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Chen S, Li L, Xu W, Xie N, Xu H, Zhou Y, Zou Y, Yi K, Zhang Z. CircMIB1 inhibits glioma development and progression through a competing endogenous RNA interaction network. Front Mol Biosci 2024; 11:1513919. [PMID: 39698112 PMCID: PMC11652353 DOI: 10.3389/fmolb.2024.1513919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 11/13/2024] [Indexed: 12/20/2024] Open
Abstract
Introduction The critical role of circular RNAs as non-coding RNAs in glioma has been extensively investigated. Therefore, we aimed to explore the role and potential molecular mechanisms of circRNA-mind bomb homolog 1 (circMIB1) in gliomas. Methods RNA sequencing was used to analyze the expression profiles of circRNAs in glioma tissues and normal brain tissues. Quantitative real-time polymerase chain reaction was implemented to examine the levels of circMIB1 in glioma cells and tissues. The circMIB1 was identified as a cyclic RNA molecule by DNA nucleic acid electrophoresis and ribonuclease R assay. The relationship between circMIB1 expression and the prognosis of glioma patients and its potential as a biomarker were analysed using Kaplan-Meier, Receiver operating characteristic curves, and Principal component analysis. Bioinformatics analysis predicted the miRNAs that bind to circMIB1 and their downstream targets, and analysed the functions of these genes. Results Firstly, a novel circRNA molecule termed circMIB1 was identified and validated by RNA sequencing. The expression of circMIB1 was significantly downregulated in glioma cells and tissues, and was closely associated with the tumor grade and survival prognosis of patients with glioma. Hence, it may be useful as a biomarker for glioma. Secondly, it was predicted that circMIB1 binds to hsa-miR-1290 based on bioinformatics analysis, which was significantly upregulated in glioma cells and tissues, and correlated with the tumor grade and overall survival of patients. Thirdly, through a series of bioinformatics analyses identified six genes downstream of hsa-miR-1290 that were significantly associated with glioma expression and prognosis, these genes are associated with cell cycle, cell necrosis and cell circadian rhythms. Discussion CircMIB1 may play a role in inhibiting glioma development through the hsa-miR-1290 competitive endogenous RNA interaction network, these findings provide new ideas and directions for the diagnosis and treatment of glioma.
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Affiliation(s)
- Simin Chen
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Longping Li
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Wei Xu
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Nanjiao Xie
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Huiting Xu
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Yongjun Zhou
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Ying Zou
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Kai Yi
- Department of Clinical Laboratory, Yiyang Central Hospital, Yiyang, Hunan, China
| | - Zuping Zhang
- School of Xiangya Basic Medical Science, Central South University, Changsha, Hunan, China
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Zhang B, Zhang H, Wang Z, Cao H, Zhang N, Dai Z, Liang X, Peng Y, Wen J, Zhang X, Zhang L, Luo P, Zhang J, Liu Z, Cheng Q, Peng R. The regulatory role and clinical application prospects of circRNA in the occurrence and development of CNS tumors. CNS Neurosci Ther 2024; 30:e14500. [PMID: 37953502 PMCID: PMC11017455 DOI: 10.1111/cns.14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/20/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Central nervous system (CNS) tumors originate from the spinal cord or brain. The study showed that even with aggressive treatment, malignant CNS tumors have high mortality rates. However, CNS tumor risk factors and molecular mechanisms have not been verified. Due to the reasons mentioned above, diagnosis and treatment of CNS tumors in clinical practice are currently fraught with difficulties. Circular RNAs (circRNAs), single-stranded ncRNAs with covalently closed continuous structures, are essential to CNS tumor development. Growing evidence has proved the numeral critical biological functions of circRNAs for disease progression: sponging to miRNAs, regulating gene transcription and splicing, interacting with proteins, encoding proteins/peptides, and expressing in exosomes. AIMS This review aims to summarize current progress regarding the molecular mechanism of circRNA in CNS tumors and to explore the possibilities of clinical application based on circRNA in CNS tumors. METHODS We have summarized studies of circRNA in CNS tumors in Pubmed. RESULTS This review summarized their connection with CNS tumors and their functions, biogenesis, and biological properties. Furthermore, we introduced current advances in clinical RNA-related technologies. Then we discussed the diagnostic and therapeutic potential (especially for immunotherapy, chemotherapy, and radiotherapy) of circRNA in CNS tumors in the context of the recent advanced research and application of RNA in clinics. CONCLUSIONS CircRNA are increasingly proven to participate in decveloping CNS tumors. An in-depth study of the causal mechanisms of circRNAs in CNS tomor progression will ultimately advance their implementation in the clinic and developing new strategies for preventing and treating CNS tumors.
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Affiliation(s)
- Bo Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Hao Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- Department of Neurosurgery, The Second Affiliated HospitalChongqing Medical UniversityChongqingChina
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- MRC Centre for Regenerative Medicine, Institute for Regeneration and RepairUniversity of EdinburghEdinburghUK
| | - Hui Cao
- Department of Psychiatry, The School of Clinical MedicineHunan University of Chinese MedicineChangshaChina
| | - Nan Zhang
- College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xisong Liang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Yun Peng
- Teaching and Research Section of Clinical NursingXiangya Hospital of Central South UniversityChangshaChina
- Department of Geriatrics, Xiangya HospitalCentral South UniversityChangshaChina
| | - Jie Wen
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Xun Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Renjun Peng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
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Zheng X, Toyama T, Siu S, Kaneko T, Sugiura H, Yamashita S, Shimoda Y, Kanamori M, Arisawa K, Endo H, Saito Y. Selenoprotein P expression in glioblastoma as a regulator of ferroptosis sensitivity: preservation of GPX4 via the cycling-selenium storage. Sci Rep 2024; 14:682. [PMID: 38182643 PMCID: PMC10770386 DOI: 10.1038/s41598-024-51259-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
Glioblastoma (GBM) is one of the most aggressive and deadly brain tumors; however, its current therapeutic strategies are limited. Selenoprotein P (SeP; SELENOP, encoded by the SELENOP gene) is a unique selenium-containing protein that exhibits high expression levels in astroglia. SeP is thought to be associated with ferroptosis sensitivity through the induction of glutathione peroxidase 4 (GPX4) via selenium supplementation. In this study, to elucidate the role of SeP in GBM, we analyzed its expression in GBM patients and found that SeP expression levels were significantly higher when compared to healthy subjects. Knock down of SeP in cultured GBM cells resulted in a decrease in GPX1 and GPX4 protein levels. Under the same conditions, cell death caused by RSL3, a ferroptosis inducer, was enhanced, however this enhancement was canceled by supplementation of selenite. These results indicate that SeP expression contributes to preserving GPX and selenium levels in an autocrine/paracrine manner, i.e., SeP regulates a dynamic cycling-selenium storage system in GBM. We also confirmed the role of SeP expression in ferroptosis sensitivity using patient-derived primary GBM cells. These findings indicate that expression of SeP in GBM can be a significant therapeutic target to overcome anticancer drug resistance.
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Affiliation(s)
- Xi Zheng
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takashi Toyama
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
| | - Stephanie Siu
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takayuki Kaneko
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hikari Sugiura
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shota Yamashita
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, 2-1 Seiryo Aoba-ku, Sendai, 980-0872, Japan
| | - Yoshiteru Shimoda
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, 2-1 Seiryo Aoba-ku, Sendai, 980-0872, Japan
| | - Masayuki Kanamori
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, 2-1 Seiryo Aoba-ku, Sendai, 980-0872, Japan
| | - Kotoko Arisawa
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hidenori Endo
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, 2-1 Seiryo Aoba-ku, Sendai, 980-0872, Japan
| | - Yoshiro Saito
- Laboratory of Molecular Biology and Metabolism, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.
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Guiducci L, Cabiati M, Santocchi E, Prosperi M, Morales MA, Muratori F, Randazzo E, Federico G, Calderoni S, Del Ry S. Expression of miRNAs in Pre-Schoolers with Autism Spectrum Disorders Compared with Typically Developing Peers and Its Effects after Probiotic Supplementation. J Clin Med 2023; 12:7162. [PMID: 38002774 PMCID: PMC10672692 DOI: 10.3390/jcm12227162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Alteration of the microbiota-gut-brain axis has been recently recognized as a possible contributor to the physiopathology of autism spectrum disorder (ASD). In this context, microRNA (miRNAs) dysfunction, implicated both in several neuropathological conditions including ASD and in different gastrointestinal disorders (GIDs), could represent an important modulating factor. In this contextual framework, we studied the transcriptional profile of specific circulating miRNAs associated with both ASD (miR-197-5p, miR-424-5p, miR-500a-5p, miR-664a-5p) and GID (miR-21-5p, miR-320a-5p, miR-31-5p, miR-223-5p) in a group of pre-schoolers with ASD and in typically developing (TD) peers. In the ASD group, we also assessed the same miRNAs after a 6-month supplementation with probiotics and their correlation with plasma levels of zonulin and lactoferrin. At baseline, the expression of miRNAs involved in ASD were significantly reduced in ASD pre-schoolers vs. TD controls. Regarding the miRNAs involved in GID, the expression levels of miR-320-5p, miR-31-5p, and miR-223-5p were significantly higher in ASD than in TD subjects, whereas miR-21-5p showed significantly reduced expression in the ASD group vs. TD group. Supplementation with probiotics did not significantly change the expression of miRNAs in the ASD population. We found a significative negative correlation between zonulin and miR-197-5p and miR-21-5p at baseline, as well as between lactoferrin and miR-223-5p after 6 months of probiotic supplementation. Our study confirms the presence of an altered profile of the miRNAs investigated in ASD versus TD peers that was not modified by supplementation with probiotics.
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Affiliation(s)
- Letizia Guiducci
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Manuela Cabiati
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Elisa Santocchi
- UFSMIA Zona Valle del Serchio, Azienda USL Toscana Nord Ovest, 55032 Castelnuovo di Garfagnana, Italy;
| | - Margherita Prosperi
- UFSMIA Valdera-Alta Val di Cecina, Azienda USL Toscana Nord Ovest, 56128 Pisa, Italy;
| | - Maria Aurora Morales
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
| | - Filippo Muratori
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
| | - Emioli Randazzo
- Unit of Pediatric Endocrinology and Diabetes, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (E.R.); (G.F.)
| | - Giovanni Federico
- Unit of Pediatric Endocrinology and Diabetes, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (E.R.); (G.F.)
| | - Sara Calderoni
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, 56128 Pisa, Italy;
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Silvia Del Ry
- CNR, Institute of Clinical Physiology, 56124 Pisa, Italy; (L.G.); (M.C.); (M.A.M.); (S.D.R.)
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Gan T, Yu J, He J. miRNA, lncRNA and circRNA: targeted molecules with therapeutic promises in Mycoplasma pneumoniae infection. Arch Microbiol 2023; 205:293. [PMID: 37477725 DOI: 10.1007/s00203-023-03636-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/02/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Mycoplasma pneumoniae (MP) is primarily recognized as a respiratory pathogen that causes community-acquired pneumonia, which can lead to acute upper and lower airway inflammation and extrapulmonary syndrome. Refractory pneumonia caused by MP can cause severe complications and even be life-threatening, particularly in infants and the elderly. It is well-known that non-coding RNAs (ncRNAs) represented by miRNAs, lncRNAs and circRNAs have been manifested to be widely involved in the regulation of gene expression. Growing evidence indicates that these ncRNAs have distinct differentiated expression in MP infection and affect multiple biological processes, playing an indispensable role in the initiation and promotion of MP infection. However, the epigenetic mechanisms involved in the development of MP infection remain unclear. This article reviews the mechanisms by which miRNAs, lncRNAs, and circRNAs mediate MP infection, such as inflammatory responses, apoptosis and pulmonary fibrosis. Focusing on miRNAs, lncRNAs and circRNAs associated with MP infection could provide new insights into this disease's early diagnosis and therapeutic approaches.
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Affiliation(s)
- Tian Gan
- The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jianwei Yu
- The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jun He
- The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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6
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Niu X, Pan Q, Zhang Q, Wang X, Liu Y, Li Y, Zhang Y, Yang Y, Mao Q. Weighted correlation network analysis identifies multiple susceptibility loci for low-grade glioma. Cancer Med 2023; 12:6379-6387. [PMID: 36305248 PMCID: PMC10028094 DOI: 10.1002/cam4.5368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The current molecular classifications cannot completely explain the polarized malignant biological behavior of low-grade gliomas (LGGs), especially for tumor recurrence. Therefore, we tried to identify suspicious hub genes related to tumor recurrence in LGGs. METHODS In this study, we constructed a gene-miRNA-lncRNA co-expression network for LGGs by a weighted gene co-expression network analysis (WGCNA). GDCRNATools and the WGCNA R package were mainly used in data analysis. RESULTS Sequencing data from 502 LGG patients were analyzed in this study. Compared with recurrent glioma tissues, we identified 774 differentially expressed (DE) mRNAs, 49 DE miRNAs, and 129 DE lncRNAs in primary LGGs and ultimately determined that the expression of MKLN1 was related to tumor recurrence in LGG. CONCLUSION This study identified the potential biomarkers for the pathogenesis and recurrence of LGGs and proposed that MKLN1 could be a potential therapeutic target.
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Affiliation(s)
- Xiaodong Niu
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qi Pan
- Department of Dermatology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Qianwen Zhang
- Department of out-patient, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanhui Liu
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Li
- Department of Anesthesia, West China Hospital, Sichuan University, Chengdu, China
| | - Yuekang Zhang
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Mao
- Department of Neurosurgery and West China Glioma Center, West China Hospital, Sichuan University, Chengdu, China
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Meta-Analysis of RNA-Seq Datasets Identifies Novel Players in Glioblastoma. Cancers (Basel) 2022; 14:cancers14235788. [PMID: 36497269 PMCID: PMC9737249 DOI: 10.3390/cancers14235788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Glioblastoma is a devastating grade IV glioma with poor prognosis. Identification of predictive molecular biomarkers of disease progression would substantially contribute to better disease management. In the current study, we performed a meta-analysis of different RNA-seq datasets to identify differentially expressed protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs). This meta-analysis aimed to improve power and reproducibility of the individual studies while identifying overlapping disease-relevant pathways. We supplemented the meta-analysis with small RNA-seq on glioblastoma tissue samples to provide an overall transcriptomic view of glioblastoma. Co-expression correlation of filtered differentially expressed PCGs and lncRNAs identified a functionally relevant sub-cluster containing DANCR and SNHG6, with two novel lncRNAs and two novel PCGs. Small RNA-seq of glioblastoma tissues identified five differentially expressed microRNAs of which three interacted with the functionally relevant sub-cluster. Pathway analysis of this sub-cluster identified several glioblastoma-linked pathways, which were also previously associated with the novel cell death pathway, ferroptosis. In conclusion, the current meta-analysis strengthens evidence of an overarching involvement of ferroptosis in glioblastoma pathogenesis and also suggests some candidates for further analyses.
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Liu J, Li H, Zhang L, Song Y, He J, Xu W, Ma C, Ren Y, Liu H. Integrative Investigation of Root-Related mRNAs, lncRNAs and circRNAs of “Muscat Hamburg” (Vitis vinifera L.) Grapevine in Response to Root Restriction through Transcriptomic Analyses. Genes (Basel) 2022; 13:genes13091547. [PMID: 36140715 PMCID: PMC9498474 DOI: 10.3390/genes13091547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/21/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
Root restriction is a physical and ecological cultivation mode which restricts plant roots into a limited container to regulate vegetative and reproduction growth by reshaping root architecture. However, little is known about related molecular mechanisms. To uncover the root-related regulatory network of endogenous RNAs under root restriction cultivation (referred to RR), transcriptome-wide analyses of mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) involved in root development were performed. During root development, RR treatment had a positive effect on root weight, typically, young roots were significantly higher than conventional cultivation (referred to NR) treatment, suggesting that root architecture reconstruction under RR was attributed to the vigorous induction into lateral roots. Furthermore, a total of 26,588 mRNAs, 1971 lncRNAs, and 2615 circRNAs were identified in root of annual “Muscat Hamburg” grapevine by the transcriptomic analyses. The expression profile of mRNAs, lncRNAs and circRNA were further confirmed by the quantitative real-time PCR (RT-qPCR). Gene ontology enrichment analysis showed that a majority of the differentially expressed mRNAs, lncRNAs and circRNAs were enriched into the categories of cellular process, metabolic process, cell part, binding, and catalytic activity. In addition, the regulatory network of endogenous RNAs was then constructed by the prediction of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA network, implying that these RNAs play significant regulatory roles for root architecture shaping in response to root restriction. Our results, for the first time, the regulatory network of competitive endogenous RNAs (ceRNAs) functions of lncRNA and circRNA was integrated, and a basis for studying the potential functions of non-coding RNAs (ncRNAs) during root development of grapevine was provided.
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Affiliation(s)
- Jingjing Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
| | - Hui Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lipeng Zhang
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
| | - Yue Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan He
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Ren
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (Y.R.); (H.L.)
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832003, China
- Correspondence: (Y.R.); (H.L.)
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Wang S, Liu C, Li Y, Qiao J, Chen X, Bao J, Li R, Xing Y. LINC00665 affects the malignant biological behavior of ovarian cancer via the miR-148b-3p/KLF5. Syst Biol Reprod Med 2022; 68:370-383. [PMID: 36016468 DOI: 10.1080/19396368.2022.2101961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
This study investigated the expression and clinical significance of long intergenic noncoding RNA 00665 (LINC00665) in ovarian cancer (OC), as well as its effect on the malignant biological behavior of OC cells. The expression of LINC00665, miR-148b-3p, and Krüppel-like factor 5 (KLF5) in OC tissues and cells were determined by RT-qPCR. Western blot was used to detect the protein expression of KLF5. The expression patterns of LINC00665 in nuclear and cytoplasm fractions were undertaken using RT-qPCR. In addition, CCK-8 assay, clone formation assay, transwell, scratch test, and flow cytometry were respectively used to detect the cell activity, proliferation, invasiveness, healing of cells, and apoptosis rate of OC cells. Furthermore, the interactions between LINC00665 and miR-148b-3p and between miR-148b-3p and KLF5 were verified by the luciferase reporter assay, and the correlations among these three genes were analyzed. LINC00665 expression was upregulated both in OC cell lines and tissues. Si-LINC00665 inhibited cell proliferation, invasion, and migration and induced apoptosis to a certain extent. The subcellular fraction assay revealed LINC00665 to be located mainly in the cytoplasm. miR-148b-3p was a target of LINC00665, and KLF5 was directly targeted by miR-148b-3p. Si-LINC00665 inhibited KLF5 expression, miR-148b-3p inhibitor promoted KLF5 expression, and si-KLF5 inhibited LINC00665 expression. Interestingly, the expression of LINC00665 was reversely associated with miR-148b-3p expression but positively correlated with KLF5. Furthermore, miR-148b-3p expression was negatively correlated with KLF5. In addition, si-KLF5 inhibited the malignant biological behavior of OC cells, whereas miR-148b-3p inhibitor had the opposite effect. Most importantly, the si-LINC00665 could reverse the promotion effect of the miR-148b-3p inhibitor on the malignant biological behavior of OC cells. LINC00665 can be used as an effective prognostic indicator of OC, which has the potential to be a new therapeutic target.
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Affiliation(s)
- Shenglan Wang
- Department of Pathophysiology, Medical College of Qinghai University, Qinghai, P.R. China
| | - Chuanchuan Liu
- Key Laboratory of Hydatidosis Research, Qinghai University Affiliated Hospital, Qinghai, P.R. China
| | - Yongchuan Li
- Department of Gynaecology, Qinghai Red Cross Hospital, Qinghai, P.R. China
| | - Jinwan Qiao
- Department of Scientific Research and Teaching, the Fifth People's Hospital of Qinghai Province, Qinghai, P.R. China
| | - Xinling Chen
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Jin Bao
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Ran Li
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Yanxia Xing
- Department of Gynaecology, the Fifth People's Hospital of Qinghai Province, Qinghai, P.R. China
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Geng X, Zhang Y, Lin X, Zeng Z, Hu J, Hao L, Xu J, Wang X, Wang H, Li Q. Exosomal circWDR62 promotes temozolomide resistance and malignant progression through regulation of the miR-370-3p/MGMT axis in glioma. Cell Death Dis 2022; 13:596. [PMID: 35817771 PMCID: PMC9273787 DOI: 10.1038/s41419-022-05056-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
Abstract
Exosome-mediated delivery of circular RNAs (circRNAs) is implicated in cancer progression. However, the role of exosomal circRNAs in the chemotherapy resistance of tumours remains poorly understood. Here we identified a novel circRNA, circWDR62. It was found that circWDR62 expression was upregulated in TMZ-resistant glioma cells and TMZ-resistant glioma cell-derived exosomes compared with their controls by using high-throughput microarray analysis and quantitative real-time polymerase chain reaction, and high circWDR62 expression was associated with poor prognosis of glioma. Functionally, downregulation of circWDR62 expression could significantly inhibit the TMZ resistance and malignant progression of glioma. Further mechanistic studies showed that circWDR62 plays a role by sponging miR-370-3p as a competing endogenous RNA. Rescue experiments confirmed that MGMT is the downstream target of the circWDR62/miR-370-3p axis in glioma. In addition, circWDR62 could be transported between TMZ-resistant and TMZ-sensitive glioma cells via exosomes. Exosomal circWDR62 from TMZ-resistant cells conferred TMZ resistance in recipient sensitive cells while also enhancing the proliferation, migration and invasion of these cells. A series of clinical and in vivo trials corroborated that exosomal circWDR62 could promote TMZ chemoresistance and malignant progression of glioma. Our results demonstrate for the first time that exosome-mediated delivery of circWDR62 can promote TMZ resistance and malignant progression via targeting of the miR-370-3p/MGMT axis in vitro and in vivo in glioma, providing a new therapeutic strategy. Moreover, exosomal circWDR62 in human serum may serve as a promising therapeutic target and prognostic marker for glioma therapy.
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Affiliation(s)
- Xiuchao Geng
- Taizhou Central Hosiptal (Taizhou University Hospital), Taizhou University, Taizhou, 318000, Zhejiang, China
- School of Medicine, Taizhou University, Taizhou, 318000, Zhejiang, China
| | - Yuhao Zhang
- Department of Neurosurgery, Zhejiang Provincial People's Hospital, Affiliated to Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
- Key Laboratory of Precise Diagnosis and Treatment of Glioma in Hebei Provience, Baoding, 071000, Hebei, China
| | - Xiaomeng Lin
- Departments of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, China
| | - Zhaomu Zeng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, China
| | - Jun Hu
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, 050091, Hebei, China
- Department of Neurosurgery, Affiliated Hospital of Chengde medical University, Chengde, 067000, Hebei, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People's Hospital, Shaoxing, 312000, Zhejiang, China
| | - Jianglong Xu
- Key Laboratory of Precise Diagnosis and Treatment of Glioma in Hebei Provience, Baoding, 071000, Hebei, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, China
| | - Xinjuan Wang
- School of Medicine, Taizhou University, Taizhou, 318000, Zhejiang, China
| | - Hong Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, 071000, Hebei, China.
- Faculty of Integrated Traditional Chinese and Western Medicine, Hebei University of Chinese Medicine, Shijiazhuang, 050091, Hebei, China.
| | - Qiang Li
- School of Medicine, Taizhou University, Taizhou, 318000, Zhejiang, China.
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11
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Sun J, Liang W, Ye S, Chen X, Zhou Y, Lu J, Shen Y, Wang X, Zhou J, Yu C, Yan C, Zheng B, Chen J, Yang Y. Whole-Transcriptome Analysis Reveals Autophagy Is Involved in Early Senescence of zj-es Mutant Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:899054. [PMID: 35720578 PMCID: PMC9204060 DOI: 10.3389/fpls.2022.899054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Senescence is a necessary stage of plant growth and development, and the early senescence of rice will lead to yield reduction and quality decline. However, the mechanisms of rice senescence remain obscure. In this study, we characterized an early-senescence rice mutant, designated zj-es (ZheJing-early senescence), which was derived from the japonica rice cultivar Zhejing22. The mutant zj-es exhibited obvious early-senescence phenotype, such as collapsed chloroplast, lesions in leaves, declined fertility, plant dwarf, and decreased agronomic traits. The ZJ-ES gene was mapped in a 458 kb-interval between the molecular markers RM5992 and RM5813 on Chromosome 3, and analysis suggested that ZJ-ES is a novel gene controlling rice early senescence. Subsequently, whole-transcriptome RNA sequencing was performed on zj-es and its wild-type rice to dissect the underlying molecular mechanism for early senescence. Totally, 10,085 differentially expressed mRNAs (DEmRNAs), 1,253 differentially expressed lncRNAs (DElncRNAs), and 614 differentially expressed miRNAs (DEmiRNAs) were identified, respectively, in different comparison groups. Based on the weighted gene co-expression network analysis (WGCNA), the co-expression turquoise module was found to be the key for the occurrence of rice early senescence. Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 14 lncRNAs possibly regulated 16 co-expressed mRNAs through 8 miRNAs, and enrichment analysis showed that most of the DEmRNAs and the targets of DElncRNAs and DEmiRNAs were involved in reactive oxygen species (ROS)-triggered autophagy-related pathways. Further analysis showed that, in zj-es, ROS-related enzyme activities were markedly changed, ROS were largely accumulated, autophagosomes were obviously observed, cell death was significantly detected, and lesions were notably appeared in leaves. Totally, combining our results here and the remaining research, we infer that ROS-triggered autophagy induces the programmed cell death (PCD) and its coupled early senescence in zj-es mutant rice.
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Affiliation(s)
- Jia Sun
- College of Life Science, Fujian A&F University, Fuzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Weifang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Shenghai Ye
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuhang Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jianfei Lu
- Zhejiang Plant Protection, Quarantine and Pesticide Management Station, Hangzhou, China
| | - Ying Shen
- Zhejiang Plant Protection, Quarantine and Pesticide Management Station, Hangzhou, China
| | - Xuming Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Jie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Chulang Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chengqi Yan
- Institute of Biotechnology, Ningbo Academy of Agricultural Science, Ningbo, China
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yong Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology for Plant Protection, Ministry of Agriculture, and Rural Affairs, Zhejiang Provincial Key Laboratory of Biotechnology for Plant Protection, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Science, Hangzhou, China
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12
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Jha A, Quesnel-Vallières M, Wang D, Thomas-Tikhonenko A, Lynch KW, Barash Y. Identifying common transcriptome signatures of cancer by interpreting deep learning models. Genome Biol 2022; 23:117. [PMID: 35581644 PMCID: PMC9112525 DOI: 10.1186/s13059-022-02681-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/27/2022] [Indexed: 01/01/2023] Open
Abstract
Background Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types. Results Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer. Conclusions Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-022-02681-3).
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Affiliation(s)
- Anupama Jha
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA.
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Philadelphia, USA. .,Department of Biochemistry and Biophysics, Philadelphia, USA.
| | - David Wang
- Department of Genetics, Philadelphia, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology and Laboratory Medicine, Philadelphia, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Philadelphia, USA
| | - Yoseph Barash
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA. .,Department of Genetics, Philadelphia, USA.
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13
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Chen P, Nie ZY, Liu XF, Zhou M, Liu XX, Wang B. CircXRCC5, as a potential novel biomarker, promotes glioma progression via the miR-490-3p/XRCC5/CLC3 ceRNA network. Neuroscience 2022; 494:104-118. [DOI: 10.1016/j.neuroscience.2021.12.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 10/18/2022]
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14
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Salami R, Salami M, Mafi A, Vakili O, Asemi Z. Circular RNAs and glioblastoma multiforme: focus on molecular mechanisms. Cell Commun Signal 2022; 20:13. [PMID: 35090496 PMCID: PMC8796413 DOI: 10.1186/s12964-021-00809-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma multiforme (GBM), as a deadly and almost incurable brain cancer, is the most invasive form of CNS tumors that affects both children and adult population. It accounts for approximately half of all primary brain tumors. Despite the remarkable advances in neurosurgery, radiotherapy, and chemotherapeutic approaches, cell heterogeneity and numerous genetic alterations in cell cycle control, cell growth, apoptosis, and cell invasion, result in an undesirable resistance to therapeutic strategies; thereby, the median survival duration for GBM patients is unfortunately still less than two years. Identifying new therapeutics and employing the combination therapies may be considered as wonderful strategies against the GBM. In this regard, circular RNAs (circRNAs), as tumor inhibiting and/or stimulating RNA molecules, can regulate the cancer-developing processes, including cell proliferation, cell apoptosis, invasion, and chemoresistance. Hereupon, these molecules have been introduced as potentially effective therapeutic targets to defeat GBM. The current study aims to investigate the fundamental molecular and cellular mechanisms in association with circRNAs involved in GBM pathogenesis. Among multiple mechanisms, the PI3K/Akt/mTOR, Wnt/β-catenin, and MAPK signaling, angiogenic processes, and metastatic pathways will be thoroughly discussed to provide a comprehensive understanding of the role of circRNAs in pathophysiology of GBM. Video Abstract.
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Affiliation(s)
- Raziyeh Salami
- Department of Clinical Biochemistry, School of Medicine, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Marziyeh Salami
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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15
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Hwang T, Kim S, Chowdhury T, Yu HJ, Kim KM, Kang H, Won JK, Park SH, Shin JH, Park CK. Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. Commun Biol 2022; 5:62. [PMID: 35042936 PMCID: PMC8766575 DOI: 10.1038/s42003-022-03011-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 12/27/2021] [Indexed: 01/09/2023] Open
Abstract
AbstractAlu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the appreciation of Alu has been limited in tumorigenesis, especially for brain tumor. To investigate the relevance of Alu to the gliomagenesis, we studied Alu element-associated post-transcriptional processes and the RNA expression of the element by performing RNA-seq for a total of 41 pairs of neurotypical and diverse glioma brain tissues. We find that A-to-I editing and circular RNA levels, as well as Alu RNA expression, are decreased overall in gliomas, compared to normal tissue. Interestingly, grade 2 oligodendrogliomas are least affected in A-to-I editing and circular RNA levels among gliomas, whereas they have a higher proportion of down-regulated Alu subfamilies, compared to the other gliomas. These findings collectively imply a unique pattern of Alu-associated transcriptomes in grade 2 oligodendroglioma, providing an insight to gliomagenesis from the perspective of an evolutionary genetic element.
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16
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Wang L, Tan Y, Chen J, Zhu Z, Zhu Y, Sun Q, Dong H, Ai C, He G, Liu Y. CircABCC1 promotes the development of glioma by sponging miR‐591 and modulating high‐mobility group A2. Ann N Y Acad Sci 2022; 1511:107-118. [PMID: 35000195 DOI: 10.1111/nyas.14717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Lei Wang
- Department of Human Anatomy, Histology and Embryology, and Institute of Neurobiology Health Science Center, Xian Jiaotong University Xi'an Shanxi China
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Ying Tan
- Department of Laboratory Medicine Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Jun Chen
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Ziyu Zhu
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Yuting Zhu
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Qiang Sun
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Hao Dong
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Chunqi Ai
- Department of Mental Health Centre Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Guohou He
- Department of Neurology Affiliated Taihe Hospital of Hubei University of Medicine Shiyan Hubei China
| | - Yong Liu
- Department of Human Anatomy, Histology and Embryology, and Institute of Neurobiology Health Science Center, Xian Jiaotong University Xi'an Shanxi China
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17
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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: 13] [Impact Index Per Article: 3.3] [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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18
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Chen M, Yan C, Zhao X. Research Progress on Circular RNA in Glioma. Front Oncol 2021; 11:705059. [PMID: 34745938 PMCID: PMC8568300 DOI: 10.3389/fonc.2021.705059] [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: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
The discovery of circular RNA (circRNA) greatly complements the traditional gene expression theory. CircRNA is a class of non-coding RNA with a stable cyclic structure. They are highly expressed, spatiotemporal-specific and conservative across species. Importantly, circRNA participates in the occurrence of many kinds of tumors and regulates the tumor development. Glioma is featured by limited therapy and grim prognosis. Cancer-associated circRNA compromises original function or creates new effects in glioma, thus contributing to oncogenesis. Therefore, this article reviews the biogenesis, metabolism, functions and properties of circRNA as a novel potential biomarker for gliomas. We elaborate the expression characteristics, interaction between circRNA and other molecules, aiming to identify new targets for early diagnosis and treatment of gliomas.
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Affiliation(s)
- Mengyu Chen
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chunyan Yan
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xihe Zhao
- Department of Clinical Oncology, Shengjing Hospital of China Medical University, Shenyang, China
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19
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Li X, Zhang J, Zhang M, Qi X, Wang S, Teng J. Construction and comprehensive analysis of a competitive endogenous RNA network to reveal potential biomarkers for the malignant differentiation of glioma. Medicine (Baltimore) 2021; 100:e27248. [PMID: 34596120 PMCID: PMC8483826 DOI: 10.1097/md.0000000000027248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) can act as microRNA (miRNA) sponges to regulate protein-coding gene expression; therefore, lncRNAs are considered major components of the competitive endogenous RNA (ceRNA) network and have attracted growing attention. This study explored the regulatory mechanisms and functional roles of lncRNAs as ceRNAs in the malignant differentiation of low-grade glioma (LGG) to glioblastoma (GBM) and their potential impact on the prognosis of patients with GBM. METHODS LncRNA and messenger RNA (mRNA) data were extracted from the Cancer Genome Atlas (TCGA) database from 156 GBM samples and 529 LGG samples. Separately, the miRNA expression data were downloaded from the Gene Expression Omnibus database, with the GSE112009 dataset containing miRNA expression data from 10 GBM samples and 15 LGG samples. Weighted gene coexpression network analysis was performed to screen the glioma grade-related lncRNAs. Then, a ceRNA network was established. The database for annotation, visualization, and integrated discovery was adopted to conduct functional enrichment analysis based on 57 upregulated differentially expressed mRNAs in the ceRNA network. Finally, Kaplan-Meier curves were created for the survival analysis of 13 hub lncRNA by combining the clinical data of GBM patients in TCGA. RESULTS A ceRNA network including 16 lncRNAs, 18 miRNAs, and 78 mRNAs specific to the malignant differentiation of LGG to GBM was established. The 57 upregulated differentially expressed mRNAs in the ceRNA network were significantly enriched in 35 gene ontology terms and 5 pathways. The survival analysis showed that 2 lncRNAs (LINC00261 and HOXA10-AS) were prognostic biomarkers for patients with GBM in TCGA. CONCLUSION The proposed ceRNA network may help elucidate the regulatory mechanism by which lncRNAs function as ceRNAs and contribute to the malignant differentiation of LGG to GBM. Importantly, the candidate lncRNAs, miRNAs, and mRNAs involved in the ceRNA network can be further evaluated as potential therapeutic targets and prognostic biomarkers for GBM.
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Affiliation(s)
- Xin Li
- Weifang Traditional Chinese Medicine Hospital, WeiFang, China
| | - Jingwen Zhang
- School of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Min Zhang
- School of Statistics, Renmin University of China, Beijing, China
| | - Xianghua Qi
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Shiyuan Wang
- School of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Jing Teng
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, JiNan, China
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20
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Sun Y, Ma G, Xiang H, Wang X, Wang H, Zhang Y, Qie F, Li C. circFLNA promotes glioblastoma proliferation and invasion by negatively regulating miR‑199‑3p expression. Mol Med Rep 2021; 24:786. [PMID: 34498720 PMCID: PMC8441964 DOI: 10.3892/mmr.2021.12426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/28/2021] [Indexed: 01/22/2023] Open
Abstract
Glioblastoma (GBM) is one of the most common and malignant types of primary cancer in the central nervous system; however, the clinical outcomes of patients with GBM remain poor. Circular RNAs (circRNAs) have been revealed to serve important roles in diverse biological processes, such as regulating cell proliferation, epithelial-mesenchymal transition and tumor development. However, the underlying biological function of circRNA filamin A (circFLNA) and its potential role in GBM remain to be determined. The present study aimed to identify differentially expressed circRNAs in GBM. Reverse transcription-quantitative PCR was used to analyze the expression levels of circFLNA. The results demonstrated that the expression levels of circFLNA were significantly upregulated in clinical GBM samples and GBM cells compared with adjacent healthy brain tissues and normal human astrocytes, respectively. The results of the Cell Counting Kit-8 and Transwell assays revealed that circFLNA knockdown significantly inhibited the proliferative and invasive abilities of GBM cell lines. Moreover, high circFLNA expression levels were associated with a worse prognosis in GBM. MicroRNA (miR)-199-3p was subsequently predicted to be target of circFLNA. The inhibitory effect of miR-199-3p on cell proliferation and invasion was partially reversed following circFLNA knockdown. In conclusion, the findings of the present study identified novel roles for circFLNA in GBM and indicated that the circFLNA/miR-199-3p signaling axis may serve an important role in GBM progression. Therefore, circFLNA may represent a novel target for the diagnosis and treatment of GBM.
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Affiliation(s)
- Yu Sun
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Guangtao Ma
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Hongtao Xiang
- Department of Gastroenterology, The Fourth Hospital of Daqing, Daqing, Heilongjiang 163001, P.R. China
| | - Xiaomin Wang
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Hanmei Wang
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Yan Zhang
- Department of The Heart of Non‑Invasive Examination, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Fuzhong Qie
- Department of Neurosurgery, Daqing Oil Field General Hospital, Daqing, Heilongjiang 163001, P.R. China
| | - Chenlong Li
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150001, P.R. China
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21
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Song W, Qiu J, Yin L, Hong X, Dai W, Tang D, Liu D, Dai Y. Integrated analysis of competing endogenous RNA networks in peripheral blood mononuclear cells of systemic lupus erythematosus. J Transl Med 2021; 19:362. [PMID: 34419106 PMCID: PMC8380341 DOI: 10.1186/s12967-021-03033-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/07/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease with a complicated pathogenesis, and its aetiology has not been clearly unveiled. The lack of effective diagnosis and treatment methods makes it necessary to explore the molecular mechanism of SLE. We aimed to identify some critical signalling pathways and key competing endogenous RNAs (ceRNAs) underlying the molecular mechanism of SLE and to map out the systematic signalling networks by integrating the data on different kinds of RNAs. METHODS Peripheral blood mononuclear cells (PBMCs) were collected from both SLE patients and healthy subjects, RNA was extracted from the PBMCs, and RNA libraries including ribosomal RNA-depleted strand-specific libraries and small RNA libraries were built for deep RNA sequencing (RNA-seq). RNA-seq yielded differential expression profiles of lncRNAs/circRNAs/miRNAs/mRNAs related to SLE. The DAVID database (v. 6.8) was employed for Gene Ontology (GO) and KEGG pathway analysis. ceRNA networks (circRNA/lncRNA-miRNA-mRNA) were constructed and visualized using Cytoscape software (v. 3.5.0). The TargetScan and miRanda databases were used to predict target relationships in ceRNA networks. qRT-PCR was used to verify our data. RESULTS Differential expression of ceRNAs related to SLE was detected in SLE patients' PBMCs: 644 mRNAs (384 upregulated, 260 downregulated), 326 miRNAs (223 upregulated, 103 downregulated), 221 lncRNAs (79 upregulated, 142 downregulated), and 31 circRNAs (21 upregulated, 10 downregulated). We drew ceRNA signalling networks made up of the differentially expressed mRNAs/miRNAs/lncRNAs/circRNAs mentioned above, and the hub genes included IRF5, IFNAR2, TLR7, IRAK4, STAT1, STAT2, C2, and Tyk2. These hub genes were involved in ceRNA signalling pathways, such as the IL-17 signalling pathway and type I interferon signalling pathway. CONCLUSIONS We explored the differential expression profiles of various kinds of ceRNAs and integrated signalling networks constructed by ceRNAs. Our findings offer new insights into the pathogenesis of SLE and hint at therapeutic strategies.
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Affiliation(s)
- Wencong Song
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China
- The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Jie Qiu
- School of Computer Science and Engineering, Yulin Normal University, Yulin, China
| | - Lianghong Yin
- The First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, 78712, USA
| | - Donge Tang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin NO. 924 Hospital, Guilin, 541002, China.
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
| | - Yong Dai
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College, Jinan University (Shenzhen Peoples Hospital), Shenzhen, 518020, China.
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory of Guilin NO. 924 Hospital, Guilin, 541002, China.
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22
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Xia M, Duan LJ, Lu BN, Pang YZ, Pang ZR. LncRNA AFAP1-AS1/miR-27b-3p/VEGF-C axis modulates stemness characteristics in cervical cancer cells. Chin Med J (Engl) 2021; 134:2091-2101. [PMID: 34334630 PMCID: PMC8440026 DOI: 10.1097/cm9.0000000000001665] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: Long non-coding RNA (lncRNA) actin filament-associated protein 1 antisense RNA 1 (AFAP1-AS1) functions as a competing endogenous RNA to regulate target genes expression by sponging microRNAs (miRs) to play cancer-promoting roles in cancer stem cells. However, the regulatory mechanism of AFAP1-AS1 in cervical cancer (CC) stem cells is unknown. The present study aimed to provide a new therapeutic target for the clinical treatment of CC. Methods: Hyaluronic acid receptor cluster of differentiation 44 variant exon 6 (CD44v6)(+) CC cells were isolated by flow cytometry (FCM). Small interfering RNAs of AFAP1-AS1 (siAFAP1-AS1) were transfected into the (CD44v6)(+) cells. The levels of AFAP1-AS1 were measured by quantitative real-time PCR (qRT-PCR). Sphere formation assay, cell cycle analysis, and Western blotting were used to detect the effect of siAFAP1-AS1. RNA pull-down and luciferase reporter assay were used to verify the relationship between miR-27b-3p and AFAP1-AS1 or vascular endothelial growth factor (VEGF)-C. Results: CD44v6(+) CC cells had remarkable stemness and a high level of AFAP1-AS1. However, AFAP1-AS1 knockdown with siAFAP1-AS1 suppressed the cell cycle transition of G(1)/S phase and inhibited self-renewal of CD44v6(+) CC cells, the levels of the stemness markers octamer-binding transcription factor 4 (OCT4), osteopontin (OPN), and cluster of differentiation 133 (CD133), and the epithelial-mesenchymal transition (EMT)-related proteins Twist1, matrix metalloprotease (MMP)-9, and VEGF-C. In the mechanism study, miR-27b-3p/VEGF-C signaling was demonstrated to be a key downstream of AFAP1-AS1 in the CD44v6(+) CC cells. Conclusions: LncRNA AFAP1-AS1 knockdown inhibits the CC cell stemness by upregulating miR-27b-3p to suppress VEGF-C.
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Affiliation(s)
- Meng Xia
- School of Pharmacy, Minzu University of China, Beijing 100081, China Department of Orthopedics, Bayannaoer City Hospital, Bayannaoer, Inner Mongolia 015000, China Guangxi Zhuang Yao Medicine Center of Engineering and Technology, Guangxi University of Chinese Medicine, Nanning, Guangxi 530200, China Key Laboratory of Ethnomedicine of Ministry of Education, Minzu University of China, Beijing 100081, China
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circRNA derived from CLSPN (circCLSPN) is an oncogene in human glioblastoma multiforme by regulating cell growth, migration and invasion via ceRNA pathway. J Biosci 2021. [DOI: 10.1007/s12038-021-00185-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Sun J, Yin A, Zhang W, Lv J, Liang Y, Li H, Li Y, Li X. CircUBAP2 Inhibits Proliferation and Metastasis of Clear Cell Renal Cell Carcinoma via Targeting miR-148a-3p/FOXK2 Pathway. Cell Transplant 2021; 29:963689720925751. [PMID: 32425115 PMCID: PMC7563813 DOI: 10.1177/0963689720925751] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the prominent histological subtype of renal cell carcinoma (RCC) with high incidence of local recurrence and distant metastasis. It has been documented that circular ribonucleic acids (circRNAs) play crucial roles in the development of cancers; however, study on exploring the role of circRNAs in ccRCC still remains limited. In the present study, we aimed to evaluate the biological function of a novel circRNA UBAP2 (circUBAP2) in ccRCC and the underlying mechanism. Our results showed that circUBAP2 expression was significantly down-regulated in ccRCC tissues and cell lines. Overexpression of circUBAP2 significantly inhibited the proliferation, migration, and invasion of ccRCC cells. MiR-148a-3p was a target miRNA of circUBAP2 in ccRCC cells, and its expression levels in ccRCC tissues and cell lines were negatively correlated with circUBAP2 levels. Moreover, miR-148a-3p reversed the inhibitory effects of circUBAP2 on cell proliferation, migration, and invasion in ccRCC cells. Additionally, forkhead box K2 (FOXK2) was found to be a target gene of miR-148a-3p and regulated by miR-148a-3p in ccRCC cells. Furthermore, knockdown of FOXK2 reversed the inhibitory effects of miR-148a-3p inhibitor on ccRCC cells. In conclusion, these findings indicated that circUBAP2 functioned as a novel tumor suppressor in ccRCC through regulating the miR-148a-3p/FOXK2 axis. Therefore, circUBAP2 might serve as a potential therapeutic target for the treatment of ccRCC.
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Affiliation(s)
- Jiping Sun
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China.,Both the authors contributed equally to this article
| | - Aiping Yin
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China.,Both the authors contributed equally to this article
| | - Wenjing Zhang
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Jia Lv
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Yu Liang
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Huixian Li
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Yan Li
- Department of Nephrology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
| | - Xudong Li
- Department of Urology, the First Affiliated Hospital of Medical College, Xi'an Jiaotong University, China
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25
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Wang T, Mao P, Feng Y, Cui B, Zhang B, Chen C, Xu M, Gao K. Blocking hsa_circ_0006168 suppresses cell proliferation and motility of human glioblastoma cells by regulating hsa_circ_0006168/miR-628-5p/IGF1R ceRNA axis. Cell Cycle 2021; 20:1181-1194. [PMID: 34024251 PMCID: PMC8265815 DOI: 10.1080/15384101.2021.1930357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND hsa_circ_0006168 is an oncogenic circular RNA in esophageal cancer. However, its role remains unclarified in tumor progression of gliomas, especially in glioblastoma (GBM). METHODS Cell counting kit-8 assay, transwell assays, western blotting, and xenograft experiment, as well as colony formation assay and flow cytometry were performed to measure cell proliferation and motility. Expression of hsa_circ_0006168, microRNA (miR)-628-3p, insulin‑like growth factor 1 receptor (IGF1R), and Ras/extracellular signal regulated kinases (Erk)-related proteins were determined by quantitative real-time polymerase chain reaction and western blotting. The physical interaction was confirmed by dual-luciferase reporter assay and RNA pull-down assay. RESULTS hsa_circ_0006168 and IGF1R were upregulated, and miR-628-5p was downregulated in human GBM tissues and cells. Functionally, blocking hsa_circ_0006168 and overexpressing miR-628-5p suppressed cell proliferation, migration, invasion, and expression of Vimentin and Snail (mesenchymal markers) in A172 and LN229 cells, accompanied with increased E-cadherin (epithelial marker), decreased colony formation, and promoted apoptosis rate. Silencing miR-628-5p counteracted the suppression of hsa_circ_0006168 deficiency on these behaviors, and restoring IGF1R blocked miR-628-5p-mediated inhibition as well. More importantly, hsa_circ_0006168 knockdown could delay xenograft tumor growth in vivo and lower Ras and phosphorylated Erk1/2 expression in vitro and in vivo. Mechanically, hsa_circ_0006168 targeted and sponged miR-628-5p, and IFG1R was a novel target for miR-628-5p. Inhibiting miR-628-5p could abrogate in vitro role of hsa_circ_0006168 knockdown, and similarly IGF1R upregulation counteracted miR-628-5p role. CONCLUSION Silencing hsa_circ_0006168 might suppress GBM proliferation and motility via serving as competitive endogenous RNA for miR-628-5p and regulating IGF1R/Ras/Erk pathway.
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Affiliation(s)
- Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Ping Mao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Yong Feng
- Department of Neurosurgery, The Hancheng People's Hospital, Weinan, Shannxi, China
| | - Bo Cui
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
| | - Bin Zhang
- Department of Neurosurgery, Bao Ji Affiliated Hospital of Xi'an Medical University, Baoji, Shannxi, China
| | - Chen Chen
- Department of Neurosurgery, Mianxian Hospital, Mianxian, Shannxi, China
| | - Mingjie Xu
- Department of Neurosurgery, Traditional Chinese Medicine Hospital of Xixiang, Hanzhong, Shannxi, China
| | - Ke Gao
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shannxi, China
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Warburg effect-promoted exosomal circ_0072083 releasing up-regulates NANGO expression through multiple pathways and enhances temozolomide resistance in glioma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:164. [PMID: 33975615 PMCID: PMC8111743 DOI: 10.1186/s13046-021-01942-6] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/11/2021] [Indexed: 12/20/2022]
Abstract
Background Temozolomide (TMZ) resistance limits its application in glioma. Exosome can carry circular RNAs (circRNAs) to regulate drug resistance via sponging microRNAs (miRNAs). miRNAs can control mRNA expression by regulate the interaction with 3’UTR and methylation. Nanog homeobox (NANOG) is an important biomarker for TMZ resistance. Hitherto, it is unknown about the role of exosomal hsa_circ_0072083 (circ_0072083) in TMZ resistance in glioma, and whether it is associated with NANOG via regulating miRNA sponge and methylation. Methods TMZ-resistant (n = 36) and sensitive (n = 33) patients were recruited. The sensitive cells and constructed resistant cells were cultured and exposed to TMZ. circ_0072083, miR-1252-5p, AlkB homolog H5 (ALKBH5) and NANOG levels were examined via quantitative reverse transcription polymerase chain reaction and western blot. The half maximal inhibitory concentration (IC50) of TMZ, cell proliferation, apoptosis, migration and invasion were analyzed via Cell Counting Kit-8, colony formation, flow cytometry, wound healing and transwell assays. The in vivo function was assessed using xenograft model. The N6-methyladenosine (m6A) level was analyzed via methylated RNA immunoprecipitation (MeRIP). Target relationship was investigated via dual-luciferase reporter assay and RNA immunoprecipitation. Warburg effect was investigated via lactate production, glucose uptake and key enzymes expression. Exosome was isolated and confirmed via transmission electron microscopy and specific protein expression. Results circ_0072083 expression was increased in TMZ-resistant glioma tissues and cells. circ_0072083 knockdown restrained the resistance of resistant cells via decreasing IC50 of TMZ, proliferation, migration, invasion and xenograft tumor growth and increasing apoptosis. circ_0072083 silence reduced NANOG expression via blocking ALKBH5-mediated demethylation. circ_0072083 could regulate NANOG and ALKBH5 via targeting miR-1252-5p to control TMZ resistance. Warburg effect promoted the release of exosomal circ_0072083 in resistant cells. Exosomal circ_0072083 from resistant cells increased the resistance of sensitive cells to TMZ in vitro and xenograft model. Exosomal circ_0072083 level was enhanced in resistant patients, and it had a diagnostic value and indicated a lower overall survival in glioma. Conclusion Exosomal circ_0072083 promoted TMZ resistance via increasing NANOG via regulating miR-1252-5p-mediated degradation and demethylation in glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01942-6.
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Zhang J, Chen Z, Liu X, Yang C, Xie D. Gain of circBRAF Represses Glioma Progression by Regulating miR-1290/FBXW7 Axis. Neurochem Res 2021; 46:1203-1213. [PMID: 33650075 DOI: 10.1007/s11064-021-03259-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Dysregulated circular RNAs (circRNAs) have been confirmed to partake in the modulation of the glioma progression. Here, we intended to explore the role of circBRAF in glioma and the possible action mechanism. The expression levels of circBRAF, microRNA (miR)-1290 and F-box and WD repeat domain containing 7 (FBXW7) were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) or western blot. Cell viability was assessed by 3-(4, 5)-dimethylthiazole-2-y1)-2, 5-biphenyl tetrazolium bromide (MTT) assay. Cell cycle distribution was determined by flow cytometry. Cell migration and invasion were evaluated through Trans-well assay. Related protein levels were detected by western blot. Targeted relation among circBRAF, miR-1290 and FBXW7 was validated by dual-luciferase reporter, RNA immunoprecipitation (RIP) and pull-down assays. Xenograft model was constructed to explore the function of circBRAF in vivo. Expression of circBRAF and FBXW7 was decreased in glioma tissues and cells. Upregulation of circBRAF inhibited glioma cell proliferation and metastasis in vitro. MiR-1290 was upregulated in glioma, which was sponged by circBRAF. Besides, circBRAF elevated FBXW7 expression by targeting miR-1290. Introduction of miR-1290 or FBXW7 knockdown could counteract the inhibitory effects of circBRAF upregulation on the malignant phenotypes of glioma cells. Overexpression of circBRAF repressed the tumor growth in vivo. Upregulation of circBRAF suppressed glioma evolvement in vitro and in vivo by regulating miR-1290/FBXW7 axis, broadening the cognition of glioma progression.
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Affiliation(s)
- Jinchao Zhang
- Department of Neurosurgery, Yingtan People's Hospital, No. 116, Shenglixi Road, Yingtan, 335000, Jiangxi, China.
| | - Zhi Chen
- Department of Neurosurgery, Yingtan People's Hospital, No. 116, Shenglixi Road, Yingtan, 335000, Jiangxi, China
| | - Xinjun Liu
- Department of Neurosurgery, Yingtan People's Hospital, No. 116, Shenglixi Road, Yingtan, 335000, Jiangxi, China
| | - Chonglin Yang
- Department of Neurosurgery, Yingtan People's Hospital, No. 116, Shenglixi Road, Yingtan, 335000, Jiangxi, China
| | - Donggen Xie
- Department of Neurosurgery, Yingtan People's Hospital, No. 116, Shenglixi Road, Yingtan, 335000, Jiangxi, China
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28
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Rahnama S, Bakhshinejad B, Farzam F, Bitaraf A, Ghazimoradi MH, Babashah S. Identification of dysregulated competing endogenous RNA networks in glioblastoma: A way toward improved therapeutic opportunities. Life Sci 2021; 277:119488. [PMID: 33862117 DOI: 10.1016/j.lfs.2021.119488] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/16/2021] [Accepted: 04/04/2021] [Indexed: 12/17/2022]
Abstract
Glioblastoma is recognized as one of the leading causes of death worldwide. Although there have been considerable advancements in understanding the causative molecular mechanisms of this malignancy, effective therapeutic strategies are still in limited use. It has been revealed that non-coding RNAs (ncRNAs) play critical roles in glioblastoma development, while interactions between the regulatory molecules such as long ncRNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs) remain to be fully deciphered. Over the recent years, researchers have discovered a new category of RNA molecules called competing endogenous RNA (ceRNA). This kind of RNA can contribute to molecular interactions in the form of ceRNA networks (ceRNETs). Multiple lines of evidence have demonstrated that dysregulation of various ceRNA networks is involved in glioblastoma development. Therefore, gaining insights into these dysregulations might offer potential for the early diagnosis of glioblastoma patients and identification of efficient therapeutic targets. In this review, we provide an overview of recent discoveries on ceRNA networks and the involvement of dysregulated networks in posing limitations to temozolomide therapy. We also describe signaling pathways relevant to the progression of glioblastoma.
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Affiliation(s)
- Saghar Rahnama
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amirreza Bitaraf
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Wang Z, Wang Q, Bao Z, Guo L, Chen H, Lv T, Xu T, Zhang X, Zhou C, Sun L. LINC00174 is a favorable prognostic biomarker in glioblastoma via promoting proliferative phenotype. Cancer Biomark 2021; 28:421-427. [PMID: 32390602 DOI: 10.3233/cbm-191026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To investigate the expression pattern, prognostic value and biological functional of LINC00174 in glioma. METHODS In total, 140 glioma samples were collected as discovery cohort. TCGA RNA sequence dataset was obtained as validation set. Kaplan-Meier survival and multivariate Cox analysis were performed to evaluate survival difference. Furthermore, the biological function of LINC00174 was analyzed by clonogenic and intracranial tumor model assays. RESULTS Overexpressed LINC00174 was significantly correlated with tumor grade as well as the higher mortality in survival analysis both in the discovery and the validation GBM cohorts. Besides, LINC00174 served as an independent prognostic indicator in glioblastoma patients. Additionally, knock down of LINC00174 expression significantly suppressed GBM cells' proliferation both in vitro and vivo. CONCLUSION LINC00174 acts as an oncogene in glioma and may be a new potential therapeutic target.
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Affiliation(s)
- Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiangwei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoshi Bao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liemei Guo
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongjin Chen
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Lv
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianqi Xu
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohua Zhang
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Caifang Zhou
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lihua Sun
- Department of Neurosurgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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The GAUGAA Motif Is Responsible for the Binding between circSMARCA5 and SRSF1 and Related Downstream Effects on Glioblastoma Multiforme Cell Migration and Angiogenic Potential. Int J Mol Sci 2021; 22:ijms22041678. [PMID: 33562358 PMCID: PMC7915938 DOI: 10.3390/ijms22041678] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/04/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) are a large class of RNAs with regulatory functions within cells. We recently showed that circSMARCA5 is a tumor suppressor in glioblastoma multiforme (GBM) and acts as a decoy for Serine and Arginine Rich Splicing Factor 1 (SRSF1) through six predicted binding sites (BSs). Here we characterized RNA motifs functionally involved in the interaction between circSMARCA5 and SRSF1. Three different circSMARCA5 molecules (Mut1, Mut2, Mut3), each mutated in two predicted SRSF1 BSs at once, were obtained through PCR-based replacement of wild-type (WT) BS sequences and cloned in three independent pcDNA3 vectors. Mut1 significantly decreased its capability to interact with SRSF1 as compared to WT, based on the RNA immunoprecipitation assay. In silico analysis through the “Find Individual Motif Occurrences” (FIMO) algorithm showed GAUGAA as an experimentally validated SRSF1 binding motif significantly overrepresented within both predicted SRSF1 BSs mutated in Mut1 (q-value = 0.0011). U87MG and CAS-1, transfected with Mut1, significantly increased their migration with respect to controls transfected with WT, as revealed by the cell exclusion zone assay. Immortalized human brain microvascular endothelial cells (IM-HBMEC) exposed to conditioned medium (CM) harvested from U87MG and CAS-1 transfected with Mut1 significantly sprouted more than those treated with CM harvested from U87MG and CAS-1 transfected with WT, as shown by the tube formation assay. qRT-PCR showed that the intracellular pro- to anti-angiogenic Vascular Endothelial Growth Factor A (VEGFA) mRNA isoform ratio and the amount of total VEGFA mRNA secreted in CM significantly increased in Mut1-transfected CAS-1 as compared to controls transfected with WT. Our data suggest that GAUGAA is the RNA motif responsible for the interaction between circSMARCA5 and SRSF1 as well as for the circSMARCA5-mediated control of GBM cell migration and angiogenic potential.
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Guan Y, Guan A, Chen L, Gong A. LINC00461 facilitates HNSCC development and reduces chemosensitivity by impairing miR-195-mediated inhibition of HOXA10. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:74-86. [PMID: 33869744 PMCID: PMC8027536 DOI: 10.1016/j.omto.2021.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022]
Abstract
Homeobox A10 (HOXA10) has been regarded to serve as an oncogene in head and neck squamous cell carcinoma (HNSCC). This study was intended to explore the interaction among the long intergenic noncoding RNA 00461 (LINC00461), microRNA (miR)-195, and HOXA10, and to investigate its role in epithelial-mesenchymal transition (EMT) and chemoresistance in HNSCC. The effects of LINC00461, miR-195, and HOXA10 on the EMT and chemoresistance of HNSCC cells were analyzed by comprehensive analysis of gain- and loss-of-function techniques. The intimate relationships among LINC00461, miR-195, and HOXA10 were investigated by several procedures such as RNA-binding protein immunoprecipitation, RNA pull-down, and dual-luciferase reporter assays. A xenotransplantation tumor model in nude mice was established for the assessment of the tumorigenic ability of the cells in vivo. Our findings indicated that LINC00461 was highly expressed in HNSCC and its overexpression induced EMT and precipitated the chemoresistance of HNSCC cells to cisplatin. The LINC00461 could bind to miR-195 while miR-195 targeted HOXA10 independently. Moreover, LINC00461 impaired miR-195-mediated inhibition of HOXA10 to induce EMT and increase the chemoresistance in HNSCC. Tumor weight and volume were reduced by lentivirus-mediated elevation of miR-195 by inhibition of HOXA10, which could be annulled by LINC00461 overexpression. LINC00461 downregulates the expression of miR-195 to subsequently upregulate the expression of HOXA10, thereby promoting EMT and enhancing chemoresistance in HNSCC.
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Affiliation(s)
- Yifang Guan
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong, P.R. China
| | - Aizhong Guan
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong, P.R. China
| | - Long Chen
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong, P.R. China
| | - Aimei Gong
- Department of Stomatology, Linyi People's Hospital, Linyi 276000, Shandong, P.R. China
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Wang Z, Lu Y, Sheng B, Ding Y, Cheng X. Long-noncoding RNA LINC00461 promotes proliferation and invasion of nonsmall cell lung cancer cells via targeting miR-518a-3p/WDR1 pathway. J Recept Signal Transduct Res 2020; 42:80-87. [PMID: 33233986 DOI: 10.1080/10799893.2020.1850786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are a class of RNAs participating in many biological processes such as imprinting, alternative splicing and RNA decay. Recently, lncRNAs have drawn a great deal of attention for their critical role in cancer progression. LINC00461, a newly identified lncRNA, has been reported to be significantly overexpressed in breast cancer and markedly expedited breast cancer progression. However, the specific role of LINC00461 in nonsmall cell lung cancer (NSCLC) remains unknown. In this study, we for the first time showed the biological functions of LINC00461 in NSCLC. Our results demonstrated that LINC00461 was significantly up-regulated in NSCLC tissues and cell lines. Furthermore, knockdown of LINC00461 inhibited NSCLC cell proliferation and invasion in vitro as well as suppressed tumor growth and metastasis in vivo. We also performed luciferase reporter assays and found that LINC00461 functioned as a sponge for miR-518a-3p and WDR1 was a target of miR-518a-3p. Taken together, we suggested an essential role of LINC00461/miR-518a-3p/WDR1 axis in NSCLC, which could be used as a potential therapeutic target for NSCLC treatment.
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Affiliation(s)
- Zuopei Wang
- Department of Thoracic Surgery, Shanghai Pudong New area People's Hospital, Shanghai, China
| | - Yi Lu
- Department of Thoracic Surgery, Shanghai Pudong New area People's Hospital, Shanghai, China
| | - Bo Sheng
- Department of Thoracic Surgery, Shanghai Pudong New area People's Hospital, Shanghai, China
| | - Yi Ding
- Department of Thoracic Surgery, Shanghai Pudong New area People's Hospital, Shanghai, China
| | - Xiaoke Cheng
- Department of Scientific Research, Shanghai Pudong New area People's Hospital, Shanghai, China
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Wei B, Wang L, Zhao J. Circular RNA hsa_circ_0005114-miR-142-3p/miR-590-5p-adenomatous polyposis coli protein axis as a potential target for treatment of glioma. Oncol Lett 2020; 21:58. [PMID: 33281969 PMCID: PMC7709550 DOI: 10.3892/ol.2020.12320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glioma is the most common type of brain tumor and is associated with a high mortality rate. Despite recent advances in treatment options, the overall prognosis in patients with glioma remains poor. Studies have suggested that circular (circ)RNAs serve important roles in the development and progression of glioma and may have potential as therapeutic targets. However, the expression profiles of circRNAs and their functions in glioma have rarely been studied. The present study aimed to screen differentially expressed circRNAs (DECs) between glioma and normal brain tissues using sequencing data collected from the Gene Expression Omnibus database (GSE86202 and GSE92322 datasets) and explain their mechanisms based on the competing endogenous (ce)RNA regulatory hypothesis. In total, 424 commonly downregulated DECs (with the Gene_symbol annotated in the circBase database) in these two datasets were identified. Using the CircInteractome and Starbase databases, 18 micro (mi)RNAs (miRs) were predicted to interact with DECs, while 22 glioma-related genes obtained from the Comparative Toxicogenomics Database were predicted to be regulated by 15 miRNAs via the miRwalk 2.0 database. A ceRNA network was established based on 115 DECs, 15 miRNAs and 22 mRNAs. LinkedOmics online analysis using The Cancer Genome Atlas (TCGA) data showed that hsa-miR-142-3p/hsa-miR-590-5p and their target gene adenomatous polyposis coli protein (APC) were all significantly associated with overall survival rate and their prognosis trend was opposite, revealing that high expression levels of hsa-miR-142-3p/hsa-miR-590-5 were associated with a poor overall survival rate, while high APC expression with a good overall survival rate. UALCAN analysis using TCGA data of glioblastoma multiforme and the GSE25632 and GSE103229 microarray datasets showed that hsa-miR-142-3p/hsa-miR-590-5p was upregulated and APC was downregulated. Thus, hsa-miR-142-3p/hsa-miR-590-5p-APC-related circ/ceRNA axes may be important in glioma, and hsa_circ_0005114 interacted with both of these miRNAs. Functional analysis showed that hsa_circ_0005114 was involved in insulin secretion, while APC was associated with the Wnt signaling pathway. In conclusion, hsa_circ_0005114-miR-142-3p/miR-590-5p-APC ceRNA axes may be potential targets for the treatment of glioma.
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Affiliation(s)
- Bo Wei
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Le Wang
- Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Jingwei Zhao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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Han C, Wang S, Wang H, Zhang J. Knockdown of circ-TTBK2 Inhibits Glioma Progression by Regulating miR-1283 and CHD1. Cancer Manag Res 2020; 12:10055-10065. [PMID: 33116862 PMCID: PMC7568596 DOI: 10.2147/cmar.s252916] [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: 03/07/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
Background Dysregulated circular RNAs (circRNAs) are involved in the development of glioma. This paper aims to analyze the role and mechanism of circRNA tau tubulin kinase 2 (circ-TTBK2) in glioma progression. Methods The glioma samples and normal brain tissues were collected. The levels of circ-TTBK2, microRNA-1283 (miR-1283) and chromodomain helicase DNA-binding protein 1 (CHD1) were examined via quantitative reverse transcription polymerase chain reaction or Western blot. Cell proliferation, migration, invasion and glycolysis were determined via 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide, transwell assay, Western blot, glucose and lactate assay kits. The target relationship was analyzed via dual-luciferase reporter assay. The xenograft model was established using U251 cells. Results circ-TTBK2 expression was increased in glioma tissues and cells. circ-TTBK2 knockdown suppressed glioma cell proliferation, migration, invasion and glycolysis. circ-TTBK2 was a sponge for miR-1283, and knockdown of miR-1283 reversed the effect of circ-TTBK2 silence on glioma progression. CHD1 was targeted via miR-1283, and miR-1283 repressed glioma cell proliferation, migration, invasion and glycolysis via decreasing CHD1. Knockdown of circ-TTBK2-reduced CHD1 expression by mediating miR-1283. Silence of circ-TTBK2 reduced xenograft tumor growth. Conclusion Down-regulation of circ-TTBK2 suppressed glioma development by regulating miR-1283 and CHD1, providing a new mechanism for understanding glioma pathogenesis.
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Affiliation(s)
- Chengchen Han
- Department of Neurosurgery, The Sixth Medical Center of PLA General Hospital, Beijing 100048, People's Republic of China
| | - Shuwei Wang
- Department of Neurosurgery, The Sixth Medical Center of PLA General Hospital, Beijing 100048, People's Republic of China
| | - Hongwei Wang
- Department of Neurosurgery, The Sixth Medical Center of PLA General Hospital, Beijing 100048, People's Republic of China
| | - Jianning Zhang
- Department of Neurosurgery, The Sixth Medical Center of PLA General Hospital, Beijing 100048, People's Republic of China
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De Novo A-to-I RNA Editing Discovery in lncRNA. Cancers (Basel) 2020; 12:cancers12102959. [PMID: 33066171 PMCID: PMC7650826 DOI: 10.3390/cancers12102959] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Long non-coding RNAs are emerging as key regulators of gene expression at both transcriptional and translational levels, and their alterations (in expression or sequence) are linked to tumorigenesis and tumor progression. RNA editing has the unique ability to change the RNA sequence without altering the integrity or sequence of genomic DNA, with adenosine to inosine (A-to-I) RNA editing being the most common event in humans. With the ability to change the genetic information after transcription, RNA editing is an essential player in the transcriptome and proteome enrichment; however, when deregulated, it can contribute to cell transformation. In this article, we performed the first deep de novo editing survey in lncRNA, demonstrating that RNA editing is a pervasive phenomenon involving lncRNAs important in the brain and brain cancer. Our study will open a new field of research in which the interplay between lncRNA and RNA editing can add novel insights into cancer. Abstract Background: Adenosine to inosine (A-to-I) RNA editing is the most frequent editing event in humans. It converts adenosine to inosine in double-stranded RNA regions (in coding and non-coding RNAs) through the action of the adenosine deaminase acting on RNA (ADAR) enzymes. Long non-coding RNAs, particularly abundant in the brain, account for a large fraction of the human transcriptome, and their important regulatory role is becoming progressively evident in both normal and transformed cells. Results: Herein, we present a bioinformatic analysis to generate a comprehensive inosinome picture in long non-coding RNAs (lncRNAs), using an ad hoc index and searching for de novo editing events in the normal brain cortex as well as in glioblastoma, a highly aggressive human brain cancer. We discovered >10,000 new sites and 335 novel lncRNAs that undergo editing, never reported before. We found a generalized downregulation of editing at multiple lncRNA sites in glioblastoma samples when compared to the normal brain cortex. Conclusion: Overall, our study discloses a novel layer of complexity that controls lncRNAs in the brain and brain cancer.
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Zhu X, Jiang L, Yang H, Chen T, Wu X, Lv K. Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. Cancer Cell Int 2020; 20:393. [PMID: 32821246 PMCID: PMC7429694 DOI: 10.1186/s12935-020-01488-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/07/2020] [Indexed: 02/08/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis. Recent research has demonstrated that competitive endogenous RNA (ceRNA) network which long noncoding RNAs (lncRNAs) act as microRNA (miRNA) sponges to regulate mRNA expression were closely related to tumor development. However, the regulatory mechanisms and functional roles of ceRNA network in the pathogenesis of GBM are remaining poorly understood. Methods In this study, we systematically analyzed the expression profiles of lncRNA and mRNA (GSE51146 dataset) and miRNA (GSE65626 dataset) from GEO database. Then, we constructed a ceRNA network with the dysregulated genes by bioinformatics methods. The TCGA and GSE4290 dataset were used to confirm the expression and prognostic value of candidate mRNAs. Results In total, 3413 differentially expressed lncRNAs and mRNAs, 305 differentially expressed miRNAs were indentified in GBM samples. Then a ceRNA network containing 3 lncRNAs, 5 miRNAs, and 60 mRNAs was constructed. The overall survival analysis of TCGA databases indicated that two mRNAs (C1s and HSD3B7) were remarkly related with the prognosis of GBM. Conclusion The ceRNA network may increase our understanding to the pathogenesis of GBM. In general, the candidate mRNAs from the ceRNA network can be predicted as new therapeutic targets and prognostic biomarkers for GBM.
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Affiliation(s)
- Xiaolong Zhu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Hui Yang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Tianbing Chen
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Xingwei Wu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
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Wu H, Tian X, Zhu C. Knockdown of lncRNA PVT1 inhibits prostate cancer progression in vitro and in vivo by the suppression of KIF23 through stimulating miR-15a-5p. Cancer Cell Int 2020; 20:283. [PMID: 32624708 PMCID: PMC7330980 DOI: 10.1186/s12935-020-01363-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) greatly threatens men's lives, with high incidence and mortality. Recently, the research of long non-coding RNAs (lncRNAs) has made breakthroughs in the development of human cancers. This study aimed to figure out the role and action mechanism of lncRNA PVT1 (PVT1) in PCa. METHODS The expression of PVT1, microRNA-15a-5p (miR-15a-5p) and kinesin family member 23 (KIF23) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation, apoptosis, migration and invasion were assessed by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT), flow cytometry and transwell assays, respectively. The protein levels of KIF23 and proliferation, apoptosis, and epithelial-mesenchymal transition (EMT)-related markers were quantified by western blot. The relationship between miR-15a-5p and PVT1 or KIF23 was predicted by starBase v2.0 and verified by dual-luciferase reporter assay. Xenograft assay was conducted to determine the role of PVT1 in vivo. RESULTS The expression of PVT1 and KIF23 was enhanced, while miR-15a-5p expression was reduced in PCa tissues and cells. PVT1 interference inhibited proliferation, migration and invasion but promoted apoptosis of PCa cells. MiR-15a-5p was a target of PVT1, and KIF23 was a target of miR-15a-5p. The inhibition of miR-15a-5p reversed the effects of PVT1 interference and suppressed the roles of KIF23 knockdown. KIF23 expression was regulated by PVT1 through miR-15a-5p. PVT1 interference blocked PCa progression in vivo. CONCLUSION PVT1 knockdown had effects on the progression of PCa by inhibiting the expression of KIF23 via enriching miR-15a-5p in vitro and in vivo, suggesting that PVT1 might be a novel biomarker for the treatment of PCa.
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Affiliation(s)
- Huijuan Wu
- Department of Telemedicine and Internet Medical Center, The Huaihe Hospital of Henan University, No. 115 Ximen Avenue, Kaifeng, 475000 Henan China
| | - Xin Tian
- Department of Urology Surgery, The Huaihe Hospital of Henan University, Kaifeng, Henan China
| | - Chaoyang Zhu
- Department of Urology Surgery, The Huaihe Hospital of Henan University, Kaifeng, Henan China
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miR-6869-5p Inhibits Glioma Cell Proliferation and Invasion via Targeting PGK1. Mediators Inflamm 2020; 2020:9752372. [PMID: 32565733 PMCID: PMC7260655 DOI: 10.1155/2020/9752372] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 04/21/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Accumulating studies have suggested the dysregulated microRNAs (miRNAs) play important roles in brain tumors, including glioma. miR-6869-5p has been documented to be aberrantly expressed in diverse cancers. However, the precise role of miR-6869-5p in glioma remains poorly understood. This study is aimed at evaluating its modifying effects on glioma. Significantly decreased expression of miR-6869-5p was found in glioma tissues and cells. Negative association was documented between miR-6869-5p and PGK1 in glioma cells, and PGK1 was demonstrated to be a targeted gene of this miRNA by luciferase reporter assay. miR-6869-5p regulated glioma cell proliferation and invasion via targeting PGK1. In addition, the survival analysis had suggested that low miR-6869-5p expression predicted poor prognosis of glioma patients. This study has suggested that miR-6869-5p is a useful tumor suppressor and prognostic marker in glioma.
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Wang DW, Lou XQ, Liu ZL, Zhang N, Pang L. LncRNA SNHG1 protects SH-SY5Y cells from hypoxic injury through miR-140-5p/Bcl-XL axis. Int J Neurosci 2020; 131:336-345. [PMID: 32186226 DOI: 10.1080/00207454.2020.1744594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: Hypoxic brain injury is one of the major causes of neurodevelopmental impairment and cardiovascular disability. LncRNA SNHG1 works as a critical factor in hypoxic induced injury, however, the potential mechanism is still not known well.Methods: The expression level of small nucleolar RNA host gene 1 (SNHG1) and miR-140-5p was detected by qRT-PCR. The western blot assay was performed to measure the level of Bcl-XL and apoptosis-related proteins. The target relationship between lncRNA SNHG1 and miR-140-5p, as well as miR-140-5p and Bcl-XL was detected by dual luciferase reporter gene assay. Cell apoptosis was assessed using Annexin V/PI staining by flow cytometry. Cell viability was analyzed by MTT assay.Results: Oxygen glucose deprivation (OGD) treatment inhibited SNHG1 and Bcl-XL expression and enhanced miR-140-5p expression. OGD treatment-induced cell viability inhibition, cell apoptosis promotion were partially abrogated when SH-SY5Y cells were transfected with pcDNA3.1-SNHG1 or miR-140-5p inhibitor. Moreover, luciferase reporter assay revealed that lncRNA SNHG1 bound directly to miR-140-5p, and miR-140-5p directly targeted Bcl-XL. The protective effect of SNHG1 overexpressing on cell apoptosis induced by OGD was attenuated after transfected with miR-140-5p mimic or sh-Bcl-XL in SH-SY5Y cells.Conclusion: LncRNA SNHG1-modulated miR-140-5p inhibition regulates Bcl-XL expression, thereby reducing cell apoptosis and recovering cell viability of SH-SY5Y cells. The results in this study provide novel insight into the mechanism of SNHG1 mediated signaling pathway during hypoxic brain injury.
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Affiliation(s)
- Da-Wei Wang
- Department of Emergency, The First Hospital of Jilin University, Changchun, PR China
| | - Xiao-Qian Lou
- Department of Endocrinology, The First Hospital of Jilin University, Changchun, PR China
| | - Zuo-Long Liu
- Department of Emergency, The First Hospital of Jilin University, Changchun, PR China
| | - Nan Zhang
- Department of Emergency, The First Hospital of Jilin University, Changchun, PR China
| | - Li Pang
- Department of Emergency, The First Hospital of Jilin University, Changchun, PR China
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Sun J, Jiang R, Song M, Yao J, Hou S, Zhu Y, Ji X, Sheng H, Tang Z, Liu Q, Jia Z, Shi W, Shi J. Pathological Grade-Associated Transcriptome Profiling of lncRNAs and mRNAs in Gliomas. Front Oncol 2020; 10:253. [PMID: 32211318 PMCID: PMC7076085 DOI: 10.3389/fonc.2020.00253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/14/2020] [Indexed: 11/19/2022] Open
Abstract
The aim of the present study was to explore the expression profiles of lncRNAs and mRNAs in glioma patients and to elucidate any potential relationship between lncRNAs and mRNAs in glioma. High-throughput transcriptome sequencing of mRNAs and lncRNAs from six normal tissues and 16 glioma tissues (grade II, six cases; grade III, four cases; and grade IV, six cases) was performed. Series test of cluster (STC) analysis was used to screen significant trending models associated with glioma. Gene co-expression networks were constructed for the differentially expressed lncRNAs and mRNAs, and gene-ontology (GO) and pathway-enrichment analyses were further performed. Quantitative real-time PCR was performed to validate the five most differentially expressed lncRNAs and mRNAs. After filtering the raw sequencing data, we found 578 lncRNAs and 3,216 mRNAs that were significantly dysregulated in glioma (fold change ≥ 2, p < 0.05). Twenty model profiles of lncRNA and 10 model profiles of mRNA were summarized, and three patterns of lncRNAs and two patterns of mRNAs were of clinical significance. Three gene co-expression networks between mRNAs and lncRNAs were built to clarify the relationship between lncRNAs and mRNAs in glioma. GO and pathway analyses indicated that the differentially expressed lncRNAs and mRNAs were enriched in several biological processes and signaling pathways associated with tumorigenesis. Both lncRNAs and mRNAs exhibited dynamic differential expression profiles that indicated their potential roles in different degrees of glioma malignancy. A series of bioinformatics analyses indicated that most of these lncRNAs and mRNAs are involved in important biological processes and pathways associated with the pathogenesis of glioma. These results provide potential directions and valuable resources for future investigations via the comprehensive integration of these lncRNAs and mRNAs.
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Affiliation(s)
- Junlong Sun
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Neurosurgery, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Rui Jiang
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Mengruo Song
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Junzhong Yao
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Shiqiang Hou
- Department of Neurosurgery, Chuzhou Clinical College of Anhui Medical University, The First Peoples Hospital Chuzhou, Chuzhou, China
| | - Yunhua Zhu
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Xiang Ji
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Hao Sheng
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Zhongyu Tang
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Qianqian Liu
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Zhongzheng Jia
- Medical Image Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Wei Shi
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
| | - Jinlong Shi
- Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair and Department of Neurosurgery, The Affiliated Hospital of Nantong University, Nantong, China
- Department of Clinic Research Center, The Affiliated Hospital of Nantong University, Nantong, China
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Kong X, Hu S, Yuan Y, Du Y, Zhu Z, Song Z, Lu S, Zhao C, Yan D. Analysis of lncRNA, miRNA and mRNA-associated ceRNA networks and identification of potential drug targets for drug-resistant non-small cell lung cancer. J Cancer 2020; 11:3357-3368. [PMID: 32231742 PMCID: PMC7097957 DOI: 10.7150/jca.40729] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Drug resistance to chemotherapeutic drugs or targeted medicines is an obstacle encountered in the treatment of non-small-cell lung cancer (NSCLC). However, the mechanisms of competing endogenous RNA (ceRNA) on the drug resistance in NSCLC are rarely reported. In this paper, the comprehensive expression profiles of lncRNAs and mRNAs in drug-resistant NSCLC cells were obtained by RNA sequencing. Methods: The dysregulated lncRNAs, miRNAs and mRNAs in drug-resistant NSCLC cell lines were identified by RNA-sequencing and bioinformatics methods. Results: A total of 39 dysregulated lncRNAs and 650 dysregulated mRNAs were identified between drug-resistant NSCLC cell lines and their parental cell lines. Additionally, 33 lncRNA-miRNA-mRNA pathways in the ceRNA network in drug-resistant NSCLC were constructed through bioinformatics methods and ceRNA regulatory rules. These comprised 12 dysregulated lncRNAs, five dysregulated miRNAs, and eight dysregulated mRNAs. In addition, lncRNA ATP2B1/miR-222-5p/TAB2 and lncRNA HUWE1/miR-222-5p/TAB2 were identified as potential ceRNA networks involved in drug resistance to NSCLC. Conclusions: The current study provides a promising therapeutic strategy against the lncRNA-miRNA-mRNA ceRNA regulatory network for NSCLC treatment and deepens our comprehension of the ceRNA regulatory mechanisms related to drug resistance to NSCLC.
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Affiliation(s)
- Xiangzhen Kong
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Shousen Hu
- Department of Otolaryngology Head and Neck Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongliang Yuan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Yue Du
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Zijia Zhu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Zhizhen Song
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Shanshan Lu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Chang Zhao
- Department of Otolaryngology Head and Neck Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dan Yan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
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Jin T, Liu M, Liu Y, Li Y, Xu Z, He H, Liu J, Zhang Y, Ke Y. Lcn2-derived Circular RNA (hsa_circ_0088732) Inhibits Cell Apoptosis and Promotes EMT in Glioma via the miR-661/RAB3D Axis. Front Oncol 2020; 10:170. [PMID: 32154171 PMCID: PMC7047435 DOI: 10.3389/fonc.2020.00170] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Glioma is the most common malignant tumor of the central nervous system, and often displays invasive growth. Recently, circular RNA (circRNA), which is a novel non-coding type of RNA, has been shown to play a vital role in glioma tumorigenesis. However, the functions and mechanism of lipocalin-2 (Lcn2)-derived circular RNA (hsa_circ_0088732) in glioma progression remain unclear. Methods: We evaluated hsa_circ_0088732 expression by fluorescence in situ hybridization (FISH), Sanger sequencing, and PCR assays. Cell apoptosis was evaluated by flow cytometry and Hoechst 33258 staining. Transwell migration and invasion assays were performed to measure cell metastasis and viability. In addition, the target miRNA of hsa_circ_0088732 and the target gene of miR-661 were predicted by a bioinformatics analysis, and the interactions were verified by dual-luciferase reporter assays. RAB3D expression was analyzed by an immunochemistry assay, and E-cadherin, N-cadherin, and vimentin protein expression were examined by western blot assays. A mouse xenograft model was developed and used to analyze the effects of hsa_circ_0088732 on glioma growth in vivo. Results: We verified that hsa_circ_0088732 is circular and highly expressed in glioma tissues. Knockdown of hsa_circ_0088732 induced glioma cell apoptosis and inhibited glioma cell migration, invasion, and epithelial-mesenchymal transition (EMT). We found that hsa_circ_0088732 negatively regulated miR-661 by targeting miR-661, and RAB3D was a target gene of miR-661. In addition, inhibition of miR-661 promoted glioma cell metastasis and suppressed cell apoptosis. Knockdown of RAB3D induced cell apoptosis and suppressed cell metastasis. Moreover, hsa_circ_0088732 accelerated glioma progression through its effects on the miR-661/RAB3D axis. Finally, results from a mouse xenograft model confirmed that knockdown of hsa_circ_0088732 induced miR-661 expression, resulting in suppression of RAB3D expression and inhibition of tumor growth in vivo. Conclusion: We demonstrated that hsa_circ_0088732 facilitated glioma progression by sponging miR-661 to increase RAB3D expression. This study provides a theoretical basis for understanding the development and occurrence of glioma, as well as for the development of targeted drugs.
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Affiliation(s)
- Tao Jin
- The National Key Clinical Specialty, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Department of Neurosurgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Mingfa Liu
- Department of Neurosurgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Yan Liu
- Department of Neurosurgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Yuanzhi Li
- Department of Neurosurgery, Affiliated Hengyang Hospital of Southern Medical University (Hengyang Central Hospital), Hengyang, China
| | - Zhennan Xu
- Department of Neurosurgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, China
| | - Haoqi He
- The National Key Clinical Specialty, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Liu
- The National Key Clinical Specialty, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuxuan Zhang
- The National Key Clinical Specialty, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yiquan Ke
- The National Key Clinical Specialty, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, Department of Neurosurgery, The Engineering Technology Research Center of Education Ministry of China, Zhujiang Hospital, Southern Medical University, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
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Sun J, Li B, Shu C, Ma Q, Wang J. Functions and clinical significance of circular RNAs in glioma. Mol Cancer 2020; 19:34. [PMID: 32061256 PMCID: PMC7023692 DOI: 10.1186/s12943-019-1121-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
CircRNAs are a class of single-stranded RNA molecules with a covalently closed loop structure and have been characterized by high stability, abundance, conservation, and display tissue/developmental stage-specific expression, furthermore, based on the abundance in distinct body fluids or exosomes, circRNAs present novel biomarkers and targets for the diagnosis and prognosis of cancers. Recently, the regulatory mechanisms of biogenesis and molecular functions, including miRNAs and RBPs sponge, translation as well as transcriptional and splicing regulation, have been gradually uncovered, although various aspects remained to be elucidated in combination with deep-sequence and bioinformatics. Accumulating studies have indicated that circRNAs are more enriched in neuronal tissues partly due to the abundance of specific genes promoting circularization, suggesting dysregulation of circRNAs is closely related to diseases of the nervous system, including glioma. In this review, we elaborate on the biogenesis, functions, databases as well as novel advances especially involved in the molecular pathways, highlight its great value as diagnostic or therapeutic targets in glioma.
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Affiliation(s)
- Jikui Sun
- School of Medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, People's Republic of China.,Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Banban Li
- Qilu Hospital, Shandong University, 107 Cultural West Road, Jinan, 250012, People's Republic of China.,Department of Hematology, Taian Central Hospital, 29 Longtan Road, Taian, 271000, People's Republic of China
| | - Chang Shu
- Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Quanfeng Ma
- Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China
| | - Jinhuan Wang
- School of Medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, People's Republic of China. .,Tianjin Cerebral Vascular and Neural Degenerative Disease Key Laboratory, Tianjin Neurosurgery Institute, Department of Neurosurgery, Tianjin Huan Hu Hospital, Tianjin, 300350, People's Republic of China.
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44
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Fu XZ, Zhang XY, Qiu JY, Zhou X, Yuan M, He YZ, Chun CP, Cao L, Ling LL, Peng LZ. Whole-transcriptome RNA sequencing reveals the global molecular responses and ceRNA regulatory network of mRNAs, lncRNAs, miRNAs and circRNAs in response to copper toxicity in Ziyang Xiangcheng (Citrus junos Sieb. Ex Tanaka). BMC PLANT BIOLOGY 2019; 19:509. [PMID: 31752684 PMCID: PMC6873749 DOI: 10.1186/s12870-019-2087-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Copper (Cu) toxicity has become a potential threat for citrus production, but little is known about related mechanisms. This study aims to uncover the global landscape of mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in response to Cu toxicity so as to construct a regulatory network of competing endogenous RNAs (ceRNAs) and to provide valuable knowledge pertinent to Cu response in citrus. RESULTS Tolerance of four commonly used rootstocks to Cu toxicity was evaluated, and 'Ziyang Xiangcheng' (Citrus junos) was found to be the most tolerant genotype. Then the roots and leaves sampled from 'Ziyang Xiangcheng' with or without Cu treatment were used for whole-transcriptome sequencing. In total, 5734 and 222 mRNAs, 164 and 5 lncRNAs, 45 and 17 circRNAs, and 147 and 130 miRNAs were identified to be differentially expressed (DE) in Cu-treated roots and leaves, respectively, in comparison with the control. Gene ontology enrichment analysis showed that most of the DEmRNAs and targets of DElncRNAs and DEmiRNAs were annotated to the categories of 'oxidation-reduction', 'phosphorylation', 'membrane', and 'ion binding'. The ceRNA network was then constructed with the predicted pairs of DEmRNAs-DEmiRNAs and DElncRNAs-DEmiRNAs, which further revealed regulatory roles of these DERNAs in Cu toxicity. CONCLUSIONS A large number of mRNAs, lncRNAs, circRNAs, and miRNAs in 'Ziyang Xiangcheng' were altered in response to Cu toxicity, which may play crucial roles in mitigation of Cu toxicity through the ceRNA regulatory network in this Cu-tolerant rootstock.
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Affiliation(s)
- Xing-Zheng Fu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China.
| | - Xiao-Yong Zhang
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Jie-Ya Qiu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Xue Zhou
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Meng Yuan
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Yi-Zhong He
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Chang-Pin Chun
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Li Cao
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Li-Li Ling
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China
| | - Liang-Zhi Peng
- Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, 400712, China.
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Liu K, Guo Y, Zheng K, Zou C, Wu H, Wang S, Ou L, Wang Y, Huang B, Wang X. Identification of the circRNA-miRNA-mRNA regulatory network of Hsp90 inhibitor-induced cell death in colorectal cancer by integrated analysis. Gene 2019; 727:144232. [PMID: 31715300 DOI: 10.1016/j.gene.2019.144232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/16/2019] [Accepted: 10/27/2019] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is a global disease with high incidence and mortality rate. Hsp90 inhibitors induce cell death in various cancers, including CRC. However, the underlying mechanisms need to be clarified further. In this study, Caco-2 cells were treated with 0.25 μM SNX-2112, an Hsp90 inhibitor, for 48 h; subsequently, whole-transcriptome sequencing was performed. At the mRNA level in SNX-2112-treated Caco-2 cells, 1588 genes were upregulated, and 433 genes were downregulated. Six genes were found to be associated with necroptosis and apoptosis, and these 6 upregulated genes were validated by RT-qPCR. Hundred and six miRNAs were upregulated, and 48 miRNAs were downregulated in SNX-2112-treated Caco-2 cells. Eleven downregulated miRNAs were found to interact with the 6 upregulated genes. Moreover, 676 circRNAs were upregulated, and 291 circRNAs were downregulated in SNX-2112-treated Caco-2 cells. Among them, 126 circRNAs were found to be the target of the 11 downregulated miRNAs. The circRNA-miRNA-mRNA regulatory network of Hsp90 inhibitor-induced cell death in colorectal cancer was constructed. This regulatory network extends the underlying mechanism of Hsp90 and improves our understanding of Hsp90 inhibitors as potential targeted therapeutic agents.
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Affiliation(s)
- Kaisheng Liu
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China
| | - Yaomin Guo
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong, China
| | - Chang Zou
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China
| | - Haixiong Wu
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, Guangdong, China
| | - Ling Ou
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China
| | - Bowan Huang
- Department of Anesthesiology, Central People's Hospital of Zhanjiang, Zhanjiang 524000, Guangdong, China.
| | - Xiao Wang
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, Guangdong, China.
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Cheng Z, Luo C, Guo Z. LncRNA-XIST/microRNA-126 sponge mediates cell proliferation and glucose metabolism through the IRS1/PI3K/Akt pathway in glioma. J Cell Biochem 2019; 121:2170-2183. [PMID: 31680298 DOI: 10.1002/jcb.29440] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
Abstract
Abnormal glucose metabolism may contribute to cancer progression. Glioma represents a cancer resulting from an imbalance between glucose metabolism and tumor growth. However, the molecular mechanisms responsible for dysregulated brain glucose metabolism and lactate accumulation in glioma remain to be elucidated. The present study identified a long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) as a candidate to mediate glucose metabolism in glioma. Cell viability, migration, invasion, and resistance to apoptosis were evaluated in lncRNA-XIST-depleted glioblastoma cells by short hairpin RNA. Glucose uptake, lactate production, as well as levels of glucose transporter 1 (GLUT1) and GLUT3, were measured. Luciferase assay, RNA pull-down, and RNA immunoprecipitation were performed to validate the interactions among lncRNA-XIST, microRNA-126 (miR-126), and insulin receptor substrate 1 (IRS1). An in vivo analysis was carried out in nude mice bearing glioblastoma cell xenografts. The study found that lncRNA-XIST knockdown inhibited cell viability, migration, invasion, resistance to apoptosis, and glucose metabolism of glioblastoma cells. LncRNA-XIST functioned as a competing endogenous RNA of miR-126 and then regulated IRS1/PI3K/Akt pathway in glioblastoma cells. In vivo results demonstrated lncRNA-XIST knockdown reduces the tumorigenicity of glioblastoma cells. Taken together, we demonstrated a novel cellular mechanism that was dependent of the lncRNA-XIST/miR-126/IRS1/PI3K/Akt pathway in enhanced glucose metabolism in glioma.
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Affiliation(s)
- Zhihua Cheng
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Cong Luo
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Zhilin Guo
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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Identification of differentially expressed genes and fusion genes associated with malignant progression of spinal cord gliomas by transcriptome analysis. Sci Rep 2019; 9:13583. [PMID: 31537867 PMCID: PMC6753211 DOI: 10.1038/s41598-019-50072-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 09/05/2019] [Indexed: 11/25/2022] Open
Abstract
Glioma, the most common histological subtype of primary spinal cord tumors, is considered as a rare central nervous system neoplasm. In this study, 9 glioma samples (4 of grade II and 5 of grade IV with H3K27M positive) were analyzed to examine the molecular mechanisms underlying the malignant progression of gliomas, transcriptome sequencing. Differentially expressed genes (DEGs) in grade IV vs. grade II were analyzed by using the Limma package in R. Enrichment analysis was performed for the individual DEGs through VennPlex software and the Database for Annotation. Gene mutations and fusions were analyzed using the Genome Analysis Toolkit and STAR-Fusion. A total of 416 DEGs were identified in grade IV vs. grade II. Functional analysis of the DEGs showed that GALR1 and GRM5 of neuroactive ligand-receptor interactions signaling pathways may be relaed to malignant progression of gliomas. Further systematic transcriptional profiling identified 11 in-frame/frameshift gene fusions in the tumors. Notably, one novel gene fusions, GATSL2-GTF2I was detected in all of the grade II samples. In summary, the molecular alterations observed in glioma progression may improve the characterization of different human spinal cord glioma grades. The transcriptome analysis of intramedullary spinal cord glioma will provide a new candidate gene list for further mechanism research.
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Zhang L, Mao J. Long-Chain Noncoding RNA PVT1 Gene Polymorphisms Are Associated with the Risk and Prognosis of Colorectal Cancer in the Han Chinese Population. Genet Test Mol Biomarkers 2019; 23:728-736. [PMID: 31509024 DOI: 10.1089/gtmb.2019.0078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: To investigate the association between long-chain noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) gene polymorphisms and the risk and prognosis of colorectal cancer (CRC) in the Han Chinese population. Methods: A cohort of 225 Han Chinese CRC patients and 225 healthy controls was analyzed for the PVT1 gene genotypes at the loci rs1221464062, rs1366023633, rs1252200336, and rs1273526412. The levels of PVT1 mRNA, hsa-miR-455-5p, and hsa-miR-455-3p in both cancerous tissues and paracancerous normal tissues of the CRC patients were determined by reverse transcription polymerase chain reaction. The survival rate of CRC patients was recorded after 3 years of follow-up. Results: The risk of developing CRC in subjects with the ID genotype of the PVT1 gene locus rs1252200336 was 2.71 times higher compared with the type II genotype; and the D allele was a risk factor for CRC. The survival of CRC patients with the ID/DD genotypes of the PVT1 gene rs1252200336 locus was significantly lower compared with the II genotype. In both the cancerous tissues and the paracancerous normal tissues of CRC patients, the level of lncRNA PVT1 was negatively correlated with the hsa-miR-455-5p and hsa-miR-455-3p levels. In subjects carrying the ID/DD genotypes of the PVT1 gene rs1252200336 locus, the level of the lncRNA PVT1 in cancerous tissues was significantly higher compared with the II genotype, whereas the hsa-miR-455-3p level was significantly lower compared with the II genotype. Conclusion: The PVT1 gene rs1252200336 locus polymorphisms are associated with the risk of developing CRC in the Han Chinese population. The rs1252200336 locus deletion mutation (D) may impact the binding of hsa-miR-455-5p to the lncRNA PVT1 and its role in the development and progression of CRC.
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Affiliation(s)
- Lei Zhang
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiehong Mao
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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49
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Guo X, Luo Z, Xia T, Wu L, Shi Y, Li Y. Identification of miRNA signature associated with BMP2 and chemosensitivity of TMZ in glioblastoma stem-like cells. Genes Dis 2019; 7:424-439. [PMID: 32884997 PMCID: PMC7452549 DOI: 10.1016/j.gendis.2019.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/12/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Glioblastoma multiform (GBM) is the most lethal intracranial tumor in adults. Glioblastoma stem-like cells (GSCs) are responsible for tumorigenesis and chemotherapy resistance. BMPs are known to increase temozolomide (TMZ) response in GSCs, however, the intracellular molecular mechanism remains largely unknown. In this study, we built a GSC cell model called U87S, and performed RNA sequencing to identify differentially expressed (DE) miRNA profiles in U87S cells treated with BMP2, TMZ or combined BMP2 and TMZ respectively. Bioinformatics analysis revealed that most DE miRNAs were involved in the cancer pathways, suggesting their crucial roles in gliomagenesis. Eight miRNAs from RNA-seq were validated. Four out of these miRNAs (has-miR-199a-3p, hsa-miR-374b-5p, hsa-miR-320d, and hsa-miR-339-5p) were found significantly up-regulated in GBM tumor tissues. One of them, hsa-miR-199a-3p, was significantly correlated with the survival of GBM patients, and differentially expressed in U87S cells. Expression of hsa-miR-199a-3p was up-regulated by BMP. Overexpression of hsa-miR-199a-3p in U87S cells inhibited cell viability and enhanced the cytotoxicity of TMZ. And activation of BMP boosted the effect of hsa-miR-199a-3p on cell viability and TMZ-mediated cytotoxicity. Besides, expressions of five predicted targets of hsa-miR-199a-3p were evaluated. Four of them were differentially expressed in GBM tumors. And one of them, SLC22A18, was associated with the survival of GBM patients. In the end, a hsa-miR-199a-3p-mediated ceRNA network was constructed for the convenience of future study. Together, our data provided DE miRNA expression profiles associated with BMP2 and TMZ in GSCs, which might lead to finding out miRNA-based target therapies that specially target GSCs.
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Affiliation(s)
- Xiaoyu Guo
- Life Science Institute, Chongqing Medical University, Chongqing, China
| | - Ziguo Luo
- Life Science Institute, Chongqing Medical University, Chongqing, China
| | - Tong Xia
- Life Science Institute, Chongqing Medical University, Chongqing, China
| | - Lanxiang Wu
- Life Science Institute, Chongqing Medical University, Chongqing, China
| | - Yanshu Shi
- Department of Radiology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Ying Li
- Life Science Institute, Chongqing Medical University, Chongqing, China
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50
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MiR-1261/circ-PTPRZ1/PAK1 pathway regulates glioma cell growth and invasion. Hum Cell 2019; 32:540-547. [DOI: 10.1007/s13577-019-00271-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/19/2019] [Indexed: 12/21/2022]
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