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Xia C, Wang T, Hahm B. Triggering Degradation of Host Cellular Proteins for Robust Propagation of Influenza Viruses. Int J Mol Sci 2024; 25:4677. [PMID: 38731896 PMCID: PMC11083682 DOI: 10.3390/ijms25094677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Following infection, influenza viruses strive to establish a new host cellular environment optimized for efficient viral replication and propagation. Influenza viruses use or hijack numerous host factors and machinery not only to fulfill their own replication process but also to constantly evade the host's antiviral and immune response. For this purpose, influenza viruses appear to have formulated diverse strategies to manipulate the host proteins or signaling pathways. One of the most effective tactics is to specifically induce the degradation of the cellular proteins that are detrimental to the virus life cycle. Here, we summarize the cellular factors that are deemed to have been purposefully degraded by influenza virus infection. The focus is laid on the mechanisms for the protein ubiquitination and degradation in association with facilitated viral amplification. The fate of influenza viral infection of hosts is heavily reliant on the outcomes of the interplay between the virus and the host antiviral immunity. Understanding the processes of how influenza viruses instigate the protein destruction pathways could provide a foundation for the development of advanced therapeutics to target host proteins and conquer influenza.
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Affiliation(s)
- Chuan Xia
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Ting Wang
- Department of Bioengineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China;
| | - Bumsuk Hahm
- Departments of Surgery & Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212, USA
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2
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Yuan J, Pan J, Zhang X, Gao R. TRIM21 reduces H1N1-induced inflammation and apoptosis by regulating the TBK1-IRF3 signaling pathway in A549 cells. Arch Virol 2024; 169:74. [PMID: 38480558 DOI: 10.1007/s00705-024-05989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/29/2023] [Indexed: 04/10/2024]
Abstract
Triple motif protein 21 (TRIM21) has an antiviral function that inhibits various viral infections. However, its role in the progress of influenza A virus (IAV) infection is unclear. In this study, we investigated the role and molecular mechanism of TRIM21 in IAV infection. RT-qPCR was used to determine the level of TRIM21 mRNA, and ELISA was used to measure the levels of IFN-α, IFN-β, IL-6, and TNF-α. The levels of the TRIM21, NP, TBK1, IRF3, p-TBK1, and p-IRF3 proteins were estimated by Western blot. The results showed that, after IAV infection, TRIM21 was upregulated in clinical patient serum and A549 cells, and this was correlated with the IFN response. Overexpression of TRIM21 reduced IAV replication and transcription in in vitro cell experiments. TRIM21 also increased IFN-α and IFN-β levels and decreased IL-6 and TNF-α levels in A549 cells. In addition, overexpression of TRIM21 inhibited IAV-induced apoptosis. Further experiments demonstrated that TBK1-IRF3 signaling was activated by TRIM21 and was involved in the inhibitory effect of TRIM21 on virus replication. In summary, our study suggests that TRIM21 inhibits viral replication by activating the TBK1-IRF3 signaling pathway, further inhibiting the infection process of IAV.
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Affiliation(s)
- Juan Yuan
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China
| | - Jianli Pan
- The Special Department, Xi'an Children's Hospital, Xi'an, 710003, Shaanxi, China
| | - Xiaofang Zhang
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China
| | - Rui Gao
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China.
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3
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Yin L, Liu X, Yao Y, Yuan M, Luo Y, Zhang G, Pu J, Liu P. Gut microbiota-derived butyrate promotes coronavirus TGEV infection through impairing RIG-I-triggered local type I interferon responses via class I HDAC inhibition. J Virol 2024; 98:e0137723. [PMID: 38197629 PMCID: PMC10878070 DOI: 10.1128/jvi.01377-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024] Open
Abstract
Gut microbiota-derived metabolites are important for the replication and pathogenesis of many viruses. However, the roles of bacterial metabolites in swine enteric coronavirus (SECoV) infection remain poorly understood. Recent studies show that SECoVs infection in vivo significantly alters the composition of short-chain fatty acids (SCFAs)-producing gut microbiota. This prompted us to investigate whether and how SCFAs impact SECoV infection. Employing alphacoronavirus transmissible gastroenteritis virus (TGEV), a major cause of diarrhea in piglets, as a model, we found that SCFAs, particularly butyrate, enhanced TGEV infection both in porcine intestinal epithelial cells and swine testicular (ST) cells at the late stage of viral infection. This effect depended on the inhibited productions of virus-induced type I interferon (IFN) and downstream antiviral IFN-stimulated genes (ISGs) by butyrate. Mechanistically, butyrate suppressed the expression of retinoic acid-inducible gene I (RIG-I), a key viral RNA sensor, and downstream mitochondrial antiviral-signaling (MAVS) aggregation, thereby impairing type I IFN responses and increasing TGEV replication. Using pharmacological and genetic approaches, we showed that butyrate inhibited RIG-I-induced type I IFN signaling by suppressing class I histone deacetylase (HDAC). In summary, we identified a novel mechanism where butyrate enhances TGEV infection by suppressing RIG-I-mediated type I IFN responses. Our findings highlight that gut microbiota-derived metabolites like butyrate can be exploited by SECoV to dampen innate antiviral immunity and establish infection in the intestine.IMPORTANCESwine enteric coronaviruses (SECoVs) infection in vivo alters the composition of short-chain fatty acids (SCFAs)-producing gut microbiota, but whether microbiota-derived SCFAs impact coronavirus gastrointestinal infection is largely unknown. Here, we demonstrated that SCFAs, particularly butyrate, substantially increased alphacoronavirus TGEV infection at the late stage of infection, without affecting viral attachment or internalization. Furthermore, enhancement of TGEV by butyrate depended on impeding virus-induced type I interferon (IFN) responses. Mechanistically, butyrate suppressed the cytoplasmic viral RNA sensor RIG-I expression and downstream type I IFN signaling activation by inhibiting class I HDAC, thereby promoting TGEV infection. Our work reveals novel functions of gut microbiota-derived SCFAs in enhancing enteric coronavirus infection by impairing RIG-I-dependent type I IFN responses. This implies that bacterial metabolites could be therapeutic targets against SECoV infection by modulating antiviral immunity in the intestine.
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Affiliation(s)
- Lingdan Yin
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiang Liu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yao Yao
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Mengqi Yuan
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yi Luo
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Juan Pu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Pinghuang Liu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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4
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Husain M. Influenza Virus Host Restriction Factors: The ISGs and Non-ISGs. Pathogens 2024; 13:127. [PMID: 38392865 PMCID: PMC10893265 DOI: 10.3390/pathogens13020127] [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: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza virus has been one of the most prevalent and researched viruses globally. Consequently, there is ample information available about influenza virus lifecycle and pathogenesis. However, there is plenty yet to be known about the determinants of influenza virus pathogenesis and disease severity. Influenza virus exploits host factors to promote each step of its lifecycle. In turn, the host deploys antiviral or restriction factors that inhibit or restrict the influenza virus lifecycle at each of those steps. Two broad categories of host restriction factors can exist in virus-infected cells: (1) encoded by the interferon-stimulated genes (ISGs) and (2) encoded by the constitutively expressed genes that are not stimulated by interferons (non-ISGs). There are hundreds of ISGs known, and many, e.g., Mx, IFITMs, and TRIMs, have been characterized to restrict influenza virus infection at different stages of its lifecycle by (1) blocking viral entry or progeny release, (2) sequestering or degrading viral components and interfering with viral synthesis and assembly, or (3) bolstering host innate defenses. Also, many non-ISGs, e.g., cyclophilins, ncRNAs, and HDACs, have been identified and characterized to restrict influenza virus infection at different lifecycle stages by similar mechanisms. This review provides an overview of those ISGs and non-ISGs and how the influenza virus escapes the restriction imposed by them and aims to improve our understanding of the host restriction mechanisms of the influenza virus.
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Affiliation(s)
- Matloob Husain
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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5
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Lefkowitz RB, Miller CM, Martinez-Caballero JD, Ramos I. Epigenetic Control of Innate Immunity: Consequences of Acute Respiratory Virus Infection. Viruses 2024; 16:197. [PMID: 38399974 PMCID: PMC10893272 DOI: 10.3390/v16020197] [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: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by acute respiratory viruses induce a systemic innate immune response, which can be measured by the increased levels of expression of inflammatory genes in immune cells. There is growing evidence that these acute viral infections, alongside transient transcriptomic responses, induce epigenetic remodeling as part of the immune response, such as DNA methylation and histone modifications, which might persist after the infection is cleared. In this article, we first review the primary mechanisms of epigenetic remodeling in the context of innate immunity and inflammation, which are crucial for the regulation of the immune response to viral infections. Next, we delve into the existing knowledge concerning the impact of respiratory virus infections on the epigenome, focusing on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Influenza A Virus (IAV), and Respiratory Syncytial Virus (RSV). Finally, we offer perspectives on the potential consequences of virus-induced epigenetic remodeling and open questions in the field that are currently under investigation.
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Affiliation(s)
- Rivka Bella Lefkowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan David Martinez-Caballero
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Husain M. Influenza A Virus and Acetylation: The Picture Is Becoming Clearer. Viruses 2024; 16:131. [PMID: 38257831 PMCID: PMC10820114 DOI: 10.3390/v16010131] [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: 12/25/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Influenza A virus (IAV) is one of the most circulated human pathogens, and influenza disease, commonly known as the flu, remains one of the most recurring and prevalent infectious human diseases globally. IAV continues to challenge existing vaccines and antiviral drugs via its ability to evolve constantly. It is critical to identify the molecular determinants of IAV pathogenesis to understand the basis of flu severity in different populations and design improved antiviral strategies. In recent years, acetylation has been identified as one of the determinants of IAV pathogenesis. Acetylation was originally discovered as an epigenetic protein modification of histones. But, it is now known to be one of the ubiquitous protein modifications of both histones and non-histone proteins and a determinant of proteome complexity. Since our first observation in 2007, significant progress has been made in understanding the role of acetylation during IAV infection. Now, it is becoming clearer that acetylation plays a pro-IAV function via at least three mechanisms: (1) by reducing the host's sensing of IAV infection, (2) by dampening the host's innate antiviral response against IAV, and (3) by aiding the stability and function of viral and host proteins during IAV infection. In turn, IAV antagonizes the host deacetylases, which erase acetylation, to facilitate its replication. This review provides an overview of the research progress made on this subject so far and outlines research prospects for the significance of IAV-acetylation interplay.
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Affiliation(s)
- Matloob Husain
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
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Chen R, Han X, Xu H, Xu J, Cao T, Shan Y, He F, Fang W, Li X. N-terminal domain of classical swine fever virus N pro induces proteasomal degradation of specificity protein 1 with reduced HDAC1 expression to evade from innate immune responses. J Virol 2023; 97:e0111523. [PMID: 37796122 PMCID: PMC10617410 DOI: 10.1128/jvi.01115-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Of the flaviviruses, only CSFV and bovine viral diarrhea virus express Npro as the non-structural protein which is not essential for viral replication but functions to dampen host innate immunity. We have deciphered a novel mechanism with which CSFV uses to evade the host antiviral immunity by the N-terminal domain of its Npro to facilitate proteasomal degradation of Sp1 with subsequent reduction of HDAC1 and ISG15 expression. This is distinct from earlier findings involving Npro-mediated IRF3 degradation via the C-terminal domain. This study provides insights for further studies on how HDAC1 plays its role in antiviral immunity, and if and how other viral proteins, such as the core protein of CSFV, the nucleocapsid protein of porcine epidemic diarrhea virus, or even other coronaviruses, exert antiviral immune responses via the Sp1-HDAC1 axis. Such research may lead to a deeper understanding of viral immune evasion strategies as part of their pathogenetic mechanisms.
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Affiliation(s)
- Rong Chen
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Xiao Han
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Hankun Xu
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Jidong Xu
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Tong Cao
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Ying Shan
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Fang He
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Weihuan Fang
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
| | - Xiaoliang Li
- Zhejiang University Institute of Preventive Veterinary Medicine & Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
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8
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Rehman UU, Ghafoor D, Ullah A, Ahmad R, Hanif S. Epigenetics regulation during virus-host interaction and their effects on the virus and host cell. Microb Pathog 2023; 182:106271. [PMID: 37517745 DOI: 10.1016/j.micpath.2023.106271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/07/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Epigenetics, a field of study focused on cellular gene regulation independent of DNA sequence alterations, encompasses DNA methylation, histone modification and microRNA modification. Epigenetics processes play a pivotal role in governing the life cycles of viruses, enabling their transmission, persistence, and maintenance with in host organisms. This review examines the epigenetics regulation of diverse virus including orthomoxyviruses, coronavirus, retroviridae, mononegavirales, and poxviruses among others. The investigation encompasses ten representative viruses from these families. Detailed exploration of the epigenetic mechanisms underlying each virus type, involving miRNA modification, histone modification and DNA methylation, sheds light on the intricate and multifaceted epigenetic interplay between viruses and their hosts. Furthermore, this review investigates the influence of these epigenetic processes on infection cycles, emphasizing the utilization of epigenetics by viruses such as Epstein-Barr virus and Human immunodeficiency virus (HIV) to regulate gene expression during chronic or latent infections, control latency, and transition to lytic infection. Finally, the paper explores the novel treatments possibilities stemming from this epigenetic understanding.
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Affiliation(s)
- Ubaid Ur Rehman
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Dawood Ghafoor
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430064, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Asad Ullah
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Riaz Ahmad
- Medical Genetics Research Laboratory, Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Sumaira Hanif
- Department of Biological Sciences, International Islamic University, Islamabad, 45320, Pakistan
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Donnarumma F, Tucci V, Ambrosino C, Altucci L, Carafa V. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Clin Epigenetics 2022; 14:182. [PMID: 36539894 PMCID: PMC9769039 DOI: 10.1186/s13148-022-01402-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Chromatin structural organization, gene expression and proteostasis are intricately regulated in a wide range of biological processes, both physiological and pathological. Protein acetylation, a major post-translational modification, is tightly involved in interconnected biological networks, modulating the activation of gene transcription and protein action in cells. A very large number of studies describe the pivotal role of the so-called acetylome (accounting for more than 80% of the human proteome) in orchestrating different pathways in response to stimuli and triggering severe diseases, including cancer. NAA60/NatF (N-terminal acetyltransferase F), also named HAT4 (histone acetyltransferase type B protein 4), is a newly discovered acetyltransferase in humans modifying N-termini of transmembrane proteins starting with M-K/M-A/M-V/M-M residues and is also thought to modify lysine residues of histone H4. Because of its enzymatic features and unusual cell localization on the Golgi membrane, NAA60 is an intriguing acetyltransferase that warrants biochemical and clinical investigation. Although it is still poorly studied, this review summarizes current findings concerning the structural hallmarks and biological role of this novel targetable epigenetic enzyme.
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Affiliation(s)
- Federica Donnarumma
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy
| | - Valeria Tucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Concetta Ambrosino
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.47422.370000 0001 0724 3038Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Lucia Altucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Vincenzo Carafa
- grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
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Xu M, Xia S, Wang M, Liu X, Li X, Chen W, Wang Y, Li H, Xia C, Chen J, Wu J. Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection. PLoS Pathog 2022; 18:e1010794. [PMID: 36070294 PMCID: PMC9451060 DOI: 10.1371/journal.ppat.1010794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/04/2022] [Indexed: 11/18/2022] Open
Abstract
Influenza virus has the ability to circumvent host innate immune system through regulating certain host factors for its effective propagation. However, the detailed mechanism is still not fully understood. Here, we report that a host sphingolipid metabolism-related factor, sphingosine kinase 2 (SPHK2), upregulated during influenza A virus (IAV) infection, promotes IAV infection in an enzymatic independent manner. The enhancement of the virus replication is not abolished in the catalytic-incompetent SPHK2 (G212E) overexpressing cells. Intriguingly, the sphingosine-1-phosphate (S1P) related factor HDAC1 also plays a crucial role in SPHK2-mediated IAV infection. We found that SPHK2 cannot facilitate IAV infection in HDAC1 deficient cells. More importantly, SPHK2 overexpression diminishes the IFN-β promoter activity upon IAV infection, resulting in the suppression of type I IFN signaling. Furthermore, ChIP-qPCR assay revealed that SPHK2 interacts with IFN-β promoter through the binding of demethylase TET3, but not with the other promoters regulated by TET3, such as TGF-β1 and IL6 promoters. The specific regulation of SPHK2 on IFN-β promoter through TET3 can in turn recruit HDAC1 to the IFN-β promoter, enhancing the deacetylation of IFN-β promoter, therefore leading to the inhibition of IFN-β transcription. These findings reveal an enzymatic independent mechanism on host SPHK2, which associates with TET3 and HDAC1 to negatively regulate type I IFN expression and thus facilitates IAV propagation.
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Affiliation(s)
- Mengqiong Xu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Sisi Xia
- Department of Biological Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Mei Wang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xiaolian Liu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Xin Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Weijie Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Yaohao Wang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
| | - Hongjian Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Chuan Xia
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, China
- College of Basic Medical Sciences, Dalian Medical University, Dalian, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Jun Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, Guangdong, China
- * E-mail: (HL); (CX); (JC); (JW)
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
- Foshan Institute of Medical Microbiology, Foshan, Guangdong, China
- * E-mail: (HL); (CX); (JC); (JW)
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Abstract
Protein acetylation plays an important role during virus infection. Thus, it is not surprising that viruses always evolve elaborate mechanisms to regulate the functions of histone deacetylases (HDACs), the essential transcriptional and epigenetic regulators for deacetylation. Porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus, causes severe diarrhea in suckling piglets and has the potential to infect humans. In this study, we found that PDCoV infection inhibited cellular HDAC activity. By screening the expressions of different HDAC subfamilies after PDCoV infection, we unexpectedly found that HDAC2 was cleaved. Ectopic expression of HDAC2 significantly inhibited PDCoV replication, while the reverse effects could be observed after treatment with an HDAC2 inhibitor (CAY10683) or the knockdown of HDAC2 expression by specific siRNA. Furthermore, we demonstrated that PDCoV-encoded nonstructural protein 5 (nsp5), a 3C-like protease, was responsible for HDAC2 cleavage through its protease activity. Detailed analyses showed that PDCoV nsp5 cleaved HDAC2 at glutamine 261 (Q261), and the cleaved fragments (amino acids 1 to 261 and 262 to 488) lost the ability to inhibit PDCoV replication. Interestingly, the Q261 cleavage site is highly conserved in HDAC2 homologs from other mammalian species, and the nsp5s encoded by seven tested mammalian coronaviruses also cleaved HDAC2, suggesting that cleaving HDAC2 may be a common strategy used by different mammalian coronaviruses to antagonize the antiviral role of HDAC2. IMPORTANCE As an emerging porcine enteropathogenic coronavirus that possesses the potential to infect humans, porcine deltacoronavirus (PDCoV) is receiving increasing attention. In this work, we found that PDCoV infection downregulated cellular histone deacetylase (HDAC) activity. Of particular interest, the viral 3C-like protease, encoded by the PDCoV nonstructural protein 5 (nsp5), cleaved HDAC2, and this cleavage could be observed in the context of PDCoV infection. Furthermore, the cleavage of HDAC2 appears to be a common strategy among mammalian coronaviruses, including the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), to antagonize the antiviral role of HDAC2. To our knowledge, PDCoV nsp5 is the first identified viral protein that can cleave cellular HDAC2. Results from our study provide new targets to develop drugs combating coronavirus infection.
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12
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Prescott L. SARS-CoV-2 3CLpro whole human proteome cleavage prediction and enrichment/depletion analysis. Comput Biol Chem 2022; 98:107671. [PMID: 35429835 PMCID: PMC8958254 DOI: 10.1016/j.compbiolchem.2022.107671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
A novel coronavirus (SARS-CoV-2) has devastated the globe as a pandemic that has killed millions of people. Widespread vaccination is still uncertain, so many scientific efforts have been directed toward discovering antiviral treatments. Many drugs are being investigated to inhibit the coronavirus main protease, 3CLpro, from cleaving its viral polyprotein, but few publications have addressed this protease’s interactions with the host proteome or their probable contribution to virulence. Too few host protein cleavages have been experimentally verified to fully understand 3CLpro’s global effects on relevant cellular pathways and tissues. Here, I set out to determine this protease’s targets and corresponding potential drug targets. Using a neural network trained on cleavages from 392 coronavirus proteomes with a Matthews correlation coefficient of 0.985, I predict that a large proportion of the human proteome is vulnerable to 3CLpro, with 4898 out of approximately 20,000 human proteins containing at least one putative cleavage site. These cleavages are nonrandomly distributed and are enriched in the epithelium along the respiratory tract, brain, testis, plasma, and immune tissues and depleted in olfactory and gustatory receptors despite the prevalence of anosmia and ageusia in COVID-19 patients. Affected cellular pathways include cytoskeleton/motor/cell adhesion proteins, nuclear condensation and other epigenetics, host transcription and RNAi, ribosomal stoichiometry and nascent-chain detection and degradation, ubiquitination, pattern recognition receptors, coagulation, lipoproteins, redox, and apoptosis. This whole proteome cleavage prediction demonstrates the importance of 3CLpro in expected and nontrivial pathways affecting virulence, lead me to propose more than a dozen potential therapeutic targets against coronaviruses, and should therefore be applied to all viral proteases and subsequently experimentally verified.
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Histone deacetylase 3 contributes to the antiviral innate immunity of macrophages by interacting with FOXK1 to regulate STAT1/2 transcription. Cell Rep 2022; 38:110302. [PMID: 35081346 DOI: 10.1016/j.celrep.2022.110302] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 11/16/2021] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
It is well known that interferon (IFN)-α/-β activates the JAK/STAT signaling pathway and suppresses viral replication through the induction of IFN stimulated genes (ISGs). Here, we report that knockout of HDAC3 from macrophages results in the decreased expression of STAT1 and STAT2, leading to defective antiviral immunity in cells and mice. Further studies show that HDAC3 interacts with a conserved transcription factor Forkhead Box K1 (FOXK1), co-localizes with FOXK1 at the promoter of STAT1 and STAT2, and is required for protecting FOXK1 from lysosomal system-mediated degradation. FOXK1-deficient macrophages also show low STAT1 and STAT2 expression with defective responses to viruses. Thus, our studies uncover the biological importance of HDAC3 in regulating the antiviral immunity of macrophages through interacting with FOXK1 to regulate the expression of STAT1 and STAT2.
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14
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Ahmed F, Husain M. Human N-Alpha-Acetyltransferase 60 Promotes Influenza A Virus Infection by Dampening the Interferon Alpha Signaling. Front Immunol 2022; 12:771792. [PMID: 35095845 PMCID: PMC8790067 DOI: 10.3389/fimmu.2021.771792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
N-alpha-acetyltransferase 60 (NAA60) is the most recently discovered N-terminal acetyltransferase and found only in multicellular eukaryotes. NAA60 localizes to the Golgi complex and is one of the only two N-terminal acetyltransferases known to localize to an organelle. Furthermore, NAA60 possesses a unique ability of catalyzing the acetylation of membrane-anchored proteins at the N-terminus and histones at the lysine side chains. Herein, we demonstrate that NAA60 exhibits proviral properties during influenza A virus (IAV) infection by interfering with the interferon (IFN) α signaling. We found that the depletion and overexpression of NAA60 reduced and enhanced, respectively, the IAV growth in a cell type- and IAV strain-independent manner. Mechanistically, the IAV-induced expression of IFNα was increased and decreased in NAA60-depleted and -overexpressing cells, respectively. Furthermore, the depletion of NAA60 enhanced the level of phosphorylated STAT1 transcription factor as well as the expression of several IFN-stimulated genes (ISGs) such as MX1, CH25H, IFITM3, ISG15 and viperin in infected cells. Whereas the overexpression of NAA60 produced opposite results. Finally, similar results were obtained when the NAA60-depleted cells were treated with purified IFNα. These findings, in conjunction with our recent findings where N-terminal acetylation of many host proteins increased in response to the IAV infection, indicate an important role of N-terminal acetylation during IAV replication.
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15
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Shiimori M, Nukiwa R, Imai Y. Dynamics of the host chromatin three-dimensional response to influenza virus infection. Int Immunol 2021; 33:541-545. [PMID: 34282455 DOI: 10.1093/intimm/dxab043] [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: 06/02/2021] [Accepted: 07/19/2021] [Indexed: 11/14/2022] Open
Abstract
The spatial organization of chromatin is known to be highly dynamic in response to environmental stress. However, it remains unknown how chromatin dynamics contributes to or modulates the pathogenesis of immune and infectious diseases. Influenza virus is a single-stranded RNA virus, and transcription and replication of the virus genome occur in the nucleus. Since viral infection is generally associated with virus-driven hijack of the host cellular machineries, influenza virus may utilize and/or affect the nuclear system. In this review article, we focus on recent studies showing that the three-dimensional structure of chromatin changes with influenza virus infection, which affects the pathology of infection. Also, we discuss studies showing the roles of epigenetics in influenza virus infection. Understanding how this affects immune responses may lead to novel strategies to combat immune and infectious diseases.
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Affiliation(s)
- Masami Shiimori
- Laboratory of Regulation for Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Ryota Nukiwa
- Laboratory of Regulation for Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
| | - Yumiko Imai
- Laboratory of Regulation for Intractable Infectious Diseases, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka 567-0085, Japan
- Laboratory for Infectious Systems, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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16
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Porcine Epidemic Diarrhea Virus Inhibits HDAC1 Expression To Facilitate Its Replication via Binding of Its Nucleocapsid Protein to Host Transcription Factor Sp1. J Virol 2021; 95:e0085321. [PMID: 34232065 DOI: 10.1128/jvi.00853-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus causing acute intestinal infection in pigs, with high mortality often seen in neonatal pigs. The newborns rely on innate immune responses against invading pathogens because of lacking adaptive immunity. However, how PEDV disables the innate immunity of newborns toward severe infection remains unknown. We found that PEDV infection led to reduced expression of histone deacetylases (HDACs), especially HDAC1, in porcine IPEC-J2 cells. HDACs are considered important regulators of innate immunity. We hypothesized that PEDV interacts with certain host factors to regulate HDAC1 expression in favor of its replication. We show that HDAC1 acted as a negative regulator of PEDV replication in IPEC-J2 cells, as shown by chemical inhibition, gene knockout, and overexpression. A GC-box (GCCCCACCCCC) within the HDAC1 promoter region was identified for Sp1 binding in IPEC-J2 cells. Treatment of the cells with Sp1 inhibitor mithramycin A inhibited HDAC1 expression, indicating direct regulation of HDAC1 expression by Sp1. Of the viral proteins that were overexpressed in IPEC-J2 cells, the N protein was found to be present in the nuclei and more inhibitory to HDAC1 transcription. The putative nuclear localization sequence 261PKKNKSR267 contributed to its nuclear localization. The N protein interacted with Sp1 and interfered with its binding to the promoter region, thereby inhibiting its transcriptional activity for HDAC1 expression. Our findings reveal a novel mechanism of PEDV evasion of the host responses, offering implications for studying the infection processes of other coronaviruses. IMPORTANCE The enteric coronavirus porcine epidemic diarrhea virus (PEDV) causes fatal acute intestinal infection in neonatal pigs that rely on innate immune responses. Histone deacetylases (HDACs) play important roles in innate immune regulation. Our study found PEDV suppresses HDAC1 expression via the interaction of its N protein and porcine Sp1, which identified a novel mechanism of PEDV evasion of the host responses to benefit its replication. This study suggests that other coronaviruses, including SARS-CoV and SARS-CoV-2, also make use of their N proteins to intercept the host immune responses in favor of their infection.
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17
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Acetylation, Methylation and Allysine Modification Profile of Viral and Host Proteins during Influenza A Virus Infection. Viruses 2021; 13:v13071415. [PMID: 34372620 PMCID: PMC8310381 DOI: 10.3390/v13071415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/08/2021] [Accepted: 07/18/2021] [Indexed: 12/18/2022] Open
Abstract
Protein modifications dynamically occur and regulate biological processes in all organisms. Towards understanding the significance of protein modifications in influenza virus infection, we performed a global mass spectrometry screen followed by bioinformatics analyses of acetylation, methylation and allysine modification in human lung epithelial cells in response to influenza A virus infection. We discovered 8 out of 10 major viral proteins and 245 out of 2280 host proteins detected to be differentially modified by three modifications in infected cells. Some of the identified proteins were modified on multiple amino acids residues and by more than one modification; the latter occurred either on different or same residues. Most of the modified residues in viral proteins were conserved across >40 subtypes of influenza A virus, and influenza B or C viruses and located on the protein surface. Importantly, many of those residues have already been determined to be critical for the influenza A virus. Similarly, many modified residues in host proteins were conserved across influenza A virus hosts like humans, birds, and pigs. Finally, host proteins undergoing the three modifications clustered in common functional networks of metabolic, cytoskeletal, and RNA processes, all of which are known to be exploited by the influenza A virus.
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18
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Keshavarz M, Sabbaghi A, Koushki K, Miri SM, Sarshari B, Vahdat K, Ghaemi A. Epigenetic reprogramming mechanisms of immunity during influenza A virus infection. Microbes Infect 2021; 23:104831. [PMID: 33878459 DOI: 10.1016/j.micinf.2021.104831] [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: 09/30/2020] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
This paper reviews epigenetic mechanisms by which influenza viruses affect cellular gene activity to control their life cycles, aiming to provide new insights into the complexity of functional interactions between viral and cellular factors, as well as to introduce novel targets for therapeutic intervention and vaccine development against influenza infections.
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Affiliation(s)
- Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Ailar Sabbaghi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Khadijeh Koushki
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Miri
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Behrang Sarshari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Katayoun Vahdat
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
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19
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McKellar J, Rebendenne A, Wencker M, Moncorgé O, Goujon C. Mammalian and Avian Host Cell Influenza A Restriction Factors. Viruses 2021; 13:522. [PMID: 33810083 PMCID: PMC8005160 DOI: 10.3390/v13030522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022] Open
Abstract
The threat of a new influenza pandemic is real. With past pandemics claiming millions of lives, finding new ways to combat this virus is essential. Host cells have developed a multi-modular system to detect incoming pathogens, a phenomenon called sensing. The signaling cascade triggered by sensing subsequently induces protection for themselves and their surrounding neighbors, termed interferon (IFN) response. This response induces the upregulation of hundreds of interferon-stimulated genes (ISGs), including antiviral effectors, establishing an antiviral state. As well as the antiviral proteins induced through the IFN system, cells also possess a so-called intrinsic immunity, constituted of antiviral proteins that are constitutively expressed, creating a first barrier preceding the induction of the interferon system. All these combined antiviral effectors inhibit the virus at various stages of the viral lifecycle, using a wide array of mechanisms. Here, we provide a review of mammalian and avian influenza A restriction factors, detailing their mechanism of action and in vivo relevance, when known. Understanding their mode of action might help pave the way for the development of new influenza treatments, which are absolutely required if we want to be prepared to face a new pandemic.
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Affiliation(s)
- Joe McKellar
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Antoine Rebendenne
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Mélanie Wencker
- Centre International de Recherche en Infectiologie, INSERM/CNRS/UCBL1/ENS de Lyon, 69007 Lyon, France;
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, CNRS, Université de Montpellier, CEDEX 5, 34293 Montpellier, France; (J.M.); (A.R.)
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20
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Host factors involved in influenza virus infection. Emerg Top Life Sci 2020; 4:389-398. [PMID: 33210707 DOI: 10.1042/etls20200232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/30/2020] [Indexed: 12/17/2022]
Abstract
Influenza virus causes an acute febrile respiratory disease in humans that is commonly known as 'flu'. Influenza virus has been around for centuries and is one of the most successful, and consequently most studied human viruses. This has generated tremendous amount of data and information, thus it is pertinent to summarise these for, particularly interdisciplinary readers. Viruses are acellular organisms and exist at the interface of living and non-living. Due to this unique characteristic, viruses require another organism, i.e. host to survive. Viruses multiply inside the host cell and are obligate intracellular pathogens, because their relationship with the host is almost always harmful to host. In mammalian cells, the life cycle of a virus, including influenza is divided into five main steps: attachment, entry, synthesis, assembly and release. To complete these steps, some viruses, e.g. influenza utilise all three parts - plasma membrane, cytoplasm and nucleus, of the cell; whereas others, e.g. SARS-CoV-2 utilise only plasma membrane and cytoplasm. Hence, viruses interact with numerous host factors to complete their life cycle, and these interactions are either exploitative or antagonistic in nature. The host factors involved in the life cycle of a virus could be divided in two broad categories - proviral and antiviral. This perspective has endeavoured to assimilate the information about the host factors which promote and suppress influenza virus infection. Furthermore, an insight into host factors that play a dual role during infection or contribute to influenza virus-host adaptation and disease severity has also been provided.
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21
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Stubbs BJ, Koutnik AP, Goldberg EL, Upadhyay V, Turnbaugh PJ, Verdin E, Newman JC. Investigating Ketone Bodies as Immunometabolic Countermeasures against Respiratory Viral Infections. MED 2020; 1:43-65. [PMID: 32838361 PMCID: PMC7362813 DOI: 10.1016/j.medj.2020.06.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Respiratory viral infections remain a scourge, with seasonal influenza infecting millions and killing many thousands annually and viral pandemics, such as COVID-19, recurring every decade. Age, cardiovascular disease, and diabetes mellitus are risk factors for severe disease and death from viral infection. Immunometabolic therapies for these populations hold promise to reduce the risks of death and disability. Such interventions have pleiotropic effects that might not only target the virus itself but also enhance supportive care to reduce cardiopulmonary complications, improve cognitive resilience, and facilitate functional recovery. Ketone bodies are endogenous metabolites that maintain cellular energy but also feature drug-like signaling activities that affect immune activity, metabolism, and epigenetics. Here, we provide an overview of ketone body biology relevant to respiratory viral infection, focusing on influenza A and severe acute respiratory syndrome (SARS)-CoV-2, and discuss the opportunities, risks, and research gaps in the study of exogenous ketone bodies as novel immunometabolic interventions in these diseases.
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Affiliation(s)
| | - Andrew P Koutnik
- Institute for Human and Machine Cognition, Pensacola, FL, USA
- Department of Molecular Pharmacology and Physiology, USF, Tampa, FL, USA
| | | | - Vaibhav Upadhyay
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, UCSF, San Francisco, CA, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - John C Newman
- Buck Institute for Research on Aging, Novato, CA, USA
- Division of Geriatrics, UCSF, San Francisco, CA, USA
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22
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Histone Deacetylase 6 Knockout Mice Exhibit Higher Susceptibility to Influenza A Virus Infection. Viruses 2020; 12:v12070728. [PMID: 32640546 PMCID: PMC7411611 DOI: 10.3390/v12070728] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
The host innate defence against influenza virus infection is an intricate system with a plethora of antiviral factors involved. We have identified host histone deacetylase 6 (HDAC6) as an anti-influenza virus factor in cultured cells. Consistent with this, we report herein that HDAC6 knockout (KO) mice are more susceptible to influenza virus A/PR/8/1934 (H1N1) infection than their wild type (WT) counterparts. The KO mice lost weight faster than the WT mice and, unlike WT mice, could not recover their original body weight. Consequently, more KO mice succumbed to infection, which corresponded with higher lung viral loads. Conversely, the expression of the critical innate antiviral response genes interferon alpha/beta, CD80, CXCL10 and IL15 was significantly downregulated in KO mouse lungs compared to WT mouse lungs. These data are consistent with the known function of HDAC6 of de-acetylating the retinoic acid inducible gene-I (RIG-I) and activating the host innate antiviral response cascade. Loss of HDAC6 thus leads to a blunted innate response and increased susceptibility of mice to influenza A virus infection.
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23
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Nehme Z, Pasquereau S, Herbein G. Targeting histone epigenetics to control viral infections. HISTONE MODIFICATIONS IN THERAPY 2020. [PMCID: PMC7453269 DOI: 10.1016/b978-0-12-816422-8.00011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the past decades, many studies have significantly broadened our understanding of complex virus-host interactions to control chromatin structure and dynamics.1, 2 However, the role and impact of such modifications during viral infections is not fully revealed. Indeed, this type of regulation is bidirectional between the virus and the host. While viral replication and gene expression are significantly impacted by histone modifications on the viral chromatin,3 studies have shown that some viral pathogens dynamically manipulate cellular epigenetic factors to enhance their own survival and pathogenesis, as well as escape the immune system defense lines.4 In this dynamic, histone posttranslational modifications (PTMs) appear to play fundamental roles in the regulation of chromatin structure and recruitment of other factors.5 Genuinely, those PTMs play a vital role in lytic infection, latency reinforcement, or, conversely, viral reactivation.6 In this chapter, we will examine and review the involvement of histone modifications as well as their potential manipulation to control infections during various viral life cycle stages, highlighting their prospective implications in the clinical management of human immunodeficiency virus (HIV), herpes simplex virus (HSV), human cytomegalovirus (HCMV), hepatitis B and C viruses (HBV and HCV, respectively), Epstein–Barr virus (EBV), and other viral diseases. Targeting histone modifications is critical in setting the treatment of chronic viral infections with both lytic and latent stages (HIV, HCMV, HSV, RSV), virus-induced cancers (HBV, HCV, EBV, KSHV, HPV), and epidemic/emerging viruses (e.g. influenza virus, arboviruses).
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24
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Galvin HD, Husain M. Influenza A virus-induced host caspase and viral PA-X antagonize the antiviral host factor, histone deacetylase 4. J Biol Chem 2019; 294:20207-20221. [PMID: 31757810 DOI: 10.1074/jbc.ra119.010650] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
Influenza A virus (IAV) effectively manipulates host machinery to replicate. There is a growing evidence that an optimal acetylation environment in the host cell is favorable to IAV proliferation and vice versa. The histone deacetylases (HDACs), a family of 18 host enzymes classified into four classes, are central to negatively regulating the acetylation level, hence the HDACs would not be favorable to IAV. Indeed, by using the RNAi and overexpression strategies, we found that human HDAC4, a class II member, possesses anti-IAV properties and is a component of host innate antiviral response. We discovered that IAV multiplication was augmented in HDAC4-depleted cells and abated in HDAC4-supplemented cells. Likewise, the expression of IFITM3, ISG15, and viperin, some of the critical markers of host anti-IAV response was abated in HDAC4-depleted cells and augmented in HDAC4-supplemented cells. In turn, IAV strongly antagonizes the HDAC4, by down-regulating its expression both at the mRNA level via viral RNA endonuclease PA-X and at the polypeptide level by inducing its cleavage via host caspase 3 in infected cells. Such HDAC4 polypeptide cleavage resulted in a ∼30 kDa fragment that is also observed in some heterologous systems and may have a significant role in IAV replication.
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Affiliation(s)
- Henry D Galvin
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
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25
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Gatla HR, Muniraj N, Thevkar P, Yavvari S, Sukhavasi S, Makena MR. Regulation of Chemokines and Cytokines by Histone Deacetylases and an Update on Histone Decetylase Inhibitors in Human Diseases. Int J Mol Sci 2019; 20:E1110. [PMID: 30841513 PMCID: PMC6429312 DOI: 10.3390/ijms20051110] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/12/2022] Open
Abstract
Histone acetyltransferases (HATs) and histone deacetylases (HDACs) counteract with each other to regulate gene expression by altering chromatin structure. Aberrant HDAC activity was reported in many human diseases including wide range of cancers, viral infections, cardiovascular complications, auto-immune diseases and kidney diseases. HDAC inhibitors are small molecules designed to block the malignant activity of HDACs. Chemokines and cytokines control inflammation, immunological and other key biological processes and are shown to be involved in various malignancies. Various HDACs and HDAC inhibitors were reported to regulate chemokines and cytokines. Even though HDAC inhibitors have remarkable anti-tumor activity in hematological cancers, they are not effective in treating many diseases and many patients relapse after treatment. However, the role of HDACs and cytokines in regulating these diseases still remain unclear. Therefore, understanding exact mechanisms and effector functions of HDACs are urgently needed to selectively inhibit them and to establish better a platform to combat various malignancies. In this review, we address regulation of chemokines and cytokines by HDACs and HDAC inhibitors and update on HDAC inhibitors in human diseases.
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Affiliation(s)
- Himavanth Reddy Gatla
- Department of Pediatric Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
| | - Nethaji Muniraj
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
| | - Prashanth Thevkar
- Department of Microbiology, New York University, New York, NY 10016, USA.
| | - Siddhartha Yavvari
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Sahithi Sukhavasi
- Center for Distance Learning, GITAM University, Visakhapatnam, AP 530045, India.
| | - Monish Ram Makena
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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26
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Suppression of the SAP18/HDAC1 complex by targeting TRIM56 and Nanog is essential for oncogenic viral FLICE-inhibitory protein-induced acetylation of p65/RelA, NF-κB activation, and promotion of cell invasion and angiogenesis. Cell Death Differ 2019; 26:1970-1986. [PMID: 30670829 DOI: 10.1038/s41418-018-0268-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/14/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Kaposi's sarcoma (KS), a highly invasive and angiogenic tumor of endothelial spindle-shaped cells, is the most common AIDS-associated cancer caused by KS-associated herpesvirus (KSHV) infection. KSHV-encoded viral FLICE-inhibitory protein (vFLIP) is a viral oncogenic protein, but its role in the dissemination and angiogenesis of KSHV-induced cancers remains unknown. Here, we report that vFLIP facilitates cell migration, invasion, and angiogenesis by downregulating the SAP18-HDAC1 complex. vFLIP degrades SAP18 through a ubiquitin-proteasome pathway by recruiting E3 ubiquitin ligase TRIM56. Further, vFLIP represses HDAC1, a protein partner of SAP18, by inhibiting Nanog occupancy on the HDAC1 promoter. Notably, vFLIP impairs the interaction between the SAP18/HDAC1 complex and p65 subunit, leading to enhancement of p65 acetylation and NF-κB activation. Our data suggest a novel mechanism of vFLIP activation of the NF-κB by decreasing the SAP18/HDAC1 complex to promote the acetylation of p65 subunit, which contributes to vFLIP-induced activation of the NF-κB pathway, cell invasion, and angiogenesis. These findings advance our understanding of the mechanism of KSHV-induced pathogenesis, and providing a rationale for therapeutic targeting of the vFLIP/SAP18/HDAC1 complex as a novel strategy of AIDS-KS.
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27
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Nutsford AN, Galvin HD, Ahmed F, Husain M. The Class IV human deacetylase, HDAC11, exhibits anti-influenza A virus properties via its involvement in host innate antiviral response. Cell Microbiol 2018; 21:e12989. [PMID: 30511515 DOI: 10.1111/cmi.12989] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/06/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023]
Abstract
Histone deacetylase 11 (HDAC11) is most recently discovered deacetylase. Here, we demonstrate that human HDAC11 exhibits anti-influenza A virus (IAV) properties. We found that knockdown of HDAC11 expression augments IAV growth kinetics in human lung epithelial cells A549 by up to 1 log. One of the ways HDAC11 exerts its anti-IAV function is by being a part of IAV-induced host antiviral response. We found that the kinetics of both IAV- and interferon-induced innate antiviral response is significantly delayed in HDAC11-depleted cells. Further, in the absence of HDAC11 expression, there was a significant decrease in the expression of interferon-stimulated genes-IFITM3, ISG15, and viperin-previously implicated in anti-IAV function. One of the ways IAV antagonises HDAC11 is by downregulating its expression in host cells. We found that there was up to 93% reduction in HDAC11 transcript levels in A549 cells in response to IAV infection. HDAC11 is the smallest HDAC with majority of its polypeptide assigned to catalytic domain. Evolutionarily, it seems to be the least evolved and most closely related to common ancestral HDAC gene(s). Furthermore, HDAC11 has also been described as a deacylase. Therefore, our findings present exciting prospects for further investigations into significance of HDAC11 in virus infections.
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Affiliation(s)
- Ashley N Nutsford
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Henry D Galvin
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Farjana Ahmed
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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28
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Ma G, Chen L, Luo J, Wang B, Wang C, Li M, Huang C, Du J, Ma J, Chang Y, He H. Histone acetyl transferase TIP60 inhibits the replication of influenza a virus by activation the TBK1-IRF3 pathway. Virol J 2018; 15:172. [PMID: 30409205 PMCID: PMC6225679 DOI: 10.1186/s12985-018-1079-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/10/2018] [Indexed: 11/15/2022] Open
Abstract
Influenza A virus (IAV) is an important pathogen that poses a severe threat to the health of humans. Nucleoprotein (NP) of IAV plays crucial roles in the viral life cycle by interacting with various cellular factors. Histone Acetyl Transferase TIP60 is a key target of several viral proteins during infection, including HIV-1 Tat, HPV E6, HTLV-1 p30II and HCMV UL27 proteins. However, Whether the interaction between the IAV NP and TIP60, and the role of TIP60 in IAV life cycle are largely unknown. Here, we showed that IAV infection up-regulated TIP60 protein and RNA expression. Overexpression of TIP60 inhibited viral protein and RNA expression and reduced the progeny viral titer. Further study revealed that TIP60 inhibited viral replication through activation of TBK1-IRF3 signaling pathway. Furthermore, we demonstrated that the NP protein of IAV interacted with TIP60. Together, these results indicate that TIP60 play a repressor in IAV infection, and it may be a possible target for antiviral drugs.
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Affiliation(s)
- Guoyao Ma
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Lin Chen
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Luo
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Bo Wang
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengmin Wang
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Meng Li
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengmei Huang
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Du
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiajun Ma
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.,University of the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yungfu Chang
- Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Hongxuan He
- National Research Center for Wildlife Borne Diseases, Institute of Zoology, Chinese Academy of Sciences, No.1-5 Beichenxilu, Chaoyang District, Beijing, 100101, People's Republic of China.
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29
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The Involvement of Histone H3 Acetylation in Bovine Herpesvirus 1 Replication in MDBK Cells. Viruses 2018; 10:v10100525. [PMID: 30261679 PMCID: PMC6213513 DOI: 10.3390/v10100525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/14/2022] Open
Abstract
During bovine herpesvirus 1 (BoHV-1) productive infection in cell cultures, partial of intranuclear viral DNA is present in nucleosomes, and viral protein VP22 associates with histones and decreases histone H4 acetylation, indicating the involvement of histone H4 acetylation in virus replication. In this study, we demonstrated that BoHV-1 infection at the late stage (at 24 h after infection) dramatically decreased histone H3 acetylation [at residues K9 (H3K9ac) and K18 (H3K18ac)], which was supported by the pronounced depletion of histone acetyltransferases (HATs) including CBP/P300 (CREB binding protein and p300), GCN5L2 (general control of amino acid synthesis yeast homolog like 2) and PCAF (P300/CBP-associated factor). The depletion of GCN5L2 promoted by virus infection was partially mediated by ubiquitin-proteasome pathway. Interestingly, the viral replication was enhanced by HAT (histone acetyltransferase) activator CTPB [N-(4-Chloro-3-trifluoromethylphenyl)-2-ethoxy-6-pentadecylbenzamide], and vice versa, inhibited by HAT inhibitor Anacardic acid (AA), suggesting that BoHV-1 may take advantage of histone acetylation for efficient replication. Taken together, we proposed that the HAT-dependent histone H3 acetylation plays an important role in BoHV-1 replication in MDBK (Madin-Darby bovine kidney) cells.
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30
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Nguyen TH, Liu X, Su ZZ, Hsu ACY, Foster PS, Yang M. Potential Role of MicroRNAs in the Regulation of Antiviral Responses to Influenza Infection. Front Immunol 2018; 9:1541. [PMID: 30022983 PMCID: PMC6039551 DOI: 10.3389/fimmu.2018.01541] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022] Open
Abstract
Influenza is a major health burden worldwide and is caused by influenza viruses that are enveloped and negative stranded RNA viruses. Little progress has been achieved in targeted intervention, either at a population level or at an individual level (to treat the cause), due to the toxicity of drugs and ineffective vaccines against influenza viruses. MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in gene expression, cell differentiation, and tissue development and have been shown to silence viral replication in a sequence-specific manner. Investigation of these small endogenous nucleotides may lead to new therapeutics against influenza virus infection. Here, we describe our current understanding of the role of miRNAs in host defense response against influenza virus, as well as their potential and limitation as new therapeutic approaches.
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Affiliation(s)
- Thi Hiep Nguyen
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Xiaoming Liu
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Zhen Zhong Su
- Department of Respiratory Medicine, The Second Hospital, Jilin University, ChangChun, China
| | - Alan Chen-Yu Hsu
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Medicine and Public Health, The University of Newcastle, Callaghan, NSW, Australia
| | - Paul S Foster
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
| | - Ming Yang
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Callaghan, NSW, Australia.,Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, Australia
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31
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Xia B, Lu J, Wang R, Yang Z, Zhou X, Huang P. miR-21-3p Regulates Influenza A Virus Replication by Targeting Histone Deacetylase-8. Front Cell Infect Microbiol 2018; 8:175. [PMID: 29888214 PMCID: PMC5981164 DOI: 10.3389/fcimb.2018.00175] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022] Open
Abstract
Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection. Subsequently, we demonstrated that IAV replication was essential for the regulation of these miRNAs, and bioinformatic analysis revealed that the targets of these miRNAs affected biological processes relevant to IAV replication. Specifically, miR-21-3p was found to be down-regulated in IAV-infected A549 cells and selected for further detailed analysis. Target prediction and functional study illustrated that miR-21-3p repressed the expression of HDAC8 by targeting its 3′UTR. Furthermore, we confirmed miR-21-3p could promote virus replication, which was similar to the result of knocking down HDAC8, indicating that miR-21-3p promoted IAV replication by suppressing HDAC8 expression. Altogether, our results suggest a potential host defense against IAV through down-regulation of miR-21-3p.
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Affiliation(s)
- Binghui Xia
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jiansheng Lu
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Rong Wang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Zhixin Yang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiaowei Zhou
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Peitang Huang
- Laboratory of Protein Engineering, Beijing Institute of Biotechnology, Beijing, China
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32
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Flotillin proteins recruit sphingosine to membranes and maintain cellular sphingosine-1-phosphate levels. PLoS One 2018; 13:e0197401. [PMID: 29787576 PMCID: PMC5963794 DOI: 10.1371/journal.pone.0197401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/30/2018] [Indexed: 01/09/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) is an important lipid signalling molecule. S1P is produced via intracellular phosphorylation of sphingosine (Sph). As a lipid with a single fatty alkyl chain, Sph may diffuse rapidly between cellular membranes and through the aqueous phase. Here, we show that the absence of microdomains generated by multimeric assemblies of flotillin proteins results in reduced S1P levels. Cellular phenotypes of flotillin knockout mice, including changes in histone acetylation and expression of Isg15, are recapitulated when S1P synthesis is perturbed. Flotillins bind to Sph in vitro and increase recruitment of Sph to membranes in cells. Ectopic re-localisation of flotillins within the cell causes concomitant redistribution of Sph. The data suggest that flotillins may directly or indirectly regulate cellular sphingolipid distribution and signalling.
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33
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Zheng J, Perlman S. Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host. Curr Opin Virol 2018; 28:43-52. [PMID: 29172107 PMCID: PMC5835172 DOI: 10.1016/j.coviro.2017.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/02/2017] [Indexed: 12/25/2022]
Abstract
Respiratory viruses, especially influenza A viruses and coronaviruses such as MERS-CoV, represent continuing global threats to human health. Despite significant advances, much needs to be learned. Recent studies in virology and immunology have improved our understanding of the role of the immune system in protection and in the pathogenesis of these infections and of co-evolution of viruses and their hosts. These findings, together with sophisticated molecular structure analyses, omics tools and computer-based models, have helped delineate the interaction between respiratory viruses and the host immune system, which will facilitate the development of novel treatment strategies and vaccines with enhanced efficacy.
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Affiliation(s)
- Jian Zheng
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States
| | - Stanley Perlman
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, IA 52242, United States.
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34
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Chen L, Wang C, Luo J, Su W, Li M, Zhao N, Lyu W, Attaran H, He Y, Ding H, He H. Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Front Immunol 2017; 8:1757. [PMID: 29312300 PMCID: PMC5733105 DOI: 10.3389/fimmu.2017.01757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza A viruses (IAVs) take advantage of the host acetylation system for their own benefit. Whether the nucleoprotein (NP) of IAVs undergoes acetylation and the interaction between the NP and the class I histone deacetylases (HDACs) were largely unknown. Here, we showed that the NP protein of IAV interacted with HDAC1, which downregulated the acetylation level of NP. Using mass spectrometry, we identified lysine 103 as an acetylation site of the NP. Compared with wild-type protein, two K103 NP mutants, K103A and K103R, enhanced replication efficiency of the recombinant viruses in vitro. We further demonstrated that HDAC1 facilitated viral replication via two paths: promoting the nuclear retention of NP and inhibiting TBK1-IRF3 pathway. Our results lead to a new mechanism for regulating NP acetylation, indicating that HDAC1 may be a possible target for antiviral drugs.
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Affiliation(s)
- Lin Chen
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Chengmin Wang
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Luo
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wen Su
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Meng Li
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Wenting Lyu
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Hamidreza Attaran
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yapeng He
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hua Ding
- Department of Infectious Diseases, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Hongxuan He
- National Research Center for Wildlife Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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35
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van de Wakker SI, Fischer MJ, Oosting RS. New drug-strategies to tackle viral-host interactions for the treatment of influenza virus infections. Eur J Pharmacol 2017; 809:178-190. [DOI: 10.1016/j.ejphar.2017.05.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022]
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36
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Nagesh PT, Hussain M, Galvin HD, Husain M. Histone Deacetylase 2 Is a Component of Influenza A Virus-Induced Host Antiviral Response. Front Microbiol 2017; 8:1315. [PMID: 28769891 PMCID: PMC5511851 DOI: 10.3389/fmicb.2017.01315] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/29/2017] [Indexed: 11/13/2022] Open
Abstract
Host cells produce variety of antiviral factors that create an antiviral state and target various stages of influenza A virus (IAV) life cycle to inhibit infection. However, IAV has evolved various strategies to antagonize those antiviral factors. Recently, we reported that a member of class I host histone deacetylases (HDACs), HDAC1 possesses an anti-IAV function. Herein, we provide evidence that HDAC2, another class I member and closely related to HDAC1 in structure and function, also possesses anti-IAV properties. In turn, IAV, like HDAC1, dysregulates HDAC2, mainly at the polypeptide level through proteasomal degradation to potentially minimize its antiviral effect. We found that IAV downregulated the HDAC2 polypeptide level in A549 cells in an H1N1 strain-independent manner by up to 47%, which was recovered to almost 100% level in the presence of proteasome-inhibitor MG132. A further knockdown in HDAC2 expression by up to 90% via RNA interference augmented the growth kinetics of IAV in A549 cells by more than four-fold after 24 h of infection. Furthermore, the knockdown of HDAC2 expression decreased the IAV-induced phosphorylation of the transcription factor, Signal Transducer and Activator of Transcription I (STAT1) and the expression of interferon-stimulated gene, viperin in infected cells by 41 and 53%, respectively. The role of HDAC2 in viperin expression was analogous to that of HDAC1, but it was not in the phosphorylation of STAT1. This indicated that, like HDAC1, HDAC2 is a component of IAV-induced host innate antiviral response and performs both redundant and non-redundant functions vis-a-vis HDAC1; however, IAV dysregulates them both in a redundant manner.
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Affiliation(s)
- Prashanth T Nagesh
- Department of Microbiology and Immunology, University of OtagoDunedin, New Zealand.,Department of Microbiology, New York University School of Medicine, New YorkNY, United States
| | - Mazhar Hussain
- Department of Microbiology and Immunology, University of OtagoDunedin, New Zealand
| | - Henry D Galvin
- Department of Microbiology and Immunology, University of OtagoDunedin, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of OtagoDunedin, New Zealand
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37
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Roles of HDACs in the Responses of Innate Immune Cells and as Targets in Inflammatory Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1024:91-110. [DOI: 10.1007/978-981-10-5987-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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38
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Erwin-Cohen RA, Porter AI, Pittman PR, Rossi CA, DaSilva L. Human transcriptome response to immunization with live-attenuated Venezuelan equine encephalitis virus vaccine (TC-83): Analysis of whole blood. Hum Vaccin Immunother 2016; 13:169-179. [PMID: 27870591 PMCID: PMC5287313 DOI: 10.1080/21645515.2016.1227900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is an important human and animal alphavirus pathogen transmitted by mosquitoes. The virus is endemic in Central and South America, but has also caused equine outbreaks in southwestern areas of the United States. In an effort to better understand the molecular mechanisms of the development of immunity to this important pathogen, we performed transcriptional analysis from whole, unfractionated human blood of patients who had been immunized with the live-attenuated vaccine strain of VEEV, TC-83. We compared changes in the transcriptome between naïve individuals who were mock vaccinated with saline to responses of individuals who received TC-83. Significant transcriptional changes were noted at days 2, 7, and 14 following vaccination. The top canonical pathways revealed at early and intermediate time points (days 2 and 7) included the involvement of the classic interferon response, interferon-response factors, activation of pattern recognition receptors, and engagement of the inflammasome. By day 14, the top canonical pathways included oxidative phosphorylation, the protein ubiquitination pathway, natural killer cell signaling, and B-cell development. Biomarkers were identified that differentiate between vaccinees and control subjects, at early, intermediate, and late stages of the development of immunity as well as markers which were common to all 3 stages following vaccination but distinct from the sham-vaccinated control subjects. The study represents a novel examination of molecular processes that lead to the development of immunity against VEEV in humans and which may be of value as diagnostic targets, to enhance modern vaccine design, or molecular correlates of protection.
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Affiliation(s)
- Rebecca A Erwin-Cohen
- a Virology Division, United States Army Military Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Aimee I Porter
- a Virology Division, United States Army Military Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Phillip R Pittman
- b Division of Medicine, United States Army Military Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Cynthia A Rossi
- c Diagnostics Systems Division, United States Army Military Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Luis DaSilva
- d Center for Aerobiological Sciences, United States Army Military Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
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39
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Söderholm S, Fu Y, Gaelings L, Belanov S, Yetukuri L, Berlinkov M, Cheltsov AV, Anders S, Aittokallio T, Nyman TA, Matikainen S, Kainov DE. Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction. Viruses 2016; 8:v8100269. [PMID: 27690086 PMCID: PMC5086605 DOI: 10.3390/v8100269] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 09/13/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022] Open
Abstract
Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV–host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 199 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the 665 remains unknown. Studying anti-influenza efficacy and immuno/neuro-modulating properties of these compounds and their combinations as well as potential viral and host resistance to them may lead to the discovery of novel modulators of IAV–host interactions, which might be more effective than the currently available anti-influenza therapeutics.
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Affiliation(s)
- Sandra Söderholm
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
| | - Yu Fu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Lana Gaelings
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Sergey Belanov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Laxman Yetukuri
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Mikhail Berlinkov
- Institute of Mathematics and Computer Science, Ural Federal University, Yekaterinburg 620083, Russia.
| | - Anton V Cheltsov
- Q-Mol L.L.C. in Silico Pharmaceuticals, San Diego, CA 92037, USA.
| | - Simon Anders
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
- Department of Mathematics and Statistics, University of Turku, Turku 20014, Finland.
| | | | - Sampsa Matikainen
- Finnish Institute of Occupational Health, Helsinki 00250, Finland.
- Department of Rheumatology, Helsinki University Hospital, University of Helsinki, Helsinki 00015, Finland.
| | - Denis E Kainov
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00014, Finland.
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40
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Chen DY, Husain M. Caspase-mediated degradation of host cortactin that promotes influenza A virus infection in epithelial cells. Virology 2016; 497:146-156. [PMID: 27471953 DOI: 10.1016/j.virol.2016.07.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 01/09/2023]
Abstract
Influenza A virus (IAV) is well-known to exploit host factors to its advantage. Here, we report that IAV exploits host cortactin, an actin filament-stabilising protein for infection in epithelial cells. By using RNA interference-mediated knockdown and overexpression approach, we demonstrate that cortactin promotes IAV infection. However, cortactin polypeptide undergoes the degradation during late IAV infection. By perturbing the lysosome and proteasome, two main compartments governing the degradation of mammalian proteins, we demonstrate that a lysosome-associated apoptotic pathway mediates the degradation of cortactin in IAV-infected cells. However, we could not detect cleaved cortactin fragments by western blotting using the antibodies recognising either N-terminal/Central or C-terminal cortactin regions, which suggested the presence of multiple caspase cleavage sites. Indeed, CaspDB, a recently-described database predicted up to 35 caspase cleavage motifs present across cortactin polypeptide. The data presented indicate that host cortactin potentially has a dual but contrasting role during IAV infection.
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Affiliation(s)
- Da-Yuan Chen
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matloob Husain
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
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