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Sharma RK, Calderon C, Vivas-Mejia PE. Targeting Non-coding RNA for Glioblastoma Therapy: The Challenge of Overcomes the Blood-Brain Barrier. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:678593. [PMID: 35047931 PMCID: PMC8757885 DOI: 10.3389/fmedt.2021.678593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant form of all primary brain tumors, and it is responsible for around 200,000 deaths each year worldwide. The standard therapy for GBM treatment includes surgical resection followed by temozolomide-based chemotherapy and/or radiotherapy. With this treatment, the median survival rate of GBM patients is only 15 months after its initial diagnosis. Therefore, novel and better treatment modalities for GBM treatment are urgently needed. Mounting evidence indicates that non-coding RNAs (ncRNAs) have critical roles as regulators of gene expression. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are among the most studied ncRNAs in health and disease. Dysregulation of ncRNAs is observed in virtually all tumor types, including GBMs. Several dysregulated miRNAs and lncRNAs have been identified in GBM cell lines and GBM tumor samples. Some of them have been proposed as diagnostic and prognostic markers, and as targets for GBM treatment. Most ncRNA-based therapies use oligonucleotide RNA molecules which are normally of short life in circulation. Nanoparticles (NPs) have been designed to increase the half-life of oligonucleotide RNAs. An additional challenge faced not only by RNA oligonucleotides but for therapies designed for brain-related conditions, is the presence of the blood-brain barrier (BBB). The BBB is the anatomical barrier that protects the brain from undesirable agents. Although some NPs have been derivatized at their surface to cross the BBB, optimal NPs to deliver oligonucleotide RNA into GBM cells in the brain are currently unavailable. In this review, we describe first the current treatments for GBM therapy. Next, we discuss the most relevant miRNAs and lncRNAs suggested as targets for GBM therapy. Then, we compare the current drug delivery systems (nanocarriers/NPs) for RNA oligonucleotide delivery, the challenges faced to send drugs through the BBB, and the strategies to overcome this barrier. Finally, we categorize the critical points where research should be the focus in order to design optimal NPs for drug delivery into the brain; and thus move the Oligonucleotide RNA-based therapies from the bench to the clinical setting.
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Affiliation(s)
- Rohit K. Sharma
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Carlos Calderon
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Pablo E. Vivas-Mejia
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR, United States
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2
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Zhao Z, Zhang C, Li M, Yu X, Liu H, Chen Q, Wang J, Shen S, Jiang J. Integrative Analysis of miRNA-mediated Competing Endogenous RNA Network Reveals the lncRNAs-mRNAs Interaction in Glioblastoma Stem Cell Differentiation. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200511074226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background:
Competing endogenous RNA (ceRNA) networks play a pivotal role in
tumor diagnosis and progression. Numerous studies have explored the functional landscape and
prognostic significance of ceRNA interaction within differentiated tumor cells.
Objective:
We propose a new perspective by exploring ceRNA networks in the process of
glioblastoma stem cell (GSC) differentiation.
Methods:
In this study, expression profiles of lncRNAs and mRNAs were compared between GSCs
and differentiated glioblastoma cells. Using a comprehensive computational method, miRNAmediated
and GSC differentiation-associated ceRNA crosstalk between lncRNAs and mRNAs was
identified. A ceRNA network was then established to select potential candidates that regulate GSC
differentiation.
Results:
Based on the specific ceRNA network related to GSC differentiation, we identified lnc
MYOSLID: 11 as a ceRNA that regulated the expression of the downstream gene PXN by
competitively binding with hsa-miR-149-3p. After Kaplan-Meier (KM) survival analysis, the
expression of PXN gene (PPXN = 0.0015) and lnc MYOSLID: 11 (PMYOSLID: 11=0.041) showed
significant correlation with glioblastoma in 160 patients from TCGA.
Conclusion:
This result sheds light on a potential way of studying the ceRNA network, which can
provide clues for developing new diagnostic methods and finding therapeutic targets for clinical
treatment of glioblastoma.
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Affiliation(s)
- Zhenyu Zhao
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Cheng Zhang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao tong University School of Medicine, Shanghai, China
| | - Mi Li
- Department of Mathematics & Statistics, Boston University, Boston, MA, United States
| | - Xinguang Yu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Hailong Liu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Qi Chen
- National Engineering Laboratory for Medical Big Data Application Technology, Chinese PLA General Hospital, Beijing, China
| | - Jian Wang
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Shaopin Shen
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Jingjing Jiang
- Clinical Data and Specimen Repositories, Chinese PLA General Hospital, Beijing, China
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3
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Cheng F, Liu J, Zhang Y, You Q, Chen B, Cheng J, Deng C. Long Non-Coding RNA UBA6-AS1 Promotes the Malignant Properties of Glioblastoma by Competitively Binding to microRNA-760 and Enhancing Homeobox A2 Expression. Cancer Manag Res 2021; 13:379-392. [PMID: 33469379 PMCID: PMC7813458 DOI: 10.2147/cmar.s287676] [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: 10/19/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Background The dysregulation of long non-coding RNAs is a frequent finding in glioblastoma (GBM) and is considered as a crucial mechanism contributing to GBM oncogenesis and progression. The biological roles and underlying mechanisms of action of UBA6 antisense RNA 1 (UBA6-AS1) in GBM have been rarely investigated. Therefore, the aim of the present study was to investigate in detail the role of UBA6-AS1 in the modulation of the malignant properties of GBM and explore the possible underlying mechanism(s). Methods The expression of UBA6-AS1 in GBM was determined via reverse transcription-quantitative PCR. Cell Counting Kit-8 assay, flow cytometric analysis, Transwell migration and invasion assays, and in vivo tumorigenicity assay were applied to elucidate the biological effects of UBA6-AS1 on GBM cells. The possible biological events associated with UBA6-AS1 were investigated by luciferase reporter, RNA immunoprecipitation (RIP) and rescue assays. Results UBA6-AS1 was overexpressed in GBM, which was consistent with the data from The Cancer Genome Atlas database. In the case of UBA6-AS1 depletion, GBM cell proliferation, migration and invasion were notably decreased and cell apoptosis was enhanced in vitro. Additionally, knockdown of UBA6-AS1 suppressed the proliferation of GBM cells in vivo. Mechanistically, UBA6-AS1 functioned as a competing endogenous RNA by adsorbing miR-760 and, consequently, upregulating homeobox A2 (HOXA2) expression. Rescue experiments demonstrated that the UBA6-AS1 silencing-mediated regulatory effects on GBM cells were reversed by the decrease of miR-760 or restoration of HOXA2 expression. Conclusion Therefore, the results of the present study revealed that UBA6-AS1 promoted the malignant progression of GBM via targeting the miR-760/HOXA2 axis, thereby representing a promising effective target for the treatment of GBM.
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Affiliation(s)
- Feifei Cheng
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Jiang Liu
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Yundong Zhang
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Qiuxiang You
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Bo Chen
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Jing Cheng
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
| | - Chunyan Deng
- Department of Neurology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, People's Republic of China
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4
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Li H, Yan R, Chen W, Ding X, Liu J, Chen G, Zhao Q, Tang Y, Lv S, Liu S, Yu Y. Long non coding RNA SLC26A4-AS1 exerts antiangiogenic effects in human glioma by upregulating NPTX1 via NFKB1 transcriptional factor. FEBS J 2021; 288:212-228. [PMID: 32255252 DOI: 10.1111/febs.15325] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 01/07/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022]
Abstract
Malignant gliomas are a heterogeneous group of brain tumors with a poor prognosis, which is largely due to its aggressive invasiveness and angiogenesis. In recent years, it has been found that multiple long noncoding RNAs (lncRNAs) participate in a wide range of biological functions including angiogenesis through the regulation of gene expression in cancers. In this study, we investigate and report the novel role of lncRNA SLC26A4-AS1 in gliomas, with a novel mechanism involving transcription factors NFKB1 and NPTX1. We determined that SLC26A4-AS1 was downregulated in human glioma tissues and cells. Furthermore, overexpression of SLC26A4-AS1 or NPTX1 restrained the aggressiveness of glioma cells and their pro-angiogenic ability. SLC26A4-AS1 was also found to upregulate NPTX1 by recruiting NFKB1 into the NPTX1 promoter. Moreover, silencing of either NPTX1 or NFKB1 restored the aggressive and pro-angiogenic properties of glioma cells in the presence of SLC26A4-AS1. Taken together, we demonstrate that SLC26A4-AS1 promotes NPTX1 transcriptional activity by recruiting NFKB1 and thus exerting antiangiogenic effects on glioma cells. This study provides an experimental basis for the intervention of SLC26A4-AS1 in the treatment of gliomas.
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MESH Headings
- Animals
- Brain Neoplasms/blood supply
- Brain Neoplasms/genetics
- Brain Neoplasms/metabolism
- Brain Neoplasms/pathology
- C-Reactive Protein/antagonists & inhibitors
- C-Reactive Protein/genetics
- C-Reactive Protein/metabolism
- Case-Control Studies
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Glioblastoma/blood supply
- Glioblastoma/genetics
- Glioblastoma/metabolism
- Glioblastoma/pathology
- Humans
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- NF-kappa B p50 Subunit/antagonists & inhibitors
- NF-kappa B p50 Subunit/genetics
- NF-kappa B p50 Subunit/metabolism
- Neoplasm Grading
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/pathology
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neuroglia/metabolism
- Neuroglia/pathology
- Promoter Regions, Genetic
- RNA, Long Noncoding/agonists
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Signal Transduction
- Sulfate Transporters/genetics
- Sulfate Transporters/metabolism
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Haijun Li
- Department of Neurology, Taizhou Second People's Hospital, China
| | - Raoyu Yan
- Ankang Ward, Taizhou Second People's Hospital, China
| | - Weiqing Chen
- Clinical Laboratory, Taizhou Women and Children Hospital, China
| | - Xiaofei Ding
- Central Laboratory, Taizhou University Medical School, China
| | - Jiaming Liu
- School of Basic Medical Sciences, Wenzhou Medical University, China
| | - Guang Chen
- Central Laboratory, Taizhou University Medical School, China
| | - Qunfeng Zhao
- Blood Transfusion Division, Taizhou Municipal Hospital, China
| | - Yiping Tang
- Blood Transfusion Division, Taizhou Municipal Hospital, China
| | - Siye Lv
- Blood Transfusion Division, Taizhou Municipal Hospital, China
| | - Shuangchun Liu
- Blood Transfusion Division, Taizhou Municipal Hospital, China
| | - Ying Yu
- Infection Medicine, Taizhou Municipal Hospital, China
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5
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Singh P, Singh A, Shah S, Vataliya J, Mittal A, Chitkara D. RNA Interference Nanotherapeutics for Treatment of Glioblastoma Multiforme. Mol Pharm 2020; 17:4040-4066. [PMID: 32902291 DOI: 10.1021/acs.molpharmaceut.0c00709] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleic acid therapeutics for RNA interference (RNAi) are gaining attention in the treatment and management of several kinds of the so-called "undruggable" tumors via targeting specific molecular pathways or oncogenes. Synthetic ribonucleic acid (RNAs) oligonucleotides like siRNA, miRNA, shRNA, and lncRNA have shown potential as novel therapeutics. However, the delivery of such oligonucleotides is significantly hampered by their physiochemical (such as hydrophilicity, negative charge, and instability) and biopharmaceutical features (in vivo serum stability, fast renal clearance, interaction with extracellular proteins, and hindrance in cellular internalization) that markedly reduce their biological activity. Recently, several nanocarriers have evolved as suitable non-viral vectors for oligonucleotide delivery, which are known to either complex or conjugate with these oligonucleotides efficiently and also overcome the extracellular and intracellular barriers, thereby allowing access to the tumoral micro-environment for the better and desired outcome in glioblastoma multiforme (GBM). This Review focuses on the up-to-date advancements in the field of RNAi nanotherapeutics utilized for GBM treatment.
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Affiliation(s)
- Prabhjeet Singh
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Aditi Singh
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Shruti Shah
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Jalpa Vataliya
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Anupama Mittal
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
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6
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Liu Z, Wang X, Yang G, Zhong C, Zhang R, Ye J, Zhong Y, Hu J, Ozal B, Zhao S. Construction of lncRNA-associated ceRNA networks to identify prognostic lncRNA biomarkers for glioblastoma. J Cell Biochem 2020; 121:3502-3515. [PMID: 32277520 DOI: 10.1002/jcb.29625] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) serve as competitive endogenous RNAs (ceRNAs) that play significant regulatory roles in the pathogenesis of tumors. However, the role of lncRNAs, especially the lncRNA-related ceRNA regulatory network, in glioblastoma (GBM) has not been fully elucidated. The goal of the current study was to construct lncRNA-microRNA-mRNA-related ceRNA networks for further investigation of their mechanism of action in GBM. We downloaded data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases and identified differential lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs) associated with GBM. A ceRNA network was constructed and analyzed to examine the relationship between lncRNAs and patients' overall survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGGs) were used to analyze the related mRNAs to indirectly explain the mechanism of action of lncRNAs. The potential effective drugs for the treatment of GBM were identified using the connectivity map (CMap). After integrated analysis, we obtained a total of 210 differentially expressed lncRNAs, 90 differentially expressed miRNAs, and 2508 differentially expressed mRNAs (DEmRNAs) from the TCGA and GEO databases. Using these differential genes, we constructed a lncRNA-associated ceRNA network. Six lncRNAs in the ceRNA network were associated with the overall survival of patients with GBM. Through KEGG analysis, it was found that the DEmRNAs involved in the network are related to cancer-associated pathways, for instance, mitogen-activated protein kinase and Ras signaling pathways. CMap analysis revealed four small-molecule compounds that could be used as drugs for the treatment of GBM. In this study, a multi-database joint analysis was used to construct a lncRNA-related ceRNA network to help identify the regulatory functions of lncRNAs in the pathogenesis of GBM.
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Affiliation(s)
- Zhendong Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoxiong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Guang Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chen Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ruotian Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Junyi Ye
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yingqiang Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Junlong Hu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
| | - Beylerli Ozal
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China.,Central Research Laboratory, Bashkir State Medical University, Ufa, Russia
| | - Shiguang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.,The Laboratory of Neurosurgery, Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang, China
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7
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Abstract
Glioma, the most common and aggressive type of brain tumor, has a poor prognosis. Glioma stem cells (GSCs) are thought to be responsible for glioma genesis, proliferation, resistance to chemoradiotherapy, and recurrence. Long non-coding RNAs (lncRNAs) have been viewed as a prospective novel target in glioma therapy in recent years due to their functional roles in GSC biological processes. However, how lncRNAs interact with GSCs and the underlining mechanisms associated with these interactions are not yet clear. In this review, we briefly illustrate recent advancements in the functional roles of lncRNA and their potential mechanisms in GSCs.
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Affiliation(s)
- Lei Wang
- Department of Neurosurgery, Hunan Cancer Hospital and The Afliated Cancer Hospital of Xiangya School, Central South University, Changsha, Hunan, China (mainland)
| | - Zhengwen He
- Department of Neurosurgery, Hunan Cancer Hospital and The Afliated Cancer Hospital of Xiangya School, Central South University, Changsha, Hunan, China (mainland)
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8
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Ye J, Zhu J, Chen H, Qian J, Zhang L, Wan Z, Chen F, Sun S, Li W, Luo C. A novel lncRNA-LINC01116 regulates tumorigenesis of glioma by targeting VEGFA. Int J Cancer 2019; 146:248-261. [PMID: 31144303 DOI: 10.1002/ijc.32483] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/16/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022]
Abstract
Brain glioma is the most common malignant tumor of the central nervous system, and one of the leading causes of death in patients with intracranial tumors. The clinical outcome of glioma is usually poor due to abundant vascularity, fast growth and susceptibility of invasion to normal brain tissues. Our microarray study showed that lncRNA-LINC01116 was significantly upregulated in glioma tissues and played an important role in cell proliferation, cycle, migration, invasion and angiogenesis. In addition, vascular endothelial growth factor (VEGFA) may be the major target genes in the downstream of lncRNA-LINC01116. Dual luciferase assay showed that LINC01116 and VEGFA both contained a miR-31-5p binding site, and LINC01116 could regulate the expression of VEGFA through competitive absorption of miR-31-5p. RNA immunoprecipitation indicated that LINC01116 and VEGFA were present in the miR-31-5p-RISC complex, and biotinylated miR-31-5p pull-down assay suggested that there was a competitive relationship between LINC01116 and VEGFA to bind with miR-31-5p. Collectively, our study has identified a novel lncRNA-LINC01116 and clarified the role and mechanism of LINC01116 in the tumorigenesis of glioma. LINC01116 may prove to be a potential target for the clinical diagnosis and treatment of glioma.
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Affiliation(s)
- Jingliang Ye
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Neurosurgery, 72 Group Military Hospital of CPLA, Huzhou, China
| | - Junle Zhu
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huairui Chen
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun Qian
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lei Zhang
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiping Wan
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feng Chen
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuhan Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - Wen Li
- Center of Reproductive Medicine, Shanghai Changzheng Hospital, Shanghai, China
| | - Chun Luo
- Department of Neurosurgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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9
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Li D, Lu J, Li H, Qi S, Yu L. Identification of a long noncoding RNA signature to predict outcomes of glioblastoma. Mol Med Rep 2019; 19:5406-5416. [PMID: 31059035 PMCID: PMC6522932 DOI: 10.3892/mmr.2019.10184] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/15/2019] [Indexed: 12/20/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a novel class of gene regulators involved in tumor biogenesis. Glioblastoma is the most common and malignant type of brain tumor. The function and prognostic significance of lncRNAs in glioblastoma remain unclear. In the present study, updated gene annotations were adopted to investigate lncRNA expression profiles in publicly available glioma microarray datasets from the Gene Expression Omnibus and the Repository for Molecular Brain Neoplasia Data. In a training set of 108 samples of glioblastoma, using univariate Cox regression analysis with a permutation P<0.005, four lncRNAs, including insulin‑like growth factor binding protein 7‑antisense 1 (IGFBP7‑AS1), were significantly associated with patient overall survival. These four lncRNAs were integrated as an expression‑based molecular signature to divide patients in the training set into high‑risk and low‑risk subgroups, with distinct survival rates (hazard ratio, 2.72; 95% CI, 1.71‑4.31; P<0.001). The prognostic value of the lncRNA signature was confirmed in two additional datasets comprising a total of 147 samples from patients with glioblastoma. The prognostic value of this signature was independent of age and Karnofsky performance status. This signature was also able to predict different outcomes in cases of glioblastoma associated with an isocitrate dehydrogenase 1 mutation. Further bioinformatics analyses revealed that 'epithelial‑mesenchymal transition' and 'p53 pathway' gene sets were enriched in glioblastoma samples with higher IGFBP7‑AS1 expression. Furthermore, in vitro experiments demonstrated that knockdown of IGFBP7‑AS1 inhibited the viability, migration and invasion of U87 and U251 glioma cells. In conclusion, the present study identified a lncRNA signature able to predict glioblastoma outcomes, and provided novel information regarding the role of IGFBP7‑AS1 in glioma development.
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Affiliation(s)
- Depei Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Jie Lu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Hong Li
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Lei Yu
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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10
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Zan XY, Li L. Construction of lncRNA-mediated ceRNA network to reveal clinically relevant lncRNA biomarkers in glioblastomas. Oncol Lett 2019; 17:4369-4374. [PMID: 30944630 PMCID: PMC6444437 DOI: 10.3892/ol.2019.10114] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 02/07/2019] [Indexed: 12/27/2022] Open
Abstract
Cross-talk between competing endogenous RNAs (ceRNAs) play key roles in tumor development. In this study, we performed exon-level expression profiling on 26 glioblastomas (GBMs) and 6 controls to identify long non-coding RNAs (lncRNAs) of GBM initiation and progression using lncRNA-mediated ceRNA network (LMCN). The mRNA and lncRNA expression data, as well as miRNA-target interactions were firstly collected. Then, we used hypergeometric test to detect the lncRNA-mRNA interactions, followed by the construction of LMCN based on Pearson correlation coefficient. With the goal of investigation of the network organization, degree distribution of LMCN was performed. Next, the synergistic, competing lncRNA modules were identified using jActiveModule plug-in of Cytoscape. Moreover, we implemented the pathway analysis for its mRNAs in the module to explore the functions of significant lncRNAs. Using the criteria of degrees >50, 8 hub genes were identified, including EPB41L4A-AS1, ZRANB2-AS2, XIST, HOTAIR, TRAF3IP2-AS1, TPT1-AS1, PVT1 and DLG1-AS1. Furthermore, 1 synergistic, competitive module was identified. In this module, lncRNAs XIST and PVT1 were also the hubs in the synergistic, competing lncRNA module. Functional annotation demonstrated that 5 pathways were identified, including cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and mTOR signaling pathway. We have successfully identified several hubs (such as XIST and PVT1) and significant pathways (for instance, cytokine-cytokine receptor interaction, and neuroactive ligand-receptor interactions) for GBM via establishing the LMCN. These findings might offer potential biomarkers to early diagnose, and predict GBM prognosis in the future.
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Affiliation(s)
- Xiang-Yang Zan
- Department of Neurosurgery, Affiliated Traditional Chinese Medical Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830000, P.R. China
| | - Luo Li
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao, Shandong 266071, P.R. China
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11
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Fawzy MS, Ellawindy A, Hussein MH, Khashana MS, Darwish MK, Abdel-Daim MM, Toraih EA. Long noncoding RNA H19, and not microRNA miR-326, is over-expressed and predicts survival in glioblastoma. Biochem Cell Biol 2018; 96:832-839. [PMID: 30096248 DOI: 10.1139/bcb-2018-0122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Glioblastoma (GB) represents the most common malignant brain tumor, which, despite extensive research, remains of poor prognosis. The focus of recent studies of GB pathogenesis has shifted to the study of the role of noncoding RNAs (ncRNAs). In this study, we examined the expression levels of the microRNA miR-326 and the long ncRNA H19 (on which a miR-326 putative binding site was found by in-silico analysis) in brain tumor tissue from GB patients as compared to cancer-free brain tissue. Relative expression levels of miR-326 were not found to be significantly altered in GB patients. By comparison, H19 was consistently over-expressed in all GB patients (p < 0.001), and correlated with poorer overall survival (OS) and progression-free survival (PFS) (p = 0.026 and p = 0.045, respectively). At a cutoff value of 5.27, H19 up-regulation could predict OS in GB patients, with a 71.4% sensitivity and 59.6% specificity (p = 0.026). The current GB patients were clustered by the multivariate analysis into 4 groups based on miR-326 and H19 expression profiles, age at diagnosis, and PFS. Our data suggest a role for H19 in the pathogenesis of GB and could be a potential prognostic biomarker for GB.
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Affiliation(s)
- Manal S Fawzy
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.,Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar, Saudi Arabia
| | - Alia Ellawindy
- Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | | | | | - Marwa K Darwish
- Department of Chemistry, Biochemistry Branch, Faculty of Science, Suez University, Suez, Egypt
| | - Mohamed M Abdel-Daim
- Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Eman A Toraih
- Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.,Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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12
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Dianatpour A, Ghafouri-Fard S. Long Non Coding RNA Expression Intersecting Cancer and Spermatogenesis: A Systematic Review. Asian Pac J Cancer Prev 2017; 18:2601-2610. [PMID: 29072050 PMCID: PMC5747377 DOI: 10.22034/apjcp.2017.18.10.2601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Numerous similarities have been noted between gametogenic and tumorigenic programs in features
such as global hypomethylation, immune evasion, immortalization, meiosis induction, and migration. In addition, aberrant
expression of testis specific genes has been detected in various cancers which has led to categorization of these genes
as “cancer-testis genes”. Most of the examples identified in this category are protein encoding. However, recent studies
have revealed that non-coding RNAs, including long non coding RNAs (lncRNAs), may have essential regulatory
roles in telomere biology, chromatin dynamics, modulation of gene expression and genome structural organization.
All of these functions are implicated in both gametogenic and tumorigenic programs. Methods: In the present study,
we conducted a computerized search of the MEDLINE/PUBMED and Embase databases with the key words lncRNA,
gametogenesis, testis and cancer. Results: We found a number of lncRNAs with essential roles and notable expression
in both gametogenic and cancer tissues. Conclusions: Comparison between cancer tissues and gametogenic tissues
has shown that numerous lncRNAs are expressed in both, playing similar roles in processes modulated by signaling
pathways such as Wnt/β-catenin and PI3K/AKT/mTOR. Evaluation of expression patterns and functions of these
genes should pave the way to discovery of biomarkers for early detection, prognostic assessment and evaluation of
therapeutic responses in cancers.
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Affiliation(s)
- Ali Dianatpour
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran.
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13
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Reon BJ, Anaya J, Zhang Y, Mandell J, Purow B, Abounader R, Dutta A. Expression of lncRNAs in Low-Grade Gliomas and Glioblastoma Multiforme: An In Silico Analysis. PLoS Med 2016; 13:e1002192. [PMID: 27923049 PMCID: PMC5140055 DOI: 10.1371/journal.pmed.1002192] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/28/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Each year, over 16,000 patients die from malignant brain cancer in the US. Long noncoding RNAs (lncRNAs) have recently been shown to play critical roles in regulating neurogenesis and brain tumor progression. To better understand the role of lncRNAs in brain cancer, we performed a global analysis to identify and characterize all annotated and novel lncRNAs in both grade II and III gliomas as well as grade IV glioblastomas (glioblastoma multiforme [GBM]). METHODS AND FINDINGS We determined the expression of all lncRNAs in over 650 brain cancer and 70 normal brain tissue RNA sequencing datasets from The Cancer Genome Atlas (TCGA) and other publicly available datasets. We identified 611 induced and 677 repressed lncRNAs in glial tumors relative to normal brains. Hundreds of lncRNAs were specifically expressed in each of the three lower grade glioma (LGG) subtypes (IDH1/2 wt, IDH1/2 mut, and IDH1/2 mut 1p19q codeletion) and the four subtypes of GBMs (classical, mesenchymal, neural, and proneural). Overlap between the subtype-specific lncRNAs in GBMs and LGGs demonstrated similarities between mesenchymal GBMs and IDH1/2 wt LGGs, with 2-fold higher overlap than would be expected by random chance. Using a multivariate Cox regression survival model, we identified 584 and 282 lncRNAs that were associated with a poor and good prognosis, respectively, in GBM patients. We developed a survival algorithm for LGGs based on the expression of 64 lncRNAs that was associated with patient prognosis in a test set (hazard ratio [HR] = 2.168, 95% CI = 1.765-2.807, p < 0.001) and validation set (HR = 1.921, 95% CI = 1.333-2.767, p < 0.001) of patients from TCGA. The main limitations of this study are that further work is needed to investigate the clinical relevance of our findings, and that validation in an independent dataset is needed to determine the robustness of our survival algorithm. CONCLUSIONS This work identifies a panel of lncRNAs that appear to be prognostic in gliomas and provides a critical resource for future studies examining the role of lncRNAs in brain cancers.
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Affiliation(s)
- Brian J. Reon
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jordan Anaya
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ying Zhang
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - James Mandell
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Benjamin Purow
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - Roger Abounader
- Division of Neuro-Oncology, Neurology Department, University of Virginia Health System, Old Medical School, Charlottesville, Virginia, United States of America
| | - Anindya Dutta
- Department of Biochemistry, University of Virginia, Charlottesville, Virginia, United States of America
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14
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Lv D, Wang X, Dong J, Zhuang Y, Huang S, Ma B, Chen P, Li X, Zhang B, Li Z, Jin B. Systematic characterization of lncRNAs' cell-to-cell expression heterogeneity in glioblastoma cells. Oncotarget 2016; 7:18403-14. [PMID: 26918340 PMCID: PMC4951297 DOI: 10.18632/oncotarget.7580] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/11/2016] [Indexed: 12/30/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant adult brain tumor generally associated with high level of cellular heterogeneity and a dismal prognosis. Long noncoding RNAs (lncRNAs) are emerging as novel mediators of tumorigenesis. Recently developed single-cell RNA-seq provides an unprecedented way for analysis of the cell-to-cell variability in lncRNA expression profiles. Here we comprehensively examined the expression patterns of 2,003 lncRNAs in 380 cells from five primary GBMs and two glioblastoma stem-like cell (GSC) lines. Employing the self-organizing maps, we displayed the landscape of the lncRNA expression dynamics for individual cells. Further analyses revealed heterogeneous nature of lncRNA in abundance and splicing patterns. Moreover, lncRNA expression variation is also ubiquitously present in the established GSC lines composed of seemingly identical cells. Through comparative analysis of GSC and corresponding differentiated cell cultures, we defined a stemness signature by the set of 31 differentially expressed lncRNAs, which can disclose stemness gradients in five tumors. Additionally, based on known classifier lncRNAs for molecular subtypes, each tumor was found to comprise individual cells representing four subtypes. Our systematic characterization of lncRNA expression heterogeneity lays the foundation for future efforts to further understand the function of lncRNA, develop valuable biomarkers, and enhance knowledge of GBM biology.
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Affiliation(s)
- Dekang Lv
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Jun Dong
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Yan Zhuang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Shuyu Huang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Binbin Ma
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, 116023, Liaoning, P.R. China
| | - Puxiang Chen
- Department of Obstetrics and Gynecology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, P.R. China
| | - Xiaodong Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Bo Zhang
- Department of Neurosurgery, The Second Hospital of Dalian Medical University, Dalian, 116023, Liaoning, P.R. China
| | - Zhiguang Li
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, P.R. China
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15
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Long Non-Coding RNAs: The Key Players in Glioma Pathogenesis. Cancers (Basel) 2015; 7:1406-24. [PMID: 26230711 PMCID: PMC4586776 DOI: 10.3390/cancers7030843] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (LncRNAs) represent a novel class of RNAs with no functional protein-coding ability, yet it has become increasingly clear that interactions between lncRNAs with other molecules are responsible for important gene regulatory functions in various contexts. Given their relatively high expressions in the brain, lncRNAs are now thought to play important roles in normal brain development as well as diverse disease processes including gliomagenesis. Intriguingly, certain lncRNAs are closely associated with the initiation, differentiation, progression, recurrence and stem-like characteristics in glioma, and may therefore be exploited for the purposes of sub-classification, diagnosis and prognosis. LncRNAs may also serve as potential therapeutic targets as well as a novel biomarkers in the treatment of glioma. In this article, the functional aspects of lncRNAs, particularly within the central nervous system (CNS), will be briefly discussed, followed by highlights of the important roles of lncRNAs in mediating critical steps during glioma development. In addition, the key lncRNA players and their possible mechanistic pathways associated with gliomagenesis will be addressed.
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