1
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Song B, Huang Y, Ma J, Yu L, Yu Y, Peng C, Wu W. Construction and Analysis of ceRNA Networks Reveal the Key Genes Associated with Bovine Herpesvirus Type 1 Infection. Infect Drug Resist 2023; 16:5729-5740. [PMID: 37670981 PMCID: PMC10476657 DOI: 10.2147/idr.s411034] [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: 05/17/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023] Open
Abstract
Background Virus infection can cause the changes of lncRNA expression levels to regulate the interaction between virus and host, but the relationship between BHV-1 infection and lncRNA has not been reported. Methods In this study, in order to reveal the molecular mechanism of RNA in BoHV-1 infection, the Madin-Darby bovine kidney (MDBK) cells were infected with BoHV-1, transcriptome sequencing were performed by next-generation sequencing at 18 h or 24 h or 33 h of viral infection and then based on the competitive endogenous RNA (ceRNA) theory, lncRNA-miRNA-mRNA networks were constructed using these high-throughput sequencing data. The network analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for functional annotation and exploration of ncRNA ceRNAs in BoHV-1 infection. Results The results showed that 48 lncRNAs, 123 mRNAs and 20 miRNAs as differentially expressed genes, and the mitogen activated protein kinase (MAPK) pathway and calcium signaling pathway were significantly enriched in the ceRNA network. Some differentially expressed lncRNA genes were randomly selected for verification by RT-qPCR, and the results showed that their expression trend was consistent with the results of transcriptome sequencing data. Conclusion This study revealed that BoHV-1 infection can affect the expression of RNAs in MDBK cells and the regulation of ceRNA network to carry out corresponding biological functions in the host, but further experimental studies are still necessary to prove the hub genes function in ceRNA network and the molecular mechanism in BoHV-1 infection.
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Affiliation(s)
- Baifen Song
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yanmei Huang
- The College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, People’s Republic of China
| | - Jinzhu Ma
- The College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, People’s Republic of China
| | - Liquan Yu
- The College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, People’s Republic of China
| | - Yongzhong Yu
- The College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, People’s Republic of China
| | - Chen Peng
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Wenxue Wu
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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2
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Rao G, Peng X, Tian Y, Fu X, Zhang Y. Circular RNAs in hepatocellular carcinoma: biogenesis, function, and pathology. Front Genet 2023; 14:1106665. [PMID: 37485335 PMCID: PMC10361733 DOI: 10.3389/fgene.2023.1106665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. Both genetic and environmental factors through a multitude of underlying molecular mechanisms participate in the pathogenesis of HCC. Recently, numerous studies have shown that circular RNAs (circRNAs), an emerging class of non-coding RNAs characterized by the presence of covalent bonds linking 3' and 5' ends, play an important role in the initiation and progression of cancers, including HCC. In this review, we outline the current status of the field of circRNAs, with an emphasis on the functions and mechanisms of circRNAs in HCC and its microenvironment. We also summarize and discuss recent advances of circRNAs as biomarkers and therapeutic targets. These efforts are anticipated to throw new insights into future perspectives about circRNAs in basic, translational and clinical research, eventually advancing the diagnosis, prevention and treatment of HCC.
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Affiliation(s)
- Guocheng Rao
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Xi Peng
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yan Tian
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yuwei Zhang
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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3
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Gupta S, Singh P, Tasneem A, Almatroudi A, Rahmani AH, Dohare R, Parveen S. Integrative Multiomics and Regulatory Network Analyses Uncovers the Role of OAS3, TRAFD1, miR-222-3p, and miR-125b-5p in Hepatitis E Virus Infection. Genes (Basel) 2022; 14:42. [PMID: 36672782 PMCID: PMC9859139 DOI: 10.3390/genes14010042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The hepatitis E virus (HEV) is a long-ignored virus that has spread globally with time. It ranked 6th among the top risk-ranking viruses with high zoonotic spillover potential; thus, considering its viral threats is a pressing priority. The molecular pathophysiology of HEV infection or the underlying cause is limited. Therefore, we incorporated an unbiased, systematic methodology to get insights into the biological heterogeneity associated with the HEV. Our study fetched 93 and 2016 differentially expressed genes (DEGs) from chronic HEV (CHEV) infection in kidney-transplant patients, followed by hub module selection from a weighted gene co-expression network (WGCN). Most of the hub genes identified in this study were associated with interferon (IFN) signaling pathways. Amongst the genes induced by IFNs, the 2'-5'-oligoadenylate synthase 3 (OAS3) protein was upregulated. Protein-protein interaction (PPI) modular, functional enrichment, and feed-forward loop (FFL) analyses led to the identification of two key miRNAs, i.e., miR-222-3p and miR-125b-5p, which showed a strong association with the OAS3 gene and TRAF-type zinc finger domain containing 1 (TRAFD1) transcription factor (TF) based on essential centrality measures. Further experimental studies are required to substantiate the significance of these FFL-associated genes and miRNAs with their respective functions in CHEV. To our knowledge, it is the first time that miR-222-3p has been described as a reference miRNA for use in CHEV sample analyses. In conclusion, our study has enlightened a few budding targets of HEV, which might help us understand the cellular and molecular pathways dysregulated in HEV through various factors. Thus, providing a novel insight into its pathophysiology and progression dynamics.
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Affiliation(s)
- Sonam Gupta
- Molecular Virology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Prithvi Singh
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Alvea Tasneem
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ravins Dohare
- Mathematical and Computational Biology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shama Parveen
- Molecular Virology Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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4
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Zhu B, Gao J, Zhang Y, Liao B, Zhu S, Li C, Liao J, Liu J, Jiang C, Zeng J. CircRNA/miRNA/mRNA axis participates in the progression of partial bladder outlet obstruction. BMC Urol 2022; 22:191. [PMID: 36434693 PMCID: PMC9700926 DOI: 10.1186/s12894-022-01132-2] [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: 07/02/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More and more evidence showed that circRNA/miRNA/mRNA axis played a vital role in the pathogenesis of some diseases. However, the role of circRNA/miRNA/mRNA axis in partial bladder outlet obstruction (pBOO) remains unknown. Our study aimed to explore the complex regulatory mechanism of circRNA/miRNA/mRNA axis in pBOO. METHODS The pBOO rat model was established, and the bladder tissues were collected for mRNA sequencing. The differentially expressed mRNAs were analyzed by high-throughput sequencing, and the GO and KEGG analysis of the differentially expressed mRNAs were performed. Competing endogenous RNAs (ceRNAs) analysis identified the potential regulation function of circRNA/miRNA/mRNA axis in pBOO. qRT-PCR detected the expression of circRNA/miRNA/mRNA. miRanda software was performed to predict the relationship between circRNA and miRNA, miRNA and mRNA. RESULTS Compared with the sham group, a total of 571 mRNAs were differentially expressed in the pBOO group, of which 286 were up-regulated and 285 were down-regulated. GO analysis showed that the mRNAs were mainly involved in cellular process, single-organism process, and cell, etc. KEGG analysis showed that the enriched signaling pathways were metabolic pathways, cell adhesion molecules (CAMs), and HTLV-I infection, etc. Based on the previous transcriptome data and differentially expressed circRNAs, we drew the ceRNA network regulation diagram. qRT-PCR results confirmed that chr3:113195876|113197193/rno-miR-30c-1-3p/Gata4, chr1:126188351|126195625/rno-miR-153-5p/Diaph3, and chr9:81258380|81275269/rno-miR-135b-5p/Pigr axis may have ceRNA function. miRanda confirmed there have the binding sites of circRNA/miRNA/mRNA axis. CONCLUSIONS CircRNA/miRNA/mRNA axis was involved in the progression of pBOO. Our research on the circRNA/miRNA/mRNA axis revealed new pathogenesis and treatment strategies for pBOO.
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Affiliation(s)
- Baoyi Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jun Gao
- grid.410737.60000 0000 8653 1072Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518 Guangdong People’s Republic of China
| | - Yuying Zhang
- Department of Child Health Care, Shenzhen Longhua Maternity and Child Health Care Hospital, Shenzhen, 518000 Guangdong People’s Republic of China
| | - Baojian Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China ,grid.9227.e0000000119573309Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510700 Guangdong People’s Republic of China
| | - Sihua Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chunling Li
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Junhao Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianjia Liu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chonghe Jiang
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianwen Zeng
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
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Song Y, Li J, Mao Y, Zhang X. ceRNAshiny: An Interactive R/Shiny App for Identification and Analysis of ceRNA Regulation. Front Mol Biosci 2022; 9:865408. [PMID: 35647026 PMCID: PMC9136144 DOI: 10.3389/fmolb.2022.865408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The competing endogenous RNA (ceRNA) network is a newly discovered post-transcriptional regulation that controls both physiological and pathological progresses. Increasing research studies have been pivoted on this theory to explore the function of novel non-coding RNAs, pseudogenes, circular RNAs, and messenger RNAs. Although there are several R packages or computational tools to analyze ceRNA networks, an urgent need for easy-to-use computational tools still remains to identify ceRNA regulation. Besides, the conventional tools were mainly devoted to investigating ceRNAs in malignancies instead of those in neurodegenerative diseases. To fill this gap, we developed ceRNAshiny, an interactive R/Shiny application, which integrates widely used computational methods and databases to provide and visualize the construction and analysis of the ceRNA network, including differential gene analysis and functional annotation. In addition, demo data in ceRNAshiny could provide ceRNA network analyses about neurodegenerative diseases such as Parkinson's disease. Overall, ceRNAshiny is a user-friendly application that benefits all researchers, especially those who lack an established bioinformatic pipeline and are interested in studying ceRNA networks.
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Affiliation(s)
- Yueqiang Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jia Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiming Mao
- Department of Thoracic Surgery, Suzhou Kowloon Hospital, School of Medicine, Shanghai Jiao Tong University, Suzhou, China
| | - Xi Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Rehabilitation, Huashan Hospital, Fudan University, Shanghai, China
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6
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Yang M, Li J, Deng S, Fan H, Peng Y, Ye G, Wang J, Wei J, Jiang X, Xu Z, Qing L, Wang F, Yang Y, Liu Y. Competitive Endogenous RNA Network Activates Host Immune Response in SARS-CoV-2-, panH1N1 (A/California/07/2009)-, and H7N9 (A/Shanghai/1/2013)-Infected Cells. Cells 2022; 11:cells11030487. [PMID: 35159296 PMCID: PMC8834034 DOI: 10.3390/cells11030487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/16/2022] [Accepted: 01/27/2022] [Indexed: 02/05/2023] Open
Abstract
The global outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still ongoing, as is research on the molecular mechanisms underlying cellular infection by coronaviruses, with the hope of developing therapeutic agents against this pandemic. Other important respiratory viruses such as 2009 pandemic H1N1 and H7N9 avian influenza virus (AIV), influenza A viruses, are also responsible for a possible outbreak due to their respiratory susceptibility. However, the interaction of these viruses with host cells and the regulation of post-transcriptional genes remains unclear. In this study, we detected and analyzed the comparative transcriptome profiling of SARS-CoV-2, panH1N1 (A/California/07/2009), and H7N9 (A/Shanghai/1/2013) infected cells. The results showed that the commonly upregulated genes among the three groups were mainly involved in autophagy, pertussis, and tuberculosis, which indicated that autophagy plays an important role in viral pathogenicity. There are three groups of commonly downregulated genes involved in metabolic pathways. Notably, unlike panH1N1 and H7N9, SARS-CoV-2 infection can inhibit the m-TOR pathway and activate the p53 signaling pathway, which may be responsible for unique autophagy induction and cell apoptosis. Particularly, upregulated expression of IRF1 was found in SARS-CoV-2, panH1N1, and H7N9 infection. Further analysis showed SARS-CoV-2, panH1N1, and H7N9 infection-induced upregulation of lncRNA-34087.27 could serve as a competitive endogenous RNA to stabilize IRF1 mRNA by competitively binding with miR-302b-3p. This study provides new insights into the molecular mechanisms of influenza A virus and SARS-CoV-2 infection.
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MESH Headings
- A549 Cells
- Animals
- COVID-19/genetics
- COVID-19/immunology
- COVID-19/virology
- HEK293 Cells
- Host-Pathogen Interactions/immunology
- Humans
- Immunity/genetics
- Immunity/immunology
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza A Virus, H7N9 Subtype/immunology
- Influenza A Virus, H7N9 Subtype/physiology
- Influenza, Human/genetics
- Influenza, Human/immunology
- Influenza, Human/virology
- Interferon Regulatory Factor-1/genetics
- Interferon Regulatory Factor-1/immunology
- Interferon Regulatory Factor-1/metabolism
- MicroRNAs/genetics
- MicroRNAs/immunology
- MicroRNAs/metabolism
- Pandemics/prevention & control
- RNA/genetics
- RNA/immunology
- RNA/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/immunology
- RNA, Long Noncoding/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Messenger/metabolism
- RNA-Seq/methods
- SARS-CoV-2/physiology
- Signal Transduction/genetics
- Signal Transduction/immunology
- Transcriptome/genetics
- Transcriptome/immunology
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Affiliation(s)
- Minghui Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Jin Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518406, China;
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China;
| | - Hao Fan
- Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA;
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Guoguo Ye
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Jun Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Jinli Wei
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Xiao Jiang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Zhixiang Xu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Ling Qing
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Fuxiang Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
- Correspondence: (Y.Y.); (Y.L.)
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People’s Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China; (M.Y.); (Y.P.); (G.Y.); (J.W.); (J.W.); (X.J.); (Z.X.); (L.Q.); (F.W.)
- Correspondence: (Y.Y.); (Y.L.)
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7
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Barbagallo D, Palermo CI, Barbagallo C, Battaglia R, Caponnetto A, Spina V, Ragusa M, Di Pietro C, Scalia G, Purrello M. Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells. Cell Mol Life Sci 2022; 79:75. [PMID: 35039944 PMCID: PMC8763136 DOI: 10.1007/s00018-021-04119-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.
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Affiliation(s)
- Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy.
| | - Concetta Ilenia Palermo
- U.O.C. Laboratory Analysis Unit, A.O.U. Policlinico‑Vittorio Emanuele, 95123, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Vittoria Spina
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
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8
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Cheng J, Lin Y, Xu L, Chen K, Li Q, Xu K, Ning L, Kang J, Cui T, Huang Y, Zhao X, Wang D, Li Y, Su X, Yang B. ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. Nucleic Acids Res 2022; 50:D928-D933. [PMID: 34723320 PMCID: PMC8728225 DOI: 10.1093/nar/gkab1029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/15/2022] Open
Abstract
As a means to aid in the investigation of viral infection mechanisms and identification of more effective antivirus targets, the availability of a source which continually collects and updates information on the virus and host ncRNA-associated interaction resources is essential. Here, we update the ViRBase database to version 3.0 (http://www.virbase.org/ or http://www.rna-society.org/virbase/). This update represents a major revision: (i) the total number of interaction entries is now greater than 820,000, an approximately 70-fold increment, involving 116 virus and 36 host organisms, (ii) it supplements and provides more details on RNA annotations (including RNA editing, RNA localization and RNA modification), ncRNA SNP and ncRNA-drug related information and (iii) it provides two additional tools for predicting binding sites (IntaRNA and PRIdictor), a visual plug-in to display interactions and a website which is optimized for more practical and user-friendly operation. Overall, ViRBase v3.0 provides a more comprehensive resource for virus and host ncRNA-associated interactions enabling researchers a more effective means for investigation of viral infections.
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Affiliation(s)
- Jun Cheng
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Yunqing Lin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Linfu Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kechen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kaixin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Juanjuan Kang
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Huang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yanhui Li
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Beijing, PR China
| | - Xi Su
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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9
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Abstract
Most of the transcribed human genome codes for noncoding RNAs (ncRNAs), and long noncoding RNAs (lncRNAs) make for the lion's share of the human ncRNA space. Despite growing interest in lncRNAs, because there are so many of them, and because of their tissue specialization and, often, lower abundance, their catalog remains incomplete and there are multiple ongoing efforts to improve it. Consequently, the number of human lncRNA genes may be lower than 10,000 or higher than 200,000. A key open challenge for lncRNA research, now that so many lncRNA species have been identified, is the characterization of lncRNA function and the interpretation of the roles of genetic and epigenetic alterations at their loci. After all, the most important human genes to catalog and study are those that contribute to important cellular functions-that affect development or cell differentiation and whose dysregulation may play a role in the genesis and progression of human diseases. Multiple efforts have used screens based on RNA-mediated interference (RNAi), antisense oligonucleotide (ASO), and CRISPR screens to identify the consequences of lncRNA dysregulation and predict lncRNA function in select contexts, but these approaches have unresolved scalability and accuracy challenges. Instead-as was the case for better-studied ncRNAs in the past-researchers often focus on characterizing lncRNA interactions and investigating their effects on genes and pathways with known functions. Here, we focus most of our review on computational methods to identify lncRNA interactions and to predict the effects of their alterations and dysregulation on human disease pathways.
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10
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Qi M, Liu B, Li S, Ni Z, Li F. Construction and Investigation of Competing Endogenous RNA Networks and Candidate Genes Involved in SARS-CoV-2 Infection. Int J Gen Med 2021; 14:6647-6659. [PMID: 34675627 PMCID: PMC8520483 DOI: 10.2147/ijgm.s335162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Introduction The current COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2 is a quickly developing global health crisis, yet the mechanisms of pathogenesis in COVID-19 are not fully understood. Methods The RNA sequencing data of SARS-CoV-2-infected cells was obtained from the Gene Expression Omnibus (GEO). The differentially expressed mRNAs (DEmRNAs), long non-coding RNAs (DElncRNAs), and microRNAs (DEmiRNAs) were identified by edgeR, and the SARS-CoV-2-associated competing endogenous RNA (ceRNA) network was constructed based on the prediction of bioinformatic databases. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted with the SARS-CoV-2-related DEmRNAs, and the protein–protein interaction network was also built basing on STRING database. The ROC analysis was performed for assessing the diagnostic efficiency of hub genes. Results The results indicated that SARS-CoV-2-related DEmRNAs were associated with the interferon signaling pathway and other antiviral processes, such as IFNL3, IFNL1 and CH25H. Our analysis suggested that lncRNA NEAT1 might regulate the host immune response through two miRNAs, hsa-miR-374-5p and hsa-miR-155-5p, which control the expression of SOCS1, IL6, IL1B, CSF1R, CD274, TLR6, and TNF. Additionally, IFI6, HRASLS2, IGFBP4 and PTN may be potential targets based on an analysis comparing the transcriptional responses of SARS-CoV-2 infection with that of other respiratory viruses. Discussion The unique ceRNA network identified potential non-coding RNAs and their possible targets as well as a new perspective to understand the molecular mechanisms of the host immune response to SARS-CoV-2. This study may also aid in the development of innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Mingran Qi
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, People's Republic of China
| | - Bin Liu
- Cardiovascular Disease Center, The First Hospital of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuai Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, People's Republic of China
| | - Zhaohui Ni
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, People's Republic of China.,The Key Laboratory for Bionics Engineering, Ministry of Education, Jilin University, Changchun, Jilin, People's Republic of China.,Engineering Research Center for Medical Biomaterials of Jilin Province, Jilin University, Changchun, Jilin, People's Republic of China.,Key Laboratory for Health Biomedical Materials of Jilin Province, Jilin University, Changchun, Jilin, People's Republic of China
| | - Fan Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, Jilin, People's Republic of China.,The Key Laboratory for Bionics Engineering, Ministry of Education, Jilin University, Changchun, Jilin, People's Republic of China.,Engineering Research Center for Medical Biomaterials of Jilin Province, Jilin University, Changchun, Jilin, People's Republic of China.,Key Laboratory for Health Biomedical Materials of Jilin Province, Jilin University, Changchun, Jilin, People's Republic of China.,State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, People's Republic of China
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11
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Ye J, Li J, Zhao P. Roles of ncRNAs as ceRNAs in Gastric Cancer. Genes (Basel) 2021; 12:genes12071036. [PMID: 34356052 PMCID: PMC8305186 DOI: 10.3390/genes12071036] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
Although ignored in the past, with the recent deepening of research, significant progress has been made in the field of non-coding RNAs (ncRNAs). Accumulating evidence has revealed that microRNA (miRNA) response elements regulate RNA. Long ncRNAs, circular RNAs, pseudogenes, miRNAs, and messenger RNAs (mRNAs) form a competitive endogenous RNA (ceRNA) network that plays an essential role in cancer and cardiovascular, neurodegenerative, and autoimmune diseases. Gastric cancer (GC) is one of the most common cancers, with a high degree of malignancy. Considerable progress has been made in understanding the molecular mechanism and treatment of GC, but GC’s mortality rate is still high. Studies have shown a complex ceRNA crosstalk mechanism in GC. lncRNAs, circRNAs, and pseudogenes can interact with miRNAs to affect mRNA transcription. The study of the involvement of ceRNA in GC could improve our understanding of GC and lead to the identification of potential effective therapeutic targets. The research strategy for ceRNA is mainly to screen the different miRNAs, lncRNAs, circRNAs, pseudogenes, and mRNAs in each sample through microarray or sequencing technology, predict the ceRNA regulatory network, and, finally, conduct functional research on ceRNA. In this review, we briefly discuss the proposal and development of the ceRNA hypothesis and the biological function and principle of ceRNAs in GC, and briefly introduce the role of ncRNAs in the GC’s ceRNA network.
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Affiliation(s)
- Junhong Ye
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China;
| | - Jifu Li
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China;
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China;
- Correspondence: ; Tel.: +86-23-6825-0885
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12
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Chen L, Wang C, Sun H, Wang J, Liang Y, Wang Y, Wong G. The bioinformatics toolbox for circRNA discovery and analysis. Brief Bioinform 2021; 22:1706-1728. [PMID: 32103237 PMCID: PMC7986655 DOI: 10.1093/bib/bbaa001] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
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Affiliation(s)
- Liang Chen
- Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University
| | | | - Huiyan Sun
- School of Artificial Intelligence, Jilin University
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science and Bond Life Science Center, University of Missouri
| | - Yanchun Liang
- College of Computer Science and Technology, Jilin University
| | - Yan Wang
- College of Computer Science and Technology, Jilin University
| | - Garry Wong
- Faculty of Health Sciences, University of Macau
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13
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Li W, Liu JQ, Chen M, Xu J, Zhu D. Circular RNA in cancer development and immune regulation. J Cell Mol Med 2020; 26:1785-1798. [PMID: 33277969 PMCID: PMC8918416 DOI: 10.1111/jcmm.16102] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/14/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of single‐stranded RNAs with closed loop structures formed by covalent bonds of head and tail. Exploration of circRNAs is continually increasing; however, their functional relevance largely remains to be elucidated. In general, they are stable, abundant, conserved and expressed in tissue‐specific manner. These distinct properties and their diverse cellular actions indicate that circRNAs modulate transcription and translation, and may even function as translation templates. Growing evidence reveals that circRNAs contribute to various physiological and pathological processes, including the initiation and progression of cancer. In this review, we present the current knowledge about circRNAs in cancer development, as well as their potential for use as biomarkers and even therapeutic targets. CircRNA’s role in immune regulation and antitumour immunotherapy is also discussed. In addition, possible challenges in antitumour therapy are raised, and current progress and future perspectives are provided.
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Affiliation(s)
- Weizhen Li
- Department of Laboratory Medicine, Sixth Affiliated Hospital of Yangzhou University, Taizhou, China.,Department of Laboratory Medicine, Affiliated Taixing Hospital of Bengbu Medical College, Taizhou, China
| | - Jia-Qiang Liu
- Department of Oral and Cranio-Maxillofacial, Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Chen
- Department of Laboratory Medicine, Sixth Affiliated Hospital of Yangzhou University, Taizhou, China.,Department of Laboratory Medicine, Affiliated Taixing Hospital of Bengbu Medical College, Taizhou, China
| | - Jiang Xu
- Department of Rehabilitation, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Di Zhu
- School of Pharmacy and Shanghai Pudong Hospital, Fudan University, Shanghai, China
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14
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Yan L, Li K, Feng Z, Zhang Y, Han R, Ma J, Zhang J, Wu X, Liu H, Jiang Y, Zhang Y, Zhu Y. lncRNA CERS6-AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR-125a-5p to upregulate BAP1 expression. Mol Carcinog 2020; 59:1199-1208. [PMID: 32808708 DOI: 10.1002/mc.23249] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/21/2022]
Abstract
Long noncoding RNAs (lncRNAs) can act as oncogene and tumor suppressor genes in many types of cancers including breast cancer (BC). Our previous study has indicated microRNA (miR)-125a-5p was downregulated and function as a tumor suppressor in BC. However, its upstream regulation mechanism is still unclear. In this study, we used bioinformatics algorithms, RNA pulldown assay, and dual-luciferase reports assay to predict and confirm lncRNA CERS6-AS1 interacted with miR-125a-5p. Then we found CERS6-AS1 was upregulated in BC tissues. Experimental results of tumor growth in nude mice show that CERS6-AS1 promotes tumor growth. Furthermore, CERS6-AS1 regulated BC susceptibility gene 1-associated protein 1 (BAP1) expression via sponging miR-125a-5p via Western blot analysis and quantitative polymerase chain reaction arrays. Finally, we showed that miR-125a-5p had opposing effects to those of CERS6-AS1 on BC cells, demonstrating that CERS6-AS1 may promote cell proliferation and inhibit cell apoptosis via sponging miR-125a-5p. Our results indicated CERS6-AS1 promote BC cell proliferation and inhibit cell apoptosis via sponging miR-125a-5p to upregulate BAP1 expression.
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Affiliation(s)
- Liang Yan
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Kai Li
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
| | - Zunyong Feng
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yizongheng Zhang
- Department of Clinical Medicine, The First College of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Renrui Han
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Jinzhu Ma
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Jieling Zhang
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
| | - Xu Wu
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Haijun Liu
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yuxin Jiang
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yao Zhang
- Anhui Provincial Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu, Anhui, China
| | - Yiping Zhu
- Department of Clinical Diagnostics, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, Anhui, China
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15
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Arora S, Singh P, Dohare R, Jha R, Ali Syed M. Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19). Gene 2020; 762:145057. [PMID: 32805314 PMCID: PMC7428439 DOI: 10.1016/j.gene.2020.145057] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
Bioinformatics analysis of mouse mRNA expression dataset for presumptive SARS-CoV-2 targets. Induction of ISGs-Isg15, Oasl1, Usp18 and Ddx58 with no marked changes in the expression of IFNs. No induction of ACE2 and TMPRSS2, raising implications for host factor limitations. Identification of ceRNA network including miR-124-3p, Ddx58, lncRNA (Gm26917) and circRNAs (Ppp1r10, C330019G07RiK). Virus regulates the expression of lnc and circRNAs, acting as sponges for miR-124-3p targeting Ddx58.
COVID-19 is a lurking calamitous disease caused by an unusual virus, SARS-CoV-2, causing massive deaths worldwide. Nonetheless, explicit therapeutic drugs or clinically approved vaccines are not available for COVID-19. Thus, a comprehensive research is crucially needed to decode the pathogenic tools, plausible drug targets, committed to the development of efficient therapy. Host-pathogen interactions via host cellular components is an emerging field of research in this respect. miRNAs have been established as vital players in host-virus interactions. Moreover, viruses have the capability to manoeuvre the host miRNA networks according to their own obligations. Besides protein coding mRNAs, noncoding RNAs might also be targeted in infected cells and viruses can exploit the host miRNA network via ceRNA effect. We have predicted a ceRNA network involving one miRNA (miR-124-3p), one mRNA (Ddx58), one lncRNA (Gm26917) and two circRNAs (Ppp1r10, C330019G07RiK) in SARS-CoV infected cells. We have identified 4 DEGs-Isg15, Ddx58, Oasl1, Usp18 by analyzing a mRNA GEO dataset. There is no notable induction of IFNs and IFN-induced ACE2, significant receptor responsible for S-protein binding mediated viral entry. Pathway enrichment and GO analysis conceded the enrichment of pathways associated with interferon signalling and antiviral-mechanism by IFN-stimulated genes. Further, we have identified 3 noncoding RNAs, playing as potential ceRNAs to the genes associated with immune mechanisms. This integrative analysis has identified noncoding RNAs and their plausible targets, which could effectively enhance the understanding of molecular mechanisms associated with viral infection. However, validation of these targets is further corroborated to determine their therapeutic efficacy.
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Affiliation(s)
- Shweta Arora
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Rishabh Jha
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mansoor Ali Syed
- Translational Research Lab, Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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16
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Lin Y, Liu T, Cui T, Wang Z, Zhang Y, Tan P, Huang Y, Yu J, Wang D. RNAInter in 2020: RNA interactome repository with increased coverage and annotation. Nucleic Acids Res 2020; 48:D189-D197. [PMID: 31906603 PMCID: PMC6943043 DOI: 10.1093/nar/gkz804] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.
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Affiliation(s)
- Yunqing Lin
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuncong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100730, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279; or
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17
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Dai M, Feng M, Xie T, Zhang X. Long non-coding RNA and MicroRNA profiling provides comprehensive insight into non-coding RNA involved host immune responses in ALV-J-infected chicken primary macrophage. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 100:103414. [PMID: 31200006 DOI: 10.1016/j.dci.2019.103414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/10/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression in infected chickens. Macrophages play a crucial role in host defense against invading pathogens. In the present study, whole transcriptome analysis was performed to analyze the host factors including genes, microRNA (miRNA), long non-coding RNA (lncRNA) and their regulatory network in chicken primary monocyte-derived macrophages (MDMs). In total, 128 differentially expressed (DE) lncRNAs and 15 DE miRNAs were identified in MDMs at 3 h post infection (hpi), and 30 DE lncRNAs and 8 DE miRNAs were identified in MDMs at 36 hpi during ALV-J infection. We further constructed the DE lncRNAs-mRNAs, miRNA-mRNAs and lncRNAs-miRNA-mRNAs interaction networks. The results suggested that DE lncRNAs and miRNAs are involved in the regulation of CCND3 and SOCS5 in Jak-STAT signaling pathway via ceRNA network in ALV-J-infected MDMs at 3 hpi. In addition, lncRNAs including XLOC_672329, ALDBGALG0000001429, XLOC_016500 and ALDBGALG0000000253 cis-regulating CH25H, CISH, IL-1β and CD80 respectively in MDMs at 3 hpi participated in host antiviral responses. Our findings give a comprehensive view of the connection between non-coding RNA and ALV-J in chicken primary macrophages, and provide an excellent resource for further studies of epigenetic effects on ALV-J disease resistance breeding as well as immune system and genomic researches.
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Affiliation(s)
- Manman Dai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, People's Republic of China.
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, 510642, Guangdong, China.
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China; Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, 510642, Guangdong, China.
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18
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Chen F, Li Z, Deng C, Yan H. Integration analysis for novel lncRNA markers predicting tumor recurrence in human colon adenocarcinoma. J Transl Med 2019; 17:299. [PMID: 31470869 PMCID: PMC6717325 DOI: 10.1186/s12967-019-2049-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/25/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Numerous evidence has suggested that long non-coding RNA (lncRNA) acts an important role in tumor biology. This study focuses on the identification of novel prognostic lncRNA biomarkers predicting tumor recurrence in human colon adenocarcinoma. METHODS We obtained the research data from The Cancer Genome Atlas (TCGA) database. The interaction among different expressed lncRNA, miRNA and mRNA markers between colon adenocarcinoma patients with and without tumor recurrence were verified with miRcode, starBase and miRTarBase databases. We established the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network based on the verified association between the selected markers. We performed the functional enrichment analysis to obtain better understanding of the selected lncRNAs. Then we use multivariate logistic regression to identify the prognostic lncRNA markers with covariates. We also generated a nomogram predicting tumor recurrence risk based on the identified lncRNA biomarkers and clinical covariates. RESULTS We included 12,727 lncRNA, 1881 miRNA and 47,761 mRNA profiling and clinical features for 113 colon adenocarcinoma patients obtained from the TCGA database. After filtration, we used 37 specific lncRNAs, 60 miRNAs and 148 mRNAs in the ceRNA network analysis. We identified five lncRNAs as prognostic lncRNA markers predicting tumor recurrence in colon adenocarcinoma, in which four of them were identified for the first time. Finally, we generated a nomogram illustrating the association between the identified lncRNAs and the tumor recurrence risk in colon adenocarcinoma. CONCLUSIONS The four newly identified lncRNA biomarkers might be potential prognostic biomarkers predicting tumor recurrence in colon adenocarcinoma. We recommend that further clinical and fundamental researches be conducted on the identified lncRNA markers.
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Affiliation(s)
- Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
| | - Zhe Li
- First Affiliated Hospital of Xi’an Jiaotong University, 277 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
| | - Changyu Deng
- Department of Preventive Medicine, Shantou University Medical College, 22 Xinling Road, Jinping District, Shantou, 515041 Guangdong China
| | - Hong Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, 76 Yanta Xilu Road, Xi’an, 710061 Shaanxi China
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19
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Zeng N, Wang T, Chen M, Yuan Z, Qin J, Wu Y, Gao L, Shen Y, Chen L, Wen F. Cigarette smoke extract alters genome-wide profiles of circular RNAs and mRNAs in primary human small airway epithelial cells. J Cell Mol Med 2019; 23:5532-5541. [PMID: 31140741 PMCID: PMC6653042 DOI: 10.1111/jcmm.14436] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/11/2019] [Accepted: 05/15/2019] [Indexed: 02/05/2023] Open
Abstract
As a novel kind of non-coding RNA, circular RNAs (circRNAs) were involved in various biological processes. However, the role of circRNAs in the developmental process of chronic obstructive pulmonary disease (COPD) is still unclear. In the present study, by using a cell model of COPD in primary human small airway epithelial cells (HSAECs) treated with or without cigarette smoke extract (CSE), we uncovered 4,379 previously unknown circRNAs in human cells and 903 smoke-specific circRNAs, with the help of RNA-sequencing and bioinformatic analysis. Moreover, 3,872 up- and 4,425 down-regulated mRNAs were also identified under CSE stimulation. Furthermore, a putative circRNA-microRNA-mRNA network was constructed for in-depth mechanism exploration, which indicated that differentially expressed circRNAs could influence expression of some key genes that participate in response to pentose phosphate pathway, ATP-binding cassette (ABC) transporters, glycosaminoglycan biosynthesis pathway and cancer-related pathways. Our research indicated that cigarette smoke had an influence on the biogenesis of circRNAs and mRNAs. CircRNAs might be involved in the response to CSE in COPD through the circRNA-mediated ceRNA networks.
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Affiliation(s)
- Ni Zeng
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Tao Wang
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Mei Chen
- Department of Respiratory and Critical Care Medicine, Chengdu Fifth People's Hospital, Chengdu, China
| | - Zhicheng Yuan
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jiangyue Qin
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yanqiu Wu
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Lijuan Gao
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Yongchun Shen
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Lei Chen
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Fuqiang Wen
- Division of Pulmonary Diseases, State Key Laboratory of Biotherapy of China, Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
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20
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Zurawska A, Mycko MP, Selmaj KW. Circular RNAs as a novel layer of regulatory mechanism in multiple sclerosis. J Neuroimmunol 2019; 334:576971. [PMID: 31163273 DOI: 10.1016/j.jneuroim.2019.576971] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/23/2019] [Indexed: 12/18/2022]
Abstract
Multiple sclerosis (MS) is believed to be an autoimmune disease of the central nervous system (CNS) in which autoreactive immune cells recognizing myelin antigens lead to demyelination and axonal injury. Mechanisms inducing and controlling the pathogenesis of MS have not been fully elucidated. Recent studies suggest an important role of epigenetic processes during the development of MS. One of the most significant discoveries in the field of epigenetic contribution to immune response has been the recognition of a group of microRNAs (miRNAs). These single-stranded non-coding RNA molecules regulate the expression of genes encoding proteins and have already been shown to be involved in pathogenesis of MS. Some miRNAs enhance generation of pro-inflammatory immune cells by promoting Th1 and Th17 pathways and others contribute to regulatory and tissue repair processes. The miRNA-dependent controlling process of autoimmune reactions is highly complex because of miRNA redundancy and multitarget nature of most of these molecules. Recently it was discovered that circular RNAs (circRNA) representing a new class of RNA possess a unique ability to control miRNAs by blocking their activity. CircRNAs are called natural miRNA "sponges" as the single circRNA molecule is able to neutralize several miRNAs and thus might determine the availability of miRNAs for their posttranscription regulation. Thus, circRNAs emerged as critical factors in epigenetic regulation of many human diseases including MS. In addition, in contrary to other RNA species they are very stable in the blood and other biological fluids and thus might be considered as a candidate for a biomarker of MS.
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Affiliation(s)
- Anna Zurawska
- Department of Neurology, Laboratory of Neuroimmunology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Marcin P Mycko
- Department of Neurology, Laboratory of Neuroimmunology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Krzysztof W Selmaj
- Department of Neurology, Laboratory of Neuroimmunology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland.
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21
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Bakre AA, Maleki A, Tripp RA. MicroRNA and Nonsense Transcripts as Putative Viral Evasion Mechanisms. Front Cell Infect Microbiol 2019; 9:152. [PMID: 31139579 PMCID: PMC6519394 DOI: 10.3389/fcimb.2019.00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
Viral proteins encode numerous antiviral activities to modify the host immunity. In this article, we hypothesize that viral genomes and gene transcripts interfere with host gene expression using passive mechanisms to deregulate host microRNA (miRNA) activity. We postulate that various RNA viruses mimic or block binding between a host miRNA and its target transcript, a phenomenon mediated by the miRNA seed site at the 5′ end of miRNA. Virus-encoded miRNA seed sponges (vSSs) can potentially bind to host miRNA seed sites and prevent interaction with their native targets thereby relieving native miRNA suppression. In contrast, virus-encoded miRNA seed mimics (vSMs) may mediate considerable downregulation of host miRNA activity. We analyzed genomes from diverse RNA viruses for vSS and vSM signatures and found an abundance of these motifs indicating that this may be a mechanism of deceiving host immunity. Employing respiratory syncytial virus and measles virus as models, we reveal that regions surrounding vSS or vSM motifs have features characteristics of pre-miRNA templates and show that RSV viral transcripts are processed into small RNAs that may behave as vSS or vSM effectors. These data suggest that complex molecular interactions likely occur at the host-virus interface. Identifying the mechanisms in the network of interactions between the host and viral transcripts can help uncover ways to improve vaccine efficacy, therapeutics, and potentially mitigate the adverse events that may be associated with some vaccines.
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Affiliation(s)
- Abhijeet A Bakre
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ali Maleki
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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22
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Comprehensive analysis of circRNAs expression profiles in different periods of MDBK cells infected with bovine viral diarrhea virus. Res Vet Sci 2019; 125:52-60. [PMID: 31146221 DOI: 10.1016/j.rvsc.2019.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/24/2018] [Accepted: 05/03/2019] [Indexed: 02/07/2023]
Abstract
CircRNAs play an important regulatory role in the regulation of disease. However, we have a limited understanding of the role of circRNAs in the host's complex protective and pathological mechanisms of BVDV infection. Transcriptome analysis of circRNAs in host cells after BVDV infection may allow us to understand the biological functions of circRNAs in the regulation of BVDV infection. Here, we identified a total of 19,118 circRNAs from the MBDK cells (at 12 h, 24 h, and 48 h post-infection) infected with BVDV by using RNA-seq technology. We confirmed several circRNAs using RT-PCR and DNA sequencing, and qRT-PCR analysis was performed to identify several circRNAs expression and circRNAs resistance to RNase R digestion. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that the host genes of differentially expressed circRNAs were involved in the regulation of cell proliferation, apoptosis, cycle and viral infection related signaling pathways. These results indicate that circRNA in host cells plays a broad regulatory role after BVDV infection and provides a valuable resource for studying circRNA biology in host cells after BVDV infection.
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23
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Zhang Y, Tao Y, Liao Q. Long noncoding RNA: a crosslink in biological regulatory network. Brief Bioinform 2019; 19:930-945. [PMID: 28449042 DOI: 10.1093/bib/bbx042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) had been defined as a novel class of functional RNAs longer than 200 nucleotides around a decade ago. It is widely acknowledged that lncRNAs play a significant role in regulation of gene expression, but the biological and molecular mechanisms are diverse and complex, and remain to be determined. Especially, the regulatory network of lncRNAs associated with other biological molecules is still a controversial matter, thus becoming a new frontier of the studies on transcriptome. Recent advance in high-throughput sequencing technologies and bioinformatics approaches may be an accelerator to lift the mysterious veil. In this review, we will outline well-known associations between lncRNAs and other biological molecules, demonstrate the diverse bioinformatics approaches applied in prediction and analysis of lncRNA interaction and perform a case study for lncRNA linc00460 to concretely decipher the lncRNA regulatory network.
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Affiliation(s)
- Yuwei Zhang
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Yang Tao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
| | - Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medicine School of Ningbo University, Ningbo, Zhejiang, China
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24
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Russo F, Fiscon G, Conte F, Rizzo M, Paci P, Pellegrini M. Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer. Methods Mol Biol 2019; 1819:75-92. [PMID: 30421400 DOI: 10.1007/978-1-4939-8618-7_4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the last decade noncoding RNAs (ncRNAs) have been extensively studied in several biological processes and human diseases including cancer. microRNAs (miRNAs) are the best-known class of ncRNAs. miRNAs are small ncRNAs of around 20-22 nucleotides (nt) and are crucial posttranscriptional regulators of protein coding genes. Recently, new classes of ncRNAs, longer than miRNAs have been discovered. Those include intergenic noncoding RNAs (lincRNAs) and circular RNAs (circRNAs). These novel types of ncRNAs opened a very exciting field in biology, leading researchers to discover new relationships between miRNAs and long noncoding RNAs (lncRNAs), which act together to control protein coding gene expression. One of these new discoveries led to the formulation of the "competing endogenous RNA (ceRNA) hypothesis." This hypothesis suggests that an lncRNA acts as a sponge for miRNAs reducing their expression and causing the upregulation of miRNA targets. In this chapter we first discuss some recent discoveries in this field showing the mutual regulation of miRNAs, lncRNAs, and protein-coding genes in cancer. We then discuss the general approaches for the study of ceRNAs and present in more detail a recent computational approach to explore the ability of lncRNAs to act as ceRNAs in human breast cancer that has been shown to be, among the others, the most precise and promising.
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Affiliation(s)
- Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Milena Rizzo
- Institute of Clinical Physiology, National Research Council (CNR), Pisa, Italy.,Istituto Toscano Tumori (ITT), Firenze, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "A. Ruberti" (IASI), National Research Council (CNR), Rome, Italy
| | - Marco Pellegrini
- Institute of Informatics and Telematics (IIT), National Research Council (CNR), Pisa, Italy
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25
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Yang L, Fu J, Zhou Y. Circular RNAs and Their Emerging Roles in Immune Regulation. Front Immunol 2018; 9:2977. [PMID: 30619334 PMCID: PMC6305292 DOI: 10.3389/fimmu.2018.02977] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/04/2018] [Indexed: 01/16/2023] Open
Abstract
Circular ribonucleic acid (RNA) molecules (circRNAs) are covalently closed loop RNA molecules with no 5' end caps or 3' poly (A) tails, which are generated by back-splicing. Originally, circRNAs were considered to be byproducts of aberrant splicing. However, in recent years, development of high-throughput sequencing has led to gradual recognition of functional circRNAs, and increasing numbers of studies have elucidated their roles in cancer, neurologic diseases, and cardiovascular disorders. Nevertheless, studies of the functions of circRNAs in the immune system are relatively scarce. In this review, we detail relevant research on the biogenesis and classification of circRNAs, describe their functional mechanisms and approaches to their investigation, and summarize recent studies of circRNA function in the immune system.
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Affiliation(s)
- Lan Yang
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jinrong Fu
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yufeng Zhou
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai, China
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26
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Li R, Wang Y, Song X, Sun W, Zhang J, Liu Y, Li H, Meng C, Zhang J, Zheng Q, Lv C. Potential regulatory role of circular RNA in idiopathic pulmonary fibrosis. Int J Mol Med 2018; 42:3256-3268. [PMID: 30272257 PMCID: PMC6202105 DOI: 10.3892/ijmm.2018.3892] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive type of interstitial pneumonia with unknown causes, poor prognosis and no effective therapy available. Circular RNAs (circRNAs), which serve as potential therapeutic targets and diagnostic biomarkers for certain diseases, represent a recent hotspot in the field of RNA research. In the present study, a total of 67 significantly dysregulated circRNAs were identified in the plasma of IPF patients by using a circRNA microarray. Among these circRNAs, 38 were upregulated, whereas 29 were downregulated. Further validation of the results by polymerase chain reaction analysis indicated that Homo sapiens (hsa)_circRNA_100906, hsa_circRNA_102100 and hsa_circRNA_102348 were significantly upregulated, whereas hsa_circRNA_101225, hsa_circRNA_104780 and hsa_circRNA_101242 were downregulated in plasma samples of IPF patients compared with those in samples from healthy controls. The majority of differentially expressed circRNAs were generated from exonic regions. The host genes of the differentially expressed circRNAs were involved in the regulation of the cell cycle, adherens junctions and RNA transport. The competing endogenous RNA (ceRNA) network of the circRNAs/micro(mi)RNAs/mRNAs indicated that circRNA-protected mRNA participated in transforming growth factor-β1, hypoxia-inducible factor-1, Wnt, Janus kinase, Rho-associated protein kinase, vascular endothelial growth factor, mitogen-activated protein kinase, Hedgehog and nuclear factor κB signalling pathways or functioned as biomarkers for pulmonary fibrosis. Furthermore, luciferase reporter assays confirmed that hsa_circRNA_100906 and hsa_circRNA_102348 directly interact with miR-324-5p and miR-630, respectively, which were downregulated in IPF patients. The present study provided a novel avenue for exploring the underlying molecular mechanisms of IPF disease.
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Affiliation(s)
- Rongrong Li
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Youlei Wang
- School of Special Education, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Xiaodong Song
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Wenjing Sun
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, P.R. China
| | - Jinjin Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Yuxia Liu
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Hongbo Li
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Chao Meng
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Jie Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Qingyin Zheng
- School of Special Education, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Changjun Lv
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
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27
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Pan T, Sun X, Liu Y, Li H, Deng G, Lin H, Wang S. Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 96:217-229. [PMID: 29177640 DOI: 10.1007/s11103-017-0684-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/18/2017] [Indexed: 05/19/2023]
Abstract
1599 novel circRNAs and 1583 heat stress-specific circRNAs were identified in Arabidopsis. Heat stress enhanced accumulation of circRNAs remarkably. Heat stress altered the sizes of circRNAs, numbers of circularized exons and alterative circularization events. A putative circRNA-mediated ceRNA networks under heat stress was established. Heat stress retards plant growth and destabilizes crop yield. The noncoding RNAs were demonstrated to be involved in plant response to heat stress. As a newly-characterized class of noncoding RNAs, circular RNAs (circRNAs) play important roles in transcriptional and post-transcriptional regulation. A few recent investigations indicated that plant circRNAs were differentially expressed under abiotic stress. However, little is known about how heat stress mediates biogenesis of circRNAs in plants. Here, we uncovered 1599 previously-unknown circRNAs and 1583 heat-specific circRNAs, by RNA-sequencing and bioinformatic analysis. Our results indicated that much more circRNAs were expressed under heat stress than in control condition. Besides, heat stress also increased the length of circRNAs, the quantity of circularized exons, and alternative circularization events. Moreover, we observed a positive correlation between expression patterns of some circRNAs and their parental genes. The prediction of ceRNA (competing endogenous RNA) networks indicated that differentially-expressed circRNAs could influence expression of many important genes, that participate in response to heat stress, hydrogen peroxide, and phytohormone signaling pathways, by interacting with the corresponding microRNAs. Together, our observations indicated that heat stress had great impacts on the biogenesis of circRNAs. Heat-induced circRNAs might participate in plant response to heat stress through the circRNA-mediated ceRNA networks.
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Affiliation(s)
- Ting Pan
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuqiang Sun
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangxuan Liu
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangbin Deng
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Honghui Lin
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Songhu Wang
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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Shuwen H, Qing Z, Yan Z, Xi Y. Competitive endogenous RNA in colorectal cancer: A systematic review. Gene 2017; 645:157-162. [PMID: 29273554 DOI: 10.1016/j.gene.2017.12.036] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/30/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Colorectal cancer is one of the most common malignant tumours. Competitive endogenous RNA (ceRNA) networks have been hypothesized, in which various RNAs regulate each other's expression using microRNA response elements (MREs). Recent evidence has highlighted the crucial regulatory roles of ceRNA networks in colorectal cancer. In this review, we summarize the present research methods as well as the currently known ceRNA competitors and targets in colorectal cancer. In addition, we discuss the significance of ceRNA and shortcomings of current studies of colorectal cancer.
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Affiliation(s)
- Han Shuwen
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Zhou Qing
- Department of Critical Care Medicine, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Zheng Yan
- Department of Pathology, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Yang Xi
- Department of Intervention and Radiotherapy, Huzhou Central Hospital, Huzhou, Zhejiang Province, China.
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29
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Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X, Cao Y, Hazi W, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget 2017; 8:97165-97177. [PMID: 29228601 PMCID: PMC5722553 DOI: 10.18632/oncotarget.21835] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.
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Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
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30
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Wang M, Yu F, Wu W, Zhang Y, Chang W, Ponnusamy M, Wang K, Li P. Circular RNAs: A novel type of non-coding RNA and their potential implications in antiviral immunity. Int J Biol Sci 2017; 13:1497-1506. [PMID: 29230098 PMCID: PMC5723916 DOI: 10.7150/ijbs.22531] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/08/2017] [Indexed: 12/23/2022] Open
Abstract
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), are ubiquitously expressed in eukaryotic cells during post-transcriptional processes. Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. With advances in high-throughput sequencing technology, numerous circRNAs have been identified in plants, animals and humans. Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression. More importantly, circRNAs serve as microRNA (miRNA) sponges and crucial regulators of gene expression. Additionally, circRNAs modulate pre-mRNA alternative splicing and possess protein-coding capacity. CircRNAs exhibit altered expression under pathological conditions and are strongly associated with the development of various human diseases. Interestingly, circRNAs can also induce antiviral immune responses. A recent study found that the delivery of circRNAs generated in vitro activates RIG-I-mediated innate immune responses and provides protection against viral infection. The antiviral dsRNA-binding proteins, NF90/NF110, act as key regulators in circRNA biogenesis. NF90/NF110 are also functional in inhibiting viral replication through binding to viral mRNAs. In this review, we provide a comprehensive overview on the classification, biogenesis and functions of circRNAs. We also discuss the critical role of circRNAs in eliciting antiviral immunity, providing evidence for the potential implications of circRNAs in antiviral therapies.
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Affiliation(s)
| | | | | | | | | | | | - Kun Wang
- Institute for Translational Medicine, Medical College of Qingdao University, Dengzhou Road 38, Qingdao 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, Medical College of Qingdao University, Dengzhou Road 38, Qingdao 266021, China
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31
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Tang L, Chen HY, Hao NB, Tang B, Guo H, Yong X, Dong H, Yang SM. microRNA inhibitors: Natural and artificial sequestration of microRNA. Cancer Lett 2017; 407:139-147. [PMID: 28602827 DOI: 10.1016/j.canlet.2017.05.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNAs) is post-transcriptional regulator of mRNA. However, the prevalence and activity of miRNA are regulated by other regulators. miRNA inhibitors are natural or artificial RNA transcripts that sequestrate miRNAs and decrease or even eliminate miRNA activity. Competing endogenous RNAs (ceRNAs) are natural and intracellular miRNA inhibitors that compete to bind to shared miRNA recognition elements (MREs) to decrease microRNA availability and relieve the repression of target RNAs. In recent years, studies have revealed that ceRNA crosstalk is involved in many pathophysiological processes and adds a new dimension to miRNA regulation. Artificial miRNA inhibitors are RNA transcripts that are synthesized via chemical and genetic methods. Artificial miRNA inhibitors can be used in miRNA loss-of-function research and gene therapies for certain diseases. In this review, we summarize the recent advances in the two different types of miRNA inhibitors.
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Affiliation(s)
- Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong-Yan Chen
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Ning-Bo Hao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hong Guo
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xin Yong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hui Dong
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Shi-Ming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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32
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Kang S, Park S, Yoon S, Min H. Machine learning-based identification of endogenous cellular microRNA sponges against viral microRNAs. Methods 2017; 129:33-40. [PMID: 28323040 DOI: 10.1016/j.ymeth.2017.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/02/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions. Here we present a computational approach for the prediction of endogenous human miRNA sponge candidates targeting viral miRNAs derived from pathogenic human viruses. Viral miRNA binding sites were predicted using a newly-developed machine learning-based method, and candidate interactions between miRNAs and sponge RNAs were experimentally validated using luciferase reporter assay, western blot analysis, and flow cytometry. We found that BX649188.1 functions as a potential natural miRNA sponge against kshv-miR-K12-7-3p.
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Affiliation(s)
- Soowon Kang
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seunghyun Park
- Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea; Electrical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Sungroh Yoon
- Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea; Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Hyeyoung Min
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
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33
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Sardina DS, Alaimo S, Ferro A, Pulvirenti A, Giugno R. A novel computational method for inferring competing endogenous interactions. Brief Bioinform 2016; 18:1071-1081. [DOI: 10.1093/bib/bbw084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 12/14/2022] Open
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34
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The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene 2016; 36:1112-1122. [PMID: 27530352 DOI: 10.1038/onc.2016.278] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/25/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023]
Abstract
The expression of long non-coding RNAs (lncRNAs) is dysregulated in hepatocellular carcinoma (HCC). However, the functions and contributions of lncRNAs remain largely unknown. Here, we identified a critical role of SNHG6-003 in HCC. We found that five SNHG6 transcripts were differentially expressed in HCC tissues while only the SNHG6-003 had an oncogenic function. Ectopic expression of SNHG6-003 in HCC cells promoted cell proliferation and induced drug resistance, whereas SNHG6-003 knockdown promoted apoptosis. Moreover, SNHG6-003 functioned as a competitive endogenous RNA (ceRNA), effectively becoming sponge for miR-26a/b and thereby modulating the expression of transforming growth factor-β-activated kinase 1 (TAK1). Importantly, expression analysis revealed that both SNHG6-003 and TAK1 were upregulated in human cancers, exhibiting a co-expression pattern. In HCC patients, high expression of SNHG6-003 closely correlated with tumor progression and shorter survival. Thus, targeting the ceRNA network involving SNHG6-003 may be used as a treatment strategy against HCC.
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35
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Le TD, Zhang J, Liu L, Li J. Computational methods for identifying miRNA sponge interactions. Brief Bioinform 2016; 18:577-590. [DOI: 10.1093/bib/bbw042] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 12/14/2022] Open
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36
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Abstract
The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
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Affiliation(s)
- Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
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37
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Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells. Sci Rep 2016; 6:20263. [PMID: 26838068 PMCID: PMC4738309 DOI: 10.1038/srep20263] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
Microglia cells in the brain play essential role during Japanese Encephalitis Virus (JEV) infection and may lead to change in microRNA (miRNA) and mRNA profile. These changes may together control disease outcome. Using Affymetrix microarray platform, we profiled cellular miRNA and mRNA expression at multiple time points during viral infection in human microglial (CHME3) cells. In silico analysis of microarray data revealed a phased pattern of miRNAs expression, associated with JEV replication and provided unique signatures of infection. Target prediction and pathway enrichment analysis identified anti correlation between differentially expressed miRNA and the gene expression at multiple time point which ultimately affected diverse signaling pathways including Notch signaling pathways in microglia. Activation of Notch pathway during JEV infection was demonstrated in vitro and in vivo. The expression of a subset of miRNAs that target multiple genes in Notch signaling pathways were suppressed and their overexpression could affect JEV induced immune response. Further analysis provided evidence for the possible presence of cellular competing endogenous RNA (ceRNA) associated with innate immune response. Collectively, our data provide a uniquely comprehensive view of the changes in the host miRNAs induced by JEV during cellular infection and identify Notch pathway in modulating microglia mediated inflammation.
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38
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Wang P, Ning S, Zhang Y, Li R, Ye J, Zhao Z, Zhi H, Wang T, Guo Z, Li X. Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer. Nucleic Acids Res 2015; 43:3478-89. [PMID: 25800746 PMCID: PMC4402541 DOI: 10.1093/nar/gkv233] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 03/05/2015] [Indexed: 12/13/2022] Open
Abstract
Recent studies have suggested that long non-coding RNAs (lncRNAs) can interact with microRNAs (miRNAs) and indirectly regulate miRNA targets though competing interactions. However, the molecular mechanisms underlying these interactions are still largely unknown. In this study, these lncRNA–miRNA–gene interactions were defined as lncRNA-associated competing triplets (LncACTs), and an integrated pipeline was developed to identify lncACTs that are active in cancer. Competing lncRNAs had sponge features distinct from non-competing lncRNAs. In the lncACT cross-talk network, disease-associated lncRNAs, miRNAs and coding-genes showed specific topological patterns indicative of their competence and control of communication within the network. The construction of global competing activity profiles revealed that lncACTs had high activity specific to cancers. Analyses of clustered lncACTs revealed that they were enriched in various cancer-related biological processes. Based on the global cross-talk network and cluster analyses, nine cancer-specific sub-networks were constructed. H19- and BRCA1/2-associated lncACTs were able to discriminate between two groups of patients with different clinical outcomes. Disease-associated lncACTs also showed variable competing patterns across normal and cancer patient samples. In summary, this study uncovered and systematically characterized global properties of human lncACTs that may have prognostic value for predicting clinical outcome in cancer patients.
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Affiliation(s)
- Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ronghong Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Jingrun Ye
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zuxianglan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tingting Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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