1
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Zhu Z, Fan H, Fodor E. Defining the minimal components of the influenza A virus replication machinery via an in vitro reconstitution system. PLoS Biol 2023; 21:e3002370. [PMID: 37943954 PMCID: PMC10662765 DOI: 10.1371/journal.pbio.3002370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
During influenza A virus infection, the viral RNA polymerase transcribes the viral negative-sense segmented RNA genome and replicates it in a two-step process via complementary RNA within viral ribonucleoprotein (vRNP) complexes. While numerous viral and host factors involved in vRNP functions have been identified, dissecting the roles of individual factors remains challenging due to the complex cellular environment in which vRNP activity has been studied. To overcome this challenge, we reconstituted viral transcription and a full cycle of replication in a test tube using vRNPs isolated from virions and recombinant factors essential for these processes. This novel system uncovers the minimal components required for influenza virus replication and also reveals new roles of regulatory factors in viral replication. Moreover, it sheds light on the molecular interplay underlying the temporal regulation of viral transcription and replication. Our highly robust in vitro system enables systematic functional analysis of factors modulating influenza virus vRNP activity and paves the way for imaging key steps of viral transcription and replication.
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Affiliation(s)
- Zihan Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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2
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Chu KB, Quan FS. Respiratory Viruses and Virus-like Particle Vaccine Development: How Far Have We Advanced? Viruses 2023; 15:v15020392. [PMID: 36851606 PMCID: PMC9965150 DOI: 10.3390/v15020392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
With technological advancements enabling globalization, the intercontinental transmission of pathogens has become much easier. Respiratory viruses are one such group of pathogens that require constant monitoring since their outbreak leads to massive public health crises, as exemplified by the influenza virus, respiratory syncytial virus (RSV), and the recent coronavirus disease 2019 (COVID-19) outbreak caused by the SARS-CoV-2. To prevent the transmission of these highly contagious viruses, developing prophylactic tools, such as vaccines, is of considerable interest to the scientific community. Virus-like particles (VLPs) are highly sought after as vaccine platforms for their safety and immunogenicity profiles. Although several VLP-based vaccines against hepatitis B and human papillomavirus have been approved for clinical use by the United States Food and Drug Administration, VLP vaccines against the three aforementioned respiratory viruses are lacking. Here, we summarize the most recent progress in pre-clinical and clinical VLP vaccine development. We also outline various strategies that contributed to improving the efficacy of vaccines against each virus and briefly discuss the stability aspect of VLPs that makes it a highly desired vaccine platform.
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Affiliation(s)
- Ki-Back Chu
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, Core Research Institute (CRI), Kyung Hee University, Seoul 02447, Republic of Korea
| | - Fu-Shi Quan
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, Core Research Institute (CRI), Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Medical Zoology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
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3
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Zhang L, Ye X, Liu Y, Zhang Z, Xia X, Dong S. Research progress on the effect of traditional Chinese medicine on the activation of PRRs-mediated NF-κB signaling pathway to inhibit influenza pneumonia. Front Pharmacol 2023; 14:1132388. [PMID: 37089926 PMCID: PMC10119400 DOI: 10.3389/fphar.2023.1132388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Influenza pneumonia has challenged public health and social development. One of the hallmarks of severe influenza pneumonia is overproduction of pro-inflammatory cytokines and chemokines, which result from the continuous activation of intracellular signaling pathways, such as the NF-κB pathway, mediated by the interplay between viruses and host pattern recognition receptors (PRRs). It has been reported that traditional Chinese medicines (TCMs) can not only inhibit viral replication and inflammatory responses but also affect the expression of key components of PRRs and NF-κB signaling pathways. However, whether the antiviral and anti-inflammatory roles of TCM are related with its effects on NF-κB signaling pathway activated by PRRs remains unclear. Here, we reviewed the mechanism of PRRs-mediated activation of NF-κB signaling pathway following influenza virus infection and summarized the influence of anti-influenza TCMs on inflammatory responses and the PRRs/NF-κB signaling pathway, so as to provide better understanding of the mode of action of TCMs in the treatment of influenza pneumonia.
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Affiliation(s)
- Ling Zhang
- The Affiliated Anning First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xiong Ye
- The Affiliated Anning First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yuntao Liu
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhongde Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhongde Zhang, ; Xueshan Xia, ; Shuwei Dong,
| | - Xueshan Xia
- The Affiliated Anning First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- *Correspondence: Zhongde Zhang, ; Xueshan Xia, ; Shuwei Dong,
| | - Shuwei Dong
- The Affiliated Anning First Hospital, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- *Correspondence: Zhongde Zhang, ; Xueshan Xia, ; Shuwei Dong,
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4
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Defective Interfering Particles of Influenza Virus and Their Characteristics, Impacts, and Use in Vaccines and Antiviral Strategies: A Systematic Review. Viruses 2022; 14:v14122773. [PMID: 36560777 PMCID: PMC9781619 DOI: 10.3390/v14122773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Defective interfering particles (DIPs) are particles containing defective viral genomes (DVGs) generated during viral replication. DIPs have been found in various RNA viruses, especially in influenza viruses. Evidence indicates that DIPs interfere with the replication and encapsulation of wild-type viruses, namely standard viruses (STVs) that contain full-length viral genomes. DIPs may also activate the innate immune response by stimulating interferon synthesis. In this review, the underlying generation mechanisms and characteristics of influenza virus DIPs are summarized. We also discuss the potential impact of DIPs on the immunogenicity of live attenuated influenza vaccines (LAIVs) and development of influenza vaccines based on NS1 gene-defective DIPs. Finally, we review the antiviral strategies based on influenza virus DIPs that have been used against both influenza virus and SARS-CoV-2. This review provides systematic insights into the theory and application of influenza virus DIPs.
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5
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Tsai M, Osman W, Adair J, ElMergawy R, Chafin L, Johns F, Farkas D, Elhance A, Londino J, Mallampalli RK. The E3 ligase subunit FBXO45 binds the interferon-λ receptor and promotes its degradation during influenza virus infection. J Biol Chem 2022; 298:102698. [PMID: 36379255 PMCID: PMC9747586 DOI: 10.1016/j.jbc.2022.102698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
Abstract
Influenza remains a major public health challenge, as the viral infection activates multiple biological networks linked to altered host innate immunity. Following infection, IFN-λ, a ligand crucial for the resolution of viral infections, is known to bind to its cognate receptor, IFNLR1, in lung epithelia. However, little is known regarding the molecular expression and regulation of IFNLR1. Here, we show that IFNLR1 is a labile protein in human airway epithelia that is rapidly degraded after influenza infection. Using an unbiased proximal ligation biotin screen, we first identified that the Skp-Cullin-F box E3 ligase subunit, FBXO45, binds to IFNLR1. We demonstrate that FBXO45, induced in response to influenza infection, mediates IFNLR1 protein polyubiquitination and degradation through the ubiquitin-proteasome system by docking with its intracellular receptor domain. Furthermore, we found ectopically expressed FBXO45 and its silencing in cells differentially regulated both IFNLR1 protein stability and interferon-stimulated gene expression. Mutagenesis studies also indicated that expression of a K319R/K320R IFNLR1 variant in cells exhibited reduced polyubiquitination, yet greater stability and proteolytic resistance to FBXO45 and influenza-mediated receptor degradation. These results indicate that the IFN-λ-IFNLR1 receptor axis is tightly regulated by the Skp-Cullin-F box ubiquitin machinery, a pathway that may be exploited by influenza infection as a means to limit antiviral responses.
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Su W, Lin XT, Zhao S, Zheng XQ, Zhou YQ, Xiao LL, Chen H, Zhang ZY, Zhang LJ, Wu XX. Tripartite motif-containing protein 46 accelerates influenza A H7N9 virus infection by promoting K48-linked ubiquitination of TBK1. Virol J 2022; 19:176. [PMID: 36329446 PMCID: PMC9632593 DOI: 10.1186/s12985-022-01907-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Avian influenza A H7N9 emerged in 2013, threatening public health and causing acute respiratory distress syndrome, and even death, in the human population. However, the underlying mechanism by which H7N9 virus causes human infection remains elusive. METHODS Herein, we infected A549 cells with H7N9 virus for different times and assessed tripartite motif-containing protein 46 (TRIM46) expression. To determine the role of TRIM46 in H7N9 infection, we applied lentivirus-based TRIM46 short hairpin RNA sequences and overexpression plasmids to explore virus replication, and changes in type I interferons and interferon regulatory factor 3 (IRF3) phosphorylation levels in response to silencing and overexpression of TRIM46. Finally, we used Co-immunoprecipitation and ubiquitination assays to examine the mechanism by which TRIM46 mediated the activity of TANK-binding kinase 1 (TBK1). RESULTS Type I interferons play an important role in defending virus infection. Here, we found that TRIM46 levels were significantly increased during H7N9 virus infection. Furthermore, TRIM46 knockdown inhibited H7N9 virus replication compared to that in the control group, while the production of type I interferons increased. Meanwhile, overexpression of TRIM46 promoted H7N9 virus replication and decrease the production of type I interferons. In addition, the level of phosphorylated IRF3, an important interferon regulatory factor, was increased in TRIM46-silenced cells, but decreased in TRIM46 overexpressing cells. Mechanistically, we observed that TRIM46 could interact with TBK1 to induce its K48-linked ubiquitination, which promoted H7N9 virus infection. CONCLUSION Our results suggest that TRIM46 negatively regulates the human innate immune response against H7N9 virus infection.
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Affiliation(s)
- Wei Su
- Department of Intensive Care Unit, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China.
| | - Xian-Tian Lin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Shuai Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiao-Qin Zheng
- Department of Lung Transplant, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Yu-Qing Zhou
- Department of Respiratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310020, Zhejiang, China
| | - Lan-Lan Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Hui Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Zheng-Yu Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Li-Jun Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China
| | - Xiao-Xin Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Centre for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qing Chun Road, Hangzhou, 310003, Zhejiang, China.
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7
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Zhao F, Xu F, Liu X, Hu Y, Wei L, Fan Z, Wang L, Huang Y, Mei S, Guo L, Yang L, Cen S, Wang J, Liang C, Guo F. SERINC5 restricts influenza virus infectivity. PLoS Pathog 2022; 18:e1010907. [PMID: 36223419 PMCID: PMC9591065 DOI: 10.1371/journal.ppat.1010907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 10/24/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
SERINC5 is a multi-span transmembrane protein that is incorporated into HIV-1 particles in producing cells and inhibits HIV-1 entry. Multiple retroviruses like HIV-1, equine infectious anemia virus and murine leukemia virus are subject to SERINC5 inhibition, while HIV-1 pseudotyped with envelope glycoproteins of vesicular stomatitis virus and Ebola virus are resistant to SERINC5. The antiviral spectrum and the underlying mechanisms of SERINC5 restriction are not completely understood. Here we show that SERINC5 inhibits influenza A virus infection by targeting virus-cell membrane fusion at an early step of infection. Further results show that different influenza hemagglutinin (HA) subtypes exhibit diverse sensitivities to SERINC5 restriction. Analysis of the amino acid sequences of influenza HA1 strains indicates that HA glycosylation sites correlate with the sensitivity of influenza HA to SERINC5, and the inhibitory effect of SERINC5 was lost when certain HA glycosylation sites were mutated. Our study not only expands the antiviral spectrum of SERINC5, but also reveals the role of viral envelope glycosylation in resisting SERINC5 restriction.
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Affiliation(s)
- Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Long Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (JW); (CL); (FG)
| | - Chen Liang
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
- * E-mail: (JW); (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (JW); (CL); (FG)
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8
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Identification of Critical Genes and Pathways for Influenza A Virus Infections via Bioinformatics Analysis. Viruses 2022; 14:v14081625. [PMID: 35893690 PMCID: PMC9332270 DOI: 10.3390/v14081625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/18/2022] [Accepted: 07/23/2022] [Indexed: 01/27/2023] Open
Abstract
Influenza A virus (IAV) requires the host cellular machinery for many aspects of its life cycle. Knowledge of these host cell requirements not only reveals molecular pathways exploited by the virus or triggered by the immune system but also provides further targets for antiviral drug development. To uncover critical pathways and potential targets of influenza infection, we assembled a large amount of data from 8 RNA sequencing studies of IAV infection for integrative network analysis. Weighted gene co-expression network analysis (WGCNA) was performed to investigate modules and genes correlated with the time course of infection and/or multiplicity of infection (MOI). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the biological functions and pathways of the genes in 5 significant modules. Top hub genes were identified using the cytoHubba plugin in the protein interaction network. The correlation between expression levels of 7 top hub genes and time course or MOI was displayed and validated, including BCL2L13, PLSCR1, ARID5A, LMO2, NDRG4, HAP1, and CARD10. Dysregulated expression of these genes potently impacted the development of IAV infection through modulating IAV-related biological processes and pathways. This study provides further insights into the underlying molecular mechanisms and potential targets in IAV infection.
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Takizawa N, Takada H, Umekita M, Igarashi M, Takahashi Y. Anti-influenza Virus Activity of Methylthio-Formycin Distinct From That of T-705. Front Microbiol 2022; 13:802671. [PMID: 35250924 PMCID: PMC8894184 DOI: 10.3389/fmicb.2022.802671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza virus epidemics result in severe illness, and occasionally influenza pandemics cause significant morbidity and mortality, although vaccines and anti-influenza virus drugs are available. By screening an in-house library, we identified methylthio-formycin (SMeFM), an adenosine analog, as a potent inhibitor of influenza virus propagation. SMeFM inhibited the propagation of influenza A and B viruses (IC50: 34.1 and 37.9 nM, respectively) and viruses showing reduced susceptibility to baloxavir and neuraminidase inhibitors but not T-705 (Favipiravir). However, the combination of T-705 and SMeFM inhibited the propagation of the influenza virus not in an antagonistic but in a slightly synergistic manner, suggesting that SMeFM has targets distinct from that of T-705. SMeFM induced A-to-C transversion mutations in virus genome RNA, and SMeFM triphosphate did not inhibit in vitro viral RNA synthesis. Our results show that SMeFM inhibits the propagation of the influenza virus by a mechanism different from that of T-705 and is a potential drug candidate to develop for anti-influenza drug.
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10
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Characterization of influenza A virus induced transposons reveals a subgroup of transposons likely possessing the regulatory role as eRNAs. Sci Rep 2022; 12:2188. [PMID: 35140280 PMCID: PMC8828846 DOI: 10.1038/s41598-022-06196-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/25/2022] [Indexed: 01/02/2023] Open
Abstract
Although many studies have observed genome-wide host transposon expression alteration during viral infection, the mechanisms of induction and the impact on the host remain unclear. Utilizing recently published influenza A virus (IAV) time series data and ENCODE functional genomics data, we characterized virus induced host differentially expressed transposons (virus-induced-TE) by investigating genome-wide spatial and functional relevance between the virus-induced-TEs and epigenomic markers (e.g. histone modification and chromatin remodelers). We found that a significant fraction of virus-induced-TEs are derived from host enhancer regions, where CHD4 binding and/or H3K27ac occupancy is high or H3K9me3 occupancy is low. By overlapping virus-induced-TEs to human enhancer RNAs (eRNAs), we discovered that a proportion of virus-induced-TEs are either eRNAs or part of enhancer RNAs. Upon further analysis of the eRNA targeted genes, we found that the virus-induced-TE related eRNA targets are overrepresented in differentially expressed host genes of IAV infected samples. Our results suggest that changing chromatin accessibility from repressive to permissive in the transposon docked enhancer regions to regulate host downstream gene expression is potentially one of the virus and host cell interaction mechanisms, where transposons are likely important regulatory genomic elements. Our study provides a new insight into the mechanisms of virus-host interaction and may lead to novel strategies for prevention and therapeutics of IAV and other virus infectious diseases.
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11
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Sayed N, Allawadhi P, Khurana A, Singh V, Navik U, Pasumarthi SK, Khurana I, Banothu AK, Weiskirchen R, Bharani KK. Gene therapy: Comprehensive overview and therapeutic applications. Life Sci 2022; 294:120375. [PMID: 35123997 DOI: 10.1016/j.lfs.2022.120375] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 02/07/2023]
Abstract
Gene therapy is the product of man's quest to eliminate diseases. Gene therapy has three facets namely, gene silencing using siRNA, shRNA and miRNA, gene replacement where the desired gene in the form of plasmids and viral vectors, are directly administered and finally gene editing based therapy where mutations are modified using specific nucleases such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regulatory interspaced short tandem repeats (CRISPR)/CRISPR-associated protein (Cas)-associated nucleases. Transfer of gene is either through transformation where under specific conditions the gene is directly taken up by the bacterial cells, transduction where a bacteriophage is used to transfer the genetic material and lastly transfection that involves forceful delivery of gene using either viral or non-viral vectors. The non-viral transfection methods are subdivided into physical, chemical and biological. The physical methods include electroporation, biolistic, microinjection, laser, elevated temperature, ultrasound and hydrodynamic gene transfer. The chemical methods utilize calcium- phosphate, DAE-dextran, liposomes and nanoparticles for transfection. The biological methods are increasingly using viruses for gene transfer, these viruses could either integrate within the genome of the host cell conferring a stable gene expression, whereas few other non-integrating viruses are episomal and their expression is diluted proportional to the cell division. So far, gene therapy has been wielded in a plethora of diseases. However, coherent and innocuous delivery of genes is among the major hurdles in the use of this promising therapy. Hence this review aims to highlight the current options available for gene transfer along with the advantages and limitations of every method.
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Affiliation(s)
- Nilofer Sayed
- Department of Pharmacy, Pravara Rural Education Society's (P.R.E.S.'s) College of Pharmacy, Shreemati Nathibai Damodar Thackersey (SNDT) Women's University, Nashik 400020, Maharashtra, India
| | - Prince Allawadhi
- Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT), Roorkee, Roorkee, Uttarakhand 247667, India
| | - Amit Khurana
- Centre for Biomedical Engineering (CBME), Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi 110016, India; Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Rajendranagar, Hyderabad 500030, Telangana, India; Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal 506166, Telangana, India; Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Pauwelsstr. 30, D-52074 Aachen, Germany.
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT), Roorkee, Roorkee, Uttarakhand 247667, India
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda 151401, Punjab, India
| | | | - Isha Khurana
- Department of Pharmaceutical Chemistry, University Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh 160014, India
| | - Anil Kumar Banothu
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Rajendranagar, Hyderabad 500030, Telangana, India
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH Aachen University Hospital, Pauwelsstr. 30, D-52074 Aachen, Germany.
| | - Kala Kumar Bharani
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science (CVSc), PVNRTVU, Mamnoor, Warangal 506166, Telangana, India.
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12
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Masterson CH, Ceccato A, Artigas A, Dos Santos C, Rocco PR, Rolandsson Enes S, Weiss DJ, McAuley D, Matthay MA, English K, Curley GF, Laffey JG. Mesenchymal stem/stromal cell-based therapies for severe viral pneumonia: therapeutic potential and challenges. Intensive Care Med Exp 2021; 9:61. [PMID: 34970706 PMCID: PMC8718182 DOI: 10.1186/s40635-021-00424-5] [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] [Received: 10/11/2021] [Accepted: 11/21/2021] [Indexed: 12/15/2022] Open
Abstract
Severe viral pneumonia is a significant cause of morbidity and mortality globally, whether due to outbreaks of endemic viruses, periodic viral epidemics, or the rarer but devastating global viral pandemics. While limited anti-viral therapies exist, there is a paucity of direct therapies to directly attenuate viral pneumonia-induced lung injury, and management therefore remains largely supportive. Mesenchymal stromal/stem cells (MSCs) are receiving considerable attention as a cytotherapeutic for viral pneumonia. Several properties of MSCs position them as a promising therapeutic strategy for viral pneumonia-induced lung injury as demonstrated in pre-clinical studies in relevant models. More recently, early phase clinical studies have demonstrated a reassuring safety profile of these cells. These investigations have taken on an added importance and urgency during the COVID-19 pandemic, with multiple trials in progress across the globe. In parallel with clinical translation, strategies are being investigated to enhance the therapeutic potential of these cells in vivo, with different MSC tissue sources, specific cellular products including cell-free options, and strategies to ‘licence’ or ‘pre-activate’ these cells, all being explored. This review will assess the therapeutic potential of MSC-based therapies for severe viral pneumonia. It will describe the aetiology and epidemiology of severe viral pneumonia, describe current therapeutic approaches, and examine the data suggesting therapeutic potential of MSCs for severe viral pneumonia in pre-clinical and clinical studies. The challenges and opportunities for MSC-based therapies will then be considered.
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Affiliation(s)
- C H Masterson
- Anaesthesia, School of Medicine, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute, National University of Ireland, Galway, Ireland
| | - A Ceccato
- Intensive Care Unit, Hospital Universitari Sagrat Cor, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Sabbadell, Spain
| | - A Artigas
- CIBER de Enfermedades Respiratorias (CIBERES), Sabbadell, Spain.,Critical Center, Corporacion Sanitaria Universitaria Parc Tauli, Autonomous University of Barcelona, Sabadell, Spain
| | - C Dos Santos
- Keenan Center for Biomedical Research, St. Michael's Hospital, Bond St, Toronto, Canada.,Interdepartmental Division of Critical Care Medicine and Institutes of Medical Sciences, University of Toronto, Toronto, Canada
| | - P R Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology for Regenerative Medicine, Rio de Janeiro, Brazil
| | - S Rolandsson Enes
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, Lund, Sweden
| | - D J Weiss
- Department of Medicine, University of Vermont College of Medicine, Burlington, VT, 05405, USA
| | - D McAuley
- Regional Intensive Care Unit, Royal Victoria Hospital, Belfast, UK.,Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - M A Matthay
- Department of Medicine and Anesthesia, University of California, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - K English
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - G F Curley
- Anaesthesia, School of Medicine, Royal College of Surgeons in Ireland, Dublin 9, Ireland
| | - J G Laffey
- Anaesthesia, School of Medicine, National University of Ireland, Galway, Ireland. .,Regenerative Medicine Institute, National University of Ireland, Galway, Ireland. .,Department of Anaesthesia and Intensive Care Medicine, Galway University Hospitals, Saolta University Hospital Group, Galway, Ireland.
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13
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Chera JS, Kumar S, Vats A, Kushwaha P, Behera M, De S. PU.1 is involved in the transcriptional up-regulation of RNA and DNA sensing pathway genes in buffalo fibroblasts. Vet Immunol Immunopathol 2021; 242:110349. [PMID: 34695651 DOI: 10.1016/j.vetimm.2021.110349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/26/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022]
Abstract
PU.1, CEBPA, and CEBPB are Lineage Determining Transcription Factors (LDTFs) that play roles in biological processes such as cell differentiation and the immune system regulation including the innate immune pathways. The roles of these LDTFs in the innate RNA and DNA sensing pathways have received little attention. We show that in buffalo fibroblasts, PU.1 causes the mRNA up-regulation of the RNA and DNA sensors such as RIG-I (65.1 fold), MDA5 (20.4 fold), IFI16-l (8.0 fold), and cGAS (60.5 fold) while CEBPA does the same but to a lesser extent (RIG-I-26.4 fold, MDA5-10.8 fold, IFI16-l- 3.3 fold and cGAS-8.6 fold). CEBPB does not appear to have a role in the up-regulation of these genes. PU.1 expression also primes the cells to develop a strong immune response against the dsRNA virus mimic polyinosinic:polycytidylic acid (poly I:C) by significantly up-regulating Interferon-β (14.9 fold change with p-value <0.0001). CEBPA up-regulates Interferon-β to a lower level than PU.1 (4.7 fold change with p-value 0.0024), whereas CEBPB exhibits non-significant up-regulation (2.1 fold with p-value of 0.1449). As PU.1 robustly up-regulates the nucleic acid sensing pathways, it can prove to be useful in improving the defence against viruses that can cause losses to animal husbandry.
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Affiliation(s)
- Jatinder Singh Chera
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sushil Kumar
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Ashutosh Vats
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Parmanand Kushwaha
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Manisha Behera
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sachinandan De
- Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India.
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14
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Verdaguer N, Ferrero DS. Special Issue: "Viral Replication Complexes". Viruses 2021; 13:v13101902. [PMID: 34696332 PMCID: PMC8539102 DOI: 10.3390/v13101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
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