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Liu Y, Yuan H, Fan J, Wang H, Xie H, Wan J, Hu X, Zhou J, Liu L. The pathogenesis mechanism and potential clinical value of lncRNA in gliomas. Discov Oncol 2024; 15:266. [PMID: 38967893 PMCID: PMC11226588 DOI: 10.1007/s12672-024-01144-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024] Open
Abstract
Glioma is the most common malignant tumor in the central nervous system, and its unique pathogenesis often leads to poor treatment outcomes and prognosis. In 2021, the World Health Organization (WHO) divided gliomas into five categories based on their histological characteristics and molecular changes. Non-coding RNA is a type of RNA that does not encode proteins but can exert biological functions at the RNA level, and long non-coding RNA (lncRNA) is a type of non-coding RNA with a length exceeding 200 nt. It is controlled by various transcription factors and plays an indispensable role in the regulatory processes in various cells. Numerous studies have confirmed that the dysregulation of lncRNA is critical in the pathogenesis, progression, and malignancy of gliomas. Therefore, this article reviews the proliferation, apoptosis, invasion, migration, angiogenesis, immune regulation, glycolysis, stemness, and drug resistance changes caused by the dysregulation of lncRNA in gliomas, and summarizes their potential clinical significance in gliomas.
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Affiliation(s)
- Yuan Liu
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Hui Yuan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - JingJia Fan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Han Wang
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - HuiYu Xie
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - JunFeng Wan
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - XueYing Hu
- Department of Clinical Medicine, School of Clinical Medical, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jie Zhou
- Dept Neurosurg, Affiliated Hosp, Southwest Med Univ, Luzhou, 646000, People's Republic of China.
| | - Liang Liu
- Dept Neurosurg, Affiliated Hosp, Southwest Med Univ, Luzhou, 646000, People's Republic of China.
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Kumar K, Dubey V, Zaidi SS, Tripathi M, Siraj F, Sharma MC, Chandra PS, Doddamani R, Dixit AB, Banerjee J. RNA Sequencing of Intraoperative Peritumoral Tissues Reveals Potential Pathways Involved in Glioma-Related Seizures. J Mol Neurosci 2023; 73:437-447. [PMID: 37268865 DOI: 10.1007/s12031-023-02125-y] [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: 04/13/2023] [Accepted: 05/18/2023] [Indexed: 06/04/2023]
Abstract
Tumor-induced changes in the peritumoral neocortex play a crucial role in generation of seizures. This study aimed to investigate the molecular mechanisms potentially involved in peritumoral epilepsy in low-grade gliomas (LGGs). Intraoperative peritumoral brain tissues resected from LGG patients with seizures (pGRS) or without seizures (pGNS) were used for RNA sequencing (RNA-seq). Comparative transcriptomics was performed to identify differentially expressed genes (DEGs) in pGRS compared to pGNS using deseq2 and edgeR packages (R). Gene set enrichment analysis (GSEA) using Gene Ontology terms and Kyoto Encyclopedia of Genes & Genomes (KEGG) pathways was performed using the clusterProfiler package (R). The expression of key genes was validated at the transcript and protein levels in the peritumoral region using real-time PCR and immunohistochemistry, respectively. A total of 1073 DEGs were identified in pGRS compared to pGNS, of which 559 genes were upregulated and 514 genes were downregulated (log2 fold-change ≥ 2, padj < 0.001). The DEGs in pGRS were highly enriched in the "Glutamatergic Synapse" and "Spliceosome" pathways, with increased expression of GRIN2A (NR2A), GRIN2B (NR2B), GRIA1 (GLUR1), GRIA3 (GLUR3), GRM5, CACNA1C, CACNA1A, and ITPR2. Moreover, increased immunoreactivity was observed for NR2A, NR2B, and GLUR1 proteins in the peritumoral tissues of GRS. These findings suggest that altered glutamatergic signaling and perturbed Ca2+ homeostasis may be potential causes of peritumoral epilepsy in gliomas. This explorative study identifies important genes/pathways that merit further characterization for their potential involvement in glioma-related seizures.
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Affiliation(s)
| | - Vivek Dubey
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India
| | - Syeda S Zaidi
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India
| | | | - Fouzia Siraj
- ICMR-National Institute of Pathology, New Delhi, India
| | | | | | | | - Aparna Banerjee Dixit
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
| | - Jyotirmoy Banerjee
- Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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Guo J, Xiao D, Lin Z, Sui C. The long non-coding RNA PANDAR regulates cell proliferation and epithelial-to-mesenchymal transition in glioma. Histol Histopathol 2023; 38:199-208. [PMID: 36073766 DOI: 10.14670/hh-18-511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Glioma is one of the most aggressive intracranial tumors in the central nervous system. The long non-coding RNA P21 associated ncRNA DNA damage activated (PANDAR) has been reported to be an oncogene or tumor suppressor in several cancers. However, the prognostic value and biological function of PANDAR in glioma have not been described. Here, we report that expression of PANDAR is significantly up-regulated in glioma tissues and cell lines. PANDAR expression was correlated with tumor size (p=0.044) and World Health Organization (WHO) grades (p=0.005), as shown by chi-squared test. Moreover, significant upregulation of PANDAR was found to correlate with poor prognosis in glioma, as shown using Kaplan-Meier method and Cox multivariate survival analysis. Furthermore, PANDAR knockdown suppressed cell proliferation, G1/S transition, migration and invasion, and promoted apoptosis in glioma cell lines (U251 and U87). PANDAR knockdown decreased expression of CDK4, Bcl-2, N-cadherin and Vimentin, but increased E-cadherin expression in glioma cells. In conclusion, our data suggest PANDAR as a potential prognostic biomarker and therapeutic candidate for glioma.
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Affiliation(s)
- Jianfeng Guo
- Department of Neurosurgy, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Deyong Xiao
- Department of Neurosurgy, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Zhijing Lin
- Department of Neurosurgy, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Chengzhi Sui
- Department of Rehabilitation, The First Affiliated Hospital of Xiamen University, Xiamen, China.
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Ghafouri-Fard S, Noroozi R, Brand S, Hussen BM, Eghtedarian R, Taheri M, Ebrahimzadeh K. Emerging Role of Non-coding RNAs in Autism Spectrum Disorder. J Mol Neurosci 2021; 72:201-216. [PMID: 34767189 DOI: 10.1007/s12031-021-01934-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023]
Abstract
Autism spectrum disorders (ASD) embrace a diverse set of neurodevelopmental diseases with a multifaceted genetic basis. Non-coding RNAs (ncRNAs) are among putative loci with critical participation in the development of ASD. Expression of some lncRNAs, namely RP11-466P24.2, SYP-AS1, STXBP5-AS1, and IFNG-AS1 has been decreased in ASD, while AK128569, CTD-2516F10.2, MSNP1AS, RPS10P2-AS1, LINC00693, LINC00689, NEAT1, TUG1, and Shank2-AS lncRNAs have been over-expressed in ASD. Expression of several miRNAs which are implicated in the immunological developmental, immune responses, and protein synthesis as well as those participating in the regulation of PI3K/Akt/mTOR and EGFR signaling pathways is dysregulated in the context of ASD. In the present article, we describe investigations which appraised the role of lncRNAs, miRNAs, and circRNAs in the pathobiology of ASD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Serge Brand
- Psychiatric Clinics, Center for Affective, Stress and Sleep Disorders, University of Basel, Basel, Switzerland
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Reyhane Eghtedarian
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Institute of Human Genetics, Jena University Hospital, 07740, Jena, Germany.
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wei Y, Zhou K, Wang C, Du X, Xiao Q, Chen C. Adsorption of miR-218 by lncRNA HOTAIR regulates PDE7A and affects glioma cell proliferation, invasion, and apoptosis. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:2973-2983. [PMID: 33425098 PMCID: PMC7791379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/07/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVE To evaluate the role of targeted adsorption of miR-218 by long-chain non-coding RNAHOTAIR to regulate PDE7A on glioma cell proliferation, invasion, and apoptosis. METHODS The expressions of lncRNA HOTAIR, miR-218, and PDE7A in glioma tissues and normal parcancer tissues, NHA and glioma cell lines were determined, and correlations among the three genes were analyzed. The subcellular localization of lncRNA HOTAIR was determined by fluorescent in situ hybridization. Dual-luciferase reporter assay was used to validate the targeted relationship between lncRNA HOTAIR/miR-218/PDE7A. Glioma cells were grouped to receive intervention of lncRNA HOTAIR or miR-218. MTT, transwell, and flow cytometry were performed to determine the proliferation, invasion, and apoptosis of cells. RESULTS Compared with the normal tissues and cells, the expression of lncRNA HOTAIR was increased while miR-218 was suppressed in glioma tissues samples and cells (all P<0.05). Inhibition of lncRNA HOTAIR expression, was able to induce apoptosis and suppress the proliferation and invasion of cells (all P<0.05). LncRNA HOTAIR is mainly localized in the cytoplasm, and is able to adsorb miR-218 as ceRNA. The effect of knockdown of HOTAIR on glioma cells could be partially rescued by miR-218 inhibitor. The expression of PDE7A was enhanced in glioma tissues and cells compared to normal tissues and cells (all P<0.05), which positively correlated with the expression of HOTAIR (r=0.546, P<0.05) and negatively correlated with the expression of miR-218 (r=0.363, P<0.05). The targeted relationship between miR-218 and PDE7A was validated: Overexpression of miR-218 was able to suppress the proliferation and invasion of glioma cells and restrain apoptosis compared to the miR-NC group (all P<0.05). The effect of miR-218 on glioma cells could be partially rescued by PDE7A. CONCLUSION lncRNA HOTAIR can adsorb miR-218 to regulate expression of PDE7A and promote the malignant biologic behavior of glioma cells.
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Affiliation(s)
- Yigong Wei
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
| | - Kun Zhou
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
| | - Cheng Wang
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
| | - Xiaolin Du
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
| | - Qing Xiao
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
| | - Changyi Chen
- Department of Neurosurgery, The Second People's Hospital of Guiyang (Jinyang Hospital) Guiyang, Guizhou Province, China
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Ahn JW, Park Y, Kang SJ, Hwang SJ, Cho KG, Lim J, Kwack K. CeRNA Network Analysis Representing Characteristics of Different Tumor Environments Based on 1p/19q Codeletion in Oligodendrogliomas. Cancers (Basel) 2020; 12:cancers12092543. [PMID: 32906679 PMCID: PMC7564449 DOI: 10.3390/cancers12092543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS). The long non-coding RNAs (lncRNAs) protects the mRNA from degradation by binding with the same miRNA by acting as a competitive endogenous RNA (ceRNA). Recently, although there is an increasing interest in lncRNAs on glioma studies, however, studies regarding their effects on OD and the 1p/19q codeletion remain limited. In our study, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. We constructed 16 coding RNA–miRNA–lncRNA networks and the ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, our results can provide insights into the possibility in the different tumor microenvironments and OS following 1p/19q codeletion through changes in the ceRNA network. Abstract Oligodendroglioma (OD) is a subtype of glioma occurring in the central nervous system. The 1p/19q codeletion is a prognostic marker of OD with an isocitrate dehydrogenase (IDH) mutation and is associated with a clinically favorable overall survival (OS); however, the exact underlying mechanism remains unclear. Long non-coding RNAs (lncRNAs) have recently been suggested to regulate carcinogenesis and prognosis in cancer patients. Here, we performed in silico analyses using low-grade gliomas from datasets obtained from The Cancer Genome Atlas to investigate the effects of ceRNA with 1p/19q codeletion on ODs. Thus, we selected modules of differentially expressed genes that were closely related to 1p/19q codeletion traits using weighted gene co-expression network analysis and constructed 16 coding RNA–miRNA–lncRNA networks. The ceRNA network participated in ion channel activity, insulin secretion, and collagen network and extracellular matrix (ECM) changes. In conclusion, ceRNAs with a 1p/19q codeletion can create different tumor microenvironments via potassium ion channels and ECM composition changes; furthermore, differences in OS may occur. Moreover, if extrapolated to gliomas, our results can provide insights into the consequences of identical gene expression, indicating the possibility of tracking different biological processes in different subtypes of glioma.
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Affiliation(s)
- Ju Won Ahn
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - YoungJoon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - Su Jung Kang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
| | - So Jung Hwang
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - Kyung Gi Cho
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
| | - JaeJoon Lim
- Department of Neurosurgery, Bundang CHA Medical Center, CHA University School of Medicine, Seongnam 13496, Korea; (S.J.H.); (K.G.C.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
| | - KyuBum Kwack
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea; (J.W.A.); (Y.P.); (S.J.K.)
- Correspondence: (J.L.); (K.K.); Tel.: +82-031-780-5688 (J.L.); +82-031-725-7141 (K.K.)
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