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Sabbaghian M, Gheitasi H, Fadaee M, Javadi Henafard H, Tavakoli A, Shekarchi AA, Poortahmasebi V. Human cytomegalovirus microRNAs: strategies for immune evasion and viral latency. Arch Virol 2024; 169:157. [PMID: 38969819 DOI: 10.1007/s00705-024-06080-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/17/2024] [Indexed: 07/07/2024]
Abstract
Viruses use various strategies and mechanisms to deal with cells and proteins of the immune system that form a barrier against infection. One of these mechanisms is the encoding and production of viral microRNAs (miRNAs), whose function is to regulate the gene expression of the host cell and the virus, thus creating a suitable environment for survival and spreading viral infection. miRNAs are short, single-stranded, non-coding RNA molecules that can regulate the expression of host and viral proteins, and due to their non-immunogenic nature, they are not eliminated by the cells of the immune system. More than half of the viral miRNAs are encoded and produced by Orthoherpesviridae family members. Human cytomegalovirus (HCMV) produces miRNAs that mediate various processes in infected cells to contribute to HCMV pathogenicity, including immune escape, viral latency, and cell apoptosis. Here, we discuss which cellular and viral proteins or cellular pathways and processes these mysterious molecules target to evade immunity and support viral latency in infected cells. We also discuss current evidence that their function of bypassing the host's innate and adaptive immune system is essential for the survival and multiplication of the virus and the spread of HCMV infection.
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Affiliation(s)
- Mohammad Sabbaghian
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Gheitasi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manouchehr Fadaee
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Shekarchi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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2
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Gao X, You X, Wang G, Liu M, Ye L, Meng Y, Luo G, Xu D, Liu M. MiR-320 inhibits PRRSV replication by targeting PRRSV ORF6 and porcine CEBPB. Vet Res 2024; 55:61. [PMID: 38750508 PMCID: PMC11097481 DOI: 10.1186/s13567-024-01309-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 02/23/2024] [Indexed: 05/18/2024] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS), a highly contagious disease caused by Porcine reproductive and respiratory syndrome virus (PRRSV), results in huge economic losses to the world pig industry. MiRNAs have been reported to be involved in regulation of viral infection. In our study, miR-320 was one of 21 common differentially expressed miRNAs of Meishan, Pietrain, and Landrace pig breeds at 9-h post-infection (hpi). Bioinformatics and experiments found that PRRSV replication was inhibited by miR-320 through directly targeting PRRSV ORF6. In addition, the expression of CCAAT enhancer binding protein beta (CEBPB) was also inhibited by miR-320 by targeting the 3' UTR of CEBPB, which significantly promotes PRRSV replication. Intramuscular injection of pEGFP-N1-miR-320 verified that miR-320 significantly inhibited the replication of PRRSV and alleviated the symptoms caused by PRRSV in piglets. Taken together, miR-320 have significant roles in the infection and may be promising therapeutic target for PRRS.
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Affiliation(s)
- Xiaoxiao Gao
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangbin You
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, 471023, China
| | - Guowei Wang
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengtian Liu
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longlong Ye
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yufeng Meng
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gan Luo
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dequan Xu
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Liu
- Colleges of Animal Science and Technology/College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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Cui YH, Liu CQ, Song XL, Yi WZ, Liu Q, Liu JM, Wu YN, Chen JY, Yang LJ, He HY, Meng J, Pan HW. Integrative Analysis of miRNA and circRNA Expression Profiles and Interaction Network in HSV-1-Infected Primary Corneal Epithelial Cells. Curr Eye Res 2024; 49:368-379. [PMID: 38164922 DOI: 10.1080/02713683.2023.2297345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE Circular RNAs (circRNAs) are products of alternative splicing with roles as competitive endogenous RNAs or microRNA sponges, regulating gene expression and biological processes. However, the involvement of circRNAs in herpes simplex keratitis remains largely unexplored. METHODS This study examines circRNA and miRNA expression profiles in primary human corneal epithelial cells infected with HSV-1, compared to uninfected controls, using microarray analysis. Bioinformatic analysis predicted the potential function of the dysregulated circRNAs and microRNA response elements (MREs) in these circRNAs, forming an interaction network between dysregulated circRNAs and miRNAs. RESULTS A total of 332 circRNAs and 16 miRNAs were upregulated, while 80 circRNAs and six miRNAs were downregulated (fold change ≥2.0 and p < 0.05). Gene ontology (GO) and KEGG pathway analyses were performed on parental genes of dysregulated circRNAs to uncover potential functions in HSV-1 infection. Notably, miR-181b-5p, miR-338-3p, miR-635, and miR-222-3p emerged as pivotal miRNAs interacting with multiple dysregulated circRNAs. CONCLUSIONS This comprehensive study offers insights into differentially expressed circRNAs and miRNAs during HSV-1 infection in corneal epithelial cells, shedding light on circRNA-miRNA interactions' potential role in herpes simplex keratitis pathogenesis.
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Affiliation(s)
- Yu-Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Chao-Qun Liu
- Department of Ophthalmology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xi-Ling Song
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wan-Zhao Yi
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Qi Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jing-Min Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Ya-Ni Wu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jian-Ying Chen
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Lv-Jun Yang
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Hui-Ying He
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Jing Meng
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hong-Wei Pan
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
- Department of Ophthalmology, the First Affiliated Hospital, Jinan University, Guangzhou, China
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Yang R, Pan M, Guo J, Huang Y, Zhang QC, Deng T, Wang J. Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication. Cell Rep 2024; 43:113833. [PMID: 38416642 DOI: 10.1016/j.celrep.2024.113833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024] Open
Abstract
Influenza A virus (IAV) represents a constant public health threat. The single-stranded, segmented RNA genome of IAV is replicated in host cell nuclei as a series of 8 ribonucleoprotein complexes (vRNPs) with RNA structures known to exert essential function to support viral replication. Here, we investigate RNA secondary structures and RNA interactions networks of the IAV genome and construct an in vivo structure model for each of the 8 IAV genome segments. Our analyses reveal an overall in vivo and in virio resemblance of the IAV genome conformation but also wide disparities among long-range and intersegment interactions. Moreover, we identify a long-range RNA interaction that exerts an essential role in genome packaging. Disrupting this structure displays reduced infectivity, attenuating virus pathogenicity in mice. Our findings characterize the in vivo RNA structural landscape of the IAV genome and reveal viral RNA structures that can be targeted to develop antiviral interventions.
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Affiliation(s)
- Rui Yang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minglei Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Huang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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5
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Cunningham CL, Frye CJ, Makowski JA, Kensinger AH, Shine M, Milback EJ, Lackey PE, Evanseck JD, Mihailescu MR. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. RNA (NEW YORK, N.Y.) 2023; 29:1754-1771. [PMID: 37604684 PMCID: PMC10578481 DOI: 10.1261/rna.079627.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/30/2023] [Indexed: 08/23/2023]
Abstract
The s2m, a highly conserved 41-nt hairpin structure in the SARS-CoV-2 genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and the subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a >99% correlation of a single nucleotide mutation at the 15th position (G15U) in Delta SARS-CoV-2. Based on 1H NMR spectroscopy assignments comparing the imino proton resonance region of s2m and the s2m G15U at 19°C, we show that the U15-A29 base pair closes, resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we show that the s2m G15U mutation drastically impacts the binding of host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on immune responses.
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Affiliation(s)
- Caylee L Cunningham
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Caleb J Frye
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Joseph A Makowski
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Adam H Kensinger
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Morgan Shine
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Ella J Milback
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Patrick E Lackey
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, Pennsylvania 16172, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
| | - Mihaela-Rita Mihailescu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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Gorbea C, Elhakiem A, Cazalla D. Shaping the host cell environment with viral noncoding RNAs. Semin Cell Dev Biol 2023; 146:20-30. [PMID: 36581481 PMCID: PMC10101873 DOI: 10.1016/j.semcdb.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Just like the cells they infect viruses express different classes of noncoding RNAs (ncRNAs). Viral ncRNAs come in all shapes and forms, and they usually associate with cellular proteins that are important for their functions. Viral ncRNAs have diverse functions, but they all contribute to the viral control of the cellular environment. Viruses utilize ncRNAs to regulate viral replication, to decide whether they should remain latent or reactivate, to evade the host immune responses, or to promote cellular transformation. In this review we describe the diverse functions played by different classes of ncRNAs expressed by adenoviruses and herpesviruses, how they contribute to the viral infection, and how their study led to insights into RNA-based mechanisms at play in host cells.
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Affiliation(s)
- Carlos Gorbea
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Abdalla Elhakiem
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Demián Cazalla
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Huang H, Liao D, Zhou G, He B, Pu R, Cui Y. MicroRNA-194-3p impacts autophagy and represses rotavirus replication via targeting silent information regulator 1. Virol J 2023; 20:210. [PMID: 37697309 PMCID: PMC10496334 DOI: 10.1186/s12985-023-02175-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 08/31/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Rotavirus (RV) is the main cause of serious diarrhea in infants and young children worldwide. Numerous studies have demonstrated that RV use host cell mechanisms to motivate their own stabilization and multiplication by degrading, enhancing, or hijacking microRNAs (miRNAs). Therefore, exploring the molecular mechanisms by which miRNAs motivate or restrain RV replication by controlling different biological processes, including autophagy, will help to better understand the pathogenesis of RV development. This study mainly explored the effect of miR-194-3p on autophagy after RV infection and its underlying mechanism of the regulation of RV replication. METHODS Caco-2 cells were infected with RV and used to measure the expression levels of miR-194-3p and silent information regulator 1 (SIRT1). After transfection with plasmids and RV infection, viral structural proteins, RV titer, cell viability, and autophagy-linked proteins were tested. The degree of acetylation of p53 was further investigated. A RV-infected neonatal mouse model was constructed in vivo and was evaluated for diarrhea symptoms and lipid droplet formation. RESULTS The results showed that miR-194-3p was reduced but SIRT1 was elevated after RV infection. Elevation of miR-194-3p or repression of SIRT1 inhibited RV replication through the regulation of autophagy. The overexpression of SIRT1 reversed the effects of miR-194-3p on RV replication. The upregulation of miR-194-3p or the downregulation of SIRT1 repressed RV replication in vivo. MiR-194-3p targeted SIRT1 to decrease p53 acetylation. CONCLUSION These results were used to determine the mechanism of miR-194-3p in RV replication, and identified a novel therapeutic small RNA molecule that can be used against RV.
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Affiliation(s)
- Haohai Huang
- Department of Clinical Pharmacy, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China.
- Medical and Pharmacy Research Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, No.1, Huangzhou Xianglong Road of Shilong Town, 523326, Dongguan, Guangdong, China.
| | - Dan Liao
- Department of Gynaecology, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Guanghui Zhou
- Department of Rehabilitation medicine, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Bin He
- Medical and Pharmacy Research Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, No.1, Huangzhou Xianglong Road of Shilong Town, 523326, Dongguan, Guangdong, China
| | - Rong Pu
- Department of Clinical Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
| | - Yejia Cui
- Department of Clinical Laboratory, SSL Central Hospital of Dongguan, Dongguan Third People's Hospital, Affiliated Dongguan Shilong People's Hospital of Southern Medical University, Dongguan, Guangdong, China
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8
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Vaswani CM, Varkouhi AK, Gupta S, Ektesabi AM, Tsoporis JN, Yousef S, Plant PJ, da Silva AL, Cen Y, Tseng YC, Batah SS, Fabro AT, Advani SL, Advani A, Leong-Poi H, Marshall JC, Garcia CC, Rocco PRM, Albaiceta GM, Sebastian-Bolz S, Watts TH, Moraes TJ, Capelozzi VL, Dos Santos CC. Preventing occludin tight-junction disruption via inhibition of microRNA-193b-5p attenuates viral load and influenza-induced lung injury. Mol Ther 2023; 31:2681-2701. [PMID: 37340634 PMCID: PMC10491994 DOI: 10.1016/j.ymthe.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/02/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023] Open
Abstract
Virus-induced lung injury is associated with loss of pulmonary epithelial-endothelial tight junction integrity. While the alveolar-capillary membrane may be an indirect target of injury, viruses may interact directly and/or indirectly with miRs to augment their replication potential and evade the host antiviral defense system. Here, we expose how the influenza virus (H1N1) capitalizes on host-derived interferon-induced, microRNA (miR)-193b-5p to target occludin and compromise antiviral defenses. Lung biopsies from patients infected with H1N1 revealed increased miR-193b-5p levels, marked reduction in occludin protein, and disruption of the alveolar-capillary barrier. In C57BL/6 mice, the expression of miR-193b-5p increased, and occludin decreased, 5-6 days post-infection with influenza (PR8). Inhibition of miR-193b-5p in primary human bronchial, pulmonary microvascular, and nasal epithelial cells enhanced antiviral responses. miR-193b-deficient mice were resistant to PR8. Knockdown of occludin, both in vitro and in vivo, and overexpression of miR-193b-5p reconstituted susceptibility to viral infection. miR-193b-5p inhibitor mitigated loss of occludin, improved viral clearance, reduced lung edema, and augmented survival in infected mice. Our results elucidate how the innate immune system may be exploited by the influenza virus and how strategies that prevent loss of occludin and preserve tight junction function may limit susceptibility to virus-induced lung injury.
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Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Amir K Varkouhi
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Sahil Gupta
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Sadiya Yousef
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Pamela J Plant
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Adriana L da Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Yuchen Cen
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Yi-Chieh Tseng
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Sabrina S Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Alexandre T Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Howard Leong-Poi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cristiana C Garcia
- Laboratory of Respiratory, Exanthematic Viruses, Enterovirus and Viral Emergencies, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Integrated Research Group on Biomarkers. René Rachou Institute, FIOCRUZ Minas, Belo Horizonte, Brazil
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Guillermo M Albaiceta
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain; Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain; CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Steffen Sebastian-Bolz
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tania H Watts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Theo J Moraes
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada; Department of Pediatrics University of Toronto and Respirology, Hospital for Sick Children, Toronto, ON, Canada
| | - Vera L Capelozzi
- Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Interdepartmental Division of Critical Care, St Michael's Hospital, University of Toronto, Toronto, ON, Canada.
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9
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Kandeel M. Oncogenic Viruses-Encoded microRNAs and Their Role in the Progression of Cancer: Emerging Targets for Antiviral and Anticancer Therapies. Pharmaceuticals (Basel) 2023; 16:ph16040485. [PMID: 37111242 PMCID: PMC10146417 DOI: 10.3390/ph16040485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Approximately 20% of all cases of human cancer are caused by viral infections. Although a great number of viruses are capable of causing a wide range of tumors in animals, only seven of these viruses have been linked to human malignancies and are presently classified as oncogenic viruses. These include the Epstein-Barr virus (EBV), human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), Merkel cell polyomavirus (MCPyV), human herpesvirus 8 (HHV8), and human T-cell lymphotropic virus type 1 (HTLV-1). Some other viruses, such as the human immunodeficiency virus (HIV), are associated with highly oncogenic activities. It is possible that virally encoded microRNAs (miRNAs), which are ideal non-immunogenic tools for viruses, play a significant role in carcinogenic processes. Both virus-derived microRNAs (v-miRNAs) and host-derived microRNAs (host miRNAs) can influence the expression of various host-derived and virus-derived genes. The current literature review begins with an explanation of how viral infections might exert their oncogenic properties in human neoplasms, and then goes on to discuss the impact of diverse viral infections on the advancement of several types of malignancies via the expression of v-miRNAs. Finally, the role of new anti-oncoviral therapies that could target these neoplasms is discussed.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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10
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Cunningham CL, Frye CJ, Makowski JA, Kensinger AH, Shine M, Milback EJ, Lackey PE, Evanseck JD, Mihailescu MR. Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.10.528014. [PMID: 36798421 PMCID: PMC9934655 DOI: 10.1101/2023.02.10.528014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The stem loop 2 motif (s2m), a highly conserved 41-nucleotide hairpin structure in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, serves as an attractive therapeutic target that may have important roles in the virus life cycle or interactions with the host. However, the conserved s2m in Delta SARS-CoV-2, a previously dominant variant characterized by high infectivity and disease severity, has received relatively less attention than that of the original SARS-CoV-2 virus. The focus of this work is to identify and define the s2m changes between Delta and SARS-CoV-2 and subsequent impact of those changes upon the s2m dimerization and interactions with the host microRNA miR-1307-3p. Bioinformatics analysis of the GISAID database targeting the s2m element reveals a greater than 99% correlation of a single nucleotide mutation at the 15 th position (G15U) in Delta SARS-CoV-2. Based on 1 H NMR assignments comparing the imino proton resonance region of s2m and the G15U at 19°C, we find that the U15-A29 base pair closes resulting in a stabilization of the upper stem without overall secondary structure deviation. Increased stability of the upper stem did not affect the chaperone activity of the viral N protein, as it was still able to convert the kissing dimers formed by s2m G15U into a stable duplex conformation, consistent with the s2m reference. However, we find that the s2m G15U mutation drastically reduces the binding affinity of the host miR-1307-3p. These findings demonstrate that the observed G15U mutation alters the secondary structure of s2m with subsequent impact on viral binding of host miR-1307-3p, with potential consequences on the immune response.
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11
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Zhang J, Li F, Sun P, Wang J, Li K, Zhao Z, Bai X, Cao Y, Bao H, Li D, Zhang J, Liu Z, Lu Z. Downregulation of miR-122 by porcine reproductive and respiratory syndrome virus promotes viral replication by targeting SOCS3. Vet Microbiol 2022; 275:109595. [DOI: 10.1016/j.vetmic.2022.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/23/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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12
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SP1/miR-92a-1-5p/SOCS5: A novel regulatory axis in feline panleukopenia virus replication. Vet Microbiol 2022; 273:109549. [PMID: 36037621 DOI: 10.1016/j.vetmic.2022.109549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) are vital post-transcriptional regulators that participate in host-pathogen interactions by modulating the expression of cellular factors. Previous studies have demonstrated that feline panleukopenia virus (FPV) alters miRNA expression levels within host cells. However, the relationship between FPV replication and host miRNAs remains unclear. Here, we demonstrated that FPV infection significantly altered cellular miR-92a-1-5p expression in F81 cells by upregulating the expression of specificity protein 1 (SP1). Furthermore, we observed that miR-92a-1-5p enhanced interferon (IFN-α/β) expression by targeting the suppressors of cytokine signaling 5 (SOCS5) that negatively regulates NF-κB signaling and inhibits FPV replication in host cells. These findings revealed that miR-92a-1-5p plays a crucial role in host defense against FPV infection.
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13
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Harper KL, Mottram TJ, Anene CA, Foster B, Patterson MR, McDonnell E, Macdonald A, Westhead D, Whitehouse A. Dysregulation of the miR‐30c/DLL4 axis by circHIPK3 is essential for KSHV lytic replication. EMBO Rep 2022; 23:e54117. [PMID: 35239998 PMCID: PMC9066072 DOI: 10.15252/embr.202154117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Katherine L Harper
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Timothy J Mottram
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Chinedu A Anene
- Centre for Cancer Genomics and Computational Biology Barts Cancer Institute Queen Mary University of London London UK
| | - Becky Foster
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Molly R Patterson
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Euan McDonnell
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Andrew Macdonald
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - David Westhead
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology University of Leeds Leeds UK
- Department of Biochemistry and Microbiology Rhodes University Grahamstown South Africa
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14
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MicroRNA ssc-miR-124a exhibits antiviral activity against porcine reproductive and respiratory syndrome virus via suppression of host genes CD163. Vet Microbiol 2021; 261:109216. [PMID: 34481271 DOI: 10.1016/j.vetmic.2021.109216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/23/2021] [Indexed: 11/22/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a serious infectious disease in the swine industry, which causes severe economic losses to current swine production worldwide. There are no effective antiviral strategies for preventing this disease. Previous studies showed that microRNAs (miRNAs) play important role in virus-host interactions. In this study, we demonstrated that the expression level of ssc-miR-124a was significantly downregulated during both high and low pathogenic PRRSV infection. Overexpression of ssc-miR-124a markedly inhibits PRRSV replication in PAMs. Luciferase reporter experiments and RISC immunoprecipitation assay were used to identify the ssc-miR-124a could directly target the 3'UTR of pig CD163 mRNA in a sequence-specific manner and that CD163 mRNA and protein levels were reduced in PAMs overexpressing ssc-miR-124a. These data not only provide new insights into virus-host interactions during PRRSV infection, but also suggest potential new antiviral strategies against PRRSV infection in the future.
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15
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Lanjanian H, Nematzadeh S, Hosseini S, Torkamanian-Afshar M, Kiani F, Moazzam-Jazi M, Aydin N, Masoudi-Nejad A. High-throughput analysis of the interactions between viral proteins and host cell RNAs. Comput Biol Med 2021; 135:104611. [PMID: 34246161 PMCID: PMC8252845 DOI: 10.1016/j.compbiomed.2021.104611] [Citation(s) in RCA: 3] [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: 05/15/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 01/18/2023]
Abstract
RNA-protein interactions of a virus play a major role in the replication of RNA viruses. The replication and transcription of these viruses take place in the cytoplasm of the host cell; hence, there is a probability for the host RNA-viral protein and viral RNA-host protein interactions. The current study applies a high-throughput computational approach, including feature extraction and machine learning methods, to predict the affinity of protein sequences of ten viruses to three categories of RNA sequences. These categories include RNAs involved in the protein-RNA complexes stored in the RCSB database, the human miRNAs deposited at the mirBase database, and the lncRNA deposited in the LNCipedia database. The results show that evolution not only tries to conserve key viral proteins involved in the replication and transcription but also prunes their interaction capability. These proteins with specific interactions do not perturb the host cell through undesired interactions. On the other hand, the hypermutation rate of NSP3 is related to its affinity to host cell RNAs. The Gene Ontology (GO) analysis of the miRNA with affiliation to NSP3 suggests that these miRNAs show strongly significantly enriched GO terms related to the known symptoms of COVID-19. Docking and MD simulation study of the obtained miRNA through high-throughput analysis suggest a non-coding RNA (an RNA antitoxin, ToxI) as a natural aptamer drug candidate for NSP5 inhibition. Finally, a significant interplay of the host RNA-viral protein in the host cell can disrupt the host cell's system by influencing the RNA-dependent processes of the host cells, such as a differential expression in RNA. Furthermore, our results are useful to identify the side effects of mRNA-based vaccines, many of which are caused by the off-label interactions with the human lncRNAs.
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Affiliation(s)
- Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajjad Nematzadeh
- Department of Computer Technologies, Beykent University, Istanbul, Turkey; Department of Computer Engineering, Faculty of Electrical and Electronics, Yildiz Technical University, Istanbul, Turkey.
| | - Shadi Hosseini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahsa Torkamanian-Afshar
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Nisantasi University, Faculty of Engineering and Architecture, Department of Computer Engineering, Turkey.
| | - Farzad Kiani
- Department of Software Engineering, Engineering and Natural Sciences Faculty, Istinye University, Istanbul, Turkey.
| | - Maryam Moazzam-Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nizamettin Aydin
- Department of Computer Engineering, Faculty of Electrical and Electronics, Yildiz Technical University, Istanbul, Turkey.
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. http://lbb.ut.ac.ir/
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16
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Rizkita LD, Astuti I. The potential of miRNA-based therapeutics in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: A review. J Pharm Anal 2021; 11:265-271. [PMID: 33782640 PMCID: PMC7989072 DOI: 10.1016/j.jpha.2021.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Since the World Health Organization (WHO) declared COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a pandemic in March 2020, and more than 117 million people worldwide have been confirmed to have been infected. Scientists, medical professionals, and other stakeholders are racing against time to find and develop effective medicines for COVID-19. However, no drug with high efficacy to treat SARS-CoV-2 infection has been approved. With the increasing popularity of gene therapy, scientists have explored the utilization of small RNAs such as microRNAs (miRNAs) as therapeutics. miRNAs are non-coding RNAs with high affinity for the 3'-UTRs of targeted messenger RNAs (mRNAs). Interactions between host cells and viral genomes may induce the upregulation or downregulation of various miRNAs. Therefore, understanding the expression patterns of these miRNAs and their functions will provide insights into potential miRNA-based therapies. This review systematically summarizes the potential targets of miRNA-based therapies for SARS-CoV-2 infection and examines the viability of possible transfection methods.
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Affiliation(s)
- Leonny Dwi Rizkita
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Indwiani Astuti
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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17
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Sun B, Yang X, Hou F, Yu X, Wang Q, Oh HS, Raja P, Pesola JM, Vanni EAH, McCarron S, Morris-Love J, Ng AHM, Church GM, Knipe DM, Coen DM, Pan D. Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency. Nat Microbiol 2021; 6:682-696. [PMID: 33558653 PMCID: PMC8221016 DOI: 10.1038/s41564-020-00860-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 11/20/2020] [Indexed: 01/30/2023]
Abstract
MicroRNA miR-138, which is highly expressed in neurons, represses herpes simplex virus 1 (HSV-1) lytic cycle genes by targeting viral ICP0 messenger RNA, thereby promoting viral latency in mice. We found that overexpressed miR-138 also represses lytic processes independently of ICP0 in murine and human neuronal cells; therefore, we investigated whether miR-138 has targets besides ICP0. Using genome-wide RNA sequencing/photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation followed by short interfering RNA knockdown of candidate targets, we identified the host Oct-1 and Foxc1 messenger mRNAs as miR-138's targets, whose gene products are transcription factors important for HSV-1 replication in neuronal cells. OCT-1 has a known role in the initiation of HSV transcription. Overexpression of FOXC1, which was not known to affect HSV-1, promoted HSV-1 replication in murine neurons and ganglia. CRISPR-Cas9 knockout of FOXC1 reduced viral replication, lytic gene expression and miR-138 repression in murine neuronal cells. FOXC1 also collaborated with ICP0 to decrease heterochromatin on viral genes and compensated for the defect of an ICP0-null virus. In summary, miR-138 targets ICP0, Oct-1 and Foxc1 to repress HSV-1 lytic cycle genes and promote epigenetic gene silencing, which together enable favourable conditions for latent infection.
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Affiliation(s)
- Boqiang Sun
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Thermo Fisher Scientific, Shanghai, China
| | - Xuewei Yang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovent Biologics, Inc., Suzhou, China
| | - Fujun Hou
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaofeng Yu
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiongyan Wang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hyung Suk Oh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Priya Raja
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jean M Pesola
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Emilia A H Vanni
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Seamus McCarron
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jenna Morris-Love
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
| | - Alex H M Ng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David M Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Donald M Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Dongli Pan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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18
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Bamunuarachchi G, Pushparaj S, Liu L. Interplay between host non-coding RNAs and influenza viruses. RNA Biol 2021; 18:767-784. [PMID: 33404285 PMCID: PMC8078518 DOI: 10.1080/15476286.2021.1872170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 01/20/2023] Open
Abstract
Influenza virus infection through seasonal epidemics and occasional pandemics has been a major public health concern for decades. Incomplete protection from vaccination and increased antiviral resistance due to frequent mutations of influenza viruses have led to a continuous need for new therapeutic options. The functional significance of host protein and influenza virus interactions has been established, but relatively less is known about the interaction of host noncoding RNAs, including microRNAs and long noncoding RNAs, with influenza viruses. In this review, we summarize host noncoding RNA profiles during influenza virus infection and the regulation of influenza virus infection by host noncoding RNAs. Influenza viral non-coding RNAs are briefly discussed. Increased understanding of the molecular regulation of influenza viral replication will be beneficial in identifying potential therapeutic targets against the influenza virus.
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Affiliation(s)
- Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Samuel Pushparaj
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
- Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, USA
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19
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Ikert H, Lynch MDJ, Doxey AC, Giesy JP, Servos MR, Katzenback BA, Craig PM. High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. Front Physiol 2021; 11:588313. [PMID: 33519501 PMCID: PMC7838646 DOI: 10.3389/fphys.2020.588313] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Circulating plasma microRNAs (miRNAs) are well established as biomarkers of several diseases in humans and have recently been used as indicators of environmental exposures in fish. However, the role of plasma miRNAs in regulating acute stress responses in fish is largely unknown. Tissue and plasma miRNAs have recently been associated with excreted miRNAs; however, external miRNAs have never been measured in fish. The objective of this study was to identify the altered plasma miRNAs in response to acute stress in rainbow trout (Oncorhynchus mykiss), as well as altered miRNAs in fish epidermal mucus and the surrounding ambient water. Small RNA was extracted and sequenced from plasma, mucus, and water collected from rainbow trout pre- and 1 h-post a 3-min air stressor. Following small RNA-Seq and pathway analysis, we identified differentially expressed plasma miRNAs that targeted biosynthetic, degradation, and metabolic pathways. We successfully isolated miRNA from trout mucus and the surrounding water and detected differences in miRNA expression 1-h post air stress. The expressed miRNA profiles in mucus and water were different from the altered plasma miRNA profile, which indicated that the plasma miRNA response was not associated with or immediately reflected in external samples, which was further validated through qPCR. This research expands understanding of the role of plasma miRNA in the acute stress response of fish and is the first report of successful isolation and profiling of miRNA from fish mucus or samples of ambient water. Measurements of miRNA from plasma, mucus, or water can be further studied and have potential to be applied as non-lethal indicators of acute stress in fish.
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Affiliation(s)
- Heather Ikert
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - John P. Giesy
- Department of Veterinary Biomedical Sciences, Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Environmental Science, Baylor University, Waco, TX, United States
| | - Mark R. Servos
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | | | - Paul M. Craig
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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20
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Wang H, Tian Z, Xu Y, Wang Q, Ding SW, Li Y. Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Front Microbiol 2020; 11:590904. [PMID: 33281788 PMCID: PMC7688628 DOI: 10.3389/fmicb.2020.590904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) causes seasonal infections and periodic pandemics in humans. The non-structural protein 1 (NS1) of IAV is the main viral antagonist of the innate immune responses that play a key role in influenza pathogenesis. However, the mechanism to disrupt the host cell homeostasis by IAV NS1 remains poorly understood. Here, we show that expression of NS1 from the WSN strain, but not PR8 strain, of IAV, markedly induced nuclear import of the host RNA interference (RNAi) factors such as Argonaute-2 and microRNA 16. We found that the single residue substitution of aspartic acid with histidine at position 101 (D101H) of IAV-PR8 NS1 was sufficient to induce the nuclear import process and to enhance the virulence of IAV-PR8 in mice. However, we observed no significant differences between the wild-type and mutant IAV-PR8 in virus titers or induction of the interferon response in lung tissues, indicating a novel role of NS1 in the virulence determination of IAV in a mammalian host. Moreover, our bioinformatic analysis of 69,057 NS1 sequences from all IAV subtypes deposited in the NCBI database revealed that the NS1-H101 gene of IAV-WSN was widespread among H1N1 viruses isolated in 1933 but disappeared completely after 1940. Thus, IAV NS1 (H101) is a mutation selected against during evolution of IAV, suggesting that mutation H101 confers an important biological phenotype.
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Affiliation(s)
- Hua Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhonghui Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Xu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Yang Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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21
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Dunn LEM, Ivens A, Netherton CL, Chapman DAG, Beard PM. Identification of a Functional Small Noncoding RNA of African Swine Fever Virus. J Virol 2020; 94:e01515-20. [PMID: 32796064 PMCID: PMC7565616 DOI: 10.1128/jvi.01515-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023] Open
Abstract
African swine fever virus (ASFV) causes a lethal hemorrhagic disease of domestic pigs, against which no vaccine is available. ASFV has a large, double-stranded DNA genome that encodes over 150 proteins. Replication takes place predominantly in the cytoplasm of the cell and involves complex interactions with host cellular components, including small noncoding RNAs (sncRNAs). A number of DNA viruses are known to manipulate sncRNA either by encoding their own or disrupting host sncRNA. To investigate the interplay between ASFV and sncRNAs, a study of host and viral small RNAs extracted from ASFV-infected primary porcine macrophages (PAMs) was undertaken. We discovered that ASFV infection had only a modest effect on host miRNAs, with only 6 miRNAs differentially expressed during infection. The data also revealed 3 potential novel small RNAs encoded by ASFV, ASFVsRNA1-3. Further investigation of ASFVsRNA2 detected it in lymphoid tissue from pigs with ASF. Overexpression of ASFVsRNA2 led to an up to 1-log reduction in ASFV growth, indicating that ASFV utilizes a virus-encoded small RNA to disrupt its own replication.IMPORTANCE African swine fever (ASF) poses a major threat to pig populations and food security worldwide. The disease is endemic to Africa and Eastern Europe and is rapidly emerging into Asia, where it has led to the deaths of millions of pigs in the last 12 months. The development of safe and effective vaccines to protect pigs against ASF has been hindered by lack of understanding of the complex interactions between ASFV and the host cell. We focused our work on characterizing the interactions between ASFV and sncRNAs. Although comparatively modest changes to host sncRNA abundances were observed upon ASFV infection, we discovered and characterized a novel functional ASFV-encoded sncRNA. The results from this study add important insights into ASFV host-pathogen interactions. This knowledge may be exploited to develop more effective ASFV vaccines that take advantage of the sncRNA system.
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Affiliation(s)
- Laura E M Dunn
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom
| | - Alasdair Ivens
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Philippa M Beard
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, United Kingdom
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22
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Degradation of MicroRNA miR-466d-3p by Japanese Encephalitis Virus NS3 Facilitates Viral Replication and Interleukin-1β Expression. J Virol 2020; 94:JVI.00294-20. [PMID: 32461319 DOI: 10.1128/jvi.00294-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/13/2020] [Indexed: 11/20/2022] Open
Abstract
Japanese encephalitis virus (JEV) infection alters microRNA (miRNA) expression in the central nervous system (CNS). However, the mechanism contributing to miRNA regulation in the CNS is not known. We discovered global degradation of mature miRNA in mouse brains and neuroblastoma (NA) cells after JEV infection. Integrative analysis of miRNAs and mRNAs suggested that several significantly downregulated miRNAs and their targeted mRNAs were clustered into an inflammation pathway. Transfection with miRNA 466d-3p (miR-466d-3p) decreased interleukin-1β (IL-1β) expression and inhibited JEV replication in NA cells. However, miR-466d-3p expression increased after JEV infection in the presence of cycloheximide, indicating that viral protein expression reduced miR-466d-3p expression. We generated all the JEV coding proteins and demonstrated NS3 helicase protein to be a potent miRNA suppressor. The NS3 proteins of Zika virus, West Nile virus, and dengue virus serotype 1 (DENV-1) and DENV-2 also decreased miR-466d-3p expression. Results from helicase-blocking assays and in vitro unwinding assays demonstrated that NS3 could unwind pre-miR-466d and induce miRNA dysfunction. Computational models and an RNA immunoprecipitation assay revealed arginine-rich domains of NS3 to be crucial for pre-miRNA binding and degradation of host miRNAs. Importantly, site-directed mutagenesis of conserved residues in NS3 revealed that R226G and R202W reduced the binding affinity and degradation of pre-miR-466d. These results expand the function of flavivirus helicases beyond unwinding duplex RNA to degrade pre-miRNAs. Hence, we revealed a new mechanism for NS3 in regulating miRNA pathways and promoting neuroinflammation.IMPORTANCE Host miRNAs have been reported to regulate JEV-induced inflammation in the CNS. We found that JEV infection could reduce expression of host miRNA. The helicase region of the NS3 protein bound specifically to miRNA precursors and could lead to incorrect unwinding of miRNA precursors, thereby reducing the expression of mature miRNAs. This observation led to two major findings. First, our results suggested that JEV NS3 protein induced miR-466d-3p degradation, which promoted IL-1β expression and JEV replication. Second, arginine molecules on NS3 were the main miRNA-binding sites, because we demonstrated that miRNA degradation was abolished if arginines at R226 and R202 were mutated. Our study provides new insights into the molecular mechanism of JEV and reveals several amino acid sites that could be mutated for a JEV vaccine.
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Sankaranarayanan R, Palani SN, Kumar A, Selvakumar A. S. P, Tennyson J. Prediction and experimental confirmation of banana bract mosaic virus encoding miRNAs and their targets. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s41544-019-0044-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Potyviridae is the largest plant infecting family under the monophyletic group Riboviria, infects many of the food, fodder and ornamental crops. Due to the higher mutation and recombination rate, potyvirids are evolving rapidly, adapting to the environmental chaos and expanding their hosts. Virus control measures are need to be updated as the economic importance of potyvirids is massive. microRNAs (miRNAs) are well known for their functional importance in eukaryotes and many viruses. Regardless of its biogenesis, whether canonical or noncanonical, microRNA centric antivirus approaches attract the researchers to the hopeful future of next-generation broad-spectrum antiviral measures.
Methods
In this study, we predicted and screened banana bract mosaic virus (BBrMV) encoding miRNAs by computation approaches and their targets on banana transcriptome using plant small RNA target analysis server (psRNAtarget). The target gene functions were annotated by Blast2GO. The predicted BBrMV miRNAs were experimentally screened by stem-loop RT-PCR.
Results
The results showed that, among the predicted BBrMV miRNAs, miRNA2 is conserved throughout BBrMV isolates and has multiple virus-specific target transcripts. In addition, primary experimental validation for the predicted miRNAs revealed that miRNA2 exists in the BBrMV infected banana leaf samples.
Conclusions
The existence of BBrMV miRNA2 is confirmed by stem-loop RT-PCR followed by cloning and sequencing. The presence of miRNA of Potyviridae is rarely addressed and would definitely spread the hope to understand the virus infectious cycle. Our report would also help to better understand and manipulate potyviral infections.
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MiR-125b Suppression Inhibits Apoptosis and Negatively Regulates Sema4D in Avian Leukosis Virus-Transformed Cells. Viruses 2019; 11:v11080728. [PMID: 31394878 PMCID: PMC6723722 DOI: 10.3390/v11080728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Subgroup J avian leukosis virus (ALV-J), an oncogenic retrovirus, causes hemangiomas and myeloid tumors in chickens. We previously showed that miR-125b is down-regulated in ALV-J-induced tumors. This study aimed to investigate the possible role of miR-125b in ALV-J-mediated infection and tumorigenesis. Knockdown of miR-125b expression in HP45 cells reduced, whereas over-expression induced late-stage apoptosis. Bioinformatics analysis and luciferase activity assays indicate that miR-125b targets Semaphorin 4D/CD100 (Sema4D) by binding the 3'-untranslated region of messenger RNA (mRNA). Up-regulation of miR-125b in the DF1 cell line suppressed Sema4D expression, whereas miR-125 down-regulation increased Sema4D expression levels. To uncover the function of Sema4D during ALV-J infection, animal infection experiments and in vitro assays were performed and show that Sema4D mRNA levels were up-regulated in ALV-J-infected tissues and cells. Finally, functional experiments show that miR-125 down-regulation and Sema4D over-expression inhibited apoptosis in HP45 cells. These results suggest that miR-125b and its target Sema4D might play an important role in the aggressive growth of HP45 cells induced by avian leukosis viruses (ALVs). These findings improve our understanding of the underlying mechanism of ALV-J infection and tumorigenesis.
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25
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Bottini S, Pratella D, Grandjean V, Repetto E, Trabucchi M. Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. Brief Bioinform 2019; 19:1290-1301. [PMID: 28605404 PMCID: PMC6291801 DOI: 10.1093/bib/bbx063] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 01/18/2023] Open
Abstract
Cross-Linking
Immunoprecipitation associated to
high-throughput sequencing (CLIP-seq) is a technique used to
identify RNA directly bound to RNA-binding proteins across the entire transcriptome in
cell or tissue samples. Recent technological and computational advances permit the
analysis of many CLIP-seq samples simultaneously, allowing us to reveal the comprehensive
network of RNA–protein interaction and to integrate it to other genome-wide analyses.
Therefore, the design and quality management of the CLIP-seq analyses are of critical
importance to extract clean and biological meaningful information from CLIP-seq
experiments. The application of CLIP-seq technique to Argonaute 2 (Ago2) protein, the main
component of the microRNA (miRNA)-induced silencing complex, reveals the direct binding
sites of miRNAs, thus providing insightful information about the role played by miRNA(s).
In this review, we summarize and discuss the most recent computational methods for
CLIP-seq analysis, and discuss their impact on Ago2/miRNA-binding site identification and
prediction with a regard toward human pathologies.
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Affiliation(s)
- Silvia Bottini
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - David Pratella
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Valerie Grandjean
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Emanuela Repetto
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Michele Trabucchi
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
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26
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Pan Q, Liu Z, Liao S, Ye L, Lu X, Chen X, Li Z, Li X, Xu YZ, Liu H. Current mechanistic insights into the role of infection in systemic lupus erythematosus. Biomed Pharmacother 2019; 117:109122. [PMID: 31226637 DOI: 10.1016/j.biopha.2019.109122] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by inflammation and abnormal production of autoantibody, but the mechanisms of the aberrant immune responses are currently unknown. Recently, growing evidence has suggested that infection plays a pivotal role in SLE. Here, we investigate the role of infectious agents (e.g., Epstein-Barr virus, parvovirus B19, human T-lymphotropic virus type 1, human immunodeficiency virus type 1, and endogenous retroviruses) in the pathogenesis of SLE. More importantly, we explore the known mechanisms underlying the involvement of infectious agents in the pathogenesis of SLE, including molecular mimicry, epitope spreading, superantigen production, bystander activation, persistent viral infection, altered apoptosis, clearance deficiency, and epigenetic alterations (e.g., DNA methylation and microRNAs). However, some infectious agents (e.g., malaria parasites, hepatitis B virus, Toxoplasma gondii, and Helicobacter pylori) may exert protective effects on SLE. Therefore, the relationship between infection and SLE is multifaceted and multidirectional, including causative and/or protective associations, which warrant further investigation in the future.
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Affiliation(s)
- Qingjun Pan
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China.
| | - Zejian Liu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Shuzhen Liao
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Lin Ye
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Xing Lu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Xiaoqun Chen
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Zhihang Li
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Xinxin Li
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Yong-Zhi Xu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China
| | - Huafeng Liu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, 524001, China.
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Wu P, Shang Q, Dweteh OA, Huang H, Zhang S, Zhong J, Hou Q, Guo X. Over expression of bmo-miR-2819 suppresses BmNPV replication by regulating the BmNPV ie-1 gene in Bombyx mori. Mol Immunol 2019; 109:134-139. [PMID: 30947109 DOI: 10.1016/j.molimm.2019.03.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen that threatens the growth and sustainability of the sericulture industry. Accumulating studies in recent years suggest that insect viruses infection can change the host microRNAs (miRNAs) expression profile and both cellular and viral miRNAs play roles in host-pathogen interactions. Until now, the functional analysis of miRNA encoded by silkworm for host-virus interaction is limited. In this study, we validate the down-regulation of bmo-miR-2819 upon BmNPV infection by qRT-PCR and confirm the BmNPV immediately early 1 gene, ie-1 is one of the targets for bmo-miR-2819 based on the results of dual luciferase report assay. Overexpression of bmo-miR-2819 can significantly decline the abundance of IE-1 protein level in BmNPV-infected silkworm larvae. Further, the expression level of polyhedrin gene and VP39 protein of BmNPV in the infected larvae after applying bmo-miR-2819 mimics was significantly decreased comparing with that of larvae with mimic control. Our results suggest that overexpression of bmo-miR-2819 could suppress BmNPV replication by down-regulating the expression of BmNPV ie-1 gene, which demonstrate that cellular miRNAs could affect virus infection by regulating the expression of virus genes.
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Affiliation(s)
- Ping Wu
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China.
| | - Qi Shang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Owusu Amanfo Dweteh
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Haoling Huang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Shaolun Zhang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Jinbo Zhong
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Qirui Hou
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Xijie Guo
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China.
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28
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Mandal P, Saha SS, Sen S, Bhattacharya A, Bhattacharya NP, Bucha S, Sinha M, Chowdhury RR, Mondal NR, Chakravarty B, Chatterjee T, Roy S, Chattapadhyay A, Sengupta S. Cervical cancer subtypes harbouring integrated and/or episomal HPV16 portray distinct molecular phenotypes based on transcriptome profiling of mRNAs and miRNAs. Cell Death Discov 2019; 5:81. [PMID: 30937183 PMCID: PMC6433907 DOI: 10.1038/s41420-019-0154-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/03/2019] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
Heterogeneity in cervical cancers (CaCx) in terms of HPV16 physical status prompted us to investigate the mRNA and miRNA signatures among the different categories of CaCx samples. We performed microarray-based mRNA expression profiling and quantitative real-time PCR-based expression analysis of some prioritised miRNAs implicated in cancer-related pathways among various categories of cervical samples. Such samples included HPV16-positive CaCx cases that harboured either purely integrated HPV16 genomes (integrated) and those that harboured episomal viral genomes, either pure or concomitant with integrated viral genomes (episomal), which were compared with normal cervical samples that were either HPV negative or positive for HPV16. The mRNA expression profile differed characteristically between integrated and episomal CaCx cases for enriched biological pathways. miRNA expression profiles also differed among CaCx cases compared with controls (upregulation—miR-21, miR-16, miR-205, miR-323; downregulation—miR-143, miR-196b, miR-203, miR-34a; progressive upregulation—miR-21 and progressive downregulation—miR-143, miR-34a, miR-196b and miR-203) in the order of HPV-negative controls, HPV16-positive non-malignant samples and HPV16-positive CaCx cases. miR-200a was upregulated in HPV16-positive cervical tissues irrespective of histopathological status. Expression of majority of the predicted target genes was negatively correlated with their corresponding miRNAs, irrespective of the CaCx subtypes. E7 mRNA expression correlated positively with miR-323 expression among episomal cases and miR-203, among integrated cases. miR-181c expression was downregulated only among the episomal CaCx cases and negatively correlated with protein coding transcript of the proliferative target gene, CKS1B of the significantly enriched “G2/M DNA Damage Checkpoint Regulation” pathway among CaCx cases. Thus, the two CaCx subtypes are distinct entities at the molecular level, which could be differentially targeted for therapy. In fact, availability of a small molecule inhibitor of CKS1B, suggests that drugging CKS1B could be a potential avenue of treating the large majority of CaCx cases harbouring episomal HPV16.
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Affiliation(s)
- Paramita Mandal
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,6Present Address: Department of Zoology, The University of Burdwan, Burdwan, West Bengal India
| | - Sweta Sharma Saha
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,Present Address: Section of Haematology/Oncology, Department of Medicine, university of Chicago, 5841 S Maryland Ave MC 2115, Chicago, IL 60637 USA
| | - Shrinka Sen
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India.,8Present Address: Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064 India
| | | | - Nitai P Bhattacharya
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Sudha Bucha
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India
| | - Mithun Sinha
- 2Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064 India.,9Present Address: Comprehensive Wound Center, Center for Regenerative Medicine and Cell Based Therapies, The Ohio State University, Columbus, OH USA
| | - Rahul Roy Chowdhury
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Nidhu Ranjan Mondal
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Biman Chakravarty
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Tanmay Chatterjee
- 3Department of Gynecology, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Sudipta Roy
- Sri Aurobindo Seva Kendra, 1H, Gariahat Road (S) Jodhpur Park, Kolkata, 700068 West Bengal India
| | | | - Sharmila Sengupta
- 1National Institute of Biomedical Genomics, Kalyani, West Bengal India
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29
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Villarreal LP, Witzany G. That is life: communicating RNA networks from viruses and cells in continuous interaction. Ann N Y Acad Sci 2019; 1447:5-20. [PMID: 30865312 DOI: 10.1111/nyas.14040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.
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Affiliation(s)
- Luis P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
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30
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Mukhopadhyay U, Chanda S, Patra U, Mukherjee A, Rana S, Mukherjee A, Chawla-Sarkar M. Synchronized Orchestration of miR-99b and let-7g Positively Regulates Rotavirus Infection by Modulating Autophagy. Sci Rep 2019; 9:1318. [PMID: 30718795 PMCID: PMC6362297 DOI: 10.1038/s41598-018-38473-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/27/2018] [Indexed: 12/18/2022] Open
Abstract
Rotavirus (RV), the major etiological agent of viral gastroenteritis in young children, kills over 200 thousand infants each year. In spite of available vaccines, rotaviral diarrhoea is still a major problem in developing countries of Asia and Africa. Therefore, the studies on RV infection and host antiviral responses are warranted. The active correlation between virus infection and activation of autophagy machinery and positive influence of autophagy on RV replication have been documented recently. Previous study from our group showed dysregulation of several cellular miRNAs during RV infection, though their significance remained largely unknown. Since cellular microRNAs (miRNAs) have been implicated in the control of several fundamental biological processes including stress response and autophagy, we focused on two miRNAs, miR-99b and let-7g, and analyzed their function to gain insight into the miRNA-autophagy crosstalk during RV infection. This study shows that RV suppresses let-7g expression but enhances miR-99b that in turn augment major autophagy regulators. Ectopic expression of let-7g and knockdown of miR-99b resulted in inhibition of autophagy, hence, reduction of RV replication. Overall, our study highlights new mechanistic insights for understanding the role of miRNAs in modulating RV infection and possibility of using RNA interference as an antiviral therapeutic target.
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Affiliation(s)
- Urbi Mukhopadhyay
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Shampa Chanda
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Upayan Patra
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Arpita Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Santanu Rana
- Department of Zoology, University of Calcutta, Kolkata, WB, India
| | - Anupam Mukherjee
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
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31
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Bilbao-Arribas M, Abendaño N, Varela-Martínez E, Reina R, de Andrés D, Jugo BM. Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq. BMC Genomics 2019; 20:62. [PMID: 30658565 PMCID: PMC6339376 DOI: 10.1186/s12864-018-5416-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/26/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short endogenous, single-stranded, noncoding small RNA molecules of approximately 22 nucleotides in length. They regulate gene expression posttranscriptionally by silencing mRNA expression, thus orchestrating many physiological processes. The Small Ruminant Lentiviruses (SRLV) group includes the Visna Maedi Virus (VMV) and Caprine Arthritis Encephalitis (CAEV) viruses, which cause a disease in sheep and goats characterized by pneumonia, mastitis, arthritis and encephalitis. Their main target cells are from the monocyte/macrophage lineage. To date, there are no studies on the role of miRNAs in this viral disease. RESULTS Using RNA-seq technology and bioinformatics analysis, the expression levels of miRNAs during different clinical stages of infection were studied. A total of 212 miRNAs were identified, of which 46 were conserved sequences in other species but found for the first time in sheep, and 12 were completely novel. Differential expression analysis comparing the uninfected and seropositive groups showed changes in several miRNAs; however, no significant differences were detected between seropositive asymptomatic and diseased sheep. The robust increase in the expression level of oar-miR-21 is consistent with its increased expression in other viral diseases. Furthermore, the target prediction of the dysregulated miRNAs revealed that they control genes involved in proliferation-related signalling pathways, such as the PI3K-Akt, AMPK and ErbB pathways. CONCLUSIONS To the best of our knowledge, this is the first study reporting miRNA profiling in sheep in response to SRLV infection. The known functions of oar-miR-21 as a regulator of inflammation and proliferation appear to be a possible cause of the lesions caused in the sheep's lungs. This miRNA could be an indicator for the severity of the lung lesions, or a putative target for therapeutic intervention.
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Affiliation(s)
- Martin Bilbao-Arribas
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Naiara Abendaño
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Endika Varela-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain
| | - Ramsés Reina
- Institute of Agrobiotechnology (CSIC-UPNA-Government of Navarra), Avenida de Pamplona 123, 31192 Mutilva, Navarra, Spain
| | - Damián de Andrés
- Institute of Agrobiotechnology (CSIC-UPNA-Government of Navarra), Avenida de Pamplona 123, 31192 Mutilva, Navarra, Spain
| | - Begoña M Jugo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, 48080, Bilbao, Spain.
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32
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Yan X, Sun J, Yuan K. miR-138 expression in oral herpes simplex and its effect on ICP0. Exp Ther Med 2019; 17:388-392. [PMID: 30651809 PMCID: PMC6307441 DOI: 10.3892/etm.2018.6912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/22/2018] [Indexed: 11/06/2022] Open
Abstract
This study aimed to investigate the micro ribonucleic acid-138 (miR-138) expression in oral herpes simplex (HS) and its effect on the expression of herpes simplex virus type 1 (HSV-1) lytic gene trans-acting factor infected cell protein 0 (ICP0). Forty-five rat models with oral HS were successfully established (the observation group) and another 40 healthy rats were selected as the control group. The miR-138 expression in serum of rats in the two groups were detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). 293T cells infected by HSV-1 were divided into Group A and Group B after 10 days of culture. Group A was transfected by miR-138 mimics and Group B was transfected by miR-138 complementary oligonucleotide inhibitor. The expression levels of miR-138 and ICP0 messenger RNA (mRNA) in the cells of the two groups were detected by RT-PCR, and the expression levels of ICP0 protein were detected by enzyme-linked immunosorbent assay (ELISA). A total of 85 rat models with oral HS were established in this study, but only 45 models were established successfully with a success rate of 56.25%. The expression level of miR-138 in the rat serum in the observation group was higher than that in the control group (P<0.05). In addition, the expression level of ICP0 mRNA in Group A was lower than that in Group B (P<0.05). Moreover, the expression level of ICP0 protein in Group A was lower than that in Group B (P<0.05). Finally, the expression level of miR-138 in HSV was increased, suggesting that the expression of miR-138 may inhibit the expression of ICP0, thus preventing the duplication of HSV-1. Therefore, the expression of miR-138 may be used as a potential therapeutic target for HSV.
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Affiliation(s)
- Xiao Yan
- Department of Stomatology, The Second Qilu Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Jing Sun
- Department of Pharmacy, The Second Qilu Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
| | - Kuifeng Yuan
- Department of Stomatology, The Second Qilu Hospital of Shandong University, Jinan, Shandong 250033, P.R. China
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33
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Kariithi HM, Boucias DG, Murungi EK, Meki IK, Demirbaş-Uzel G, van Oers MM, Vreysen MJB, Abd-Alla AMM, Vlak JM. Coevolution of hytrosaviruses and host immune responses. BMC Microbiol 2018; 18:183. [PMID: 30470186 PMCID: PMC6251100 DOI: 10.1186/s12866-018-1296-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Hytrosaviruses (SGHVs; Hytrosaviridae family) are double-stranded DNA (dsDNA) viruses that cause salivary gland hypertrophy (SGH) syndrome in flies. Two structurally and functionally distinct SGHVs are recognized; Glossina pallidipes SGHV (GpSGHV) and Musca domestica SGHV (MdSGHV), that infect the hematophagous tsetse fly and the filth-feeding housefly, respectively. Genome sizes and gene contents of GpSGHV (~ 190 kb; 160-174 genes) and MdSGHV (~ 124 kb; 108 genes) may reflect an evolution with the SGHV-hosts resulting in differences in pathobiology. Whereas GpSGHV can switch from asymptomatic to symptomatic infections in response to certain unknown cues, MdSGHV solely infects symptomatically. Overt SGH characterizes the symptomatic infections of SGHVs, but whereas MdSGHV induces both nuclear and cellular hypertrophy (enlarged non-replicative cells), GpSGHV induces cellular hyperplasia (enlarged replicative cells). Compared to GpSGHV's specificity to Glossina species, MdSGHV infects other sympatric muscids. The MdSGHV-induced total shutdown of oogenesis inhibits its vertical transmission, while the GpSGHV's asymptomatic and symptomatic infections promote vertical and horizontal transmission, respectively. This paper reviews the coevolution of the SGHVs and their hosts (housefly and tsetse fly) based on phylogenetic relatedness of immune gene orthologs/paralogs and compares this with other virus-insect models. RESULTS Whereas MdSGHV is not vertically transmitted, GpSGHV is both vertically and horizontally transmitted, and the balance between the two transmission modes may significantly influence the pathogenesis of tsetse virus. The presence and absence of bacterial symbionts (Wigglesworthia and Sodalis) in tsetse and Wolbachia in the housefly, respectively, potentially contributes to the development of SGH symptoms. Unlike MdSGHV, GpSGHV contains not only host-derived proteins, but also appears to have evolutionarily recruited cellular genes from ancestral host(s) into its genome, which, although may be nonessential for viral replication, potentially contribute to the evasion of host's immune responses. Whereas MdSGHV has evolved strategies to counteract both the housefly's RNAi and apoptotic responses, the housefly has expanded its repertoire of immune effector, modulator and melanization genes compared to the tsetse fly. CONCLUSIONS The ecologies and life-histories of the housefly and tsetse fly may significantly influence coevolution of MdSGHV and GpSGHV with their hosts. Although there are still many unanswered questions regarding the pathogenesis of SGHVs, and the extent to which microbiota influence expression of overt SGH symptoms, SGHVs are attractive 'explorers' to elucidate the immune responses of their hosts, and the transmission modes of other large DNA viruses.
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Affiliation(s)
- Henry M Kariithi
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O Box 57811, Kaptagat Rd, Loresho, Nairobi, 00200, Kenya. .,Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria. .,Present Address: US National Poultry Research Centre, Southeast Poultry Research Laboratory, USDA-ARS, 934 College Station Road, Athens, GA, 30605, USA.
| | - Drion G Boucias
- Entomology and Nematology Department, University of Florida, 970 Natural Area Drive, Gainesville, FL, 32611, USA
| | - Edwin K Murungi
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Njoro, 20115, Kenya
| | - Irene K Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria.,Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Güler Demirbaş-Uzel
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Monique M van Oers
- Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Marc J B Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Wagrammer Straße 5, A-1400, Vienna, Austria
| | - Just M Vlak
- Laboratory of Virology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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34
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Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
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Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
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35
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Ziv O, Gabryelska MM, Lun ATL, Gebert LFR, Sheu-Gruttadauria J, Meredith LW, Liu ZY, Kwok CK, Qin CF, MacRae IJ, Goodfellow I, Marioni JC, Kudla G, Miska EA. COMRADES determines in vivo RNA structures and interactions. Nat Methods 2018; 15:785-788. [PMID: 30202058 PMCID: PMC6168409 DOI: 10.1038/s41592-018-0121-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023]
Abstract
The structural flexibility of RNA underlies fundamental biological processes, but there are no methods for exploring the multiple conformations adopted by RNAs in vivo. We developed cross-linking of matched RNAs and deep sequencing (COMRADES) for in-depth RNA conformation capture, and a pipeline for the retrieval of RNA structural ensembles. Using COMRADES, we determined the architecture of the Zika virus RNA genome inside cells, and identified multiple site-specific interactions with human noncoding RNAs.
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Affiliation(s)
- Omer Ziv
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Marta M Gabryelska
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Jessica Sheu-Gruttadauria
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Luke W Meredith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zhong-Yu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Medicine (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, CA, USA
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Cambridge, UK.
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36
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Identification of virus-encoded microRNAs in divergent Papillomaviruses. PLoS Pathog 2018; 14:e1007156. [PMID: 30048533 PMCID: PMC6062147 DOI: 10.1371/journal.ppat.1007156] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/15/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNAs that regulate diverse biological processes including multiple aspects of the host-pathogen interface. Consequently, miRNAs are commonly encoded by viruses that undergo long-term persistent infection. Papillomaviruses (PVs) are capable of undergoing persistent infection, but as yet, no widely-accepted PV-encoded miRNAs have been described. The incomplete understanding of PV-encoded miRNAs is due in part to lack of tractable laboratory models for most PV types. To overcome this, we have developed miRNA Discovery by forced Genome Expression (miDGE), a new wet bench approach to miRNA identification that screens numerous pathogen genomes in parallel. Using miDGE, we screened over 73 different PV genomes for the ability to code for miRNAs. Our results show that most PVs are unlikely to code for miRNAs and we conclusively demonstrate a lack of PV miRNA expression in cancers associated with infections of several high risk HPVs. However, we identified five different high-confidence or highly probable miRNAs encoded by four different PVs (Human PVs 17, 37, 41 and a Fringilla coelebs PV (FcPV1)). Extensive in vitro assays confirm the validity of these miRNAs in cell culture and two FcPV1 miRNAs are further confirmed to be expressed in vivo in a natural host. We show that miRNAs from two PVs (HPV41 & FcPV1) are able to regulate viral transcripts corresponding to the early region of the PV genome. Combined, these findings identify the first canonical PV miRNAs and support that miRNAs of either host or viral origin are important regulators of the PV life cycle.
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37
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Li L, Gao F, Zheng H, Jiang Y, Tong W, Zhou Y, Tong G. Utilizing host endogenous microRNAs to negatively regulate the replication of porcine reproductive and respiratory syndrome virus in MARC-145 cells. PLoS One 2018; 13:e0200029. [PMID: 29969475 PMCID: PMC6029797 DOI: 10.1371/journal.pone.0200029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 06/17/2018] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) contribute to gene regulation at the post-transcriptional level and are capable of mRNA silencing by binding to target sites exhibiting high degrees of complementarity. Therefore, cloning host miRNA-recognition sequences into the genome of RNA viruses represents a rational strategy for manipulating viral replication. Here, we performed deep sequencing to obtain small-RNA (sRNA)-expression profiles from in vitro-cultured MARC-145 cells post infection with porcine reproductive and respiratory syndrome virus (PRRSV) and chose six candidate miRNAs of different abundance (miR-21, miR-140-3p, miR-185, miR-26a, miR-505, and miR-199a) for further study. Based on the full-length cDNA clone p7USC, we constructed a number of PRRSV mutants that provided complementary base-pairing target sites for the miRNAs in 3′ untranslated regions. Our results showed that all low- and moderate- abundant miRNA-target mutants showed similar growth properties, whereas the highest-abundant miRNA-target mutant blocked both viral transcription and replication. Discontinuous mutations in high-abundant miRNA-target sites subsequently recovered viral viability and propagation. These results demonstrated the copy number of endogenous miRNAs and the extent of sRNA complementarity were key factors to silence potential mRNA expression/translation, thereby determining PRRSV viability. Interestingly, the mutant containing miR-140-target sites (v140-t) showed strong suppression of viral replication from P1 to P3 in vitro, as shown by virus titer, plaque morphology, and qRT-PCR assays. To assess genetic stability, sequencing of v140-t (P1, P3, P5 and P10) revealed spontaneous mutations preferentially located among several nucleotides near the 3′ end of the insertion region and corresponding to the “seed region” of miR-140-3p, explaining the induced viral repression and the direction of virus evolution. This approach provided a general silencing strategy for limiting PRRSV replication by endogenous miRNAs in MARC-145 cells.
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Affiliation(s)
- Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Hao Zheng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, PR China
- * E-mail:
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38
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Monsanto-Hearne V, Johnson KN. miRNAs in Insects Infected by Animal and Plant Viruses. Viruses 2018; 10:E354. [PMID: 29970868 PMCID: PMC6071220 DOI: 10.3390/v10070354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/29/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses vectored by insects cause severe medical and agricultural burdens. The process of virus infection of insects regulates and is regulated by a complex interplay of biomolecules including the small, non-coding microRNAs (miRNAs). Considered an anomaly upon its discovery only around 25 years ago, miRNAs as a class have challenged the molecular central dogma which essentially typifies RNAs as just intermediaries in the flow of information from DNA to protein. miRNAs are now known to be common modulators or fine-tuners of gene expression. While recent years has seen an increased emphasis on understanding the role of miRNAs in host-virus associations, existing literature on the interaction between insects and their arthropod-borne viruses (arboviruses) is largely restricted to miRNA abundance profiling. Here we analyse the commonalities and contrasts between miRNA abundance profiles with different host-arbovirus combinations and outline a suggested pipeline and criteria for functional analysis of the contribution of miRNAs to the insect vector-virus interaction. Finally, we discuss the potential use of the model organism, Drosophila melanogaster, in complementing research on the role of miRNAs in insect vector-virus interaction.
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Affiliation(s)
- Verna Monsanto-Hearne
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
| | - Karyn N Johnson
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia.
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39
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Wang Z, Sun B, Zhu F. Epigallocatechin-3-gallate protects Kuruma shrimp Marsupeneaus japonicus from white spot syndrome virus and Vibrio alginolyticus. FISH & SHELLFISH IMMUNOLOGY 2018; 78:1-9. [PMID: 29656126 DOI: 10.1016/j.fsi.2018.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Epigallocatechin-3-gallate (EGCG) is the most abundant catechin in green tea and exhibits potential antibacterial and anticancer activities. In this study, EGCG was used in pathogen-challenge experiments in shrimp to discover its effect on the innate immune system of an invertebrate. Kuruma shrimp Marsupeneaus japonicus was used as an experimental model and challenged with white spot syndrome virus (WSSV) and the Gram-negative bacterium Vibrio alginolyticus. Pathogen-challenge experiments showed that EGCG pretreatment significantly delayed and reduced mortality upon WSSV and V. alginolyticus infection, with VP-28 copies of WSSV also reduced. Quantitative reverse transcription polymerase chain reaction revealed the positive influence of EGCG on several innate immune-related genes, including IMD, proPO, QM, myosin, Rho, Rab7, p53, TNF-alpha, MAPK, and NOS, and we observed positive influences on three immune parameters, including total hemocyte count and phenoloxidase and superoxide dismutase activities, by EGCG treatment. Additionally, results showed that EGCG treatment significantly reduced apoptosis upon V. alginolyticus challenge. These results indicated the positive role of EGCG in the shrimp innate immune system as an enhancer of immune parameters and an inhibitor of apoptosis, thereby delaying and reducing mortality upon pathogen challenge. Our findings provide insight into potential therapeutic or preventive functions associated with EGCG to enhance shrimp immunity and protect shrimp from pathogen infection.
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Affiliation(s)
- Zhi Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Baozhen Sun
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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40
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Ding YZ, Lv JL, Zhang ZW, Ma XY, Zhang J, Zhang YG. The program of antiviral agents inhibits virus infection. Arch Microbiol 2018; 200:841-846. [PMID: 29846759 DOI: 10.1007/s00203-018-1525-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/07/2017] [Accepted: 05/11/2018] [Indexed: 12/15/2022]
Abstract
Virus infections are the root cause of epidemics in the world. Vaccines and antiviral agents have been the two important methods to control viral diseases; in recent times, RNA-mediated therapeutics and prevention have received much attention. In this review, we provide an overview of the current information regarding the use of vaccines, antiviral agents, and RNA-mediated methods in controlling or preventing viral infections. We stress specifically on the potential of existing RNA-mediated methods in clinical applications.
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Affiliation(s)
- Yao-Zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China.
| | - Jan-Liang Lv
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China
| | - Zhong-Wang Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China
| | - Xiao-Yuan Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China
| | - Jie Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China
| | - Yong-Guang Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, Jiangsu, China.
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41
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Greber UF, Bartenschlager R. Editorial: An expanded view of viruses. FEMS Microbiol Rev 2018; 41:1-4. [PMID: 28087690 PMCID: PMC7108522 DOI: 10.1093/femsre/fuw044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/26/2016] [Accepted: 11/17/2016] [Indexed: 02/06/2023] Open
Affiliation(s)
- Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. E-mail: .,Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany. E-mail:
| | - Ralf Bartenschlager
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. E-mail: .,Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany. E-mail:
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42
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Abstract
As masters of genome-wide regulation, miRNAs represent a key component in the complex architecture of cellular processes. Over the last decade, it has become increasingly apparent that miRNAs have many important roles in the development of disease and cancer. Recently, however, their role in viral and bacterial gene regulation as well as host gene regulation during disease progression has become a field of interest. Due to their small size, miRNAs are the ideal mechanism for bacteria and viruses that have limited room in their genomes, as a single miRNA can target up to ~30 genes. Currently, only a limited number of miRNA and miRNA-like RNAs have been found in bacteria and viruses, a number that is sure to increase rapidly in the future. The interactions of these small noncoding RNAs in such primitive species have wide-reaching effects, from increasing viral and bacterial proliferation, better responses to stress, increased virulence, to manipulation of host immune responses to provide a more ideal environment for these pathogens to thrive. Here, we explore those roles to obtain a better grasp of just how complicated disease truly is.
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43
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Are microRNAs Important Players in HIV-1 Infection? An Update. Viruses 2018; 10:v10030110. [PMID: 29510515 PMCID: PMC5869503 DOI: 10.3390/v10030110] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 has already claimed over 35 million human lives globally. No curative treatments are currently available, and the only treatment option for over 36 million people currently living with HIV/AIDS are antiretroviral drugs that disrupt the function of virus-encoded proteins. However, such virus-targeted therapeutic strategies are constrained by the ability of the virus to develop drug-resistance. Despite major advances in HIV/AIDS research over the years, substantial knowledge gaps exist in many aspects of HIV-1 replication, especially its interaction with the host. Hence, understanding the mechanistic details of virus–host interactions may lead to novel therapeutic strategies for the prevention and/or management of HIV/AIDS. Notably, unprecedented progress in deciphering host gene silencing processes mediated by several classes of cellular small non-coding RNAs (sncRNA) presents a promising and timely opportunity for developing non-traditional antiviral therapeutic strategies. Cellular microRNAs (miRNA) belong to one such important class of sncRNAs that regulate protein synthesis. Evidence is mounting that cellular miRNAs play important roles in viral replication, either usurped by the virus to promote its replication or employed by the host to control viral infection by directly targeting the viral genome or by targeting cellular proteins required for productive virus replication. In this review, we summarize the findings to date on the role of miRNAs in HIV-1 biology.
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The Regulation of Translation in Alphavirus-Infected Cells. Viruses 2018; 10:v10020070. [PMID: 29419763 PMCID: PMC5850377 DOI: 10.3390/v10020070] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/02/2018] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
Sindbis virus (SINV) contains an RNA genome of positive polarity with two open reading frames (ORFs). The first ORF is translated from the genomic RNA (gRNA), rendering the viral non-structural proteins, whereas the second ORF is translated from a subgenomic mRNA (sgRNA), which directs the synthesis of viral structural proteins. SINV infection strongly inhibits host cell translation through a variety of different mechanisms, including the phosphorylation of the eukaryotic initiation factor eIF2α and the redistribution of cellular proteins from the nucleus to the cytoplasm. A number of motifs have been identified in SINV sgRNA, including a hairpin downstream of the AUG initiation codon, which is involved in the translatability of the viral sgRNA when eIF2 is inactivated. Moreover, a 3′-UTR motif containing three stem-loop structures is involved in the enhancement of translation in insect cells, but not in mammalian cells. Accordingly, SINV sgRNA has evolved several structures to efficiently compete for the cellular translational machinery. Mechanistically, sgRNA translation involves scanning of the 5′-UTR following a non-canonical mode and without the requirement for several initiation factors. Indeed, sgRNA-directed polypeptide synthesis occurs even after eIF4G cleavage or inactivation of eIF4A by selective inhibitors. Remarkably, eIF2α phosphorylation does not hamper sgRNA translation during the late phase of SINV infection. SINV sgRNA thus constitutes a unique model of a capped viral mRNA that is efficiently translated in the absence of several canonical initiation factors. The present review will mainly focus in the non-canonical mechanism of translation of SINV sgRNA.
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Wang Z, Zhu F. Different roles of a novel shrimp microRNA in white spot syndrome virus (WSSV) and Vibrio alginolyticus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 79:21-30. [PMID: 28986214 DOI: 10.1016/j.dci.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/30/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
In this study, Marsupeneaus japonicus microRNA-S5 (miR-S5) was found to be up-regulated 24 h post white spot syndrome virus (WSSV) or V. alginolyticus infection. The loss of function using an anti-microRNA oligonucleotide (AMO-miR-S5) showed that expression levels of multiple innate immune-related genes were affected. The expression of p53 and tumor necrosis factor-α (TNF-α) were significantly down-regulated, expression of myosin was significantly up-regulated. The miR-S5 knockdown delayed WSSV-induced death for 48 h, but the final mortality was not affected, while V. alginolyticus-induced mortality was increased by 30%. The effect of miR-S5 knockdown on phagocytosis and apoptosis rates showed that miR-S5 knock down significantly decreased phagocytosis rate of WSSV from 27.8% to 7.0%, and phagocytosis rate of V. alginolyticus from 27.2% to 21.4%, separately. WSSV-induced apoptosis decreased from 60.83% to 51.25%, but no effect on V. alginolyticus-induced apoptosis (43.72%-45.04%). We concluded that miR-S5 could be used by WSSV via regulating hemocyte phagocytosis and apoptosis processes, but helps to defend against bacterial infection by regulating the proPO system, superoxide dismutase activity and phagocytosis.
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Affiliation(s)
- Zhi Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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Zhang S, An S, Hoover K, Li Z, Li X, Liu X, Shen Z, Fang H, Ros VID, Zhang Q, Liu X. Host miRNAs are involved in hormonal regulation of HaSNPV-triggered climbing behaviour in Helicoverpa armigera. Mol Ecol 2018; 27:459-475. [PMID: 29219212 DOI: 10.1111/mec.14457] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022]
Abstract
Baculoviruses manipulate host climbing behaviour to ensure that the hosts die at elevated positions on host plants to facilitate virus proliferation and transmission, which is a process referred to as tree-top disease. However, the detailed molecular mechanism underlying tree-top disease has not been elucidated. Using transcriptome analysis, we showed that two hormone signals, juvenile hormone (JH) and 20-hydroxyecdysone (20E), are key components involved in HaSNPV-induced tree-top disease in Helicoverpa armigera larvae. RNAi-mediated knockdown and exogenous hormone treatment assays demonstrated that 20E inhibits virus-induced tree-top disease, while JH mediates tree-top disease behaviour. Knockdown of BrZ2, a downstream signal of JH and 20E, promoted HaSNPV-induced tree-top disease. We also found that two miRNAs target BrZ2 and are involved in the cross-talk regulation between 20E and JH manipulating HaSNPV replication, time to death and HaSNPV-induced tree-top disease.
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Affiliation(s)
- Songdou Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Kelli Hoover
- Department of Entomology, Pennsylvania State University, University Park, PA, USA
| | - Zhen Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiangrui Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Zhongjian Shen
- Department of Entomology, China Agricultural University, Beijing, China
| | - Haibo Fang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Qingwen Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Beijing, China
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MiR-16-5p mediates a positive feedback loop in EV71-induced apoptosis and suppresses virus replication. Sci Rep 2017; 7:16422. [PMID: 29180670 PMCID: PMC5703983 DOI: 10.1038/s41598-017-16616-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/15/2017] [Indexed: 01/29/2023] Open
Abstract
Enterovirus 71 (EV71) is the predominant causative pathogen of hand-foot-and-mouth disease (HFMD). Contrary to other HFMD-causing enterovirus, EV71 can lead to severe neurological complications, even death. MicroRNAs (miRNAs) are small non-coding RNAs that constitute the largest family of gene regulators participating in numerous biological or pathological processes. We previously reported that miR-16-5p increases with severity of HFMD by investigating the expression patterns of host miRNAs in patients with HFMD. However, the mechanisms by which EV71 induces miR-16-5p expression are not clear, and the interaction between EV71 and miR-16-5p is not yet fully understood. Here, we confirmed EV71-induced expression of miR-16-5p both in vitro and in vivo and show that upregulation of miR-16-5p by EV71 infection may occur at the posttranscriptional level. Moreover, EV71-induced caspase activation facilitates the processing of pri-miR-16-1. We also revealed that miR-16-5p can promote EV71-induced nerve cells apoptosis through activating caspase-3. In addition, we found that miR-16-5p can inhibit EV71 replication. CCNE1 and CCND1, two important cell cycle regulators, play an important role in the suppression of EV71 replication by miR-16-5p. Therefore, miR-16-5p is a positive feedback regulator in EV71-induced apoptosis and a suppressor of virus replication. These results help in understanding the interaction network between miRNA and EV71 infection and provide a potential target for the development of antiviral therapy.
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Samal J, Kandpal M, Vivekanandan P. HBeAg-induced miR-106b promotes cell growth by targeting the retinoblastoma gene. Sci Rep 2017; 7:14371. [PMID: 29085029 PMCID: PMC5662563 DOI: 10.1038/s41598-017-14652-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 10/16/2017] [Indexed: 12/20/2022] Open
Abstract
Chronic HBV infection is a major cause of hepatocellular carcinoma (HCC). The association between hepatitis B "e" antigen (HBeAg) and HCC is well-established by epidemiological studies. Nonetheless, the biological role of HBeAg in HCC remains enigmatic. We investigate the role of HBeAg in HBV-related HCC. Our findings suggest that HBeAg enhances cell proliferation and accelerates progression from G0/G1 phase to the S phase of the cell cycle in Huh7 cells. Examination of host gene expression and miRNA expression profiles reveals a total of 21 host genes and 12 host miRNAs that were differentially regulated in cells expressing HBeAg. Importantly, HBeAg induced the expression of miR-106b, an oncogenic miRNA. Interestingly, HBeAg-expression results in a significant reduction in the expression of retinoblastoma (Rb) gene, an experimentally validated target of miR-106b. Inhibition of miR-106b significantly increased the expression of the Rb gene, resulting in reduced cell proliferation and slowing of cell cycle progression from the G0/G1 phase to S phase. These observations suggest that the up-regulation of miR-106b by HBeAg contributes to the pathogenesis of HBV-related HCC by down-regulating the Rb gene. Our results highlight a role for HBeAg in HCC and provide a novel perspective on the molecular mechanisms underlying HBV-related HCC.
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Affiliation(s)
- Jasmine Samal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Manish Kandpal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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Harwig A, Landick R, Berkhout B. The Battle of RNA Synthesis: Virus versus Host. Viruses 2017; 9:v9100309. [PMID: 29065472 PMCID: PMC5691660 DOI: 10.3390/v9100309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022] Open
Abstract
Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage.
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Affiliation(s)
- Alex Harwig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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Viral Ubiquitin Ligase Stimulates Selective Host MicroRNA Expression by Targeting ZEB Transcriptional Repressors. Viruses 2017; 9:v9080210. [PMID: 28783105 PMCID: PMC5580467 DOI: 10.3390/v9080210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
Infection with herpes simplex virus-1 (HSV-1) brings numerous changes in cellular gene expression. Levels of most host mRNAs are reduced, limiting synthesis of host proteins, especially those involved in antiviral defenses. The impact of HSV-1 on host microRNAs (miRNAs), an extensive network of short non-coding RNAs that regulate mRNA stability/translation, remains largely unexplored. Here we show that transcription of the miR-183 cluster (miR-183, miR-96, and miR-182) is selectively induced by HSV-1 during productive infection of primary fibroblasts and neurons. ICP0, a viral E3 ubiquitin ligase expressed as an immediate-early protein, is both necessary and sufficient for this induction. Nuclear exclusion of ICP0 or removal of the RING (really interesting new gene) finger domain that is required for E3 ligase activity prevents induction. ICP0 promotes the degradation of numerous host proteins and for the most part, the downstream consequences are unknown. Induction of the miR-183 cluster can be mimicked by depletion of host transcriptional repressors zinc finger E-box binding homeobox 1 (ZEB1)/-crystallin enhancer binding factor 1 (δEF1) and zinc finger E-box binding homeobox 2 (ZEB2)/Smad-interacting protein 1 (SIP1), which we establish as new substrates for ICP0-mediated degradation. Thus, HSV-1 selectively stimulates expression of the miR-183 cluster by ICP0-mediated degradation of ZEB transcriptional repressors.
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