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ALV-miRNA-p19-01 Promotes Viral Replication via Targeting Dual Specificity Phosphatase 6. Viruses 2022; 14:v14040805. [PMID: 35458535 PMCID: PMC9024826 DOI: 10.3390/v14040805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of regulatory noncoding RNAs, serving as major regulators with a sequence-specific manner in multifarious biological processes. Although a series of viral families have been proved to encode miRNAs, few reports were available regarding the function of ALV-J-encoded miRNA. Here, we reported a novel miRNA (designated ALV-miRNA-p19-01) in ALV-J-infected DF-1 cells. We found that ALV-miRNA-p19-01 is encoded by the genome of the ALV-J SCAU1903 strain (located at nucleotides site 779 to 801) in a classic miRNA biogenesis manner. The transfection of DF-1 cells with ALV-miRNA-p19-01 enhanced ALV-J replication, while the blockage of ALV-miRNA-p19-01 suppressed ALV-J replication. Furthermore, our data showed that ALV-miRNA-p19-01 promotes ALV-J replication by directly targeting the cellular gene dual specificity phosphatase 6 through regulating ERK2 activity.
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52
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In silico analysis highlighting the prevalence of BCL2L1 gene and its correlation to miRNA in human coronavirus (HCoV) genetic makeup. INFECTION, GENETICS AND EVOLUTION 2022; 99:105260. [PMID: 35240314 PMCID: PMC8883758 DOI: 10.1016/j.meegid.2022.105260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/11/2021] [Accepted: 02/23/2022] [Indexed: 11/24/2022]
Abstract
The ongoing pandemic that resulted from coronavirus disease (COVID-19), which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), had been spiraling out of control with no known antiviral drugs or vaccines. Due to the extremely serious nature of the disease, it has claimed many lives, with a mortality rate of 3.4% declared by the World Health Organization (WHO) on March 3, 2020. The aim of this study is to gain an understanding of the regulatory nature of the proteins involved in COVID-19 and to explore the possibility that microRNA (miRNA) could become a major component in the decoding of the virus. In the study, we were able to correlate the host protein gene BCL2L1 with miRNA miR-23b via network analysis. MiRNAs have previously been associated with the antiviral properties of various viral diseases, such as enterovirus 71 and hepatitis. They have been reported to act as antiviral regulators, since they are an integral component in the direct regulation of viral genes. MiRNAs are also capable of enabling the virus to avoid the host immune response by suppressing the IFN-α/β signaling pathway or increasing the production of IFN-α/β and as a result, inhibiting the viral infection. Here, we explain and shed light on the various correlations in the miRNA-gene-disease association that are seen in the host proteins of COVID-19.
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53
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Zhao S, Chen G, Kong X, Chen N, Wu X. BmNPV p35 Reduces the Accumulation of Virus-Derived siRNAs and Hinders the Function of siRNAs to Facilitate Viral Infection. Front Immunol 2022; 13:845268. [PMID: 35251046 PMCID: PMC8895250 DOI: 10.3389/fimmu.2022.845268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Antiviral immunity involves various mechanisms and responses, including the RNA interference (RNAi) pathway. During long-term coevolution, viruses have gained the ability to evade this defense by encoding viral suppressors of RNAi (VSRs). It was reported that p35 of baculovirus can inhibit cellular small interference RNA (siRNA) pathway; however, the molecular mechanisms underlying p35 as a VSR remain largely unclear. Here, we showed that p35 of Bombyx mori nucleopolyhedrovirus (BmNPV) reduces the accumulation of virus-derived siRNAs (vsiRNAs) mapped to a particular region in the viral genome, leading to an increased expression of the essential genes in this region, and revealed that p35 disrupts the function of siRNAs by preventing them from loading into Argonaute-2 (Ago2). This repressive effect on the cellular siRNA pathway enhances the replication of BmNPV. Thus, our findings illustrate for the first time the inhibitory mechanism of a baculovirus VSR and how this effect influences viral infection.
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Affiliation(s)
- Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiangshuo Kong
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Nan Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou, China
- *Correspondence: Xiaofeng Wu,
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54
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Wang C, Jiang F, Zhu S. Complex Small RNA-mediated Regulatory Networks between Viruses/Viroids/Satellites and Host Plants. Virus Res 2022; 311:198704. [DOI: 10.1016/j.virusres.2022.198704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/16/2022] [Accepted: 01/29/2022] [Indexed: 12/26/2022]
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55
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Guo Y, Xu X, Tang T, Sun L, Zhang X, Shen X, Li D, Wang L, Zhao L, Xie P. miR-505 inhibits replication of Borna disease virus 1 via inhibition of HMGB1-mediated autophagy. J Gen Virol 2022; 103. [PMID: 35060474 DOI: 10.1099/jgv.0.001713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Borna disease virus 1 (BoDV-1) is a highly neurotropic RNA virus which was recently demonstrated to cause deadly human encephalitis. Viruses can modulate microRNA expression, in turn modulating cellular immune responses and regulating viral replication. A previous study indicated that BoDV-1 infection down-regulated the expression of miR-505 in rats. However, the underlying mechanism of miR-505 during BoDV-1 infection remains unknown. In this study, we found that miR-505 can inhibit autophagy activation by down-regulating the expression of its target gene HMGB1, and ultimately inhibit the replication of BoDV-1. Specifically, we found that the expression of miR-505 was significantly down-regulated in rat primary neurons stably infected with BoDV-1. Overexpression of miR-505 can inhibit the replication of BoDV-1 in cells. Bioinformatics analysis and dual luciferase reporter gene detection confirmed that during BoDV-1 infection, the high-mobility group protein B1 (HMGB1) that mediates autophagy is the direct target gene of miR-505. The expression of HMGB1 was up-regulated after BoDV-1 infection, and overexpression of miR-505 could inhibit the expression of HMGB1. Autophagy-related detection found that after infection with BoDV-1, the expression of autophagy-related proteins and autophagy-related marker LC3 in neuronal cells was significantly up-regulated. Autophagy flow experiments and transmission electron microscopy also further confirmed that BoDV-1 infection activated HMGB1-mediated autophagy. Further regulating the expression of miR-505 found that overexpression of miR-505 significantly inhibited HMGB1-mediated autophagy. The discovery of this mechanism may provide new ideas and directions for the prevention and treatment of BoDV-1 infection in the future.
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Affiliation(s)
- Yujie Guo
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xiaoyan Xu
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, PR China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Tian Tang
- Department of Laboratory Medicine, Jintang First People’s Hospital, West China Hospital Sichuan University JinTang Hospital, Chengdu, Sichuan, PR China
| | - Lin Sun
- Department of Anaesthesia and Pain, The First People’s Hospital of Chongqing Liangjiang New Area, Chongqing, PR China
| | - Xiong Zhang
- Department of Neurology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xia Shen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Dan Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, PR China
| | - Lixin Wang
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, PR China
| | - Libo Zhao
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing, PR China
| | - Peng Xie
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
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56
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Zhu Y, Zhang Z, Song J, Qian W, Gu X, Yang C, Shen N, Xue F, Tang Y. SARS-CoV-2-Encoded MiRNAs Inhibit Host Type I Interferon Pathway and Mediate Allelic Differential Expression of Susceptible Gene. Front Immunol 2022; 12:767726. [PMID: 35003084 PMCID: PMC8733928 DOI: 10.3389/fimmu.2021.767726] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the rapid spread of coronavirus disease 2019 (COVID-19), has generated a public health crisis worldwide. The molecular mechanisms of SARS-CoV-2 infection and virus–host interactions are still unclear. In this study, we identified four unique microRNA-like small RNAs encoded by SARS-CoV-2. SCV2-miR-ORF1ab-1-3p and SCV2-miR-ORF1ab-2-5p play an important role in evasion of type I interferon response through targeting several genes in type I interferon signaling pathway. Particularly worth mentioning is that highly expressed SCV2-miR-ORF1ab-2-5p inhibits some key genes in the host innate immune response, such as IRF7, IRF9, STAT2, OAS1, and OAS2. SCV2-miR-ORF1ab-2-5p has also been found to mediate allelic differential expression of COVID-19-susceptible gene OAS1. In conclusion, these results suggest that SARS-CoV-2 uses its miRNAs to evade the type I interferon response and links the functional viral sequence to the susceptible genetic background of the host.
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Affiliation(s)
- Youwei Zhu
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoyang Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weizhou Qian
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangqian Gu
- Department of Hepatobiliary Surgery, Wuxi People's Hospital Affiliated Nanjing Medical University, Wuxi, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory for Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory of Analytical Chemistry, and Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Nan Shen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Feng Xue
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai, China
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57
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Prezioso C, Ciotti M, Brazzini G, Piacentini F, Passerini S, Grimaldi A, Landi D, Nicoletti CG, Zingaropoli MA, Iannetta M, Altieri M, Conte A, Limongi D, Marfia GA, Ciardi MR, Mastroianni CM, Palamara AT, Moens U, Pietropaolo V. Diagnostic Value of JC Polyomavirus Viruria, Viremia, Serostatus and microRNA Expression in Multiple Sclerosis Patients Undergoing Immunosuppressive Treatment. J Clin Med 2022; 11:347. [PMID: 35054041 PMCID: PMC8781243 DOI: 10.3390/jcm11020347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Markers of JC polyomavirus (JCPyV) activity can be used to evaluate the risk of progressive multifocal leukoencephalopathy (PML) in treated multiple sclerosis (MS) patients. The presence of JCPyV DNA and microRNA (miR-J1-5p), the anti-JCV index and the sequence of the non-coding control region (NCCR) in urine and plasma were determined in 42 MS subjects before treatment (T0), 6 months (T6) and 12 months (T12) after natalizumab, ocrelizumab, fingolimod or dimethyl-fumarate administration and in 25 healthy controls (HC). The number of MS patients with viruria increased from 43% at T0 to 100% at T12, whereas it remained similar for the HC group (35-40%). Viremia first occurred 6 months after treatment in MS patients and increased after 12 months, whereas it was absent in HC. The viral load in urine and plasma from the MS cohort increased over time, mostly pronounced in natalizumab-treated patients, whereas it persisted in HC. The archetypal NCCR was detected in all positive urine, whereas mutations were observed in plasma-derived NCCRs resulting in a more neurotropic variant. The prevalence and miR-J1-5p copy number in MS urine and plasma dropped after treatment, whereas they remained similar in HC specimens. Viruria and miR-J1-5p expression did not correlate with anti-JCV index. In conclusion, analyzing JCPyV DNA and miR-J1-5p levels may allow monitoring JCPyV activity and predicting MS patients at risk of developing PML.
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Affiliation(s)
- Carla Prezioso
- IRCSS San Raffaele Roma, Microbiology of Chronic Neuro-Degenerative Pathologies, 00163 Rome, Italy
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Marco Ciotti
- Laboratory of Virology, Polyclinic Tor Vergata Foundation, 00133 Rome, Italy;
| | - Gabriele Brazzini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Francesca Piacentini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Sara Passerini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Alfonso Grimaldi
- Multiple Sclerosis Clinical and Research Unit, Fondazione Policlinico di Tor Vergata, 00133 Rome, Italy; (A.G.); (D.L.); (C.G.N.); (G.A.M.)
| | - Doriana Landi
- Multiple Sclerosis Clinical and Research Unit, Fondazione Policlinico di Tor Vergata, 00133 Rome, Italy; (A.G.); (D.L.); (C.G.N.); (G.A.M.)
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy;
| | - Carolina Gabri Nicoletti
- Multiple Sclerosis Clinical and Research Unit, Fondazione Policlinico di Tor Vergata, 00133 Rome, Italy; (A.G.); (D.L.); (C.G.N.); (G.A.M.)
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy;
| | - Maria Antonella Zingaropoli
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Marco Iannetta
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy;
| | - Marta Altieri
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (M.A.); (A.C.)
| | - Antonella Conte
- Department of Human Neurosciences, Sapienza University of Rome, 00185 Rome, Italy; (M.A.); (A.C.)
- IRCCS Neuromed, 86077 Pozzilli, IS, Italy
| | - Dolores Limongi
- IRCCS San Raffaele Roma, Telematic University, 00163 Rome, Italy;
| | - Girolama Alessandra Marfia
- Multiple Sclerosis Clinical and Research Unit, Fondazione Policlinico di Tor Vergata, 00133 Rome, Italy; (A.G.); (D.L.); (C.G.N.); (G.A.M.)
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy;
- Unit of Neurology, IRCCS Istituto Neurologico Mediterraneo NEUROMED, 86077 Pozzilli, IS, Italy
| | - Maria Rosa Ciardi
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Claudio Maria Mastroianni
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Institute Pasteur Italia-Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway;
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy; (G.B.); (F.P.); (S.P.); (M.A.Z.); (M.R.C.); (C.M.M.)
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58
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Cong X, Zhang J, Sun R, Pu Y. Short-term ambient particulate air pollution exposure, microRNAs, blood pressure and lung function. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118387. [PMID: 34673158 DOI: 10.1016/j.envpol.2021.118387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
Ambient particulate air pollution is a risk factor for cardiovascular and respiratory disease, yet the biological mechanisms underlying this association are not well understood. The current study aimed to investigate the mediation role of microRNAs on the association between personal PM2.5 exposure and blood pressure and lung function. One hundred and twenty adults (60 truck drivers and 60 office workers) aged 18-46 years were assessed on the June 15, 2008 and at follow-up (1- to 2-weeks later). MicroRNAs were extracted from the peripheral blood samples. Compared to truck drivers, there is a significant increase in FEF25-75, FEV1, and FEV1/FVC and a decrease in PM2.5 in office workers (all p < 0.05). According to the Bonferroni corrected threshold p-value < 6.81 × 10-5 (0.05/734) used, personal PM2.5 data showed a significant positive association with miR-644 after the adjustment for age, BMI, smoking status, and habitual alcohol use. The mediation effect of miR-644 on the association between personal PM2.5 exposure and FEF25-75 [B (95%CI) = -1.342 (-2.810, -0.113)], PEF [B (95%CI) = -1.793 (-3.926, -0.195)], and FEV1/FVC [B (95%CI) = -0.119‰ (-0.224‰, -0.026‰)] was significant only for truck drivers after the adjustment for covariates. There were no similar associations with blood pressure. These results demonstrate microRNAs to potentially mediate association of PM2.5 with lung function. Subsequent studies are needed to further elucidate the potential mechanisms of action by which the mediation effect of microRNAs is achieved with this process.
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Affiliation(s)
- Xiaowei Cong
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009, Jiangsu, China
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59
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Pawlica P, Yario TA, White S, Wang J, Moss WN, Hui P, Vinetz JM, Steitz JA. SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes. Proc Natl Acad Sci U S A 2021; 118:e2116668118. [PMID: 34903581 PMCID: PMC8719879 DOI: 10.1073/pnas.2116668118] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2-infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named CoV2-miR-O7a (for SARS-CoV-2 miRNA-like ORF7a-derived small RNA). Its abundance ranges from low to moderate as compared to host miRNAs and it associates with Argonaute proteins-core components of the RNA interference pathway. We identify putative targets for CoV2-miR-O7a, including Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which participates in interferon signaling. We demonstrate that CoV2-miR-O7a production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.
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Affiliation(s)
- Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
| | - Therese A Yario
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| | - Sylvia White
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06536
| | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06536;
- HHMI, Yale University School of Medicine, New Haven, CT 06536
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60
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Nakanishi K. Are Argonaute-Associated Tiny RNAs Junk, Inferior miRNAs, or a New Type of Functional RNAs? Front Mol Biosci 2021; 8:795356. [PMID: 34926585 PMCID: PMC8678501 DOI: 10.3389/fmolb.2021.795356] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
The biosynthesis pathways of microRNAs (miRNAs) have been well characterized with the identification of the required components. miRNAs are synthesized from the transcripts of miRNA genes and other RNAs, such as introns, transfer RNAs, ribosomal RNAs, small nucleolar RNAs, and even viral miRNAs. These small RNAs are loaded into Argonaute (AGO) proteins and recruit the effector complexes to target mRNAs, repressing their gene expression post-transcriptionally. While mature miRNAs were defined as 19–23 nucleotides (nt), tiny RNAs (tyRNAs) shorter than 19 nt have been found to bind AGOs as equivalent or lesser miRNAs compared to their full-length mature miRNAs. In contrast, my recent study revealed that when human AGO3 loads 14 nt cleavage-inducing tyRNAs (cityRNAs), comprised of the first 14 nt of their corresponding mature miRNA, it can become a comparable slicer to AGO2. This observation raises the possibility that tyRNAs play distinct roles from their mature form. This minireview focuses on human AGO-associated tyRNAs shorter than 19 nt and discusses their possible biosynthesis pathways and physiological benefits, including how tyRNAs could avoid target-directed miRNA degradation accompanied by AGO polyubiquitination.
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Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States.,Center for RNA Biology, Columbus, OH, United States
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61
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Orendain-Jaime EN, Serafín-Higuera N, Leija-Montoya AG, Martínez-Coronilla G, Moreno-Trujillo M, Sánchez-Muñoz F, Ruiz-Hernández A, González-Ramírez J. MicroRNAs Encoded by Virus and Small RNAs Encoded by Bacteria Associated with Oncogenic Processes. Processes (Basel) 2021; 9:2234. [DOI: 10.3390/pr9122234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2025] Open
Abstract
Cancer is a deadly disease and, globally, represents the second leading cause of death in the world. Although it is a disease where several factors can help its development, virus induced infections have been associated with different types of neoplasms. However, in bacterial infections, their participation is not known for certain. Among the proposed approaches to oncogenesis risks in different infections are microRNAs (miRNAs). These are small molecules composed of RNA with a length of 22 nucleotides capable of regulating gene expression by directing protein complexes that suppress the untranslated region of mRNA. These miRNAs and other recently described, such as small RNAs (sRNAs), are deregulated in the development of cancer, becoming promising biomarkers. Thus, resulting in a study possibility, searching for new tools with diagnostic and therapeutic approaches to multiple oncological diseases, as miRNAs and sRNAs are main players of gene expression and host–infectious agent interaction. Moreover, sRNAs with limited complementarity are similar to eukaryotic miRNAs in their ability to modulate the activity and stability of multiple mRNAs. Here, we will describe the regulatory RNAs from viruses that have been associated with cancer and how sRNAs in bacteria can be related to this disease.
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Affiliation(s)
- Erika Nallely Orendain-Jaime
- Facultad de Enfermería, Universidad Autónoma de Baja California, Av. Álvaro Obregón y Calle “G” S/N, Col. Nueva, Mexicali 21100, BC, Mexico
| | - Nicolás Serafín-Higuera
- Facultad de Odontología, Universidad Autónoma de Baja California, Zotoluca s/n, Fracc. Calafia, Mexicali 21040, BC, Mexico
| | - Ana Gabriela Leija-Montoya
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico
| | - Gustavo Martínez-Coronilla
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico
| | - Misael Moreno-Trujillo
- Departamento de Cuidados Intensivos, Hospital de Gineco-Pediatría #31, Instituto Mexicano del Seguro Social, Av. Sebastián Lerdo de Tejada S/N, Col. Nueva, Mexicali 21100, BC, Mexico
| | - Fausto Sánchez-Muñoz
- Departamento de Inmunología, Instituto Nacional de Cardiología, Juan Badiano No. 1, Col. Sección XVI, Tlalpan 140080, DF, Mexico
| | - Armando Ruiz-Hernández
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Centro Cívico, Mexicali 21000, BC, Mexico
| | - Javier González-Ramírez
- Facultad de Enfermería, Universidad Autónoma de Baja California, Av. Álvaro Obregón y Calle “G” S/N, Col. Nueva, Mexicali 21100, BC, Mexico
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Aso S, Kitao K, Hashimoto-Gotoh A, Sakaguchi S, Miyazawa T. Identification of Feline Foamy Virus-derived MicroRNAs. Microbes Environ 2021; 36. [PMID: 34776460 PMCID: PMC8674446 DOI: 10.1264/jsme2.me21055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs) classified as non-coding RNAs regulate various metabolic systems and viral life cycles. To date, numerous DNA viruses, many of which are members of the herpesvirus family, and a relatively small number of RNA viruses, including retroviruses, have been reported to encode and express miRNAs in infected cells. A few retroviruses have been shown to express miRNAs, and foamy viruses (FVs) were initially predicted by computational analyses to possess miRNA-coding regions. Subsequent studies on simian and bovine FVs confirmed the presence of functional and biologically active miRNA expression cassettes. We herein identified feline FV-derived miRNAs using a small RNA deep sequencing analysis. We confirmed their repressive functions on gene expression by dual-luciferase reporter assays. We found that the seed sequences of the miRNAs identified in the present study were conserved among all previously reported FFV isolates. These results suggest that FFV-derived miRNAs play a pivotal role in FFV infection.
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Affiliation(s)
- Shiro Aso
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Akira Hashimoto-Gotoh
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Osaka Medical College
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
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63
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Zaghloul HAH, Hice RH, Arensburger P, Bideshi DK, Federici BA. Extended in vivo transcriptomes of two ascoviruses with different tissue tropisms reveal alternative mechanisms for enhancing virus reproduction in hemolymph. Sci Rep 2021; 11:16402. [PMID: 34385487 PMCID: PMC8361023 DOI: 10.1038/s41598-021-95553-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
Ascoviruses are large dsDNA viruses characterized by the extraordinary changes they induce in cellular pathogenesis and architecture whereby after nuclear lysis and extensive hypertrophy, each cell is cleaved into numerous vesicles for virion reproduction. However, the level of viral replication and transcription in vesicles compared to other host tissues remains uncertain. Therefore, we applied RNA-Sequencing to compare the temporal transcriptome of Spodoptera frugiperda ascovirus (SfAV) and Trichoplusia ni ascovirus (TnAV) at 7, 14, and 21 days post-infection (dpi). We found most transcription occurred in viral vesicles, not in initial tissues infected, a remarkably novel reproduction mechanism compared to all other viruses and most other intracellular pathogens. Specifically, the highest level of viral gene expression occurred in hemolymph, for TnAV at 7 dpi, and SfAV at 14 dpi. Moreover, we found that host immune genes were partially down-regulated in hemolymph, where most viral replication occurred in highly dense accumulations of vesicles.
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Affiliation(s)
- Heba A H Zaghloul
- Interdepartmental Graduate Program in Microbiology and Institute for Integrative Genome Biology, Riverside, USA.,Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Robert H Hice
- Interdepartmental Graduate Program in Microbiology and Institute for Integrative Genome Biology, Riverside, USA
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA, 91768, USA
| | - Dennis K Bideshi
- Department of Biological Sciences, California Baptist University, Riverside, CA, 92504, USA
| | - Brian A Federici
- Interdepartmental Graduate Program in Microbiology and Institute for Integrative Genome Biology, Riverside, USA. .,Department of Entomology, University of California, Riverside, Riverside, CA, 92521, USA.
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Qi X, Cao Y, Wu S, Wu Z, Bao W. miR-129a-3p Inhibits PEDV Replication by Targeting the EDA-Mediated NF-κB Pathway in IPEC-J2 Cells. Int J Mol Sci 2021; 22:ijms22158133. [PMID: 34360898 PMCID: PMC8347983 DOI: 10.3390/ijms22158133] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Previous studies have shown that microRNAs (miRNAs) are closely related to many viral infections. However, the molecular mechanism of how miRNAs regulate porcine epidemic diarrhea virus (PEDV) infection remains unclear. In this study, we first constructed a PEDV-infected IPEC-J2 cytopathic model to validate the relationship between miR-129a-3p expression levels and PEDV resistance. Secondly, we explored the effect of miR-129a-3p on PEDV infection by targeting the 3′UTR region of the ligand ectodysplasin (EDA) gene. Finally, transcriptome sequencing was used to analyze the downstream regulatory mechanism of EDA. The results showed that after 48 h of PEDV infection, IPEC-J2 cells showed obvious pathological changes, and miR-129a-3p expression was significantly downregulated (p < 0.01). Overexpression of miR-129a-3p mimics inhibited PEDV replication in IPEC-J2 cells; silencing endogenous miR-129a-3p can promote viral replication. A dual luciferase assay showed that miR-129a-3p could bind to the 3′UTR region of the EDA gene, which significantly reduced the expression level of EDA (p < 0.01). Functional verification showed that upregulation of EDA gene expression significantly promoted PEDV replication in IPEC-J2 cells. Overexpression of miR-129a-3p can activate the caspase activation and recruitment domain 11 (CARD11) mediated NF-κB pathway, thus inhibiting PEDV replication. The above results suggest that miR-129a-3p inhibits PEDV replication in IPEC-J2 cells by activating the NF-κB pathway by binding to the EDA 3′UTR region. Our results have laid the foundation for in-depth study of the mechanism of miR-129a-3p resistance and its application in porcine epidemic diarrhea disease-resistance breeding.
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Affiliation(s)
- Xiaoyi Qi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (X.Q.); (Y.C.); (S.W.); (Z.W.)
| | - Yue Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (X.Q.); (Y.C.); (S.W.); (Z.W.)
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (X.Q.); (Y.C.); (S.W.); (Z.W.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, The Ministry of Education of China, Yangzhou 225000, China
| | - Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (X.Q.); (Y.C.); (S.W.); (Z.W.)
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China; (X.Q.); (Y.C.); (S.W.); (Z.W.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, The Ministry of Education of China, Yangzhou 225000, China
- Correspondence:
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Non-Coding RNAs and Reactive Oxygen Species–Symmetric Players of the Pathogenesis Associated with Bacterial and Viral Infections. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Infections can be triggered by a wide range of pathogens. However, there are few strains of bacteria that cause illness, but some are quite life-threatening. Likewise, viral infections are responsible for many human diseases, usually characterized by high contagiousness. Hence, as bacterial and viral infections can both cause similar symptoms, it can be difficult to determine the exact cause of a specific infection, and this limitation is critical. However, recent scientific advances have geared us up with the proper tools required for better diagnoses. Recent discoveries have confirmed the involvement of non-coding RNAs (ncRNAs) in regulating the pathogenesis of certain bacterial or viral infections. Moreover, the presence of reactive oxygen species (ROS) is also known as a common infection trait that can be used to achieve a more complete description of such pathogen-driven conditions. Thus, this opens further research opportunities, allowing scientists to explore infection-associated genetic patterns and develop better diagnosis and treatment methods. Therefore, the aim of this review is to summarize the current knowledge of the implication of ncRNAs and ROS in bacterial and viral infections, with great emphasis on their symmetry but, also, on their main differences.
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66
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Meng F, Siu GKH, Mok BWY, Sun J, Fung KSC, Lam JYW, Wong NK, Gedefaw L, Luo S, Lee TMH, Yip SP, Huang CL. Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells. Cells 2021; 10:1762. [PMID: 34359932 PMCID: PMC8307234 DOI: 10.3390/cells10071762] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 07/07/2021] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression that may be used to identify the pathological pathways influenced by disease and cellular interactions. Viral miRNAs (v-miRNAs) encoded by both DNA and RNA viruses induce immune dysregulation, virus production, and disease pathogenesis. Given the absence of effective treatment and the prevalence of highly infective SARS-CoV-2 strains, improved understanding of viral-associated miRNAs could provide novel mechanistic insights into the pathogenesis of COVID-19. In this study, SARS-CoV-2 v-miRNAs were identified by deep sequencing in infected Calu-3 and Vero E6 cell lines. Among the ~0.1% small RNA sequences mapped to the SARS-CoV-2 genome, the top ten SARS-CoV-2 v-miRNAs (including three encoded by the N gene; v-miRNA-N) were selected. After initial screening of conserved v-miRNA-N-28612, which was identified in both SARS-CoV and SARS-CoV-2, its expression was shown to be positively associated with viral load in COVID-19 patients. Further in silico analysis and synthetic-mimic transfection of validated SARS-CoV-2 v-miRNAs revealed novel functional targets and associations with mechanisms of cellular metabolism and biosynthesis. Our findings support the development of v-miRNA-based biomarkers and therapeutic strategies based on improved understanding of the pathophysiology of COVID-19.
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Affiliation(s)
- Fei Meng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Bobo Wing-Yee Mok
- Department of Microbiology, The University of Hong Kong, Hong Kong, China;
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
| | - Jiahong Sun
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Kitty S. C. Fung
- Department of Pathology, United Christian Hospital, Kwun Tong, Hong Kong, China;
| | - Jimmy Yiu-Wing Lam
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China;
| | - Nonthaphat Kent Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Lealem Gedefaw
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Shumeng Luo
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Thomas M. H. Lee
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China;
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (F.M.); (G.K.-H.S.); (J.S.); (N.K.W.); (L.G.); (S.L.)
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Perdomo HD, Hussain M, Parry R, Etebari K, Hedges LM, Zhang G, Schulz BL, Asgari S. Human blood microRNA hsa-miR-21-5p induces vitellogenin in the mosquito Aedes aegypti. Commun Biol 2021; 4:856. [PMID: 34244602 PMCID: PMC8270986 DOI: 10.1038/s42003-021-02385-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Mosquito vectors transmit various diseases through blood feeding, required for their egg development. Hence, blood feeding is a major physiological event in their life cycle, during which hundreds of genes are tightly regulated. Blood is a rich source of proteins for mosquitoes, but also contains many other molecules including microRNAs (miRNAs). Here, we found that human blood miRNAs are transported abundantly into the fat body tissue of Aedes aegypti, a key metabolic center in post-blood feeding reproductive events, where they target and regulate mosquito genes. Using an artificial diet spiked with the mimic of an abundant and stable human blood miRNA, hsa-miR-21-5p, and proteomics analysis, we found over 40 proteins showing differential expression in female Ae. aegypti mosquitoes after feeding. Of interest, we found that the miRNA positively regulates the vitellogenin gene, coding for a yolk protein produced in the mosquito fat body and then transported to the ovaries as a protein source for egg production. Inhibition of hsa-miR-21-5p followed by human blood feeding led to a statistically insignificant reduction in progeny production. The results provide another example of the involvement of small regulatory molecules in the interaction of taxonomically vastly different taxa.
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Affiliation(s)
- Hugo D. Perdomo
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
| | - Mazhar Hussain
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
| | - Rhys Parry
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia ,grid.1003.20000 0000 9320 7537School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Kayvan Etebari
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
| | - Lauren M. Hedges
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
| | - Guangmei Zhang
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
| | - Benjamin L. Schulz
- grid.1003.20000 0000 9320 7537School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Sassan Asgari
- grid.1003.20000 0000 9320 7537Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD Australia
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Nanbo A, Furuyama W, Lin Z. RNA Virus-Encoded miRNAs: Current Insights and Future Challenges. Front Microbiol 2021; 12:679210. [PMID: 34248890 PMCID: PMC8266288 DOI: 10.3389/fmicb.2021.679210] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are small non-coding RNAs that regulate eukaryotic gene expression at the post-transcriptional level and affect a wide range of biological processes. Over the past two decades, numerous virus-encoded miRNAs have been identified. Some of them are crucial for viral replication, whereas others can help immune evasion. Recent sequencing-based bioinformatics methods have helped identify many novel miRNAs, which are encoded by RNA viruses. Unlike the well-characterized DNA virus-encoded miRNAs, the role of RNA virus-encoded miRNAs remains controversial. In this review, we first describe the current knowledge of miRNAs encoded by various RNA viruses, including newly emerging viruses. Next, we discuss how RNA virus-encoded miRNAs might facilitate viral replication, immunoevasion, and persistence in their hosts. Last, we briefly discuss the challenges in the experimental methodologies and potential applications of miRNAs for diagnosis and therapeutics.
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Affiliation(s)
- Asuka Nanbo
- Molecular and Cellular Virology, Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Wakako Furuyama
- Molecular and Cellular Virology, Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Zhen Lin
- Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, LA, United States
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69
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Millard RS, Bickley LK, Bateman KS, Farbos A, Minardi D, Moore K, Ross SH, Stentiford GD, Tyler CR, van Aerle R, Santos EM. Global mRNA and miRNA Analysis Reveal Key Processes in the Initial Response to Infection with WSSV in the Pacific Whiteleg Shrimp. Viruses 2021; 13:v13061140. [PMID: 34199268 PMCID: PMC8231841 DOI: 10.3390/v13061140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
White Spot Disease (WSD) presents a major barrier to penaeid shrimp production. Mechanisms underlying White Spot Syndrome Virus (WSSV) susceptibility in penaeids are poorly understood due to limited information related to early infection. We investigated mRNA and miRNA transcription in Penaeus vannamei over 36 h following infection. Over this time course, 6192 transcripts and 27 miRNAs were differentially expressed—with limited differential expression from 3–12 h post injection (hpi) and a more significant transcriptional response associated with the onset of disease symptoms (24 hpi). During early infection, regulated processes included cytoskeletal remodelling and alterations in phagocytic activity that may assist WSSV entry and translocation, novel miRNA-induced metabolic shifts, and the downregulation of ATP-dependent proton transporter subunits that may impair cellular recycling. During later infection, uncoupling of the electron transport chain may drive cellular dysfunction and lead to high mortalities in infected penaeids. We propose that post-transcriptional silencing of the immune priming gene Dscam (downregulated following infections) by a novel shrimp miRNA (Pva-pmiR-78; upregulated) as a potential mechanism preventing future recognition of WSSV that may be suppressed in surviving shrimp. Our findings improve our understanding of WSD pathogenesis in P. vannamei and provide potential avenues for future development of prophylactics and treatments.
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Affiliation(s)
- Rebecca S. Millard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
| | - Lisa K. Bickley
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Kelly S. Bateman
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Audrey Farbos
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Diana Minardi
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Karen Moore
- Exeter Sequencing Service, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK; (A.F.); (K.M.)
| | - Stuart H. Ross
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Grant D. Stentiford
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Charles R. Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
| | - Ronny van Aerle
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Cefas Weymouth Laboratory, International Centre of Excellence for Aquatic Animal Health, Weymouth DT4 8UB, UK;
| | - Eduarda M. Santos
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; (L.K.B.); (C.R.T.)
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter EX4 4QD, UK; (K.S.B.); (S.H.R.); (G.D.S.); (R.v.A.)
- Correspondence: (R.S.M.); (E.M.S.); Tel.: +44-(0)-1392-724607 (E.M.S.)
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Franzoi AEDA, de Moraes Machado FS, de Medeiros Junior WLG, Bandeira IP, Brandão WN, Gonçalves MVM. Altered expression of microRNAs and B lymphocytes during Natalizumab therapy in multiple sclerosis. Heliyon 2021; 7:e07263. [PMID: 34179535 PMCID: PMC8214090 DOI: 10.1016/j.heliyon.2021.e07263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 01/18/2021] [Accepted: 06/05/2021] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are a family of non-translated small ribonucleic acids (RNAs) measuring 21–25 nucleotides in length that play various roles in multiple sclerosis (MS). By regulating gene expression via either mediating translational repression or cleavage of the target RNA, miRNAs can alter the expression of transcripts in different cells, such as B lymphocytes, also known as B cells. They are crucial in the pathogenesis of MS; however, they have not been extensively studied during the treatment of some drugs such as natalizumab (NTZ). NTZ is a humanized immunoglobulin G4 antibody antagonist for integrin alpha 4 (α4) used in the treatment of MS. The drug reduces the homing of lymphocytes to inflammation sites. Integrin α4 expression on the cell surface of B cells is related to MS severity, indicating a critical component in the pathogenesis of the disease. NTZ plays an important role in modifying the gene expression in B cells and the levels of miRNAs in the treatment of MS. In this review, we have described changes in gene expression in B cells and the levels of miRNAs during NTZ therapy in MS and its relapse. Studies using the experimental autoimmune encephalomyelitis (EAE) model and those involving patients with MS have described changes in the levels of microRNAs in the regulation of proteins affected by specific miRNAs, gene expression in B cells, and certain functions of B cells as well as their subpopulations. Therefore, there is a possibility that some miRNAs could be studied at different stages of MS during NTZ treatment, and these specific miRNAs can be tested as markers of therapeutic response to this drug in future studies. Physiopathology, gene expression in B cells and their subpopulations can help understand this complex puzzle involving miRNAs and the therapeutic response of patients with MS.
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Affiliation(s)
| | | | | | | | - Wesley Nogueira Brandão
- Department of Neuroimmunology at the Institute of Biological Sciences, University of São Paulo (ICB-USP), Brazil
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71
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Pasquier C, Robichon A. Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains. Heliyon 2021; 7:e07284. [PMID: 34179538 PMCID: PMC8219292 DOI: 10.1016/j.heliyon.2021.e07284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/14/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
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72
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Zhang N, Ma Y, Tian Y, Zhou Y, Tang Y, Hu S. Downregulation of microRNA‑221 facilitates H1N1 influenza A virus replication through suppression of type‑IFN response by targeting the SOCS1/NF‑κB pathway. Mol Med Rep 2021; 24:497. [PMID: 33955508 PMCID: PMC8127060 DOI: 10.3892/mmr.2021.12136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/10/2021] [Indexed: 12/23/2022] Open
Abstract
Accumulating data has indicated that host microRNAs (miRNAs/miRs) play essential roles in innate immune responses to viral infection; however, the roles and the underlying mechanisms of miRNAs in influenza A virus (IAV) replication remain unclear. The present study examined on the effects of miRNAs on hemagglutinin (H)1 neuraminidase (N)1 replication and antiviral innate immunity. Using a microarray assay, the expression profiles of miRNA molecules in IAV-infected A549 cells were analyzed. The results indicated that miR-221 was significantly downregulated in IAV-infected A549 cells. It was also observed that IAV infection decreased the expression levels of miR-221 in A549 cells in a dose- and time-dependent manner. Functionally, upregulation of miR-221 repressed IAV replication, whereas knockdown of miR-221 had an opposite effect. Subsequently, it was demonstrated that miR-221 overexpression could enhance IAV-triggered IFN-α and IFN-β production and IFN-stimulated gene expression levels, while miR-221-knockdown had the opposite effect. Target prediction and dual luciferase assays indicated that suppressor of cytokine signaling 1 (SOCS1) was a direct target of miR-221 in A549 cells. Furthermore, knockdown of SOCS1 efficiently abrogated the influences caused by miR-221 inhibition on IAV replication and the type-I IFN response. It was also found that the miR-221 positively regulated NF-κB activation in IAV-infected A549 cells. Taken together, these data suggested that miR-221-downregulation promotes IAV replication by suppressing type-I IFN response through targeting SOCS1/NF-κB pathway. These findings suggest that miR-221 may serve as a novel potential therapeutic target for IAV treatment.
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Affiliation(s)
- Nali Zhang
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
| | - Yuan Ma
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
| | - Yuheng Tian
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
| | - Yafei Zhou
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
| | - Yuhua Tang
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
| | - Shaobo Hu
- Department of Respiratory Medicine and Intensive Care Unit, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan 471009, P.R. China
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73
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Abstract
Polyomaviruses are a family of non-enveloped DNA viruses with wide host ranges. Human polyomaviruses typically cause asymptomatic infection and establish persistence but can be reactivated under certain conditions and cause severe diseases. Most well studied polyomaviruses encode a viral miRNA that regulates viral replication and pathogenesis by targeting both viral early genes and host genes. In this review, we summarize the current knowledge of polyomavirus miRNAs involved in virus infection. We review in detail the regulation of polyomavirus miRNA expression, as well as the role polyomavirus miRNAs play in viral pathogenesis by controlling both host and viral gene expression. An overview of the potential application of polyomavirus miRNA as a marker for the progression of polyomaviruses associated diseases and polyomaviruses reactivation is also included.
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Affiliation(s)
- Wei Zou
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States
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74
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Chiang C, Dvorkin S, Chiang JJ, Potter RB, Gack MU. The Small t Antigen of JC Virus Antagonizes RIG-I-Mediated Innate Immunity by Inhibiting TRIM25's RNA Binding Ability. mBio 2021; 12:e00620-21. [PMID: 33849980 PMCID: PMC8092259 DOI: 10.1128/mbio.00620-21] [Citation(s) in RCA: 13] [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: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022] Open
Abstract
JC polyomavirus (JCV), a DNA virus that leads to persistent infection in humans, is the causative agent of progressive multifocal leukoencephalopathy, a lethal brain disease that affects immunocompromised individuals. Almost nothing is currently known about how JCV infection is controlled by the innate immune response and, further, whether JCV has evolved mechanisms to antagonize antiviral immunity. Here, we show that the innate immune sensors retinoic acid-inducible gene I (RIG-I) and cGMP-AMP synthase (cGAS) control JCV replication in human astrocytes. We further identify that the small t antigen (tAg) of JCV functions as an interferon (IFN) antagonist by suppressing RIG-I-mediated signal transduction. JCV tAg interacts with the E3 ubiquitin ligase TRIM25, thereby preventing its ability to bind RNA and to induce the K63-linked ubiquitination of RIG-I, which is known to facilitate RIG-I-mediated cytokine responses. Antagonism of RIG-I K63-linked ubiquitination and antiviral signaling is also conserved in the tAg of the related polyomavirus BK virus (BKV). These findings highlight how JCV and BKV manipulate a key innate surveillance pathway, which may stimulate research into designing novel therapies.IMPORTANCE The innate immune response is the first line of defense against viral pathogens, and in turn, many viruses have evolved strategies to evade detection by the host's innate immune surveillance machinery. Investigation of the interplay between viruses and the innate immune response provides valuable insight into potential therapeutic targets against viral infectious diseases. JC polyomavirus (JCV) is associated with a lifelong, persistent infection that can cause a rare neurodegenerative disease, called progressive multifocal leukoencephalopathy, in individuals that are immunosuppressed. The molecular mechanisms of JCV infection and persistence are not well understood, and very little is currently known about the relevance of innate immunity for the control of JCV replication. Here, we define the intracellular innate immune sensors responsible for controlling JCV infection and also demonstrate a novel mechanism by which a JCV-encoded protein acts as an antagonist of the type I interferon-mediated innate immune response.
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Affiliation(s)
- Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, Florida, USA
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Steve Dvorkin
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel B Potter
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, Florida, USA
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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75
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Merino GA, Raad J, Bugnon LA, Yones C, Kamenetzky L, Claus J, Ariel F, Milone DH, Stegmayer G. Novel SARS-CoV-2 encoded small RNAs in the passage to humans. Bioinformatics 2021; 36:5571-5581. [PMID: 33244583 PMCID: PMC7717134 DOI: 10.1093/bioinformatics/btaa1002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Motivation The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. Results We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.
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Affiliation(s)
- Gabriela A Merino
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina.,Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Entre Ríos 3100, Argentina.,European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire CB101SD, UK
| | - Jonathan Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Leandro A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, UBA-CONICET, Ciudad Autónoma de Buenos Aires 1121, Argentina.,Laboratorio de Genómica y Bioinformática de Patógenos, iB3, Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
| | - Juan Claus
- Laboratorio de Virología, FBCB, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Diego H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
| | - Georgina Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe 3000, Argentina
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76
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Marchi R, Sugita B, Centa A, Fonseca AS, Bortoletto S, Fiorentin K, Ferreira S, Cavalli LR. The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review. INFECTION GENETICS AND EVOLUTION 2021; 91:104832. [PMID: 33812037 PMCID: PMC8012164 DOI: 10.1016/j.meegid.2021.104832] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/11/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
MicroRNAs are gene expression regulators, associated with several human pathologies, including the ones caused by virus infections. Although their role in infection diseases is not completely known, they can exert double functions in the infected cell, by mediating the virus infection and/or regulating the immunity-related gene targets through complex networks of virus-host cell interactions. In this systematic review, the Pubmed, EMBASE, Scopus, Lilacs, Scielo, and EBSCO databases were searched for research articles published until October 22nd, 2020 that focused on describing the role, function, and/or association of miRNAs in SARS-CoV-2 human infection and COVID-19. Following the PRISMA 2009 protocol, 29 original research articles were selected. Most of the studies reported miRNA data based on the genome sequencing of SARS-CoV-2 isolates and computational prediction analysis. The latter predicted, by at least one independent study, 1266 host miRNAs to target the viral genome. Thirteen miRNAs were identified by four independent studies to target SARS-CoV-2 specific genes, suggested to act by interfering with their cleavage and/or translation process. The studies selected also reported on viral and host miRNAs that targeted host genes, on the expression levels of miRNAs in biological specimens of COVID-19 patients, and on the impact of viral genome mutations on miRNA function. Also, miRNAs that regulate the expression levels of the ACE2 and TMPRSS2 proteins, which are critical for the virus entrance in the host cells, were reported. In conclusion, despite the limited number of studies identified, based on the search terms and eligibility criteria applied, this systematic review provides evidence on the impact of miRNAs on SARS-CoV-2 infection and COVID-19. Although most of the reported viral/host miRNAs interactions were based on in silico prediction analysis, they demonstrate the relevance of the viral/host miRNA interaction for viral activity and host responses. In addition, the identified studies highlight the potential use of miRNAs as therapeutic targets against COVID-19, and other viral human diseases (This review was registered at the International Prospective Register of Systematic Reviews (PROSPERO) database (#CRD42020199290).
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Affiliation(s)
- Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Bruna Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ariana Centa
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Aline S Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Stefanne Bortoletto
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Karine Fiorentin
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Solange Ferreira
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Luciane R Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
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77
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Islam MS, Khan MAAK. Computational analysis revealed miRNAs produced by Chikungunya virus target genes associated with antiviral immune responses and cell cycle regulation. Comput Biol Chem 2021; 92:107462. [PMID: 33640797 DOI: 10.1016/j.compbiolchem.2021.107462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 11/18/2022]
Abstract
Chikungunya virus (CHIKV) that causes chikungunya fever, is an alphavirus that belongs to the Togaviridae family containing a single-stranded RNA genome. Mosquitoes of the Aedes species act as the vectors for this virus and can be found in the blood, which can be passed from an infected person to a mosquito through mosquito bites. CHIKV has drawn much attention recently because of its potential of causing an epidemic. As the detailed mechanism of its pathogenesis inside the host system is still lacking, in this in silico research we have hypothesized that CHIKV might create miRNAs, which would target the genes associated with host cellular regulatory pathways, thereby providing the virus with prolonged refuge. Using bioinformatics approaches we found several putative miRNAs produced by CHIKV. Then we predicted the genes of the host targeted by these miRNAs. Functional enrichment analysis of these targeted genes shows the involvement of several biological pathways regulating antiviral immune stimulation, cellular proliferation, and cell cycle, thereby provide themselves with prolonged refuge and facilitate their pathogenesis, which in turn may lead to disease conditions. Finally, we analyzed a publicly available microarray dataset (GSE49985) to determine the altered expression levels of the targeted genes and found genes associated with pathways such as cell differentiation, phagocytosis, T-cell activation, response to cytokine, autophagy, Toll-like receptor signaling, RIG-I like receptor signaling and apoptosis. Our finding presents novel miRNAs and their targeted genes, which upon experimental validation could facilitate in developing new therapeutics to combat CHIKV infection and minimize CHIKV mediated diseases.
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Affiliation(s)
- Md Sajedul Islam
- Department of Biochemistry & Biotechnology, University of Barishal, Barishal, 8254, Bangladesh.
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78
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Kalhori MR, Saadatpour F, Arefian E, Soleimani M, Farzaei MH, Aneva IY, Echeverría J. The Potential Therapeutic Effect of RNA Interference and Natural Products on COVID-19: A Review of the Coronaviruses Infection. Front Pharmacol 2021; 12:616993. [PMID: 33716745 PMCID: PMC7953353 DOI: 10.3389/fphar.2021.616993] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 virus was reported for the first time in Wuhan, Hubei Province, China, and causes respiratory infection. This pandemic pneumonia killed about 1,437,835 people out of 61,308,161cases up to November 27, 2020. The disease's main clinical complications include fever, recurrent coughing, shortness of breath, acute respiratory syndrome, and failure of vital organs that could lead to death. It has been shown that natural compounds with antioxidant, anticancer, and antiviral activities and RNA interference agents could play an essential role in preventing or treating coronavirus infection by inhibiting the expression of crucial virus genes. This study aims to introduce a summary of coronavirus's genetic and morphological structure and determine the role of miRNAs, siRNAs, chemical drugs, and natural compounds in stimulating the immune system or inhibiting the virus's structural and non-structural genes that are essential for replication and infection of SARS-CoV-2.
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Affiliation(s)
- Mohammad Reza Kalhori
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Fatemeh Saadatpour
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Ehsan Arefian
- Molecular Virology Lab, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hosien Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ina Yosifova Aneva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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79
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Diggins NL, Skalsky RL, Hancock MH. Regulation of Latency and Reactivation by Human Cytomegalovirus miRNAs. Pathogens 2021; 10:pathogens10020200. [PMID: 33668486 PMCID: PMC7918750 DOI: 10.3390/pathogens10020200] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Human cytomegalovirus (HCMV) encodes 22 mature microRNAs (miRNAs), which regulate a myriad of cellular processes, including vesicular trafficking, cell cycle progression, apoptosis, and immune evasion, as well as viral gene expression. Recent evidence points to a critical role for HCMV miRNAs in mediating latency in CD34+ hematopoietic progenitor cells through modulation of cellular signaling pathways, including attenuation of TGFβ and EGFR signaling. Moreover, HCMV miRNAs can act in concert with, or in opposition to, viral proteins in regulating host cell functions. Here, we comprehensively review the studies of HCMV miRNAs in the context of latency and highlight the novel processes that are manipulated by the virus using these small non-coding RNAs.
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80
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The neglected nutrigenomics of milk: What is the role of inter-species transfer of small non-coding RNA? FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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81
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Ouyang Y, Mouillet JF, Sorkin A, Sadovsky Y. Trophoblastic extracellular vesicles and viruses: Friends or foes? Am J Reprod Immunol 2021; 85:e13345. [PMID: 32939907 PMCID: PMC7880881 DOI: 10.1111/aji.13345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022] Open
Abstract
Cells produce cytoplasmic vesicles to facilitate the processing and transport of RNAs, proteins, and other signaling molecules among intracellular organelles. Moreover, most cells release a range of extracellular vesicles (EVs) that mediate intercellular communication in both physiological and pathological settings. In addition to a better understanding of their biological functions, the diagnostic and therapeutic prospects of EVs, particularly the nano-sized small EVs (sEVs, exosomes), are currently being rigorously pursued. While EVs and viruses such as retroviruses might have evolved independently, they share a number of similar characteristics, including biogenesis pathways, size distribution, cargo, and cell-targeting mechanisms. The interplay of EVs with viruses has profound effects on viral replication and infectivity. Our research indicates that sEVs, produced by primary human trophoblasts, can endow other non-placental cell types with antiviral response. Better insights into the interaction of EVs with viruses may illuminate new ways to attenuate viral infections during pregnancy, and perhaps develop new antiviral therapeutics to protect the feto-placental unit during critical times of human development.
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Affiliation(s)
- Yingshi Ouyang
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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82
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Singh CP. Viral-encoded microRNAs in host-pathogen interactions in silkworm. Microrna 2021; 10:3-13. [PMID: 33475082 DOI: 10.2174/2211536610666210121154314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 11/22/2022]
Abstract
The mulberry silkworm Bombyx mori, apart from its well-known economic importance, has also emerged as an insect model to study host-pathogen interactions. The major concern for silkworm cultivation and the sericulture industry is the attack by various types of pathogens mainly includes viruses, fungi, bacteria and protozoa. Successful infection requires specific arsenals to counter the host immune response. MicroRNAs (miRNAs) are one of the potential arsenals which are encoded by viruses and effectively used during host-pathogen interactions. MiRNAs are short noncoding 19-25 nucleotides long endogenous RNAs that post-transcriptionally regulate expression of protein-coding genes in a sequencespecific manner. Most of the higher eukaryotes encode miRNAs and utilize them in the regulation of important cellular pathways. In silkworm, promising functions of miRNAs have been characterized in development, metamorphosis, immunity, and host-pathogen interactions. The viral miRNA-mediated fine-tuning of the viral, as well as cellular genes, is beneficial for making a cellular environment favorable for the virus proliferation. Baculovirus and cypovirus which infect silkworm have been shown to encode miRNAs and their functions are implicated in controlling the expression of both viral and host genes. In the present review, the author discusses the diverse functions of viral-encoded miRNAs in evasion of the host immune responses and reshaping of the silkworm cellular environment for replication. Besides, a basic overview of miRNA biogenesis and mechanism of action is also provided. Our increasing understanding of the viral miRNAs role in silkworm-virus interactions would not only assist us to get insights into the intricate pathways but also provide tools to deal with dreaded pathogens.
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Affiliation(s)
- C P Singh
- Department of Botany, University of Rajasthan, Jaipur-302004, Rajasthan. India
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83
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Ramesh SV, Yogindran S, Gnanasekaran P, Chakraborty S, Winter S, Pappu HR. Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis. Front Microbiol 2021; 11:614231. [PMID: 33584579 PMCID: PMC7874048 DOI: 10.3389/fmicb.2020.614231] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 02/01/2023] Open
Abstract
Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.
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Affiliation(s)
- S V Ramesh
- ICAR-Central Plantation Crops Research Institute, Kasaragod, India
| | - Sneha Yogindran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabu Gnanasekaran
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Stephan Winter
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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84
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Tang CK, Tsai CH, Wu CP, Lin YH, Wei SC, Lu YH, Li CH, Wu YL. MicroRNAs from Snellenius manilae bracovirus regulate innate and cellular immune responses of its host Spodoptera litura. Commun Biol 2021; 4:52. [PMID: 33420334 PMCID: PMC7794284 DOI: 10.1038/s42003-020-01563-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 10/18/2020] [Indexed: 01/29/2023] Open
Abstract
To avoid inducing immune and physiological responses in insect hosts, parasitoid wasps have developed several mechanisms to inhibit them during parasitism, including the production of venom, specialized wasp cells, and symbioses with polydnaviruses (PDVs). These mechanisms alter the host physiology to give the wasp offspring a greater chance of survival. However, the molecular mechanisms for most of these alterations remain unclear. In the present study, we applied next-generation sequencing analysis and identified several miRNAs that were encoded in the genome of Snellenius manilae bracovirus (SmBV), and expressed in the host larvae, Spodoptera litura, during parasitism. Among these miRNAs, SmBV-miR-199b-5p and SmBV-miR-2989 were found to target domeless and toll-7 in the host, which are involved in the host innate immune responses. Microinjecting the inhibitors of these two miRNAs into parasitized S. litura larvae not only severely decreased the pupation rate of Snellenius manilae, but also restored the phagocytosis and encapsulation activity of the hemocytes. The results demonstrate that these two SmBV-encoded miRNAs play an important role in suppressing the immune responses of parasitized hosts. Overall, our study uncovers the functions of two SmBV-encoded miRNAs in regulating the host innate immune responses upon wasp parasitism.
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Affiliation(s)
- Cheng-Kang Tang
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Chih-Hsuan Tsai
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Carol-P Wu
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Hsien Lin
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Sung-Chan Wei
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Yun-Heng Lu
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Cheng-Hsun Li
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan
| | - Yueh-Lung Wu
- Department of Entomology, National Taiwan University, Taipei, 106, Taiwan.
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85
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Islam MS, Islam ABMMK. Viral miRNAs confer survival in host cells by targeting apoptosis related host genes. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2020.100501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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86
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Liu Z, Wang J, Ge Y, Xu Y, Guo M, Mi K, Xu R, Pei Y, Zhang Q, Luan X, Hu Z, Chi Y, Liu X. SARS-CoV-2 encoded microRNAs are involved in the process of virus infection and host immune response. J Biomed Res 2021; 35:216-227. [PMID: 33963094 PMCID: PMC8193712 DOI: 10.7555/jbr.35.20200154] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The outbreak of COVID-19 caused by SARS-CoV-2 is spreading worldwide, with the pathogenesis mostly unclear. Both virus and host-derived microRNA (miRNA) play essential roles in the pathology of virus infection. This study aims to uncover the mechanism for SARS-CoV-2 pathogenicity from the perspective of miRNA. We scanned the SARS-CoV-2 genome for putative miRNA genes and miRNA targets and conducted in vivo experiments to validate the virus-encoded miRNAs and their regulatory role on the putative targets. One of such virus-encoded miRNAs, MR147-3p, was overexpressed that resulted in significantly decreased transcript levels of all of the predicted targets in human,i.e., EXOC7, RAD9A, and TFE3 in the virus-infected cells. The analysis showed that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Additionally, the genomic mutation of SARS-CoV-2 contributed to the changed miRNA repository and targets, suggesting a possible role of miRNAs in the attenuated phenotype of SARS-CoV-2 during its evolution. This study provided a comprehensive view of the miRNA-involved regulatory system during SARS-CoV-2 infection, indicating possible antiviral therapeutics against SARS-CoV-2 through intervening miRNA regulation.
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Affiliation(s)
- Zhi Liu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jianwei Wang
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yiyue Ge
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu 210009, China
| | - Yuyu Xu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mengchen Guo
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Kai Mi
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Rui Xu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yang Pei
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Qiankun Zhang
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaoting Luan
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Ying Chi
- National Health Commission Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Diseases Control and Prevention, Nanjing, Jiangsu 210009, China
| | - Xingyin Liu
- State Key Laboratory of Reproductive Medicine, Center of Global Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Pathogen Biology-Microbiology Division, Key Laboratory of Pathogen of Jiangsu Province, School of Basic Medical Science, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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87
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Singh CP. Role of microRNAs in insect-baculovirus interactions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 127:103459. [PMID: 32961323 DOI: 10.1016/j.ibmb.2020.103459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) constitute a novel class of gene expression regulators and are found to be involved in regulating a wide range of biological processes such as development, cell cycle, metabolism, apoptosis, immunity, host-pathogen interactions etc. Generally miRNAs negatively regulate the gene expression at the post-transcriptional level by binding to the complementary target mRNA sequences. These tiny molecules are abundantly found in higher eukaryotes and viruses. Most of the DNA viruses of animals and insects encode miRNAs including baculoviruses. Baculoviruses are the insect-specific viruses that cause severe infection and mortality mainly in insect larvae of the order Lepidoptera, Diptera, and Hymenoptera. These enveloped viruses have multiple applications in biotechnology and biological pest control methods. For a better understanding of baculoviruses, it is necessary to elucidate the molecular basis of insect-baculovirus interactions. Recent advancement in the technologies for studying the gene expression has accelerated the discovery of new players in the insect-baculovirus interactions. MiRNAs are the emerging and fate-determining players of host-viral interactions. The long history of host and virus co-evolution suggests that the virus keeps on evolving its arsenals to succeed in infection whereas the host continues investing in antiviral defense mechanisms. In this review, I aim to highlight the recent information and understanding of the baculovirus-encoding miRNAs and their functions in regulating viral as well as host genes. Additionally, insect-derived miRNAs response to baculovirus infection is also discussed. A detailed critical view about the regulatory roles of miRNAs in insect-baculovirus interactions will help us to understand molecular networks amid these interactions and develop a sustainable antiviral strategy.
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Affiliation(s)
- C P Singh
- Department of Botany, University of Rajasthan, Jaipur, 302004, Rajasthan, India.
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88
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Annese T, Tamma R, De Giorgis M, Ribatti D. microRNAs Biogenesis, Functions and Role in Tumor Angiogenesis. Front Oncol 2020; 10:581007. [PMID: 33330058 PMCID: PMC7729128 DOI: 10.3389/fonc.2020.581007] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
microRNAs (miRNAs) are small non-coding RNA molecules, evolutionary conserved. They target more than one mRNAs, thus influencing multiple molecular pathways, but also mRNAs may bind to a variety of miRNAs, either simultaneously or in a context-dependent manner. miRNAs biogenesis, including miRNA transcription, processing by Drosha and Dicer, transportation, RISC biding, and miRNA decay, are finely controlled in space and time. miRNAs are critical regulators in various biological processes, such as differentiation, proliferation, apoptosis, and development in both health and disease. Their dysregulation is involved in tumor initiation and progression. In tumors, they can act as onco-miRNAs or oncosuppressor-miRNA participating in distinct cellular pathways, and the same miRNA can perform both activities depending on the context. In tumor progression, the angiogenic switch is fundamental. miRNAs derived from tumor cells, endothelial cells, and cells of the surrounding microenvironment regulate tumor angiogenesis, acting as pro-angiomiR or anti-angiomiR. In this review, we described miRNA biogenesis and function, and we update the non-classical aspects of them. The most recent role in the nucleus, as transcriptional gene regulators and the different mechanisms by which they could be dysregulated, in tumor initiation and progression, are treated. In particular, we describe the role of miRNAs in sprouting angiogenesis, vessel co-option, and vasculogenic mimicry. The role of miRNAs in lymphoma angiogenesis is also discussed despite the scarcity of data. The information presented in this review reveals the need to do much more to discover the complete miRNA network regulating angiogenesis, not only using high-throughput computational analysis approaches but also morphological ones.
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Affiliation(s)
- Tiziana Annese
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Roberto Tamma
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Michelina De Giorgis
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, Section of Human Anatomy and Histology, University of Bari Medical School, Bari, Italy
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89
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Pitzalis N, Amari K, Graindorge S, Pflieger D, Donaire L, Wassenegger M, Llave C, Heinlein M. Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes. Commun Biol 2020; 3:702. [PMID: 33230160 PMCID: PMC7683744 DOI: 10.1038/s42003-020-01425-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/22/2020] [Indexed: 11/12/2022] Open
Abstract
Virus-induced plant diseases in cultivated plants cause important damages in yield. Although the mechanisms of virus infection are intensely studied at the cell biology level, only little is known about the molecular dialog between the invading virus and the host genome. Here we describe a combinatorial genome-wide approach to identify networks of sRNAs-guided post-transcriptional regulation within local Turnip mosaic virus (TuMV) infection sites in Brassica napus leaves. We show that the induction of host-encoded, virus-activated small interfering RNAs (vasiRNAs) observed in virus-infected tissues is accompanied by site-specific cleavage events on both viral and host RNAs that recalls the activity of small RNA-induced silencing complexes (RISC). Cleavage events also involve virus-derived siRNA (vsiRNA)–directed cleavage of target host transcripts as well as cleavage of viral RNA by both host vasiRNAs and vsiRNAs. Furthermore, certain coding genes act as virus-activated regulatory hubs to produce vasiRNAs for the targeting of other host genes. The observations draw an advanced model of plant-virus interactions and provide insights into the complex regulatory networking at the plant-virus interface within cells undergoing early stages of infection. Pitzalis et al. use replicative RNAseq, small RNA (sRNA)seq, and parallel analysis of RNA ends (PARE)seq analysis to identify networks of sRNAs-guided post-transcriptional regulation within local Turnip mosaic virus infection sites. This study provides insights into the complex regulatory networking at the plantvirus interface within cells undergoing early stages of infection.
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Affiliation(s)
- Nicolas Pitzalis
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (IBMP-CNRS), Université de Strasbourg, F-67000, Strasbourg, France
| | - Khalid Amari
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (IBMP-CNRS), Université de Strasbourg, F-67000, Strasbourg, France.,Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Stéfanie Graindorge
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (IBMP-CNRS), Université de Strasbourg, F-67000, Strasbourg, France
| | - David Pflieger
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (IBMP-CNRS), Université de Strasbourg, F-67000, Strasbourg, France
| | - Livia Donaire
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.,Department of Biology of Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, 30100, Murcia, Spain
| | - Michael Wassenegger
- RLP Agroscience, AlPlanta-Institute for Plant Research, 67435, Neustadt, Germany.,Centre for Organismal Studies, University of Heidelberg, 69120, Heidelberg, Germany
| | - César Llave
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (IBMP-CNRS), Université de Strasbourg, F-67000, Strasbourg, France.
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90
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Gong P, Li X, Wu W, Cao L, Zhao P, Li X, Ren B, Li J, Zhang X. A Novel MicroRNA From the Translated Region of the Giardiavirus rdrp Gene Governs Virus Copy Number in Giardia duodenalis. Front Microbiol 2020; 11:569412. [PMID: 33329426 PMCID: PMC7719678 DOI: 10.3389/fmicb.2020.569412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Giardia duodenalis is an important zoonotic parasite that can cause human and animal diarrhea. Giardiavirus (GLV) is a double-stranded RNA virus in Totiviridae family, which specifically infects trophozoites of the primitive protozoan parasite G. duodenalis. However, the GLV infectious and the pathogenicity of the G. duodenalis still remain to be confirmed. The GLV genome is 6,277 bp, which encodes two proteins (Gag and Gag-Pol). The expression of Gag-Pol protein is regulated by a-1 ribosomal frameshift. In this report, we identified a novel microRNA (GLV miRNA1) from the GLV. Split ligation northern results showed that GLV miRNA1 is a special expression product of GLV, and the precursor was also identified by primer extension. Antisense sequence of the GLV miRNA1 could increase the copy number of virus in G. duodenalis. It suggests that GLV miRNA1 governs the copy number of Giardiavirus in G. duodenalis. Most importantly, the GLV miRNA1 lies at the translated region of the rdrp gene, which is the first case that microRNA locates in the translated region of a known protein. It may be implying a novel phenomenon for miRNA biogenesis.
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Affiliation(s)
- Pengtao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xianhe Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wei Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Lili Cao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Jilin Academy of Animal Husbandry and Veterinary Medicine, Changchun, China
| | - Panpan Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Baoyan Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
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91
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Liao Y, Zhuang G, Sun A, Khan OA, Lupiani B, Reddy SM. Marek's Disease Virus Cluster 3 miRNAs Restrict Virus' Early Cytolytic Replication and Pathogenesis. Viruses 2020; 12:v12111317. [PMID: 33212952 PMCID: PMC7698348 DOI: 10.3390/v12111317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
Herpesvirus-encoded microRNAs (miRNAs) have been discovered in infected cells; however, lack of a suitable animal model has hampered functional analyses of viral miRNAs in vivo. Marek’s disease virus (MDV) (Gallid alphaherpesvirus 2, GaHV-2) genome contains 14 miRNA precursors, which encode 26 mature miRNAs, grouped into three clusters. In this study, the role of MDV-encoded cluster 3 miRNAs, also known as mdv1-miR-M8-M10, in pathogenesis was evaluated in chickens, the natural host of MDV. Our results show that deletion of cluster 3 miRNAs did not affect virus replication and plaque size in cell culture, but increased early cytolytic replication of MDV in chickens. We also observed that deletion of cluster 3 miRNAs resulted in significantly higher virus reactivation from peripheral blood lymphocytes. In addition, pathogenesis studies showed that deletion of cluster 3 miRNAs resulted in more severe atrophy of lymphoid organs and reduced mean death time, but did not affect the incidence of MDV-associated visceral tumors. We confirmed these results by generating a cluster 3 miRNA revertant virus in which the parental MDV phenotype was restored. To the best of our knowledge, our study provides the first evidence that MDV cluster 3 miRNAs play an important role in modulating MDV pathogenesis.
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92
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Pierce JB, Simion V, Icli B, Pérez-Cremades D, Cheng HS, Feinberg MW. Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. Genes (Basel) 2020; 11:E1354. [PMID: 33207533 PMCID: PMC7696723 DOI: 10.3390/genes11111354] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/18/2023] Open
Abstract
Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has led to a global pandemic, failures of local health care systems, and global economic recession. MicroRNAs (miRNAs) have recently emerged as important regulators of viral pathogenesis, particularly among RNA viruses, but the impact of host miRNAs on SARS-CoV-2 infectivity remains unknown. In this study, we utilize the combination of powerful bioinformatic prediction algorithms and miRNA profiling to predict endogenous host miRNAs that may play important roles in regulating SARS-CoV-2 infectivity. We provide a collection of high-probability miRNA binding sites within the SARS-CoV-2 genome as well as within mRNA transcripts of critical viral entry proteins ACE2 and TMPRSS2 and their upstream modulators, the interferons (IFN). By utilizing miRNA profiling datasets of SARS-CoV-2-resistant and -susceptible cell lines, we verify the biological plausibility of the predicted miRNA-target RNA interactions. Finally, we utilize miRNA profiling of SARS-CoV-2-infected cells to identify predicted miRNAs that are differentially regulated in infected cells. In particular, we identify predicted miRNA binders to SARS-CoV-2 ORFs (miR-23a (1ab), miR-29a, -29c (1ab, N), miR-151a, -151b (S), miR-4707-3p (S), miR-298 (5'-UTR), miR-7851-3p (5'-UTR), miR-8075 (5'-UTR)), ACE2 3'-UTR (miR-9-5p, miR-218-5p), TMPRSS2 3'-UTR (let-7d-5p, -7e-5p, miR-494-3p, miR-382-3p, miR-181c-5p), and IFN-α 3'-UTR (miR-361-5p, miR-410-3p). Overall, this study provides insight into potential novel regulatory mechanisms of SARS-CoV-2 by host miRNAs and lays the foundation for future investigation of these miRNAs as potential therapeutic targets or biomarkers.
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Affiliation(s)
- Jacob B. Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Basak Icli
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Daniel Pérez-Cremades
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Henry S. Cheng
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Mark W. Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
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93
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Neri L, Spezia PG, Suraci S, Macera L, Scribano S, Giusti B, Focosi D, Maggi F, Giannecchini S. Torque teno virus microRNA detection in cerebrospinal fluids of patients with neurological pathologies. J Clin Virol 2020; 133:104687. [PMID: 33176237 DOI: 10.1016/j.jcv.2020.104687] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Torque teno virus (TTV) is a widespread anellovirus that establishes persistent infections in humans and represents the most abundant component of the human virome. TTV encodes microRNAs (miRNA) which are found both in viremic and not viremic subjects being potentially ideal tools for the virus to evade the immune system response and to maintain chronic infection in the host. OBJECTIVE To investigate TTV-DNA loads and TTV-miRNAs expression in cerebrospinal fluids (CSF) from subjects under analysis for the assessment of neurological diseases. STUDY DESIGN Detection of TTV-DNA and TTV-miRNAs (e. g. miRNA t1a, t3b, and tth8) were carried out from CSF samples of 93 subjects with neurological diseases by using universal real-time PCR, real-time RT-PCR, and next-generation sequencing (NGS) analyses. RESULTS TTV-DNA was detected in 11 of 93 (12 %) CSFs with a mean TTV load of 155 copies/mL. Conversely, 29 CSF samples (31 %) were positive for at least one TTV-miRNA, while 15 (16 %) CSFs contained all the TTV-miRNAs examined. Overall, TTV-miRNA tth8 was detected in 62 % of samples, followed by TTV miRNA t3b (56 %), and t1a (29 %). Interestingly, TTV-miRNAs were found in CSF samples that were negative for the presence of TTV-DNA. Next-generation sequencing analysis carried out from 4 TTV-DNA negative CSF samples detected reads mapped in TTV-miRNA sequences region. CONCLUSIONS These results shed novel light on the relationship between TTV and the central nervous system and make compelling furthered studies for investigating the potential role of TTV-miRNAs in neurological disorders.
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Affiliation(s)
- Lorenzo Neri
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Italy
| | - Stefano Scribano
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, and Laboratory of Clinical Microbiology, ASST dei Sette Laghi, Varese, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
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94
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Zhu ZJ, Teng M, Li HZ, Zheng LP, Liu JL, Chai SJ, Yao YX, Nair V, Zhang GP, Luo J. Marek's Disease Virus ( Gallid alphaherpesvirus 2)-Encoded miR-M2-5p Simultaneously Promotes Cell Proliferation and Suppresses Apoptosis Through RBM24 and MYOD1-Mediated Signaling Pathways. Front Microbiol 2020; 11:596422. [PMID: 33224130 PMCID: PMC7669912 DOI: 10.3389/fmicb.2020.596422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) have been demonstrated for their involvement in virus biology and pathogenesis, including functioning as key determinants of virally-induced cancers. As an important oncogenic α-herpesvirus affecting poultry health, Marek’s disease virus serotype 1 [Gallid alphaherpesvirus 2 (GaHV-2)] induces rapid-onset T-cell lymphomatous disease commonly referred to as Marek’s disease (MD), an excellent biological model for the study of virally-induced cancer in the natural hosts. Previously, we have demonstrated that GaHV-2-encoded miRNAs (especially those within the Meq-cluster) have the potential to act as critical regulators of multiple processes such as virus replication, latency, pathogenesis, and/or oncogenesis. In addition to miR-M4-5p (miR-155 homolog) and miR-M3-5p, we have recently found that miR-M2-5p possibly participate in inducing MD lymphomagenesis. Here, we report the identification of two tumor suppressors, the RNA-binding protein 24 (RBM24) and myogenic differentiation 1 (MYOD1), being two biological targets for miR-M2-5p. Our experiments revealed that as a critical miRNA, miR-M2-5p promotes cell proliferation via regulating the RBM24-mediated p63 overexpression and MYOD1-mediated IGF2 signaling and suppresses apoptosis by targeting the MYOD1-mediated Caspase-3 signaling pathway. Our data present a new strategy of a single viral miRNA exerting dual role to potentially participate in the virally-induced T-cell lymphomagenesis by simultaneously promoting the cell proliferation and suppressing apoptosis.
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Affiliation(s)
- Zhi-Jian Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Man Teng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hui-Zhen Li
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China.,College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Lu-Ping Zheng
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jin-Ling Liu
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shu-Jun Chai
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yong-Xiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Guildford, United Kingdom
| | - Gai-Ping Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jun Luo
- Key Laboratory of Animal Immunology, Ministry of Agriculture and Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China.,UK-China Centre of Excellence for Research on Avian Diseases, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Animal Disease and Public Safety, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
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95
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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: 1.6] [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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96
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Lauver MD, Lukacher AE. JCPyV VP1 Mutations in Progressive MultifocalLeukoencephalopathy: Altering Tropismor Mediating Immune Evasion? Viruses 2020; 12:v12101156. [PMID: 33053912 PMCID: PMC7600905 DOI: 10.3390/v12101156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022] Open
Abstract
Polyomaviruses are ubiquitous human pathogens that cause lifelong, asymptomatic infections in healthy individuals. Although these viruses are restrained by an intact immune system, immunocompromised individuals are at risk for developing severe diseases driven by resurgent viral replication. In particular, loss of immune control over JC polyomavirus can lead to the development of the demyelinating brain disease progressive multifocal leukoencephalopathy (PML). Viral isolates from PML patients frequently carry point mutations in the major capsid protein, VP1, which mediates virion binding to cellular glycan receptors. Because polyomaviruses are non-enveloped, VP1 is also the target of the host's neutralizing antibody response. Thus, VP1 mutations could affect tropism and/or recognition by polyomavirus-specific antibodies. How these mutations predispose susceptible individuals to PML and other JCPyV-associated CNS diseases remains to be fully elucidated. Here, we review the current understanding of polyomavirus capsid mutations and their effects on viral tropism, immune evasion, and virulence.
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97
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Zhan S, Wang Y, Chen X. RNA virus-encoded microRNAs: biogenesis, functions and perspectives on application. ACTA ACUST UNITED AC 2020; 2:15. [PMID: 33209991 PMCID: PMC7548135 DOI: 10.1186/s41544-020-00056-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression at the posttranscriptional level and play a crucial role in development and many diseases. The discovery of miRNAs has greatly expanded our understanding of the intricate scenario of genome-wide regulation. Over the last two decades, hundreds of virus-encoded miRNAs have been identified, most of which are from DNA viruses. Although the number of reported RNA virus-derived miRNAs is increasing, current knowledge of their roles in physiological and pathological processes has remained lacking. In this review, we discuss the biogenesis and biological functions of RNA virus- encoded miRNAs and their proposed roles in virus-host interactions and further underscore their potential value in the diagnosis and treatment of viral diseases.
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Affiliation(s)
- Shoubin Zhan
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Yanbo Wang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
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98
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Liu J, Song XR, Zheng K, Zhang WJ, Chen HC, Liu ZF. Feedback inhibition of bovine herpesvirus 5 replication by dual-copy bhv5-miR-B10-3p. J Gen Virol 2020; 101:290-298. [PMID: 31935178 DOI: 10.1099/jgv.0.001375] [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] [Indexed: 11/18/2022] Open
Abstract
Bovine herpesvirus 5 (BoHV-5) is a pathogen of cattle responsible for fatal meningoencephalitis. Like alpha herpesvirus subfamily members, BoHV-5 also encodes microRNA in lytic infections of epithelial cells. BoHV-5-miR-B10 was the most abundant miRNA detected in a high-throughput sequencing study. Here, we evaluated the kinetics of miR-B10 expression after BoHV-5 productive infection by stem-loop real-time quantitative PCR. miR-B10 candidate target sites in the virus were predicted, and BoHV-5 UL39 was confirmed as a target gene by dual-luciferase assay with the design of an miR-B10 tough decoy (TuD). The UL39 gene encoding ribonucleotide reductase (RR) large subunit plays an important role in the early stage of BoHV-5 lytic infection. As BoHV-5-miR-B10 is located in internal and terminal repeat regions, we generated a TuD gene-integrated BoHV-5 strain, which effectively down-regulated miR-B10-3p. Strikingly, the suppression of miR-B10-3p significantly improved BoHV-5 replication. Taking these findings together, our study established an efficient method to deliver and express TuD RNA for viral miRNA suppression, and demonstrated that virus-encoded miRNA suppresses viral-genome biogenesis with a feedback mode, which might serve as a brake for viral replication. Herpesviruses infect humans and a variety of animals. Almost all herpesviruses can encode miRNAs, but the functions of these miRNAs remain to be elucidated. Most herpesvirus-encoded miRNA harbours dual copies, which is difficult to be deleted by current genetic modulation. Here, we developed an efficient method to deliver and express TuD RNA to efficiently suppress viral miRNA with multiple copies. Using this method, we demonstrated for the first time that viral miRNA feedback regulates viral replication by suppressing the expression of RR.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xian-Rong Song
- Hubei Vocational College of Bio-Technology, Wuhan 430070, PR China
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ke Zheng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wen-Jing Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Huan-Chun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zheng-Fei Liu
- Present address: State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
- Hubei Vocational College of Bio-Technology, Wuhan 430070, PR China
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99
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Bhattacharyya P, Biswas SC. Small Non-coding RNAs: Do They Encode Answers for Controlling SARS-CoV-2 in the Future? Front Microbiol 2020; 11:571553. [PMID: 33072032 PMCID: PMC7530945 DOI: 10.3389/fmicb.2020.571553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel coronavirus responsible for the current COVID-19 (coronavirus disease 2019) pandemic, which has hit the world since December 2019. It has spread to about 216 countries worldwide, affecting more than 21.7 million people so far. Although clinical trials of a number of promising antiviral drugs and vaccines against COVID-19 are underway, it is hard to predict how successful these drug- or vaccine-based therapeutics are eventually going to be in combating COVID-19 because most of such therapeutic strategies have failed against human coronaviruses such as SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus) responsible for similar pandemics in the past. In that context, we would like to bring to scientific attention another group of endogenous regulatory molecules, the small non-coding RNAs, especially the microRNAs, which are found to regulate critical cellular pathways in a number of disease conditions, including RNA viral infections. This review will focus on understanding the effect of altered microRNA expression during coronavirus-mediated infections and how it may provide clues for further exploring the pathogenesis of SARS-CoV-2, with a view of developing RNAi-based therapeutics and biomarkers against COVID-19.
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Affiliation(s)
- Pallabi Bhattacharyya
- Cell Biology & Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhas C Biswas
- Cell Biology & Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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100
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Maev IV, Karlovich TI, Burmistrov AI, Chekmazov IA, Andreev DN, Reshetnyak VI. Current Views of Torque Teno Virus (TTV) in Liver Diseases. RUSSIAN JOURNAL OF GASTROENTEROLOGY, HEPATOLOGY, COLOPROCTOLOGY 2020; 30:7-22. [DOI: 10.22416/1382-4376-2020-30-4-7-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Affiliation(s)
- I. V. Maev
- Moscow State University of Medicine and Dentistry
| | - T. I. Karlovich
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
| | | | - I. A. Chekmazov
- Central Clinical Hospital with Outpatient Care of the Russian President Administration
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