 PMCID: PMC9367289 DOI: 10.3390/cancers14153743] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive tumor of the central nervous system categorized by the World Health Organization as a Grade 4 astrocytoma. Despite treatment with surgical resection, adjuvant chemotherapy, and radiation therapy, outcomes remain poor, with a median survival of only 14-16 months. Although tumor regression is often observed initially after treatment, long-term recurrence or progression invariably occurs. Tumor growth, invasion, and recurrence is mediated by a unique population of glioblastoma stem cells (GSCs). Their high mutation rate and dysregulated transcriptional landscape augment their resistance to conventional chemotherapy and radiation therapy, explaining the poor outcomes observed in patients. Consequently, GSCs have emerged as targets of interest in new treatment paradigms. Here, we review the unique properties of GSCs, including their interactions with the hypoxic microenvironment that drives their proliferation. We discuss vital signaling pathways in GSCs that mediate stemness, self-renewal, proliferation, and invasion, including the Notch, epidermal growth factor receptor, phosphatidylinositol 3-kinase/Akt, sonic hedgehog, transforming growth factor beta, Wnt, signal transducer and activator of transcription 3, and inhibitors of differentiation pathways. We also review epigenomic changes in GSCs that influence their transcriptional state, including DNA methylation, histone methylation and acetylation, and miRNA expression. The constituent molecular components of the signaling pathways and epigenomic regulators represent potential sites for targeted therapy, and representative examples of inhibitory molecules and pharmaceuticals are discussed. Continued investigation into the molecular pathways of GSCs and candidate therapeutics is needed to discover new effective treatments for GBM and improve survival.
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Affiliation(s)
- Andrew M. Hersh
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (A.M.H.); (H.G.); (S.A.); (D.L.)
| | - Hallie Gaitsch
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (A.M.H.); (H.G.); (S.A.); (D.L.)
- NIH Oxford-Cambridge Scholars Program, Wellcome—MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | - Safwan Alomari
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (A.M.H.); (H.G.); (S.A.); (D.L.)
| | - Daniel Lubelski
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (A.M.H.); (H.G.); (S.A.); (D.L.)
| | - Betty M. Tyler
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (A.M.H.); (H.G.); (S.A.); (D.L.)
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12
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Lowe SR, Kunigelis K, Vogelbaum MA. Leveraging the neurosurgical operating room for therapeutic development in NeuroOncology. Adv Drug Deliv Rev 2022; 186:114337. [PMID: 35561836 DOI: 10.1016/j.addr.2022.114337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
Glioblastoma (GBM) remains a disease with a dismal prognosis. For all the hope and promise immunotherapies and molecular targeted therapies have shown for systemic malignancies, these treatments have failed to show any promise in GBM. In this context, the paradigm of investigation of therapeutics for this disease itself must be examined and modifications considered. The unique challenge of the presence of blood-brain and blood-tumor barriers (BBB/BTB) raises questions about both the true levels of systemic drug delivery to the affected tissues. Window-of-opportunity (WoO) trials in neuro-oncology allow for proof-of-concept at the start of a classic phase I-II-III clinical trial progression. For therapeutics that do not have the ability to cross the BBB/BTB, direct delivery into tumor and/or tumor-infiltrated brain in the setting of a surgical procedure can provide a novel route of therapeutic access. These approaches permit neurosurgeons to play a greater role in therapeutic development for brain tumors.
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13
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Zheng Y, Yue X, Fang C, Jia Z, Chen Y, Xie H, Zhao J, Yang Z, Li L, Chen Z, Bian E, Zhao B. A Novel Defined Endoplasmic Reticulum Stress-Related lncRNA Signature for Prognosis Prediction and Immune Therapy in Glioma. Front Oncol 2022; 12:930923. [PMID: 35847925 PMCID: PMC9282894 DOI: 10.3389/fonc.2022.930923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Gliomas are a group of the most aggressive primary central nervous system tumors with limited treatment options. The abnormal expression of long non-coding RNA (lncRNA) is related to the prognosis of glioma. However, the role of endoplasmic reticulum (ER) stress-associated lncRNAs in glioma prognosis has not been reported. In this paper, we obtained ER stress-related lncRNAs by co-expression analysis, and then a risk signature composed of 6 ER stress-related lncRNAs was constructed using Cox regression analysis. Glioma samples in The Cancer Genome Atlas (TCGA) were separated into high- and low-risk groups based on the median risk score. Compared with the low-risk group, patients in the high-risk group had shorter survival times. Additionally, we verified the predictive ability of these candidate lncRNAs in the testing set. Three glioma patient subgroups (cluster 1/2/3) were identified by consensus clustering. We further analysed the abundance of immune-infiltrating cells and the expression levels of immune checkpoint molecules in both three subgroups and two risk groups, respectively. Immunotherapy and anticancer drug response prediction showed that ER stress-related lncRNA risk signature positively correlates with responding to immune checkpoints and chemosensitivity. Functional analysis showed that these gene sets are enriched in the malignant process of tumors. Finally, LINC00519 was chosen for functional experiments. The silence of LINC00519 restrained the migration and invasion of glioma cells. Hence, those results indicated that ER stress-related lncRNA risk signature could be a potential treatment target and a prognosis biomarker for glioma patients.
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Affiliation(s)
- Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Cheng Fang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhuang Jia
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yuxiang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Jiajia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
- *Correspondence: Erbao Bian, ; Bing Zhao,
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
- *Correspondence: Erbao Bian, ; Bing Zhao,
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14
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Sengupta S, Mondal M, Prasasvi KR, Mukherjee A, Magod P, Urbach S, Friedmann-Morvinski D, Marin P, Somasundaram K. Differentiated glioma cell-derived Fibromodulin activates Integrin-dependent Notch signaling in endothelial cells to promote tumor angiogenesis and growth. eLife 2022; 11:78972. [PMID: 35642785 PMCID: PMC9259034 DOI: 10.7554/elife.78972] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/29/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSCs) alone can initiate and maintain tumors, but the function of non-cancer stem cells (non-CSCs) that form the tumor bulk remains poorly understood. Proteomic analysis showed a higher abundance of the extracellular matrix small leucine-rich proteoglycan fibromodulin (FMOD) in the conditioned medium of differentiated glioma cells (DGCs), the equivalent of glioma non-CSCs, compared to that of glioma stem-like cells (GSCs). DGCs silenced for FMOD fail to cooperate with co-implanted GSCs to promote tumor growth. FMOD downregulation neither affects GSC growth and differentiation nor DGC growth and reprogramming in vitro. DGC-secreted FMOD promotes angiogenesis by activating integrin-dependent Notch signaling in endothelial cells. Furthermore, conditional silencing of FMOD in newly generated DGCs in vivo inhibits the growth of GSC-initiated tumors due to poorly developed vasculature and increases mouse survival. Collectively, these findings demonstrate that DGC-secreted FMOD promotes glioma tumor angiogenesis and growth through paracrine signaling in endothelial cells and identifies a DGC-produced protein as a potential therapeutic target in glioma.
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Affiliation(s)
- Shreoshi Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Mainak Mondal
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Kaval Reddy Prasasvi
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Arani Mukherjee
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Prerna Magod
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Philippe Marin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
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15
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Chen Z, Zhong Y, Chen J, Sun S, Liu W, Han Y, Liu X, Guo C, Li D, Hu W, Zhang P, Chen Z, Chen Z, Mou Y, Yan G, Zhu W, Yin W, Sai K. Disruption of β-catenin-mediated negative feedback reinforces cAMP-induced neuronal differentiation in glioma stem cells. Cell Death Dis 2022; 13:493. [PMID: 35610201 PMCID: PMC9130142 DOI: 10.1038/s41419-022-04957-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022]
Abstract
Accumulating evidence supports the existence of glioma stem cells (GSCs) and their critical role in the resistance to conventional treatments for glioblastoma multiforme (GBM). Differentiation therapy represents a promising alternative strategy against GBM by forcing GSCs to exit the cell cycle and reach terminal differentiation. In this study, we demonstrated that cAMP triggered neuronal differentiation and compromised the self-renewal capacity in GSCs. In addition, cAMP induced negative feedback to antagonize the differentiation process by activating β-catenin pathway. Suppression of β-catenin signaling synergized with cAMP activators to eliminate GSCs in vitro and extended the survival of animals in vivo. The cAMP/PKA pathway stabilized β-catenin through direct phosphorylation of the molecule and inhibition of GSK-3β. The activated β-catenin translocated into the nucleus and promoted the transcription of APELA and CARD16, which were found to be responsible for the repression of cAMP-induced differentiation in GSCs. Overall, our findings identified a negative feedback mechanism for cAMP-induced differentiation in GSCs and provided potential targets for the reinforcement of differentiation therapy for GBM.
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Affiliation(s)
- Zhijie Chen
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.412558.f0000 0004 1762 1794Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University Lingnan Hospital, Guangzhou, 510530 China
| | - Yingqian Zhong
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Jiehong Chen
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Shuxin Sun
- grid.410643.4Department of Pancreas Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080 China
| | - Wenfeng Liu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Yu Han
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Xincheng Liu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Cui Guo
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Depei Li
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Wanming Hu
- grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Peiyu Zhang
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Zhuopeng Chen
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Zhongping Chen
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Yonggao Mou
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
| | - Guangmei Yan
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Wenbo Zhu
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Wei Yin
- grid.12981.330000 0001 2360 039XDepartment of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
| | - Ke Sai
- grid.488530.20000 0004 1803 6191Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China ,grid.488530.20000 0004 1803 6191State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060 China
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16
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Chen N, Peng C, Li D. Epigenetic Underpinnings of Inflammation: A Key to Unlock the Tumor Microenvironment in Glioblastoma. Front Immunol 2022; 13:869307. [PMID: 35572545 PMCID: PMC9100418 DOI: 10.3389/fimmu.2022.869307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults, and immunotherapies and genetic therapies for GBM have evolved dramatically over the past decade, but GBM therapy is still facing a dilemma due to the high recurrence rate. The inflammatory microenvironment is a general signature of tumors that accelerates epigenetic changes in GBM and helps tumors avoid immunological surveillance. GBM tumor cells and glioma-associated microglia/macrophages are the primary contributors to the inflammatory condition, meanwhile the modification of epigenetic events including DNA methylation, non-coding RNAs, and histone methylation and deacetylases involved in this pathological process of GBM, finally result in exacerbating the proliferation, invasion, and migration of GBM. On the other hand, histone deacetylase inhibitors, DNA methyltransferases inhibitors, and RNA interference could reverse the inflammatory landscapes and inhibit GBM growth and invasion. Here, we systematically review the inflammatory-associated epigenetic changes and regulations in the microenvironment of GBM, aiming to provide a comprehensive epigenetic profile underlying the recognition of inflammation in GBM.
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Affiliation(s)
- Nian Chen
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dan Li
- State Key Laboratory of Southwestern Characteristic Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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17
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Anti-glioblastoma effects of phenolic variants of benzoylphenoxyacetamide (BPA) with high potential for blood brain barrier penetration. Sci Rep 2022; 12:3384. [PMID: 35232976 PMCID: PMC8888627 DOI: 10.1038/s41598-022-07247-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
Glioblastomas are the most aggressive brain tumors for which therapeutic options are limited. Current therapies against glioblastoma include surgical resection, followed by radiotherapy plus concomitant treatment and maintenance with temozolomide (TMZ), however, these standard therapies are often ineffective, and average survival time for glioblastoma patients is between 12 and 18 months. We have previously reported a strong anti-glioblastoma activity of several metabolic compounds, which were synthetized based compounds, which were synthetized based on the chemical structure of a common lipid-lowering drug, fenofibrate, and share a general molecular skeleton of benzoylphenoxyacetamide (BPA). Extensive computational analyses of phenol and naphthol moieties added to the BPA skeleton were performed in this study with the objective of selecting new BPA variants for subsequent compound preparation and anti-glioblastoma testing. Initially, 81 structural variations were considered and their physical properties such as solubility (logS), blood–brain partitioning (logBB), and probability of entering the CNS calculated by the Central Nervous System—Multiparameter Optimization (MPO-CNS) algorithm were evaluated. From this initial list, 18 compounds were further evaluated for anti-glioblastoma activity in vitro. Nine compounds demonstrated desirable glioblastoma cell toxicity in cell culture, and two of them, HR51, and HR59 demonstrated significantly improved capability of crossing the model blood–brain-barrier (BBB) composed of endothelial cells, astrocytes and pericytes.
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18
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Uribe D, Niechi I, Rackov G, Erices JI, San Martín R, Quezada C. Adapt to Persist: Glioblastoma Microenvironment and Epigenetic Regulation on Cell Plasticity. BIOLOGY 2022; 11:313. [PMID: 35205179 PMCID: PMC8869716 DOI: 10.3390/biology11020313] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
Glioblastoma (GBM) is the most frequent and aggressive brain tumor, characterized by great resistance to treatments, as well as inter- and intra-tumoral heterogeneity. GBM exhibits infiltration, vascularization and hypoxia-associated necrosis, characteristics that shape a unique microenvironment in which diverse cell types are integrated. A subpopulation of cells denominated GBM stem-like cells (GSCs) exhibits multipotency and self-renewal capacity. GSCs are considered the conductors of tumor progression due to their high tumorigenic capacity, enhanced proliferation, invasion and therapeutic resistance compared to non-GSCs cells. GSCs have been classified into two molecular subtypes: proneural and mesenchymal, the latter showing a more aggressive phenotype. Tumor microenvironment and therapy can induce a proneural-to-mesenchymal transition, as a mechanism of adaptation and resistance to treatments. In addition, GSCs can transition between quiescent and proliferative substates, allowing them to persist in different niches and adapt to different stages of tumor progression. Three niches have been described for GSCs: hypoxic/necrotic, invasive and perivascular, enhancing metabolic changes and cellular interactions shaping GSCs phenotype through metabolic changes and cellular interactions that favor their stemness. The phenotypic flexibility of GSCs to adapt to each niche is modulated by dynamic epigenetic modifications. Methylases, demethylases and histone deacetylase are deregulated in GSCs, allowing them to unlock transcriptional programs that are necessary for cell survival and plasticity. In this review, we described the effects of GSCs plasticity on GBM progression, discussing the role of GSCs niches on modulating their phenotype. Finally, we described epigenetic alterations in GSCs that are important for stemness, cell fate and therapeutic resistance.
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Affiliation(s)
- Daniel Uribe
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile; (D.U.); (I.N.); (J.I.E.); (R.S.M.)
| | - Ignacio Niechi
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile; (D.U.); (I.N.); (J.I.E.); (R.S.M.)
| | - Gorjana Rackov
- Department of Immunology and Oncology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain;
| | - José I. Erices
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile; (D.U.); (I.N.); (J.I.E.); (R.S.M.)
| | - Rody San Martín
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile; (D.U.); (I.N.); (J.I.E.); (R.S.M.)
| | - Claudia Quezada
- Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia 5090000, Chile; (D.U.); (I.N.); (J.I.E.); (R.S.M.)
- Millennium Institute on Immunology and Immunotherapy, Universidad Austral de Chile, Valdivia 5090000, Chile
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19
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Sox2 induces glioblastoma cell stemness and tumor propagation by repressing TET2 and deregulating 5hmC and 5mC DNA modifications. Signal Transduct Target Ther 2022; 7:37. [PMID: 35136034 PMCID: PMC8826438 DOI: 10.1038/s41392-021-00857-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a reversible process catalyzed by the ten–eleven translocation (TET) family of enzymes (TET1, TET2, TET3) that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Altered patterns of 5hmC and 5mC are widely reported in human cancers and loss of 5hmC correlates with poor prognosis. Understanding the mechanisms leading to 5hmC loss and its role in oncogenesis will advance the development of epigenetic-based therapeutics. We show that TET2 loss associates with glioblastoma (GBM) stem cells and correlates with poor survival of GBM patients. We further identify a SOX2:miR-10b-5p:TET2 axis that represses TET2 expression, represses 5hmC, increases 5mC levels, and induces GBM cell stemness and tumor-propagating potential. In vivo delivery of a miR-10b-5p inhibitor that normalizes TET2 expression and 5hmC levels inhibits tumor growth and prolongs survival of animals bearing pre-established orthotopic GBM xenografts. These findings highlight the importance of TET2 and 5hmC loss in Sox2-driven oncogenesis and their potential for therapeutic targeting.
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20
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Zhang R, Lai W, Wang H. Quantification of Epigenetic DNA Modifications in the Subchromatin Structure Matrix Attachment Regions by Stable Isotope Dilution UHPLC-MS/MS Analysis. Anal Chem 2021; 93:15567-15572. [PMID: 34783527 DOI: 10.1021/acs.analchem.1c04151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, subchromatin structure-based quantification of epigenetic DNA modifications is limited. Matrix attachment regions (MARs), an important subchromatin structure, contain DNA elements that specifically bind chromatin to the nuclear matrix in eukaryotes and are involved in a number of diseases. Here, we exploited a high-salt extraction-based subchromatin fractionation approach for the isolation of MAR DNA and other fractions and further developed heavy stable isotope-diluted ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) for the specific quantification of epigenetic DNA modifications in the subchromatin structures. By this approach, we showed for the first time that the content of a DNA demethylation intermediate, 5-hydroxymethylcytosine (5hmdC), in MARs decreased significantly in four tested cell lines compared to the contents in genomic DNA. In particular, the content of DNA 5hmdC in the MARs of 293T cell lines decreased the most at approximately 41.09%. Together, our findings implicate that MAR DNA is less sensitive than genomic DNA to DNA demethylation.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Environment and Health, Jianghan University, Wuhan 430056, China
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21
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Site-specific quantification of 5-carboxylcytosine in DNA by chemical conversion coupled with ligation-based PCR. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.05.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Vinel C, Rosser G, Guglielmi L, Constantinou M, Pomella N, Zhang X, Boot JR, Jones TA, Millner TO, Dumas AA, Rakyan V, Rees J, Thompson JL, Vuononvirta J, Nadkarni S, El Assan T, Aley N, Lin YY, Liu P, Nelander S, Sheer D, Merry CLR, Marelli-Berg F, Brandner S, Marino S. Comparative epigenetic analysis of tumour initiating cells and syngeneic EPSC-derived neural stem cells in glioblastoma. Nat Commun 2021; 12:6130. [PMID: 34675201 PMCID: PMC8531305 DOI: 10.1038/s41467-021-26297-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/23/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms which play an essential role in normal developmental processes, such as self-renewal and fate specification of neural stem cells (NSC) are also responsible for some of the changes in the glioblastoma (GBM) genome. Here we develop a strategy to compare the epigenetic and transcriptional make-up of primary GBM cells (GIC) with patient-matched expanded potential stem cell (EPSC)-derived NSC (iNSC). Using a comparative analysis of the transcriptome of syngeneic GIC/iNSC pairs, we identify a glycosaminoglycan (GAG)-mediated mechanism of recruitment of regulatory T cells (Tregs) in GBM. Integrated analysis of the transcriptome and DNA methylome of GBM cells identifies druggable target genes and patient-specific prediction of drug response in primary GIC cultures, which is validated in 3D and in vivo models. Taken together, we provide a proof of principle that this experimental pipeline has the potential to identify patient-specific disease mechanisms and druggable targets in GBM.
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Affiliation(s)
- Claire Vinel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Gabriel Rosser
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Loredana Guglielmi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Myrianni Constantinou
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Nicola Pomella
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Xinyu Zhang
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - James R Boot
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Tania A Jones
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Anaelle A Dumas
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Vardhman Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Jeremy Rees
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
| | - Jamie L Thompson
- Stem Cell Glycobiology Group, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Juho Vuononvirta
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Suchita Nadkarni
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Tedani El Assan
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
| | - Natasha Aley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Yung-Yao Lin
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
- Stem Cell Laboratory, National Bowel Research Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 2 Newark Street, London, UK
| | - Pentao Liu
- Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sven Nelander
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Denise Sheer
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Catherine L R Merry
- Stem Cell Glycobiology Group, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Federica Marelli-Berg
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, Queen Square, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK.
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23
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Narmontė M, Gibas P, Daniūnaitė K, Gordevičius J, Kriukienė E. Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations. Front Cell Dev Biol 2021; 9:727353. [PMID: 34557494 PMCID: PMC8452964 DOI: 10.3389/fcell.2021.727353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumors. Global loss of DNA methylation and genomic 5-hydroxymethylcytosine (5hmC) is a hallmark of human cancers. Here, we used our recently developed single-base resolution approaches, hmTOP-seq and uTOP-seq, for construction of 5hmC maps and identification of large partially methylated domains (PMDs) in different NB cell subpopulations. The 5hmC profiles revealed distinct signatures characteristic to different cell lineages and stages of malignant transformation of NB cells in a conventional and oxygen-depleted environment, which often occurs in tumors. The analysis of the cell-type-specific PMD distribution highlighted differences in global genome organization among NB cells that were ascribed to the same lineage identity by transcriptomic networks. Collectively, we demonstrated a high informativeness of the integrative epigenomic and transcriptomic research and large-scale genome structure in investigating the mechanisms that regulate cell identities and developmental stages of NB cells. Such multiomics analysis, as compared with mutational studies, open new ways for identification of novel disease-associated features which bring prognostic and therapeutic value in treating this aggressive pediatric disease.
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Affiliation(s)
- Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kristina Daniūnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,Human Genome Research Group, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juozas Gordevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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24
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Pan T, Li X, Li Y, Tao Z, Yao H, Wu Y, Chen G, Zhang K, Zhou Y, Huang Y. USP7 inhibition induces apoptosis in glioblastoma by enhancing ubiquitination of ARF4. Cancer Cell Int 2021; 21:508. [PMID: 34556124 PMCID: PMC8461901 DOI: 10.1186/s12935-021-02208-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Glioblastomas (GBMs) are grade IV central nervous system tumors characterized by a poor prognosis and a short median overall survival. Effective induction of GBM cell death is difficult because the GBM cell population is genetically unstable, resistant to chemotherapy and highly angiogenic. In recent studies, ubiquitin-specific protease 7 (USP7) is shown to scavenge ubiquitin from oncogenic protein substrates, so effective inhibition of USP7 may be a potential key treatment for GBM. Methods Immunohistochemistry and western blotting were used to detect the expression of USP7 in GBM tissues. In vitro apoptosis assay of USP7 inhibition was performed by western blotting, immunofluorescence, and flow cytometry. Anti-apoptotic substrates of USP7 were defined by Co-IP and TMT proteomics. Western blotting and IP were used to verify the relationship between USP7 and its substrate. In an in vivo experiment using an intracranial xenograft model in nude mice was constructed to assess the therapeutic effect of target USP7. Results Immunohistochemistry and western blotting confirmed that USP7 was significantly upregulated in glioblastoma samples. In in vitro experiments, inhibition of USP7 in GBM induced significant apoptosis. Co-IP and TMT proteomics identified a key anti-apoptotic substrate of USP7, ADP-ribosylation factor 4 (ARF4). Western blotting and IP confirmed that USP7 interacted directly with ARF4 and catalyzed the removal of the K48-linked polyubiquitinated chain that binded to ARF4. In addition, in vivo experiments revealed that USP7 inhibition significantly suppressed tumor growth and promoted the expression of apoptotic genes. Conclusions Targeted inhibition of USP7 enhances the ubiquitination of ARF4 and ultimately mediates the apoptosis of GBM cells. In a clinical sense, P5091 as a novel specific inhibitor of USP7 may be an effective approach for the treatment of GBM. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02208-z.
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Affiliation(s)
- Tingzheng Pan
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Xuetao Li
- Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Yanyan Li
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Zhennan Tao
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Hui Yao
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Yue Wu
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Guangliang Chen
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Kai Zhang
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China
| | - Youxin Zhou
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China.
| | - Yulun Huang
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Jiangsu, Suzhou, People's Republic of China. .,Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Jiangsu, Suzhou, People's Republic of China.
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25
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Singh O, Pratt D, Aldape K. Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors. Acta Neuropathol Commun 2021; 9:148. [PMID: 34496929 PMCID: PMC8425010 DOI: 10.1186/s40478-021-01249-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
It is recognized that the tumor microenvironment (TME) plays a critical role in the biology of cancer. To better understand the role of immune cell components in CNS tumors, we applied a deconvolution approach to bulk DNA methylation array data in a large set of newly profiled samples (n = 741) as well as samples from external data sources (n = 3311) of methylation-defined glial and glioneuronal tumors. Using the cell-type proportion data as input, we used dimensionality reduction to visualize sample-wise patterns that emerge from the cell type proportion estimations. In IDH-wildtype glioblastomas (n = 2,072), we identified distinct tumor clusters based on immune cell proportion and demonstrated an association with oncogenic alterations such as EGFR amplification and CDKN2A/B homozygous deletion. We also investigated the immune cluster-specific distribution of four malignant cellular states (AC-like, OPC-like, MES-like and NPC-like) in the IDH-wildtype cohort. We identified two major immune-based subgroups of IDH-mutant gliomas, which largely aligned with 1p/19q co-deletion status. Non-codeleted gliomas showed distinct proportions of a key genomic aberration (CDKN2A/B loss) among immune cell-based groups. We also observed significant positive correlations between monocyte proportion and expression of PD-L1 and PD-L2 (R = 0.54 and 0.68, respectively). Overall, the findings highlight specific roles of the TME in biology and classification of CNS tumors, where specific immune cell admixtures correlate with tumor types and genomic alterations.
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Affiliation(s)
- Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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26
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Kucheryavenko AS, Chernomyrdin NV, Gavdush AA, Alekseeva AI, Nikitin PV, Dolganova IN, Karalkin PA, Khalansky AS, Spektor IE, Skorobogatiy M, Tuchin VV, Zaytsev KI. Terahertz dielectric spectroscopy and solid immersion microscopy of ex vivo glioma model 101.8: brain tissue heterogeneity. BIOMEDICAL OPTICS EXPRESS 2021; 12:5272-5289. [PMID: 34513256 PMCID: PMC8407834 DOI: 10.1364/boe.432758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 05/23/2023]
Abstract
Terahertz (THz) technology holds strong potential for the intraoperative label-free diagnosis of brain gliomas, aimed at ensuring their gross-total resection. Nevertheless, it is still far from clinical applications due to the limited knowledge about the THz-wave-brain tissue interactions. In this work, rat glioma model 101.8 was studied ex vivo using both the THz pulsed spectroscopy and the 0.15λ-resolution THz solid immersion microscopy (λ is a free-space wavelength). The considered homograft model mimics glioblastoma, possesses heterogeneous character, unclear margins, and microvascularity. Using the THz spectroscopy, effective THz optical properties of brain tissues were studied, as averaged within the diffraction-limited beam spot. Thus measured THz optical properties revealed a persistent difference between intact tissues and a tumor, along with fluctuations of the tissue response over the rat brain. The observed THz microscopic images showed heterogeneous character of brain tissues at the scale posed by the THz wavelengths, which is due to the distinct response of white and gray matters, the presence of different neurovascular structures, as well as due to the necrotic debris and hemorrhage in a tumor. Such heterogeneities might significantly complicate delineation of tumor margins during the intraoperative THz neurodiagnosis. The presented results for the first time pose the problem of studying the inhomogeneity of brain tissues that causes scattering of THz waves, as well as the urgent need to use the radiation transfer theory for describing the THz-wave - tissue interactions.
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Affiliation(s)
- A S Kucheryavenko
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
- Institute of Solid State Physics of the Russian Academy of Sciences, Russia
| | - N V Chernomyrdin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
- Bauman Moscow State Technical University, Russia
| | - A A Gavdush
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
- Bauman Moscow State Technical University, Russia
| | | | - P V Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
- Institute for Regenerative Medicine, Sechenov University, Russia
- Burdenko Neurosurgery Institute, Russia
| | - I N Dolganova
- Institute of Solid State Physics of the Russian Academy of Sciences, Russia
- Bauman Moscow State Technical University, Russia
- Institute for Regenerative Medicine, Sechenov University, Russia
| | - P A Karalkin
- Institute for Cluster Oncology, Sechenov University, Russia
| | | | - I E Spektor
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
| | - M Skorobogatiy
- Department of Engineering Physics, Polytechnique Montreal, Canada
| | - V V Tuchin
- Science Medical Center, Saratov State University, Russia
- Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Russia
- National Research Tomsk State University, Russia
| | - K I Zaytsev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Russia
- Bauman Moscow State Technical University, Russia
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27
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Abballe L, Miele E. Epigenetic modulators for brain cancer stem cells: Implications for anticancer treatment. World J Stem Cells 2021; 13:670-684. [PMID: 34367473 PMCID: PMC8316861 DOI: 10.4252/wjsc.v13.i7.670] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/26/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Primary malignant brain tumors are a major cause of morbidity and mortality in both adults and children, with a dismal prognosis despite multimodal therapeutic approaches. In the last years, a specific subpopulation of cells within the tumor bulk, named cancer stem cells (CSCs) or tumor-initiating cells, have been identified in brain tumors as responsible for cancer growth and disease progression. Stemness features of tumor cells strongly affect treatment response, leading to the escape from conventional therapeutic approaches and subsequently causing tumor relapse. Recent research efforts have focused at identifying new therapeutic strategies capable of specifically targeting CSCs in cancers by taking into consideration their complex nature. Aberrant epigenetic machinery plays a key role in the genesis and progression of brain tumors as well as inducing CSC reprogramming and preserving CSC characteristics. Thus, reverting the cancer epigenome can be considered a promising therapeutic strategy. Three main epigenetic mechanisms have been described: DNA methylation, histone modifications, and non-coding RNA, particularly microRNAs. Each of these mechanisms has been proven to be targetable by chemical compounds, known as epigenetic-based drugs or epidrugs, that specifically target epigenetic marks. We review here recent advances in the study of epigenetic modulators promoting and sustaining brain tumor stem-like cells. We focus on their potential role in cancer therapy.
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Affiliation(s)
- Luana Abballe
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy
| | - Evelina Miele
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy.
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28
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Mitchell K, Troike K, Silver DJ, Lathia JD. The evolution of the cancer stem cell state in glioblastoma: emerging insights into the next generation of functional interactions. Neuro Oncol 2021; 23:199-213. [PMID: 33173943 DOI: 10.1093/neuonc/noaa259] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cellular heterogeneity is a hallmark of advanced cancers and has been ascribed in part to a population of self-renewing, therapeutically resistant cancer stem cells (CSCs). Glioblastoma (GBM), the most common primary malignant brain tumor, has served as a platform for the study of CSCs. In addition to illustrating the complexities of CSC biology, these investigations have led to a deeper understanding of GBM pathogenesis, revealed novel therapeutic targets, and driven innovation towards the development of next-generation therapies. While there continues to be an expansion in our knowledge of how CSCs contribute to GBM progression, opportunities have emerged to revisit this conceptual framework. In this review, we will summarize the current state of CSCs in GBM using key concepts of evolution as a paradigm (variation, inheritance, selection, and time) to describe how the CSC state is subject to alterations of cell intrinsic and extrinsic interactions that shape their evolutionarily trajectory. We identify emerging areas for future consideration, including appreciating CSCs as a cell state that is subject to plasticity, as opposed to a discrete population. These future considerations will not only have an impact on our understanding of this ever-expanding field but will also provide an opportunity to inform future therapies to effectively treat this complex and devastating disease.
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Affiliation(s)
- Kelly Mitchell
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio
| | - Katie Troike
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case, Western Reserve University, Cleveland, Ohio
| | - Daniel J Silver
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio
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29
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Chen F, Hua J, Shen H, Wang H. Effect of TWIST1 Gene on the Proliferation and Apoptosis of Human Glioma Cell Line TJ861 by Regulating Mammalian Target of Rapamycin Signaling Pathway. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To observe TWIST1 gene expression in human glioma and study the effect human glioma cell line TJ861 on the proliferation and apoptosis, and further explore its potential mechanism to provide some reference for the targeted treatment of glioma in the future. Detection of cancer tissue
(Carcinoma tissue) in 55 patients with glioma by RT-PCR and Expression level of TWIST1 in normal and paracancerous tissues (Adjacent tissue), the human glioma cell line TJ861 was further divided into, Nonsense sequence group, (si-NS group), TWIST1 Inhibition group (si-TWIST1 group) and control
group. The glioma cells of si-NS group and si-TWIST1 group were transfected with nonsense sequence and TWIST1 siRNA respectively by liposome transfection technology. Use CCK8 assay to test the cell proliferation ability of each group at 0, 12, 24, 36, 48 and 72 hours; 48 hours after siRNA
transfection, The ability of DNA replication in each group was detected by EdU staining; Apoptosis related protein expression, in each group, was analyzed by Western blot; TUNEL staining was used to test the apoptosis rate of each group; In the end, We studied TWIST1 effect knocking down on
mTOR protein expression in human glioma cells and mTOR protein expression in cancer and adjacent tissues. TWIST1 expression in glioma cells was higher, compared with normal tissues (P <0.05); After transfection of TWIST1 siRNA into human glioma cell line TJ861 in vitro, CCK8
showed glioma cells proliferation ability in si-TWIST1 group at 12, 24, 36, 48 and 72 hours was lower, compared with the control group (P <0.05); After siRNA transfection at 48 hours, the DNA replication ability of glioma cells decreased significantly (P <0.05) with EdU
staining; The inhibition of TWIST1 increased Bax expression in glioma cells, and inhibited Bcl-2 expression (P < 0.05) with Western blot; TUNEL staining further confirmed that the apoptosis level of glioma cells in the si-TWIST1 group was higher, compared with the control group (P
<0.05). Finally, we found that mTOR protein expression in glioma was higher, compared with adjacent tissues. in vitro experiments showed that mTOR expression in glioma cells was decreased after the inhibition of TWIST1 (P <0.05). TWIST1 expression level in glioma was increased.
The inhibition of TWIST1 inhibits the proliferation of glioma by blocking the mTOR signal pathway, and promote the apoptosis of glioma.
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Affiliation(s)
- Fei Chen
- Department of Neurosurgery, The Sixth People’s Hospital of Nantong, Nantong, Jiangsu, 226011, China
| | - Jiajia Hua
- Traditional Chinese Medicine Department, The Sixth People’s Hospital of Nantong, Nantong, Jiangsu, 226011, China
| | - HongWei Shen
- Health Management Centre, The Sixth People’s Hospital of Shanghai (The East Part), Shanghai, 201306, China
| | - HongLiang Wang
- Department of Neurosurgery, The Sixth People’s Hospital of Nantong, Nantong, Jiangsu, 226011, China
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30
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Xu L, Chen Y, Huang Y, Sandanaraj E, Yu JS, Lin RYT, Dakle P, Ke XY, Chong YK, Koh L, Mayakonda A, Nacro K, Hill J, Huang ML, Gery S, Lim SW, Huang Z, Xu Y, Chen J, Bai L, Wang S, Wakimoto H, Yeo TT, Ang BT, Müschen M, Tang C, Tan TZ, Koeffler HP. Topography of transcriptionally active chromatin in glioblastoma. SCIENCE ADVANCES 2021; 7:7/18/eabd4676. [PMID: 33931443 PMCID: PMC8087410 DOI: 10.1126/sciadv.abd4676] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Molecular profiling of the most aggressive brain tumor glioblastoma (GBM) on the basis of gene expression, DNA methylation, and genomic variations advances both cancer research and clinical diagnosis. The enhancer architectures and regulatory circuitries governing tumor-intrinsic transcriptional diversity and subtype identity are still elusive. Here, by mapping H3K27ac deposition, we analyze the active regulatory landscapes across 95 GBM biopsies, 12 normal brain tissues, and 38 cell line counterparts. Analyses of differentially regulated enhancers and super-enhancers uncovered previously unrecognized layers of intertumor heterogeneity. Integrative analysis of variant enhancer loci and transcriptome identified topographies of transcriptional enhancers and core regulatory circuitries in four molecular subtypes of primary tumors: AC1-mesenchymal, AC1-classical, AC2-proneural, and AC3-proneural. Moreover, this study reveals core oncogenic dependency on super-enhancer-driven transcriptional factors, long noncoding RNAs, and druggable targets in GBM. Through profiling of transcriptional enhancers, we provide clinically relevant insights into molecular classification, pathogenesis, and therapeutic intervention of GBM.
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Affiliation(s)
- Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ye Chen
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - Yulun Huang
- Department of Neurosurgery, Dushu Lake Hospital Affiliated of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, Medical Center of Soochow University, Suzhou, 215124, China
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Edwin Sandanaraj
- Department of Research, National Neuroscience Institute, 308433, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology, and Research, 117609, Singapore
| | - John S Yu
- Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ruby Yu-Tong Lin
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Pushkar Dakle
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Xin-Yu Ke
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Yuk Kien Chong
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Lynnette Koh
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
| | - Kassoum Nacro
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 138670, Singapore
| | - Jeffrey Hill
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Mo-Li Huang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Sigal Gery
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - See Wee Lim
- Department of Research, National Neuroscience Institute, 308433, Singapore
| | - Zhengyun Huang
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Ying Xu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Jianxiang Chen
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, 311121, China
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 310015, China
| | - Longchuan Bai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tseng Tsai Yeo
- National University Cancer Institute, National University Hospital, 119074, Singapore
| | - Beng Ti Ang
- Department of Neurosurgery, National Neuroscience Institute, 308433, Singapore
- Duke-National University of Singapore Medical School, 169857, Singapore
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA
- Department of Immunobiology, Yale University, New Haven, CT 06511, USA
| | - Carol Tang
- Department of Research, National Neuroscience Institute, 308433, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- National University Cancer Institute, National University Hospital, 119074, Singapore
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31
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In silico identification of the prognostic biomarkers and therapeutic targets associated with cancer stem cell characteristics of glioma. Biosci Rep 2021; 40:225916. [PMID: 32725165 PMCID: PMC7418212 DOI: 10.1042/bsr20201037] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Glioma is the common histological subtype of malignancy in central nervous system, with a high morbidity and mortality. Cancer stem cells (CSCs) play an important role in regulating the tumorigenesis and progression of glioma; however, the prognostic biomarkers and therapeutic targets associated with CSC characteristics have not been fully acknowledged in glioma. In order to identify the prognostic stemness-related genes (SRGs) of glioma in silico, the RNA sequencing data of patients with glioma were retrieved from The Cancer Genome Atlas (TCGA) databases. The mRNA expression-based stemness index (mRNAsi) was significantly associated with the glioma histologic grade, isocitrate dehydrogenase 1 (IDH1) mutation and overall survival of glioma patients by the nonparametric test and Kaplan–Meier survival analysis. A total of 340 SRGs were identified as the overlapped stemness-related differential expressed genes (DEGs) of different histologic grade screened by the univariate Cox analysis. Based on 11 prognostic SRGs, the predict nomogram was constructed with the AUC of 0.832. Moreover, the risk score of the nomogram was an independent prognostic factor, indicating its significant applicability. Besides other eight reported biomarkers of glioma, we found that F2RL2, CLCNKA and LOXL4 were first identified as prognostic biomarkers for glioma. In conclusion, this bioinformatics study demonstrates the mRNAsi as a reliable index for the IDH1 mutation, histologic grade and OS of glioma patients and provides a well-applied model for predicting the OS for patients with glioma based on prognostic SRGs. Additionally, this in silico study also identifies three novel prognostic biomarkers (F2RL2, CLCNKA and LOXL4) for glioma patients.
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32
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WNT-Regulated Transcriptional Enhancers and Stem Cell Plasticity. Trends Cell Biol 2021; 31:525-528. [PMID: 33775538 DOI: 10.1016/j.tcb.2021.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 01/31/2023]
Abstract
Enhancer reprogramming lies at the heart of dynamic cellular processes such as differentiation and tumorigenesis. WNT signaling is an evolutionary conserved pathway that exploits transcriptional enhancers to control the state-specific transcriptional program. Recent evidences suggest several mechanisms that govern this state-specific enhancer regulation in stem cells and cancer.
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33
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Li X, Nie S, Lv Z, Ma L, Song Y, Hu Z, Hu X, Liu Z, Zhou G, Dai Z, Song T, Liu J, Wang S. Overexpression of Annexin A2 promotes proliferation by forming a Glypican 1/c-Myc positive feedback loop: prognostic significance in human glioma. Cell Death Dis 2021; 12:261. [PMID: 33712571 PMCID: PMC7954792 DOI: 10.1038/s41419-021-03547-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/25/2022]
Abstract
In order to set up a reliable prediction system for the tumor grade and prognosis in glioma patients, we clarify the complicated crosstalk of Annexin A2 (ANXA2) with Glypican 1 (GPC1) and demonstrate whether combined indexes of ANXA2 and GPC1 could improve the prognostic evaluation for glioma patients. We found that ANXA2-induced glioma cell proliferation in a c-Myc-dependent manner. ANXA2 increased the expression of GPC1 via c-Myc and the upregulated GPC1 further promoted the c-Myc level, forming a positive feedback loop, which eventually led to enhanced proliferation of glioma cells. Both mRNA and protein levels of ANXA2 were upregulated in glioma tissues and coincided with the overexpression of GPC1. Besides, we utilized tissue microarrays (TMAs) and immunohistochemistry to demonstrate that glioma patients with both high expression of ANXA2 and GPC1 tended to have higher rate of tumor recurrence and shorter overall survival (OS). In conclusion, the overexpression of ANXA2 promotes proliferation of glioma cells by forming a GPC1/c-Myc positive feedback loop, and ANXA2 together with its downstream target GPC1 could be a potential "combination biomarker" for predicting prognosis of glioma patients.
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Affiliation(s)
- Xin Li
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China.,Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Shengdan Nie
- Institute of Clinical Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Ziyang Lv
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Lingran Ma
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Yuxi Song
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Zhongxu Hu
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Xin Hu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Zhiqiang Liu
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Gaoya Zhou
- Department of Neurology, Brain Hospital of Hunan Province, Changsha, China
| | - Zhijie Dai
- Department of Institute of Metabolism and Endocrinology, Second Xiang-Ya Hospital, Central South University, Changsha, China
| | - Tao Song
- Department of Neurosurgery, Xiang-Ya Hospital, Central South University, Changsha, China.
| | - Jiajia Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China.
| | - Shan Wang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China.
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34
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Iranmanesh Y, Jiang B, Favour OC, Dou Z, Wu J, Li J, Sun C. Mitochondria's Role in the Maintenance of Cancer Stem Cells in Glioblastoma. Front Oncol 2021; 11:582694. [PMID: 33692947 PMCID: PMC7937970 DOI: 10.3389/fonc.2021.582694] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM), one of the deadliest primary brain malignancies, is characterized by a high recurrence rate due to its limited response to existing therapeutic strategies such as chemotherapy, radiation therapy, and surgery. Several mechanisms and pathways have been identified to be responsible for GBM therapeutic resistance. Glioblastoma stem cells (GSCs) are known culprits of GBM resistance to therapy. GSCs are characterized by their unique self-renewal, differentiating capacity, and proliferative potential. They form a heterogeneous population of cancer stem cells within the tumor and are further divided into different subpopulations. Their distinct molecular, genetic, dynamic, and metabolic features distinguish them from neural stem cells (NSCs) and differentiated GBM cells. Novel therapeutic strategies targeting GSCs could effectively reduce the tumor-initiating potential, hence, a thorough understanding of mechanisms involved in maintaining GSCs' stemness cannot be overemphasized. The mitochondrion, a regulator of cellular physiological processes such as autophagy, cellular respiration, reactive oxygen species (ROS) generation, apoptosis, DNA repair, and cell cycle control, has been implicated in various malignancies (for instance, breast, lung, and prostate cancer). Besides, the role of mitochondria in GBM has been extensively studied. For example, when stressors, such as irradiation and hypoxia are present, GSCs utilize specific cytoprotective mechanisms like the activation of mitochondrial stress pathways to survive the harsh environment. Proliferating GBM cells exhibit increased cytoplasmic glycolysis in comparison to terminally differentiated GBM cells and quiescent GSCs that rely more on oxidative phosphorylation (OXPHOS). Furthermore, the Warburg effect, which is characterized by increased tumor cell glycolysis and decreased mitochondrial metabolism in the presence of oxygen, has been observed in GBM. Herein, we highlight the importance of mitochondria in the maintenance of GSCs.
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Affiliation(s)
| | - Biao Jiang
- Department of Radiology, The 2nd Affiliated Hospital of Zhejiang University Medical School, Hangzhou, China
| | - Okoye C Favour
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Zhangqi Dou
- Department of Neurosurgery, The 2nd Affiliated Hospital of Zhejiang University Medical School, Hangzhou, China
| | - Jiawei Wu
- Department of Neurosurgery, The 2nd Affiliated Hospital of Zhejiang University Medical School, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, The 2nd Affiliated Hospital of Zhejiang University Medical School, Hangzhou, China
| | - Chongran Sun
- Department of Neurosurgery, The 2nd Affiliated Hospital of Zhejiang University Medical School, Hangzhou, China
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35
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Ferrer AI, Trinidad JR, Sandiford O, Etchegaray JP, Rameshwar P. Epigenetic dynamics in cancer stem cell dormancy. Cancer Metastasis Rev 2021; 39:721-738. [PMID: 32394305 DOI: 10.1007/s10555-020-09882-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer remains one of the most challenging diseases despite significant advances of early diagnosis and therapeutic treatments. Cancerous tumors are composed of various cell types including cancer stem cells capable of self-renewal, proliferation, differentiation, and invasion of distal tumor sites. Most notably, these cells can enter a dormant cellular state that is resistant to conventional therapies. Thereby, cancer stem cells have the intrinsic potential for tumor initiation, tumor growth, metastasis, and tumor relapse after therapy. Both genetic and epigenetic alterations are attributed to the formation of multiple tumor types. This review is focused on how epigenetic dynamics involving DNA methylation and DNA oxidations are implicated in breast cancer and glioblastoma multiforme. The emergence and progression of these cancer types rely on cancer stem cells with the capacity to enter quiescence also known as a dormant cellular state, which dictates the distinct tumorigenic aggressiveness between breast cancer and glioblastomas.
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Affiliation(s)
- Alejandra I Ferrer
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Jonathan R Trinidad
- Department of Biological Sciences, Rutgers University, Newark, NJ, 07102, USA
| | - Oleta Sandiford
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | | | - Pranela Rameshwar
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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36
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El Khoury LY, Fu S, Hlady RA, Wagner RT, Wang L, Eckel-Passow JE, Castle EP, Stanton ML, Thompson RH, Parker AS, Ho TH, Robertson KD. Identification of DNA methylation signatures associated with poor outcome in lower-risk Stage, Size, Grade and Necrosis (SSIGN) score clear cell renal cell cancer. Clin Epigenetics 2021; 13:12. [PMID: 33461589 PMCID: PMC7814746 DOI: 10.1186/s13148-020-00998-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite using prognostic algorithms and standard surveillance guidelines, 17% of patients initially diagnosed with low risk clear cell renal cell carcinoma (ccRCC) ultimately relapse and die of recurrent disease, indicating additional molecular parameters are needed for improved prognosis. RESULTS To address the gap in ccRCC prognostication in the lower risk population, we performed a genome-wide analysis for methylation signatures capable of distinguishing recurrent and non-recurrent ccRCCs within the subgroup classified as 'low risk' by the Mayo Clinic Stage, Size, Grade, and Necrosis score (SSIGN 0-3). This approach revealed that recurrent patients have globally hypermethylated tumors and differ in methylation significantly at 5929 CpGs. Differentially methylated CpGs (DMCpGs) were enriched in regulatory regions and genes modulating cell growth and invasion. A subset of DMCpGs stratified low SSIGN groups into high and low risk of recurrence in independent data sets, indicating that DNA methylation enhances the prognostic power of the SSIGN score. CONCLUSIONS This study reports a global DNA hypermethylation in tumors of recurrent ccRCC patients. Furthermore, DMCpGs were capable of discriminating between aggressive and less aggressive tumors, in addition to SSIGN score. Therefore, DNA methylation presents itself as a potentially strong biomarker to further improve prognostic power in patients with low risk SSIGN score (0-3).
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Affiliation(s)
- Louis Y El Khoury
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Shuang Fu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.,Hematology Laboratory, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ryan T Wagner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Erik P Castle
- Department of Urology, Mayo Clinic, Phoenix, AZ, USA
| | - Melissa L Stanton
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, AZ, USA
| | | | - Alexander S Parker
- Office of Research Affairs, University of Florida, Jacksonville, FL, USA
| | - Thai H Ho
- Division of Hematology and Medical Oncology, Mayo Clinic, 13400 E. Shea Blvd, Scottsdale, AZ, 85259, USA.
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, Epigenomics Program, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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37
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A contemporary update on glioblastoma: molecular biology, current management, and a vision towards bio-adaptable personalized care. J Neurooncol 2021; 151:103-112. [PMID: 33394264 DOI: 10.1007/s11060-020-03671-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Glioblastoma (GBM) is the most fatal brain tumor in adults. Current survival rates of GBM remain below 2 years due to GBM's aggressive cellular migration and genetically driven treatment escape pathways. Despite our rapidly increasing understanding of GBM biology, earlier diagnoses, and refined surgical techniques, only moderate survival benefits have been achieved. Nonetheless, the pressing need for better survival rates has brought forward a multitude of newer therapeutic approaches and opened the door for potential personalization of these modalities in the near future. METHODS We reviewed the published literature discussing the current state of knowledge regarding GBM biology and therapy and summarized the information that may point toward future personalized therapeutic strategies. RESULTS Several novel modalities such as oncolytic viruses, targeted immune, and molecular therapies, and tumor treating fields have been introduced. To date, there is no single treatment modality for GBM, but rather a wide spectrum of combined modalities that address intratumoral cellular and genetic variabilities. While the current state of GBM research and clinical trial landscape may hold promise, current literature lacks any fruitful progress towards personalized GBM therapy. CONCLUSION In this review, we are discussing our recent knowledge of the GBM genetic biologic landscape and the current advances in therapy, as well as providing a blueprint for an envisioned GBM management paradigm that should be personalized and adaptable to accommodate each patient's diverse genetic variations and therapy response/escape patterns.
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Chowdhury S, Ghosh S. Next Generation Sequencing and Stem Cells. Stem Cells 2021. [DOI: 10.1007/978-981-16-1638-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang H, Tao Z, Feng M, Li X, Deng Z, Zhao G, Yin H, Pan T, Chen G, Feng Z, Li Y, Zhou Y. Dual PLK1 and STAT3 inhibition promotes glioblastoma cells apoptosis through MYC. Biochem Biophys Res Commun 2020; 533:368-375. [PMID: 32962858 DOI: 10.1016/j.bbrc.2020.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/05/2020] [Indexed: 12/27/2022]
Abstract
Glioblastoma (GBM) is the deadliest primary brain tumor that is highly resistant to current treatments. Polo-like kinase 1 (PLK1) and signal transducer and activator of transcription 3 (STAT3) are highly expressed in gliomas, especially GBM. Previous studies have shown reciprocal activation between PLK1 and STAT3 and that they regulate the same pools of MYC downstream. We have demonstrated that PLK1 and STAT3 levels are elevated in gliomas compared with those in normal brain tissues, and high expression of both PLK1 and STAT3 is associated with poor prognosis in TCGA. Moreover, there was direct or indirect reciprocal regulation between PLK1 and STAT3. Furthermore, we found that PLK1 and STAT3 can regulate the same pools of MYC downstream. Compared to monotherapy, combined treatment of glioma cells with PLK1 and STAT3 inhibitors, BI2536 and Stattic, respectively, showed lower expression of MYC, synergistic induction of cell invasion and apoptosis in vitro, and tumor inhibition in xenografts. PLK1 and STAT3 were able to directly regulate the expression of MYC and induce apoptosis of glioma cells through the regulation of MYC. These findings may help develop a therapeutic strategy for dual inhibition of PLK1 and STAT3 against the tumorigenesis of glioma.
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Affiliation(s)
- Hao Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zhennan Tao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ming Feng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xuetao Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zhitong Deng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Guozheng Zhao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haoran Yin
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Tingzheng Pan
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Guangliang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Zibin Feng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yanyan Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Youxin Zhou
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China.
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Valor LM, Hervás-Corpión I. The Epigenetics of Glioma Stem Cells: A Brief Overview. Front Oncol 2020; 10:602378. [PMID: 33344253 PMCID: PMC7738619 DOI: 10.3389/fonc.2020.602378] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
Glioma stem cells (GSCs) are crucial in the formation, perpetuation and recurrence of glioblastomas (GBs) due to their self-renewal and proliferation properties. Although GSCs share cellular and molecular characteristics with neural stem cells (NSCs), GSCs show unique transcriptional and epigenetic features that may explain their relevant role in GB and may constitute druggable targets for novel therapeutic approaches. In this review, we will summarize the most important findings in GSCs concerning epigenetic-dependent mechanisms.
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Affiliation(s)
- Luis M Valor
- Unidad de Investigación, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, Spain
| | - Irati Hervás-Corpión
- Unidad de Investigación, Hospital Universitario Puerta del Mar, Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Cádiz, Spain
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Leung JY, Chia K, Ong DST, Taneja R. Interweaving Tumor Heterogeneity into the Cancer Epigenetic/Metabolic Axis. Antioxid Redox Signal 2020; 33:946-965. [PMID: 31841357 DOI: 10.1089/ars.2019.7942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Significance: The epigenomic/metabolic landscape in cancer has been studied extensively in the past decade and forms the basis of various drug targets. Yet, cancer treatment remains a challenge, with clinical trials exhibiting limited efficacy and high relapse rates. Patients respond differently to therapy, which is fundamentally attributed to tumor heterogeneity, both across and within tumors. This review focuses on the interactions between the heterogeneous tumor microenvironment (TME) and the epigenomic/metabolic axis in cancer, as well as the emerging technologies under development to aid heterogeneity studies. Recent Advances: Interlinks between epigenetics and metabolism in cancer have been reported. Emerging studies have unveiled interactions between the TME and cancer cells that play a critical role in regulating epigenetics and reprogramming cancer metabolism, suggesting a three-way cross talk. Critical Issues: This cross talk accentuates the multiplex nature of cancer, and the importance of considering tumor heterogeneity in various epigenomic/metabolic cancer studies. Future Directions: With the advancement in single-cell profiling, it may be possible to identify cancer subclones and their unique vulnerabilities to develop a multimodal therapy. Drugs targeting the TME are currently being studied, and a better understanding of the TME in regulating cancer epigenetics and metabolism may hold the key to identifying novel therapeutic targets.
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Affiliation(s)
- Jia Yu Leung
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kimberly Chia
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Lin S, Xu H, Zhang A, Ni Y, Xu Y, Meng T, Wang M, Lou M. Prognosis Analysis and Validation of m 6A Signature and Tumor Immune Microenvironment in Glioma. Front Oncol 2020; 10:541401. [PMID: 33123464 PMCID: PMC7571468 DOI: 10.3389/fonc.2020.541401] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/24/2020] [Indexed: 01/21/2023] Open
Abstract
Glioma is one of the most typical intracranial tumors, comprising about 80% of all brain malignancies. Several key molecular signatures have emerged as prognostic biomarkers, which indicate room for improvement in the current approach to glioma classification. In order to construct a more veracious prediction model and identify the potential prognosis-biomarker, we explore the differential expressed m6A RNA methylation regulators in 665 gliomas from TCGA-GBM and TCGA-LGG. Consensus clustering was applied to the m6A RNA methylation regulators, and two glioma subgroups were identified with a poorer prognosis and a higher grade of WHO classification in cluster 1. The further chi-squared test indicated that the immune infiltration was significantly enriched in cluster 1, indicating a close relation between m6A regulators and immune infiltration. In order to explore the potential biomarkers, the weighted gene co-expression network analysis (WGCNA), along with Least absolute shrinkage and selection operator (LASSO), between high/low immune infiltration and m6A cluster 1/2 groups were utilized for the hub genes, and four genes (TAGLN2, PDPN, TIMP1, EMP3) were identified as prognostic biomarkers. Besides, a prognostic model was constructed based on the four genes with a good prediction and applicability for the overall survival (OS) of glioma patients (the area under the curve of ROC achieved 0.80 (0.76-0.83) and 0.72 (0.68-0.76) in TCGA and Chinese Glioma Genome Atlas (CGGA), respectively). Moreover, we also found PDPN and TIMP1 were highly expressed in high-grade glioma from The Human Protein Atlas database and both of them were correlated with m6A and immune cell marker in glioma tissue samples. In conclusion, we construct a novel prognostic model which provides new insights into glioma prognosis. The PDPN and TIMP1 may serve as potential biomarkers for prognosis of glioma.
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Affiliation(s)
- Shaojian Lin
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Houshi Xu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Anke Zhang
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunjia Ni
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanzhi Xu
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tong Meng
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingjie Wang
- Department of Digestive Diseases, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiqing Lou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Tao Z, Li X, Wang H, Chen G, Feng Z, Wu Y, Yin H, Zhao G, Deng Z, Zhao C, Li Y, Sun T, Zhou Y. BRD4 regulates self-renewal ability and tumorigenicity of glioma-initiating cells by enrichment in the Notch1 promoter region. Clin Transl Med 2020; 10:e181. [PMID: 33135348 PMCID: PMC7533052 DOI: 10.1002/ctm2.181] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/09/2020] [Accepted: 09/12/2020] [Indexed: 12/24/2022] Open
Abstract
Bromodomain and extraterminal domain (BET) family proteins are considered to be epigenetic readers that regulate gene expression by recognizing acetyl lysine residues on histones and nonhistone chromatin factors and have been classified as curative targets for a variety of cancers. Glioma-initiating cells (GICs), which commit self-renewal, perpetual proliferation, multidirectional differentiation, and vigorous tumorigenicity, sustain the peculiar genetic and epigenetic diversification in the GBM patients, thus, GICs result in tumor recurrence. Abundant evidence demonstrates that BET proteins regulate differentiation of stem cells. However, it endures ambiguous how individual BET proteins take part in GIC advancement, and how do small molecule inhibitors like I-BET151 target functional autonomous BET proteins. Here, we validated that BRD4, not BRD2 or BRD3, has value in targeted glioma therapy. We announce a signaling pathway concerning BRD4 and Notch1 that sustains the self-renewal of GICs. Moreover, in-depth mechanistic research showed that BRD4 was concentrated at the promoter region of Notch1 and may be involved in the process of tumor metabolism. Furthermore, in intracranial models, I-BET151 eliminated U87 GICs' tumorigenicity. The outcomes of this research could be conducive to design clinical trials for treatment of glioma based on BRD4.
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Affiliation(s)
- Zhennan Tao
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xuetao Li
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Hao Wang
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Guangliang Chen
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Zibin Feng
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yue Wu
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Haoran Yin
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Guozheng Zhao
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Zhitong Deng
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Chaohui Zhao
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yanyan Li
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ting Sun
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Youxin Zhou
- Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
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Ličytė J, Gibas P, Skardžiūtė K, Stankevičius V, Rukšėnaitė A, Kriukienė E. A Bisulfite-free Approach for Base-Resolution Analysis of Genomic 5-Carboxylcytosine. Cell Rep 2020; 32:108155. [DOI: 10.1016/j.celrep.2020.108155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/10/2020] [Accepted: 08/25/2020] [Indexed: 01/01/2023] Open
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Bhargav AG, Mondal SK, Garcia CA, Green JJ, Quiñones‐Hinojosa A. Nanomedicine Revisited: Next Generation Therapies for Brain Cancer. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Adip G. Bhargav
- Mayo Clinic College of Medicine and Science Mayo Clinic 200 First Street SW Rochester MN 55905 USA
- Department of Neurologic Surgery Mayo Clinic 4500 San Pablo Rd. Jacksonville FL 32224 USA
| | - Sujan K. Mondal
- Department of Pathology University of Pittsburgh School of Medicine 200 Lothrop Street Pittsburgh PA 15213 USA
| | - Cesar A. Garcia
- Department of Neurologic Surgery Mayo Clinic 4500 San Pablo Rd. Jacksonville FL 32224 USA
| | - Jordan J. Green
- Departments of Biomedical Engineering, Neurosurgery, Oncology, Ophthalmology, Materials Science and Engineering, and Chemical and Biomolecular Engineering, Translational Tissue Engineering Center, Bloomberg‐Kimmel Institute for Cancer Immunotherapy, Institute for Nanobiotechnology Johns Hopkins University School of Medicine 400 N. Broadway, Smith 5017 Baltimore MD 21231 USA
| | - Alfredo Quiñones‐Hinojosa
- Department of Neurologic Surgery Mayo Clinic 4500 San Pablo Rd. Jacksonville FL 32224 USA
- Departments of Otolaryngology‐Head and Neck Surgery/Audiology Neuroscience, Cancer Biology, and Anatomy Mayo Clinic 4500 San Pablo Rd. Jacksonville FL 32224 USA
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Han C, He Y, Chen L, Wang J, Jiao S, Xia X, Li G, Yao S. Low Expression of APOB mRNA or Its Hypermethylation Predicts Favorable Overall Survival in Patients with Low-Grade Glioma. Onco Targets Ther 2020; 13:7243-7255. [PMID: 32801753 PMCID: PMC7394594 DOI: 10.2147/ott.s257794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background This study was performed to explore the clinical and prognostic significance of APOB mRNA expression, DNA methylation and APOB mutation in patients with low-grade glioma (LGG). Methods Bioinformatic analysis was conducted using genomic, clinical and survival data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Serum APOB protein levels were measured via immunoturbidimetry in 150 patients with LGG and 100 healthy controls from Hubei General Hospital. Results There was a negative association between the levels of APOB mRNA and DNA methylation (r=−0.355, P<0.0001) in patients with LGG from the TCGA database. Additionally, LGG patients with low levels of APOB mRNA exhibited better overall survival (OS) than those with high levels of APOB mRNA (HR=0.637, P=0.0085). The survival time of LGG patients with APOB hypermethylation was markedly longer than that of patients with APOB hypomethylation (HR=0.423, P=0.0185). The prognostic significance of APOB mRNA and DNA methylation was also validated with the CGGA cohort, and a similar conclusion was reached. APOB gene mutations were observed in 3% of patients with LGG from the TCGA database, and no association was detected between APOB mutations and OS (P=0.164). Furthermore, the levels of APOB protein were much lower in patients with LGG than in normal individuals (P=0.0022), and the expression of APOB protein was markedly different among groups when stratified by histological type (P<0.0001) and histological-molecular classification (P<0.0001). Conclusion APOB mRNA expression is negatively regulated by DNA methylation in patients with LGG. Low expression or hypermethylation of APOB might predict relatively favorable survival in patients with LGG.
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Affiliation(s)
- Chong Han
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
| | - Yang He
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China.,Department of Neurosurgery, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People's Republic of China
| | - Lifen Chen
- Department of Endocrinology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
| | - Jie Wang
- Department of Oncology, Hubei General Hospital, Wuhan, Hubei 430060, People's Republic of China
| | - Song Jiao
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
| | - Xiangping Xia
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
| | - Gang Li
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
| | - Shengtao Yao
- Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, People's Republic of China
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Reddy RG, Bhat UA, Chakravarty S, Kumar A. Advances in histone deacetylase inhibitors in targeting glioblastoma stem cells. Cancer Chemother Pharmacol 2020; 86:165-179. [PMID: 32638092 DOI: 10.1007/s00280-020-04109-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme (GBM) is a lethal grade IV glioma (WHO classification) and widely prevalent primary brain tumor in adults. GBM tumors harbor cellular heterogeneity with the presence of a small subpopulation of tumor cells, described as GBM cancer stem cells (CSCs) that pose resistance to standard anticancer regimens and eventually mediate aggressive relapse or intractable progressive GBM. Existing conventional anticancer therapies for GBM do not target GBM stem cells and are mostly palliative; therefore, exploration of new strategies to target stem cells of GBM has to be prioritized for the development of effective GBM therapy. Recent developments in the understanding of GBM pathophysiology demonstrated dysregulation of epigenetic mechanisms along with the genetic changes in GBM CSCs. Altered expression/activity of key epigenetic regulators, especially histone deacetylases (HDACs) in GBM stem cells has been associated with poor prognosis; inhibiting the activity of HDACs using histone deacetylase inhibitors (HDACi) has been promising as mono-therapeutic in targeting GBM and in sensitizing GBM stem cells to an existing anticancer regimen. Here, we review the development of pan/selective HDACi as potential anticancer agents in targeting the stem cells of glioblastoma as a mono or combination therapy.
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Affiliation(s)
- R Gajendra Reddy
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Unis Ahmad Bhat
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sumana Chakravarty
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad, 500007, Telangana, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Gibas P, Narmontė M, Staševskij Z, Gordevičius J, Klimašauskas S, Kriukienė E. Precise genomic mapping of 5-hydroxymethylcytosine via covalent tether-directed sequencing. PLoS Biol 2020; 18:e3000684. [PMID: 32275660 PMCID: PMC7176277 DOI: 10.1371/journal.pbio.3000684] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/22/2020] [Accepted: 03/27/2020] [Indexed: 01/20/2023] Open
Abstract
5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes, and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered oligonucleotide–primed sequencing), which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide. Examination of distinct conjugation chemistries suggested a structural model for the tether-directed nonhomologous polymerase priming enabling theoretical evaluation of suitable tethers at the design stage. The hmTOP-seq procedure was optimized and validated on a small model genome and mouse embryonic stem cells, which allowed construction of single-nucleotide 5hmC maps reflecting subtle differences in strand-specific CG hydroxymethylation. Collectively, hmTOP-seq provides a new valuable tool for cost-effective and precise identification of 5hmC in characterizing its biological role and epigenetic changes associated with human disease. This study describes hmTOP-seq, a bisulfite-free approach for profiling of the epigenetic mark 5-hydroxymethylcytosine (5hmC) at single-nucleotide resolution, based on direct sequence readout primed at an in situ tethered DNA oligonucleotide.
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Affiliation(s)
- Povilas Gibas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Milda Narmontė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Zdislav Staševskij
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juozas Gordevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- * E-mail: (SK); (EK)
| | - Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- * E-mail: (SK); (EK)
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Abstract
New discoveries in Glioblastoma (GBM) biology have been made using genomics data. Genomic markers are routinely integrated into clinical neurosurgical practice. In this manuscript, we review the fundamentals of genomics such as the differences between first, second, and third generation sequencing technology. We also review the impact of single cell genomics in understanding the complex heterogenous GBM microenvironment. Finally, we will discuss advances in epigenetics that have lent insights into treatment resistance. The integration of genomics into neuro-oncology clinical practice is routine and will continue to expand with the expansion of precision of medicine. We provide a primer for clinicians.
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Affiliation(s)
- John D Patterson
- Department of Neurological Surgery, University of Arkansas for Medical Sciences
| | | | - Analiz Rodriguez
- Department of Neurological Surgery, University of Arkansas for Medical Sciences
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50
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Jiang Y, Zhou J, Zhao J, Hou D, Zhang H, Li L, Zou D, Hu J, Zhang Y, Jing Z. MiR-18a-downregulated RORA inhibits the proliferation and tumorigenesis of glioma using the TNF-α-mediated NF-κB signaling pathway. EBioMedicine 2020; 52:102651. [PMID: 32062354 PMCID: PMC7016377 DOI: 10.1016/j.ebiom.2020.102651] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/05/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Glioma has a poor prognosis, and is the most common primary and lethal primary malignant tumor in the central nervous system. Retinoic acid receptor-related orphan receptor A (RORA) is a member of the ROR subfamily of orphan receptors and plays an anti-tumor role in several cancers. METHODS A cell viability assay, the Edu assay, neurosphere formation assay, and xenograft experiments were used to detect the proliferative abilities of glioma cell line, glioma stem cells (GSCs). Western blotting, ELISAs, and luciferase reporter assays were used to detect the presence of possible microRNAs. FINDINGS Our study found for the first time that RORA was expressed at low levels in gliomas, and was associated with a good prognosis. RORA overexpression inhibited the proliferation and tumorigenesis of glioma cell lines and GSCs via inhibiting the TNF-α mediated NF-κB signaling pathway. In addition, microRNA-18a had a promoting effect on gliomas, and was the possible reason for low RORA expression in gliomas. INTERPRETATION RORA may be a promising therapeutic target in the treatment of gliomas.
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Affiliation(s)
- Yang Jiang
- Department of Neurosurgery, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China; Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, China
| | - Jinpeng Zhou
- Department of Neurosurgery, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China
| | - Junshuang Zhao
- Department of Neurosurgery, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China
| | - Dianqi Hou
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, China
| | - Haiying Zhang
- International Education College, Liaoning University of Traditional Chinese Medicine, Shenyang, No. 79 Chongshan East Road, Shenyang 110042, Liaoning, China
| | - Long Li
- Department of Neurosurgery, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China
| | - Dan Zou
- The First Laboratory of Cancer Institute, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China
| | - Jiangfeng Hu
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, No. 100 Haining Road, Shanghai 200080, China
| | - Ye Zhang
- The First Laboratory of Cancer Institute, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China
| | - Zhitao Jing
- Department of Neurosurgery, the First Hospital of China Medical University, No. 155 North Nanjing Street, Shenyang 110001, Liaoning, China.
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