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Wang O, Shi D, Li Y, Zhou X, Yan H, Yao Q. lncRNA pair as candidate diagnostic signature for colorectal cancer based on the within-sample relative expression levels. Front Oncol 2022; 12:912882. [PMID: 36059706 PMCID: PMC9428707 DOI: 10.3389/fonc.2022.912882] [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: 04/05/2022] [Accepted: 07/18/2022] [Indexed: 12/09/2022] Open
Abstract
Background Early diagnosis of colorectal cancer could significantly improve the prognosis and reduce mortality. However, indeterminate diagnosis is often met in pathology diagnosis in biopsy samples. Abnormal expression of long non-coding RNA (lncRNA) is associated with the initiation and progression of colorectal cancer. It is of great value and clinical significance to explore lncRNAs as candidate diagnostic biomarkers in colorectal cancer. Methods Based on the within-sample relative expression levels of lncRNA pairs, we identified a group of candidate diagnostic biomarkers for colorectal cancer. In addition, we validated it in independent datasets produced by different laboratories and different platforms. We also tested it in colorectal cancer tissue samples using quantitative real-time polymerase chain reaction (RT-qPCR). Results A biomarker consisting of six lncRNA pairs including nine lncRNAs was identified for the diagnosis of colorectal cancer. For a total of 950 cancer samples and 247 non-cancer samples, both of the sensitivity and specificity could achieve approximately 90%. For adenoma samples, the accuracy could achieve 73%. For normal tissues from inflammatory bowel disease patients, 93% (14/15) were correctly classified as non-cancer. Furthermore, the lncRNA pair biomarker showed excellent performance in all clinical stages; even in the early stage, the accuracy could achieve 87% and 82% in stage I and II. Meanwhile, the biomarker was also robust to the microsatellite instability status. More importantly, we measured the biomarker in 35 colorectal cancer and 30 cancer-adjacent tissue samples using quantitative real-time polymerase chain reaction (RT-qPCR). The accuracy could achieve 93.3% (70/75). Specially, even in early-stage tumors (I and II), the accuracy could also achieve 90.9% (30/33). The enrichment analysis revealed that these lncRNAs were involved in highly associated cancer pathways and immune-related pathways. Immune analysis showed that these marker lncRNAs were associated with multiple immune cells, implying that they might be involved in the regulation of immune cell functions in colorectal cancer. Most of the biomarker lncRNAs were also differentially expressed between the mutant group and wild-type group of colorectal cancer driver genes. Conclusion We identified and validated six lncRNA pairs including nine lncRNAs as a biomarker for assisting in the diagnosis of colorectal cancer.
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Affiliation(s)
- Ouxi Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Di Shi
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Yaqi Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- *Correspondence: Xiaoyan Zhou, ; Haidan Yan, ; Qianlan Yao,
| | - Haidan Yan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- *Correspondence: Xiaoyan Zhou, ; Haidan Yan, ; Qianlan Yao,
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- *Correspondence: Xiaoyan Zhou, ; Haidan Yan, ; Qianlan Yao,
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2
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Tian W, Chen K, Yan G, Han X, Liu Y, Zhang Q, Liu M. A Novel Prognostic Tool for Glioma Based on Enhancer RNA-Regulated Immune Genes. Front Cell Dev Biol 2022; 9:798445. [PMID: 35127714 PMCID: PMC8811171 DOI: 10.3389/fcell.2021.798445] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Gliomas are the most malignant tumors of the nervous system. Even though their survival outcome is closely affected by immune-related genes (IRGs) in the tumor microenvironment (TME), the corresponding regulatory mechanism remains poorly characterized. Methods: Specific enhancer RNAs (eRNAs) can be found in tumors, where they control downstream genes. The present study aimed to identify eRNA-regulated IRGs, evaluate their influence on the TME, and use them to construct a novel prognostic model for gliomas. Results: Thirteen target genes (ADCYAP1R1, BMP2, BMPR1A, CD4, DDX17, ELN, FGF13, MAPT, PDIA2, PSMB8, PTPN6, SEMA6C, and SSTR5) were identified and integrated into a comprehensive risk signature, which distinguished two risk subclasses. Discrepancies between these subclasses were compared to explore potential mechanisms attributed to eRNA-regulated genes, including immune cell infiltration, clinicopathological features, survival outcomes, and chemotherapeutic drug sensitivity. Furthermore, the risk signature was used to construct a prognostic tool that was evaluated by calibration curve, clinical utility, Harrell’s concordance index (0.87; 95% CI: 0.84–0.90), and time-dependent receiver operator characteristic curves (AUCs: 0.93 and 0.89 at 3 and 5 years, respectively). The strong reliability and robustness of the established prognostic tool were validated in another independent cohort. Finally, potential subtypes were explored in patients with grade III tumors. Conclusion: Overall, eRNAs were associated with immune-related dysfunctions in the TME. Targeting of IRGs regulated by eRNAs could improve immunotherapeutic/therapeutic outcomes.
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Affiliation(s)
- Wei Tian
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Kegong Chen
- Department of Cardio-Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guangcan Yan
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Xinhao Han
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qiuju Zhang
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
| | - Meina Liu
- Department of Biostatistics, School of Public Health, Harbin Medical University, Harbin, China
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3
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Zhou K, Jiang T, Liu Y, Zhao Z, Huang L, Li G. FXYD2 mRNA expression represents a new independent factor that affects survival of glioma patients and predicts chemosensitivity of patients to temozolomide. BMC Neurol 2021; 21:438. [PMID: 34753441 PMCID: PMC8576926 DOI: 10.1186/s12883-021-02476-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/29/2021] [Indexed: 08/30/2023] Open
Abstract
PURPOSE Glioma is the most common primary intracranial tumor. Owing to the poor prognosis associated with high-grade gliomas, there is an urgent need to identify biomarkers related to prognosis and treatment sensitivity. Here, we analyze the expression of FXYD2 mRNA in gliomas, and explore its clinical prognostic value and significance in this disease. METHODS Clinical features, FXYD2 mRNA expression levels, and survival data were analyzed for 516 glioma patients from the Chinese Glioma Genome Map Project, 481 from the cancer genome map datbase and 268 from the molecular braintumor database. The expression patterns for FXYD2 mRNA were compared using the chi-square test, and overall survival (OS) of glioma patients was evaluated according to FXYD2 mRNA expression levels. The factors affecting glioma survival were evaluated by Cox univariate and multivariate regression analysis. RESULTS FXYD2 mRNA expression was related to the grade of gliomas. The higher the level, the lower the expression. Meanwhile related to the pathological classification of gliomas. Oligodendroglioma, IDH-mutant and 1p/19q-codeleted was higher than Astrocytoma, IDH-mutant, higher than Glioblastoma, IDH-wildtype. Moreover, temozolomide (TMZ) chemotherapy was found to be an independent factor affecting survival in patients with high FXYD2 mRNA expression, but not in patients with low expression. CONCLUSION FXYD2 mRNA expression represents a new independent factor affecting the survival of glioma patients and may serve as an independent prognostic indicator to predict the sensitivity of gliomas to TMZ.
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Affiliation(s)
- Kaijia Zhou
- Neuro-Oncology Surgery Department of Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China. .,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China. .,Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, 100070, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China.
| | - Yanwei Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Lijie Huang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Guanzhang Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
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Yadav B, Pal S, Rubstov Y, Goel A, Garg M, Pavlyukov M, Pandey AK. LncRNAs associated with glioblastoma: From transcriptional noise to novel regulators with a promising role in therapeutics. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:728-742. [PMID: 33996255 PMCID: PMC8099481 DOI: 10.1016/j.omtn.2021.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glioblastoma multiforme (GBM) is the most widespread and aggressive subtype of glioma in adult patients. Numerous long non-coding RNAs (lncRNAs) are deregulated or differentially expressed in GBM. These lncRNAs possess unique regulatory functions in GBM cells, ranging from high invasion/migration to recurrence. This review outlines the present status of specific involvement of lncRNAs in GBM pathogenesis, with a focus on their association with key molecular and cellular regulatory mechanisms. Also, we highlighted the potential of different novel RNA-based strategies that may be beneficial for therapeutic purposes.
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Affiliation(s)
- Bhupender Yadav
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Sonali Pal
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Yury Rubstov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Vavilova Street 7, 117312 Moscow, Russian Federation
| | - Akul Goel
- La Canada High School, La Canada Flintridge, CA 91011, USA
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Uttar Pradesh, Sector 125, Noida 201313, India
| | - Marat Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Ulitsa Miklukho-Maklaya, 16/10, 117997 Moscow, Russian Federation
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
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5
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Yu K, Yang H, Lv QL, Wang LC, Tan ZL, Zhang Z, Ji YL, Lin QX, Chen JJ, He W, Chen Z, Shen XL. Construction of a competitive endogenous RNA network and analysis of potential regulatory axis targets in glioblastoma. Cancer Cell Int 2021; 21:102. [PMID: 33579282 PMCID: PMC7881621 DOI: 10.1186/s12935-021-01789-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common primary malignant brain tumor. Because of the limited understanding of its pathogenesis, the prognosis of glioblastoma remains poor. This study was conducted to explore potential competing endogenous RNA (ceRNA) network chains and biomarkers in glioblastoma by performing integrated bioinformatics analysis. METHODS Transcriptome expression data from The Cancer Genome Atlas database and Gene Expression Omnibus were analyzed to identify differentially expressed genes between glioblastoma and normal tissues. Biological pathways potentially associated with the differentially expressed genes were explored by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, and a protein-protein interaction network was established using the STRING database and Cytoscape. Survival analysis using Gene Expression Profiling Interactive Analysis was based on the Kaplan-Meier curve method. A ceRNA network chain was established using the intersection method to align data from four databases (miRTarBase, miRcode, TargetScan, and lncBace2.0), and expression differences and correlations were verified by quantitative reverse-transcription polymerase chain reaction analysis and by determining the Pearson correlation coefficient. Additionally, an MTS assay and the wound-healing and transwell assays were performed to evaluate the effects of complement C1s (C1S) on the viability and migration and invasion abilities of glioblastoma cells, respectively. RESULTS We detected 2842 differentially expressed (DE) mRNAs, 2577 DE long non-coding RNAs (lncRNAs), and 309 DE microRNAs (miRNAs) that were dysregulated in glioblastoma. The final ceRNA network consisted of six specific lncRNAs, four miRNAs, and four mRNAs. Among them, four DE mRNAs and one DE lncRNA were correlated with overall survival (p < 0.05). C1S was significantly correlated with overall survival (p= 0.015). In functional assays, knockdown of C1S inhibited the proliferation and invasion of glioblastoma cell lines. CONCLUSIONS We established four ceRNA networks that may influence the occurrence and development of glioblastoma. Among them, the MIR155HG/has-miR-129-5p/C1S axis is a potential marker and therapeutic target for glioblastoma. Knockdown of C1S inhibited the proliferation, migration, and invasion of glioblastoma cells. These findings clarify the role of the ceRNA regulatory network in glioblastoma and provide a foundation for further research.
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Affiliation(s)
- Kai Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Huan Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Qiao-Li Lv
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi, Nanchang, People's Republic of China
| | - Li-Chong Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zi-Long Tan
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Yu-Long Ji
- Jiangxi University of Traditional Chinese Medicine, Jiangxi, Nanchang, People's Republic of China
| | - Qian-Xia Lin
- Jiangxi University of Traditional Chinese Medicine, Jiangxi, Nanchang, People's Republic of China
| | - Jun-Jun Chen
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi, Nanchang, People's Republic of China
| | - Wei He
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zhen Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Xiao-Li Shen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China.
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6
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Di Cintio F, Dal Bo M, Baboci L, De Mattia E, Polano M, Toffoli G. The Molecular and Microenvironmental Landscape of Glioblastomas: Implications for the Novel Treatment Choices. Front Neurosci 2020; 14:603647. [PMID: 33324155 PMCID: PMC7724040 DOI: 10.3389/fnins.2020.603647] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma (GBM) is the most frequent and aggressive primary central nervous system tumor. Surgery followed by radiotherapy and chemotherapy with alkylating agents constitutes standard first-line treatment of GBM. Complete resection of the GBM tumors is generally not possible given its high invasive features. Although this combination therapy can prolong survival, the prognosis is still poor due to several factors including chemoresistance. In recent years, a comprehensive characterization of the GBM-associated molecular signature has been performed. This has allowed the possibility to introduce a more personalized therapeutic approach for GBM, in which novel targeted therapies, including those employing tyrosine kinase inhibitors (TKIs), could be employed. The GBM tumor microenvironment (TME) exerts a key role in GBM tumor progression, in particular by providing an immunosuppressive state with low numbers of tumor-infiltrating lymphocytes (TILs) and other immune effector cell types that contributes to tumor proliferation and growth. The use of immune checkpoint inhibitors (ICIs) has been successfully introduced in numerous advanced cancers as well as promising results have been shown for the use of these antibodies in untreated brain metastases from melanoma and from non-small cell lung carcinoma (NSCLC). Consequently, the use of PD-1/PD-L1 inhibitors has also been proposed in several clinical trials for the treatment of GBM. In the present review, we will outline the main GBM molecular and TME aspects providing also the grounds for novel targeted therapies and immunotherapies using ICIs for GBM.
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Affiliation(s)
- Federica Di Cintio
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Lorena Baboci
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
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7
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Zottel A, Šamec N, Videtič Paska A, Jovčevska I. Coding of Glioblastoma Progression and Therapy Resistance through Long Noncoding RNAs. Cancers (Basel) 2020; 12:cancers12071842. [PMID: 32650527 PMCID: PMC7409010 DOI: 10.3390/cancers12071842] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma is the most aggressive and lethal primary brain malignancy, with an average patient survival from diagnosis of 14 months. Glioblastoma also usually progresses as a more invasive phenotype after initial treatment. A major step forward in our understanding of the nature of glioblastoma was achieved with large-scale expression analysis. However, due to genomic complexity and heterogeneity, transcriptomics alone is not enough to define the glioblastoma “fingerprint”, so epigenetic mechanisms are being examined, including the noncoding genome. On the basis of their tissue specificity, long noncoding RNAs (lncRNAs) are being explored as new diagnostic and therapeutic targets. In addition, growing evidence indicates that lncRNAs have various roles in resistance to glioblastoma therapies (e.g., MALAT1, H19) and in glioblastoma progression (e.g., CRNDE, HOTAIRM1, ASLNC22381, ASLNC20819). Investigations have also focused on the prognostic value of lncRNAs, as well as the definition of the molecular signatures of glioma, to provide more precise tumor classification. This review discusses the potential that lncRNAs hold for the development of novel diagnostic and, hopefully, therapeutic targets that can contribute to prolonged survival and improved quality of life for patients with glioblastoma.
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8
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Janaki Ramaiah M, Divyapriya K, Kartik Kumar S, Rajesh YBRD. Drug-induced modifications and modulations of microRNAs and long non-coding RNAs for future therapy against Glioblastoma Multiforme. Gene 2019; 723:144126. [PMID: 31589963 DOI: 10.1016/j.gene.2019.144126] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs are known to participate in cancer initiation, progression, and metastasis by regulating the status of chromatin epigenetics and gene expression. Although these non-coding RNAs do not possess defined protein-coding potential, they are involved in the expression and stability of messenger RNA (mRNA). The length of microRNAs (miRs) ranges between 20 and 22 nt, whereas, long non-coding RNAs (lncRNAs) length ranges between 200 nt to 1 Kb. In the case of circular RNAs (circRNAs), the size varies depending upon the length of the exon from where they were derived. Epigenetic regulations of miR and lncRNA genes will influence the gene expression by modulating histone acetylation and methylation patterns. Especially, lncRNAs will act as a scaffold for various epigenetic proteins, such as EZH2 and LSD1, and influence the chromatin epigenetic state at various genomic loci involved at silencing. Thus investigations on the expression of lncRNAs and designing drugs to modulate the expression of these genes will have a profound impact on future therapeutics against cancers such as Glioblastoma Multiforme (GBM) and also against various other diseases. With the recent advancements in genome-wide transcriptomic studies, scientists are focused on the non-coding RNAs and their regulations on various cellular processes involved in GBM and on other types of cancer as well as trying to understand possible epigenetic modulations that help in generating promising therapeutics for the future generations. In this review, the involvement of epigenetic proteins, enzymes that change chromatin architecture and epigenetic landscape and new roles of lncRNAs that are involved in GBM progression are elaborately discussed.
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Affiliation(s)
- M Janaki Ramaiah
- Laboratory of Functional Genomics and Disease Biology, School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India.
| | - Karthikeyan Divyapriya
- Laboratory of Functional Genomics and Disease Biology, School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India
| | - Sarwareddy Kartik Kumar
- Laboratory of Functional Genomics and Disease Biology, School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India
| | - Y B R D Rajesh
- Organic Synthesis and Catalysis Laboratory, School of Chemical and Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur 613401, Tamil Nadu, India
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9
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Pop S, Enciu AM, Necula LG, Tanase C. Long non-coding RNAs in brain tumours: Focus on recent epigenetic findings in glioma. J Cell Mol Med 2018; 22:4597-4610. [PMID: 30117678 PMCID: PMC6156469 DOI: 10.1111/jcmm.13781] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/07/2018] [Indexed: 02/07/2023] Open
Abstract
Glioma biology is a major focus in tumour research, primarily due to the aggressiveness and high mortality rate of its most aggressive form, glioblastoma. Progress in understanding the molecular mechanisms behind poor prognosis of glioblastoma, regardless of treatment approaches, has changed the classification of brain tumours after nearly 100 years of relying on anatomopathological criteria. Expanding knowledge in genetic, epigenetic and translational medicine is also beginning to contribute to further elucidating molecular dysregulation in glioma. Long non‐coding RNAs (lncRNAs) and their main representatives, large intergenic non‐coding RNAs (lincRNAs), have recently been under scrutiny in glioma research, revealing novel mechanisms of pathogenesis and reinforcing others. Among those confirmed was the reactivation of events significant for foetal brain development and neuronal commitment. Novel mechanisms of tumour suppression and activation of stem‐like behaviour in tumour cells have also been examined. Interestingly, these processes involve lncRNAs that are present both during normal brain development and in brain malignancies and their reactivation might be explained by epigenetic mechanisms, which we discuss in detail in the present review. In addition, the review discusses the lncRNAs‐induced changes, as well as epigenetic changes that are consequential for tumour formation, affecting, in turn, the expression of various types of lncRNAs.
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Affiliation(s)
- Sevinci Pop
- "Victor Babes" National Institute of Pathology, Bucharest, Romania
| | - Ana-Maria Enciu
- "Victor Babes" National Institute of Pathology, Bucharest, Romania.,"Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Laura G Necula
- "Victor Babes" National Institute of Pathology, Bucharest, Romania.,"Stefan N. Nicolau" National Institute of Virology, Bucharest, Romania.,Faculty of Medicine, "Titu Maiorescu" University, Bucharest, Romania
| | - Cristiana Tanase
- "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Faculty of Medicine, "Titu Maiorescu" University, Bucharest, Romania
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