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Swaraj S, Tripathi S. Interference without interferon: interferon-independent induction of interferon-stimulated genes and its role in cellular innate immunity. mBio 2024:e0258224. [PMID: 39302126 DOI: 10.1128/mbio.02582-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024] Open
Abstract
Interferons (IFNs) are multifaceted proteins that play pivotal roles in orchestrating robust antiviral immune responses and modulating the intricate landscape of host immunity. The major signaling pathway activated by IFNs is the JAK/STAT (Janus kinase/signal transducer and activator of transcription) pathway, which leads to the transcription of a battery of genes, collectively known as IFN-stimulated genes (ISGs). While the well-established role of IFNs in coordinating the innate immune response against viral infections is widely acknowledged, recent years have provided a more distinct comprehension of the functional significance attributed to non-canonical, IFN-independent induction of ISGs. In this review, we summarize the non-conventional signaling pathways of ISG induction. These alternative pathways offer new avenues for developing antiviral strategies or immunomodulation in various diseases.
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Affiliation(s)
- Shachee Swaraj
- Emerging Viral Pathogens Laboratory, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
- Microbiology & Cell Biology Department, Biological Sciences Division, Indian Institute of Science, Bengaluru, India
| | - Shashank Tripathi
- Emerging Viral Pathogens Laboratory, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
- Microbiology & Cell Biology Department, Biological Sciences Division, Indian Institute of Science, Bengaluru, India
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2
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Shi Q, Zhang P, Hu Q, Zhang T, Hou R, Yin S, Zou Y, Chen F, Jiao S, Si L, Zheng B, Chen Y, Zhan T, Liu Y, Zhu W, Qi N. Role of TOMM34 on NF-κB activation-related hyperinflammation in severely ill patients with COVID-19 and influenza. EBioMedicine 2024; 108:105343. [PMID: 39276680 PMCID: PMC11418153 DOI: 10.1016/j.ebiom.2024.105343] [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: 03/07/2024] [Revised: 08/21/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Highly pathogenic respiratory RNA viruses such as SARS-CoV-2 and its associated syndrome COVID-19 pose a tremendous threat to the global public health. Innate immune responses to SARS-CoV-2 depend mainly upon the NF-κB-mediated inflammation. Identifying unknown host factors driving the NF-κB activation and inflammation is crucial for the development of immune intervention strategies. METHODS Published single-cell RNA sequencing (scRNA-seq) data was used to analyze the differential transcriptome profiles of bronchoalveolar lavage (BAL) cells between healthy individuals (n = 27) and patients with severe COVID-19 (n = 21), as well as the differential transcriptome profiles of peripheral blood mononuclear cells (PBMCs) between healthy individuals (n = 22) and severely ill patients with COVID-19 (n = 45) or influenza (n = 16). Loss-of-function and gain-of-function assays were performed in diverse viruses-infected cells and male mice models to identify the role of TOMM34 in antiviral innate immunity. FINDINGS TOMM34, together with a list of genes encoding pro-inflammatory cytokines and antiviral immune proteins, was transcriptionally upregulated in circulating monocytes, lung epithelium and innate immune cells from individuals with severe COVID-19 or influenza. Deficiency of TOMM34/Tomm34 significantly impaired the type I interferon responses and NF-κB-mediated inflammation in various human/murine cell lines, murine bone marrow-derived macrophages (BMDMs) and in vivo. Mechanistically, TOMM34 recruits TRAF6 to facilitate the K63-linked polyubiquitination of NEMO upon viral infection, thus promoting the downstream NF-κB activation. INTERPRETATION In this study, viral induction of TOMM34 is positively correlated with the hyperinflammation in severely ill patients with COVID-19 and influenza. Our findings also highlight the physiological role of TOMM34 in the innate antiviral signallings. FUNDING A full list of funding sources can be found in the acknowledgements section.
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Affiliation(s)
- Qiwen Shi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Pengfei Zhang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Tianxin Zhang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Ruixia Hou
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shengxiang Yin
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Yilin Zou
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Fenghua Chen
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shuang Jiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Lanlan Si
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Bangjin Zheng
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Yichao Chen
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China
| | - Tingzhu Zhan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yongxiang Liu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
| | - Wenting Zhu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
| | - Nan Qi
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China; Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
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Cruz-Rivera PCDL, Eitson JL, Schoggins JW. IRF7 from the black flying fox induces a STAT1-independent ISG response in unstimulated cell lines that protects against diverse RNA viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592239. [PMID: 38746207 PMCID: PMC11092574 DOI: 10.1101/2024.05.02.592239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Bats are considered unique in their ability to harbor large numbers of viruses and serve as reservoirs for zoonotic viruses that have the potential to spill over into humans. However, these animals appear relatively resistant to the pathogenic effects of many viruses. Mounting evidence suggests that bats may tolerate viral infections due to unique immune features. These include evolutionary innovations in inflammatory pathways and in the molecules involved in viral sensing, interferon induction, and downstream interferon-induced antiviral effectors. We sought to determine whether interferon-stimulated genes (ISGs) from the black flying fox ( Pteropus alecto ) encoded proteins with unique antiviral activity relative to their human orthologs. Accordingly, we compared the antiviral activity of over 50 ISG human-bat ortholog pairs to identify differences in individual effector functions. We identified IRF7 from Pteropus alecto (Pa.IRF7) as a potent and broad-acting antiviral molecule that provides robust antiviral protection without prior activation. We show that Pa.IRF7 uniquely induces a subset of protective ISGs independent of canonical IFN signaling, which leads to protection from alphaviruses, a flavivirus, a rhabdovirus, and a paramyxovirus. In uninfected cells, Pa.IRF7 partially localizes to the nucleus and can directly bind interferon-sensitive regulatory elements (ISREs). Compared to human IRF7, Pa.IRF7 also has additional serines in its C terminal domain that contribute to antiviral activity and may serve as unique phosphorylation hubs for activation. These properties constitute major differences between bat and human IRF7 that offer additional insight into the potential uniqueness of the black flying fox immune system.
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4
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Luo P, Ji Y, Liu X, Zhang W, Cheng R, Zhang S, Qian X, Huang C. Affected inflammation-related signaling pathways in snake envenomation: A recent insight. Toxicon 2023; 234:107288. [PMID: 37703930 DOI: 10.1016/j.toxicon.2023.107288] [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: 07/23/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/15/2023]
Abstract
Snake envenomation is well known to cause grievous pathological signs, including haemorrhagic discharge, necrosis, and respiratory distress. However, inflammatory reactions are also common envenoming manifestations that lead to successive damage, such as oedema, ulceration, lymphadenectasis, systemic inflammatory response syndrome (SIRS) and even multiple organ dysfunction syndrome (MODS). Interference with the inflammatory burst is hence important in the clinical treatment of snake envenomation. Here, we summarize the typical snake toxins (or venoms) that cause inflammatory reactions and the underlying signaling pathways. In brief, inflammatory reactions are usually triggered by snake venom phospholipase A2 (svPLA2), snake venom metalloprotease (SVMP), snake venom serine protease (SVSP) and C-type lectin/snaclec (CTL) as well as disintegrin (DIS) via multiple signaling pathways. They are nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3 (NLRP3), nuclear factor kappa-B (NF-κB), mitogen-activated protein kinase (MAPK), janus kinase/signal transducer and activator of transcription (JAK-STAT) and phosphoinositide 3-Kinase/protein kinase B (PI3K/PKB also called PI3K-AKT) signaling pathways. Activation of these pathways promotes the expression of pro-inflammatory molecules such as cytokines, especially interleukin-1β (IL-1β) which causes further inflammatory cascades and manifestations, such as swelling, fever, pain, and severe complications. Remarkably, almost half of introduced snake toxins (or venoms) have anti-inflammatory effects through blocking these pathways and suppressing the expression of pro-inflammatory molecules. Investigation of affected inflammation-related signaling pathways is meaningful to achieve better clinical treatment.
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Affiliation(s)
- Peiyi Luo
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Yuxin Ji
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Xiaohan Liu
- Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China.
| | - Weiyun Zhang
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Ruoxi Cheng
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Shuxian Zhang
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Xiao Qian
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
| | - Chunhong Huang
- College of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, 330000, PR China.
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5
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Bichet MC, Adderley J, Avellaneda-Franco L, Magnin-Bougma I, Torriero-Smith N, Gearing LJ, Deffrasnes C, David C, Pepin G, Gantier MP, Lin RCY, Patwa R, Moseley GW, Doerig C, Barr JJ. Mammalian cells internalize bacteriophages and use them as a resource to enhance cellular growth and survival. PLoS Biol 2023; 21:e3002341. [PMID: 37883333 PMCID: PMC10602308 DOI: 10.1371/journal.pbio.3002341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here, we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following 8 hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage application led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a resource to promote cellular growth and metabolism.
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Affiliation(s)
- Marion C. Bichet
- School of Biological Sciences, Monash University, Clayton, Australia
- ACTALIA, Food Safety Department, Saint-Lô, France
- University of Lorraine, CNRS, LCPME, Vandœuvre-lès-Nancy, France
| | - Jack Adderley
- School of Health and Biomedical Science, RMIT University, Bundoora, Australia
| | | | | | | | - Linden J. Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Celine Deffrasnes
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Cassandra David
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Genevieve Pepin
- Medical Biology Department, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Australia
| | - Ruby CY Lin
- Centre for Infectious Diseases and Microbiology; The Westmead Institute for Medical Research, Westmead, Australia
| | - Ruzeen Patwa
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Gregory W. Moseley
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Christian Doerig
- School of Health and Biomedical Science, RMIT University, Bundoora, Australia
| | - Jeremy J. Barr
- School of Biological Sciences, Monash University, Clayton, Australia
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Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
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Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
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7
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Netherton CL, Shimmon GL, Hui JYK, Connell S, Reis AL. African Swine Fever Virus Host-Pathogen Interactions. Subcell Biochem 2023; 106:283-331. [PMID: 38159232 DOI: 10.1007/978-3-031-40086-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
African swine fever virus is a complex double-stranded DNA virus that exhibits tropism for cells of the mononuclear phagocytic system. Virus replication is a multi-step process that involves the nucleus of the host cell as well the formation of large perinuclear sites where progeny virions are assembled prior to transport to, and budding through, the plasma membrane. Like many viruses, African swine fever virus reorganises the cellular architecture to facilitate its replication and has evolved multiple mechanisms to avoid the potential deleterious effects of host cell stress response pathways. However, how viral proteins and virus-induced structures trigger cellular stress pathways and manipulate the subsequent responses is still relatively poorly understood. African swine fever virus alters nuclear substructures, modulates autophagy, apoptosis and the endoplasmic reticulum stress response pathways. The viral genome encodes for at least 150 genes, of which approximately 70 are incorporated into the virion. Many of the non-structural genes have not been fully characterised and likely play a role in host range and modifying immune responses. As the field moves towards approaches that take a broader view of the effect of expression of individual African swine fever genes, we summarise how the different steps in virus replication interact with the host cell and the current state of knowledge on how it modulates the resulting stress responses.
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8
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Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV. Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1. iScience 2022; 25:104599. [PMID: 35789859 PMCID: PMC9250025 DOI: 10.1016/j.isci.2022.104599] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/01/2022] [Accepted: 06/07/2022] [Indexed: 11/18/2022] Open
Abstract
Pattern recognition receptors (PRRs) protect against microbial invasion by detecting specific molecular patterns found in pathogens and initiating an immune response. Although microbial-derived PRR ligands have been extensively characterized, the contribution and relevance of endogenous ligands to PRR activation remains overlooked. Here, we characterize the landscape of endogenous ligands that engage RIG-I-like receptors (RLRs) upon infection by different RNA viruses. In each infection, several RNAs transcribed by RNA polymerase III (Pol3) specifically engaged RLRs, particularly the family of Y RNAs. Sensing of Y RNAs was dependent on their mimicking of viral secondary structure and their 5'-triphosphate extremity. Further, we found that HIV-1 triggered a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, inducing a transcriptome-wide change of cellular RNA 5'-triphosphorylation that licenses Y RNA immunogenicity. Overall, our work uncovers the contribution of endogenous RNAs to antiviral immunity and demonstrates the importance of this pathway in HIV-1 infection.
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Affiliation(s)
- Nicolas Vabret
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valérie Najburg
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ramya Gopal
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher McClain
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics at the Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Sreekumar Balan
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yannis Rahou
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Guillaume Beauclair
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Maxime Chazal
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Hugo Varet
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Rachel Legendre
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
- Hub Informatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP-CNRS), Institut Pasteur, Université de Paris, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Odile Sismeiro
- Transcriptome and EpiGenome Platform, BioMics, Center of Innovation and Technological Research, Institut Pasteur, Université de Paris, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Raul Y. Sanchez David
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Lise Chauveau
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nolwenn Jouvenet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY, USA
| | - Sylvie van der Werf
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
| | - Nina Bhardwaj
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Extra-mural Member, Parker Institute of Cancer Immunotherapy, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Physiology, Biophysics, & Systems Biology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anastassia V. Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
- Molecular Genetics of RNA Viruses, Department of Virology, Institut Pasteur, Université de Paris, CNRS UMR-3569, 75015 Paris, France
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9
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Thomsen EA, Andersen S, Marqvorsen MHS, Skipper KA, Paludan SR, Mikkelsen JG. Single-Cell Monitoring of Activated Innate Immune Signaling by a d2eGFP-Based Reporter Mimicking Time-Restricted Activation of IFNB1 Expression. Front Cell Infect Microbiol 2022; 11:784762. [PMID: 35118008 PMCID: PMC8803904 DOI: 10.3389/fcimb.2021.784762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/21/2021] [Indexed: 01/19/2023] Open
Abstract
The innate immune system represents a balanced first line of defense against infection. Type I interferons (IFNs) are key regulators of the response to viral infections with an essential early wave of IFN-β expression, which is conditional, time-restricted, and stochastic in its nature. The possibility to precisely monitor individual cells with active IFNB1 transcription during innate signaling requires a robust reporter system that mimics the endogenous IFN-β signal. Here, we present a reporter system based on expression of a destabilized version of eGFP (d2eGFP) from a stably integrated reporter cassette containing the IFNB1 promoter and 3'-untranslated region, enabling both spatial and temporal detection of regulated IFNB1 expression. Specifically, this reporter permits detection, quantification, and isolation of cells actively producing d2eGFP in a manner that fully mimics IFN-β production allowing tracking of IFNB1 gene activation and repression in monocytic cells and keratinocytes. Using induced d2eGFP expression as a readout for activated immune signaling at the single-cell level, we demonstrate the application of the reporter for FACS-based selection of cells with genotypes supporting cGAS-STING signaling. Our studies provide a novel approach for monitoring on/off-switching of innate immune signaling and form the basis for investigating genotypes affecting immune regulation at the single-cell level.
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10
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Abstract
The three classes of interferons (IFNs) share the ability to inhibit viral replication, activating cell transcriptional programs that regulate both innate and adaptive responses to viral and intracellular bacterial challenge. Due to their unique potency in regulating viral replication, and their association with numerous autoimmune diseases, the tightly orchestrated transcriptional regulation of IFNs has long been a subject of intense investigation. The protective role of early robust IFN responses in the context of infection with SARS-CoV-2 has further underscored the relevance of these pathways. In this viewpoint, rather than focusing on the downstream effects of IFN signaling (which have been extensively reviewed elsewhere), we will summarize the historical and current understanding of the stepwise assembly and function of factors that regulate IFNβ enhancer activity (the "enhanceosome") and highlight opportunities for deeper understanding of the transcriptional control of the ifnb gene.
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Affiliation(s)
- Andrew W Daman
- Department of Pathology, Weill Cornell Medicine, New York, NY
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11
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Chang K, Han K, Qiu W, Hu Z, Chen X, Chen X, Xie X, Wang S, Hu C, Mao H. Grass carp (Ctenopharyngodon idella) interferon regulatory factor 8 down-regulates interferon1 expression via interaction with interferon regulatory factor 2 in vitro. Mol Immunol 2021; 137:202-211. [PMID: 34280770 DOI: 10.1016/j.molimm.2021.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Interferon regulatory factor 8 (IRF8), also known as interferon consensus sequence-binding protein (ICSBP), is a negative regulatory factor of interferon (IFN) and plays an important role in cell differentiation and innate immunity in mammals. In recent years, some irf8 homologous genes have been cloned and confirmed to take part in innate immune response in fish, but the mechanism still remains unclear. In this paper, a grass carp (Ctenopharyngodon idella) irf8 gene (Ciirf8) was cloned and characterized. The deduced protein (CiIRF8) possesses a highly conserved N-terminal DNA binding domain but a less well-conserved C-terminal IRF association domain (IAD). Ciirf8 was widely expressed in all tested tissues of grass carp and up-regulated following poly(I:C) stimulation. Ciirf8 expression was also up-regulated in CIK cells upon treatment with poly(I:C). To explore the molecular mechanism of how fish IRF8 regulates ifn1 expression, the similarities and differences of grass carp IRF8 and IRF2 were compared and contrasted. Subcellular localization analysis showed that CiIRF8 is located both in the cytoplasm and nucleus; however, CiIRF2 is only located in the nucleus. The nuclear-cytoplasmic translocation of CiIRF8 was observed in CIK cells under stimulation with poly(I:C). The interaction of CiIRF8 and CiIRF2 was further confirmed by a co-immunoprecipitation assay in the nucleus. Dual-luciferase reporter assays showed that the promoter activity of Ciifn1 was significantly inhibited by co-transfection with CiIRF2 and CiIRF8. The transcription inhibition of Ciifn1 was alleviated by competitive binding of CiIRF2 and CiIRF8 to CiIRF1. In conclusion, CiIRF8 down-regulates Ciifn1 expression via interaction with CiIRF2 in cells.
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Affiliation(s)
- Kaile Chang
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Kun Han
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Weihua Qiu
- Teaching Material Research Office of Jiangxi Provincial Education Department, China
| | - Zhizhen Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xingxing Chen
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xin Chen
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiaofen Xie
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Shanghong Wang
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chengyu Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Huiling Mao
- School of Life Science, Nanchang University, Nanchang, 330031, China.
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12
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Li S, Zhu Z, Yang F, Cao W, Yang J, Ma C, Zhao Z, Tian H, Liu X, Ma J, Xiao S, Zheng H. Porcine Epidemic Diarrhea Virus Membrane Protein Interacted with IRF7 to Inhibit Type I IFN Production during Viral Infection. THE JOURNAL OF IMMUNOLOGY 2021; 206:2909-2923. [PMID: 34127522 DOI: 10.4049/jimmunol.2001186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/06/2021] [Indexed: 11/19/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic porcine enteropathogenic coronavirus causing severe enteritis and lethal watery diarrhea in piglets. PEDV infection suppresses the synthesis of type I IFN, and multiple viral proteins of PEDV have been shown to target the adaptors of innate immune pathways to inhibit type I IFN production. In this study, we identified PEDV membrane (M) protein as a new antagonist of type I IFN production in both human embryonic kidney HEK293T cells and porcine kidney PK-15 cells and determined the antagonistic mechanism used by M protein to target IFN regulatory factor 7 (IRF7), an important regulator of type I IFN production. IRF7 is phosphorylated and activated by TBK1 and IKKε in response to viral infection. We found that PEDV M protein interacted with the inhibitory domain of IRF7 and significantly suppressed TBK1/IKKε-induced IRF7 phosphorylation and dimerization of IRF7, leading to the decreased expression of type I IFN, although it did not affect the interaction between TBK1/IKKε and IRF7. As expected, overexpression of M protein significantly increased PEDV replication in porcine cells. The M proteins of both epidemic PEDV strains and vaccine strain showed similar antagonistic effect on type I IFN production, and the 1-55 region of M protein was essential for disruption of IRF7 function by interacting with IRF7. Taken together, our data identified a new, to our knowledge, IFN antagonist of PEDV, as well as a novel, to our knowledge, antagonistic mechanism evolved by PEDV to inhibit type I IFN production.
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Affiliation(s)
- Shasha Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Jinping Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Caina Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Zhenxiang Zhao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Hong Tian
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Junwu Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China; and
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13
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Reciprocal Inhibition of Immunogenic Performance in Mice of Two Potent DNA Immunogens Targeting HCV-Related Liver Cancer. Microorganisms 2021; 9:microorganisms9051073. [PMID: 34067686 PMCID: PMC8156932 DOI: 10.3390/microorganisms9051073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/29/2022] Open
Abstract
Chronic HCV infection and associated liver cancer impose a heavy burden on the healthcare system. Direct acting antivirals eliminate HCV, unless it is drug resistant, and partially reverse liver disease, but they cannot cure HCV-related cancer. A possible remedy could be a multi-component immunotherapeutic vaccine targeting both HCV-infected and malignant cells, but also those not infected with HCV. To meet this need we developed a two-component DNA vaccine based on the highly conserved core protein of HCV to target HCV-infected cells, and a renowned tumor-associated antigen telomerase reverse transcriptase (TERT) based on the rat TERT, to target malignant cells. Their synthetic genes were expression-optimized, and HCV core was truncated after aa 152 (Core152opt) to delete the domain interfering with immunogenicity. Core152opt and TERT DNA were highly immunogenic in BALB/c mice, inducing IFN-γ/IL-2/TNF-α response of CD4+ and CD8+ T cells. Additionally, DNA-immunization with TERT enhanced cellular immune response against luciferase encoded by a co-delivered plasmid (Luc DNA). However, DNA-immunization with Core152opt and TERT mix resulted in abrogation of immune response against both components. A loss of bioluminescence signal after co-delivery of TERT and Luc DNA into mice indicated that TERT affects the in vivo expression of luciferase directed by the immediate early cytomegalovirus and interferon-β promoters. Panel of mutant TERT variants was created and tested for their expression effects. TERT with deleted N-terminal nucleoli localization signal and mutations abrogating telomerase activity still suppressed the IFN-β driven Luc expression, while the inactivated reverse transcriptase domain of TERT and its analogue, enzymatically active HIV-1 reverse transcriptase, exerted only weak suppressive effects, implying that suppression relied on the presence of the full-length/nearly full-length TERT, but not its enzymatic activity. The effect(s) could be due to interference of the ectopically expressed xenogeneic rat TERT with biogenesis of mRNA, ribosomes and protein translation in murine cells, affecting the expression of immunogens. HCV core can aggravate this effect, leading to early apoptosis of co-expressing cells, preventing the induction of immune response.
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14
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Padariya M, Sznarkowska A, Kote S, Gómez-Herranz M, Mikac S, Pilch M, Alfaro J, Fahraeus R, Hupp T, Kalathiya U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021; 11:622. [PMID: 33922087 PMCID: PMC8143464 DOI: 10.3390/biom11050622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-related DNA damage resistant signature (IRDS) genes are a subgroup of interferon-stimulated genes (ISGs) found upregulated in different cancer types, which promotes resistance to DNA damaging chemotherapy and radiotherapy. Along with briefly discussing IFNs and signalling in this review, we highlighted how different IRDS genes are affected by viruses. On the contrary, different strategies adopted to suppress a set of IRDS genes (STAT1, IRF7, OAS family, and BST2) to induce (chemo- and radiotherapy) sensitivity were deliberated. Significant biological pathways that comprise these genes were classified, along with their frequently associated genes (IFIT1/3, IFITM1, IRF7, ISG15, MX1/2 and OAS1/3/L). Major upstream regulators from the IRDS genes were identified, and different IFN types regulating these genes were outlined. Functional interfaces of IRDS proteins with DNA/RNA/ATP/GTP/NADP biomolecules featured a well-defined pharmacophore model for STAT1/IRF7-dsDNA and OAS1/OAS3/IFIH1-dsRNA complexes, as well as for the genes binding to GDP or NADP+. The Lys amino acid was found commonly interacting with the ATP phosphate group from OAS1/EIF2AK2/IFIH1 genes. Considering the premise that targeting IRDS genes mediated resistance offers an efficient strategy to resensitize tumour cells and enhances the outcome of anti-cancer treatment, this review can add some novel insights to the field.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Maria Gómez-Herranz
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Magdalena Pilch
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland; (A.S.); (S.K.); (M.G.-H.); (S.M.); (M.P.); (J.A.); (R.F.); (T.H.)
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15
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Kienes I, Weidl T, Mirza N, Chamaillard M, Kufer TA. Role of NLRs in the Regulation of Type I Interferon Signaling, Host Defense and Tolerance to Inflammation. Int J Mol Sci 2021; 22:1301. [PMID: 33525590 PMCID: PMC7865845 DOI: 10.3390/ijms22031301] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Type I interferon signaling contributes to the development of innate and adaptive immune responses to either viruses, fungi, or bacteria. However, amplitude and timing of the interferon response is of utmost importance for preventing an underwhelming outcome, or tissue damage. While several pathogens evolved strategies for disturbing the quality of interferon signaling, there is growing evidence that this pathway can be regulated by several members of the Nod-like receptor (NLR) family, although the precise mechanism for most of these remains elusive. NLRs consist of a family of about 20 proteins in mammals, which are capable of sensing microbial products as well as endogenous signals related to tissue injury. Here we provide an overview of our current understanding of the function of those NLRs in type I interferon responses with a focus on viral infections. We discuss how NLR-mediated type I interferon regulation can influence the development of auto-immunity and the immune response to infection.
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Affiliation(s)
- Ioannis Kienes
- Department of Immunology, Institute for Nutritional Medicine, University of Hohenheim, 70599 Stuttgart, Germany; (I.K.); (T.W.); (N.M.)
| | - Tanja Weidl
- Department of Immunology, Institute for Nutritional Medicine, University of Hohenheim, 70599 Stuttgart, Germany; (I.K.); (T.W.); (N.M.)
| | - Nora Mirza
- Department of Immunology, Institute for Nutritional Medicine, University of Hohenheim, 70599 Stuttgart, Germany; (I.K.); (T.W.); (N.M.)
| | | | - Thomas A. Kufer
- Department of Immunology, Institute for Nutritional Medicine, University of Hohenheim, 70599 Stuttgart, Germany; (I.K.); (T.W.); (N.M.)
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16
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Irving AT, Zhang Q, Kong PS, Luko K, Rozario P, Wen M, Zhu F, Zhou P, Ng JHJ, Sobota RM, Wang LF. Interferon Regulatory Factors IRF1 and IRF7 Directly Regulate Gene Expression in Bats in Response to Viral Infection. Cell Rep 2020; 33:108345. [PMID: 33147460 PMCID: PMC8755441 DOI: 10.1016/j.celrep.2020.108345] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Bat cells and tissue have elevated basal expression levels of antiviral genes commonly associated with interferon alpha (IFNα) signaling. Here, we show Interferon Regulatory Factor 1 (IRF1), 3, and 7 levels are elevated in most bat tissues and that, basally, IRFs contribute to the expression of type I IFN ligands and high expression of interferon regulated genes (IRGs). CRISPR knockout (KO) of IRF 1/3/7 in cells reveals distinct subsets of genes affected by each IRF in an IFN-ligand signaling-dependent and largely independent manner. As the master regulators of innate immunity, the IRFs control the kinetics and maintenance of the IRG response and play essential roles in response to influenza A virus (IAV), herpes simplex virus 1 (HSV-1), Melaka virus/Pteropine orthoreovirus 3 Melaka (PRV3M), and Middle East respiratory syndrome-related coronavirus (MERS-CoV) infection. With its differential expression in bats compared to that in humans, this highlights a critical role for basal IRF expression in viral responses and potentially immune cell development in bats with relevance for IRF function in human biology.
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Affiliation(s)
- Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University International Campus, Haining, China; Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Qian Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Pui-San Kong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Katarina Luko
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Pritisha Rozario
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Ming Wen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Peng Zhou
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Justin H J Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology (A(∗)STAR), Singapore, Singapore; Institute of Medical Biology (IMB), Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
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17
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Hossain MA, Larrous F, Rawlinson SM, Zhan J, Sethi A, Ibrahim Y, Aloi M, Lieu KG, Mok YF, Griffin MDW, Ito N, Ose T, Bourhy H, Moseley GW, Gooley PR. Structural Elucidation of Viral Antagonism of Innate Immunity at the STAT1 Interface. Cell Rep 2020; 29:1934-1945.e8. [PMID: 31722208 DOI: 10.1016/j.celrep.2019.10.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 07/16/2019] [Accepted: 10/03/2019] [Indexed: 12/24/2022] Open
Abstract
To evade immunity, many viruses express interferon antagonists that target STAT transcription factors as a major component of pathogenesis. Because of a lack of direct structural data, these interfaces are poorly understood. We report the structural analysis of full-length STAT1 binding to an interferon antagonist of a human pathogenic virus. The interface revealed by transferred cross-saturation NMR is complex, involving multiple regions in both the viral and cellular proteins. Molecular mapping analysis, combined with biophysical characterization and in vitro/in vivo functional assays, indicates that the interface is significant in disease caused by a pathogenic field-strain lyssavirus, with critical roles for contacts between the STAT1 coiled-coil/DNA-binding domains and specific regions within the viral protein. These data elucidate the potentially complex nature of IFN antagonist/STAT interactions, and the spatial relationship of protein interfaces that mediate immune evasion and replication, providing insight into how viruses can regulate these essential functions via single multifunctional proteins.
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Affiliation(s)
- Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Florence Larrous
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Stephen M Rawlinson
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Jingyu Zhan
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Ashish Sethi
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Youssef Ibrahim
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Maria Aloi
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Kim G Lieu
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Naoto Ito
- Laboratory of Zoonotic Diseases, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Toyoyuki Ose
- Faculty of Advanced Life Science, Hokkaido University, 060-0810 Sapporo, Japan
| | - Hervé Bourhy
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; Unité Lyssavirus, Epidémiologie et Neuropathologie - CNR de la RAGE, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia; Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton Campus, VIC 3800, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC 3010, Australia.
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18
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Schwanke H, Stempel M, Brinkmann MM. Of Keeping and Tipping the Balance: Host Regulation and Viral Modulation of IRF3-Dependent IFNB1 Expression. Viruses 2020; 12:E733. [PMID: 32645843 PMCID: PMC7411613 DOI: 10.3390/v12070733] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
The type I interferon (IFN) response is a principal component of our immune system that allows to counter a viral attack immediately upon viral entry into host cells. Upon engagement of aberrantly localised nucleic acids, germline-encoded pattern recognition receptors convey their find via a signalling cascade to prompt kinase-mediated activation of a specific set of five transcription factors. Within the nucleus, the coordinated interaction of these dimeric transcription factors with coactivators and the basal RNA transcription machinery is required to access the gene encoding the type I IFN IFNβ (IFNB1). Virus-induced release of IFNβ then induces the antiviral state of the system and mediates further mechanisms for defence. Due to its key role during the induction of the initial IFN response, the activity of the transcription factor interferon regulatory factor 3 (IRF3) is tightly regulated by the host and fiercely targeted by viral proteins at all conceivable levels. In this review, we will revisit the steps enabling the trans-activating potential of IRF3 after its activation and the subsequent assembly of the multi-protein complex at the IFNβ enhancer that controls gene expression. Further, we will inspect the regulatory mechanisms of these steps imposed by the host cell and present the manifold strategies viruses have evolved to intervene with IFNβ transcription downstream of IRF3 activation in order to secure establishment of a productive infection.
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Affiliation(s)
- Hella Schwanke
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Stempel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Melanie M. Brinkmann
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany; (H.S.); (M.S.)
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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19
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Kim JH, Yoon JE, Nikapitiya C, Kim TH, Uddin MB, Lee HC, Kim YH, Hwang JH, Chathuranga K, Chathuranga WAG, Choi HS, Kim CJ, Jung JU, Lee CH, Lee JS. Small Heterodimer Partner Controls the Virus-Mediated Antiviral Immune Response by Targeting CREB-Binding Protein in the Nucleus. Cell Rep 2020; 27:2105-2118.e5. [PMID: 31091449 DOI: 10.1016/j.celrep.2019.04.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/01/2019] [Accepted: 04/15/2019] [Indexed: 01/16/2023] Open
Abstract
Small heterodimer partner (SHP) is an orphan nuclear receptor that acts as a transcriptional co-repressor by interacting with nuclear receptors and transcription factors. Although SHP plays a negative regulatory function in various signaling pathways, its role in virus infection has not been studied. Here, we report that SHP is a potent negative regulator of the virus-mediated type I IFN signaling that maintains homeostasis within the antiviral innate immune system. Upon virus infection, SHP interacts specifically with CREB-binding protein (CBP) in the nucleus, thereby obstructing CBP/β-catenin interaction competitively. Consequently, SHP-deficient cells enhance antiviral responses, including transcription of the type I IFN gene, upon virus infection. Furthermore, SHP-deficient mice show higher levels of IFN production and are more resistant to influenza A virus infection. Our results suggest that SHP is a nuclear regulator that blocks transcription of the type I IFN gene to inhibit excessive innate immune responses.
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Affiliation(s)
- Jae-Hoon Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea; Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Ji-Eun Yoon
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Tae-Hwan Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Md Bashir Uddin
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea; Faculty of Veterinary & Animal Science, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Hyun-Cheol Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jung Hwan Hwang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - W A Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hueng-Sik Choi
- National Creative Research Initiatives Center for Nuclear Receptor Signals and Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, Republic of Korea
| | - Chul-Joong Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea.
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Kuroda M, Nishiguchi M, Ugawa N, Ishikawa E, Kawabata Y, Okamoto S, Sasaki W, Miyatake Y, Sebe M, Masumoto S, Tsutsumi R, Harada N, Sakaue H. Interferon regulatory factor 7 mediates obesity-associated MCP-1 transcription. PLoS One 2020; 15:e0233390. [PMID: 32437400 PMCID: PMC7241760 DOI: 10.1371/journal.pone.0233390] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/04/2020] [Indexed: 11/18/2022] Open
Abstract
Hypertrophy, associated with adipocyte dysfunction, causes increased pro-inflammatory adipokine, and abnormal glucose and lipid metabolism, leading to insulin resistance and obesity-related-health problems. By combining DNA microarray and genomic data analyses to predict DNA binding motifs, we identified the transcription factor Interferon Regulatory Factor 7 (IRF7) as a possible regulator of genes related to adipocyte hypertrophy. To investigate the role of IRF7 in adipocytes, we examined gene expression patterns in 3T3-L1 cells infected with a retrovirus carrying the IRF7 gene and found that enforced IRF7 expression induced the expression of monocyte chemoattractant protein-1 (MCP-1), a key initial adipokine in the chronic inflammation of obesity. CRISPR/Cas9 mediated-suppression of IRF7 significantly reduced MCP-1 mRNA. Luciferase assays, chromatin immunoprecipitation PCR analysis and gel shift assay showed that IRF7 transactivates the MCP-1 gene by binding to its proximal Interferon Stimulation Response Element (ISRE), a putative IRF7 binding motif. IRF7 knockout mice exhibited lower expression of MCP-1 in epidydimal white adipose tissue under high-fat feeding conditions, suggesting the transcription factor is physiologically important for inducing MCP-1. Taken together, our results suggest that IRF7 transactivates MCP-1 mRNA in adipocytes, and it may be involved in the adipose tissue inflammation associated with obesity.
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Affiliation(s)
- Masashi Kuroda
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Misa Nishiguchi
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Naho Ugawa
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Etsuko Ishikawa
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Yasuyo Kawabata
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Saya Okamoto
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Waka Sasaki
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Yumiko Miyatake
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Mayu Sebe
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Saeko Masumoto
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima-city, Fukushima, Japan
| | - Rie Tsutsumi
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
| | - Nagakatsu Harada
- Department of Health and Nutrition, Faculty of Nursing and Nutrition, The University of Shimane, Izumo-city, Shimane, Japan
| | - Hiroshi Sakaue
- Department of Nutrition and Metabolism, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima-city, Tokushima, Japan
- Diabetes Therapeutics and Research Center, Tokushima University, Tokushima-city, Tokushima, Japan
- * E-mail:
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21
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Marineau A, Khan KA, Servant MJ. Roles of GSK-3 and β-Catenin in Antiviral Innate Immune Sensing of Nucleic Acids. Cells 2020; 9:cells9040897. [PMID: 32272583 PMCID: PMC7226782 DOI: 10.3390/cells9040897] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/23/2022] Open
Abstract
The rapid activation of the type I interferon (IFN) antiviral innate immune response relies on ubiquitously expressed RNA and DNA sensors. Once engaged, these nucleotide-sensing receptors use distinct signaling modules for the rapid and robust activation of mitogen-activated protein kinases (MAPKs), the IκB kinase (IKK) complex, and the IKK-related kinases IKKε and TANK-binding kinase 1 (TBK1), leading to the subsequent activation of the activator protein 1 (AP1), nuclear factor-kappa B (NF-κB), and IFN regulatory factor 3 (IRF3) transcription factors, respectively. They, in turn, induce immunomodulatory genes, allowing for a rapid antiviral cellular response. Unlike the MAPKs, the IKK complex and the IKK-related kinases, ubiquitously expressed glycogen synthase kinase 3 (GSK-3) α and β isoforms are active in unstimulated resting cells and are involved in the constitutive turnover of β-catenin, a transcriptional coactivator involved in cell proliferation, differentiation, and lineage commitment. Interestingly, studies have demonstrated the regulatory roles of both GSK-3 and β-catenin in type I IFN antiviral innate immune response, particularly affecting the activation of IRF3. In this review, we summarize current knowledge on the mechanisms by which GSK-3 and β-catenin control the antiviral innate immune response to RNA and DNA virus infections.
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Affiliation(s)
- Alexandre Marineau
- Faculty of Pharmacy, Université de Montréal, Montréal, QC H3C3J7, Canada;
| | - Kashif Aziz Khan
- Department of Biology, York University, Toronto, ON M3J1P3, Canada;
| | - Marc J. Servant
- Faculty of Pharmacy, Université de Montréal, Montréal, QC H3C3J7, Canada;
- Réseau Québécois de Recherche sur les Médicaments (RQRM), Montréal, QC H3T1C5, Canada
- Correspondence: ; Tel.: +1-514-343-7966
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22
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Cao L, Ji Y, Zeng L, Liu Q, Zhang Z, Guo S, Guo X, Tong Y, Zhao X, Li CM, Chen Y, Guo D. P200 family protein IFI204 negatively regulates type I interferon responses by targeting IRF7 in nucleus. PLoS Pathog 2019; 15:e1008079. [PMID: 31603949 PMCID: PMC6818788 DOI: 10.1371/journal.ppat.1008079] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/29/2019] [Accepted: 09/12/2019] [Indexed: 01/19/2023] Open
Abstract
Interferon-inducible p200 family protein IFI204 was reported to be involved in DNA sensing, and subsequently induces the production of type I interferons and proinflammatory mediators. However, its function in the regulation of antiviral innate immune signaling pathway remains unclear. Here we reported a novel role of IFI204 that specifically inhibits the IRF7-mediated type I interferons response during viral infection. IFI204 and other p200 family proteins are highly expressed in mouse hepatitis coronavirus-infected bone marrow-derived dendritic cells. The abundant IFI204 could significantly interact with IRF7 in nucleus by its HIN domain and prevent the binding of IRF7 with its corresponding promoter. Moreover, other p200 family proteins that possess HIN domain could also inhibit the IRF7-mediated type I interferons. These results reveal that, besides the positive regulation function in type I interferon response at the early stage of DNA virus infection, the interferon-inducible p200 family proteins such as IFI204 could also negatively regulate the IRF7-mediated type I interferon response after RNA virus infection to avoid unnecessary host damage from hyper-inflammatory responses. The regulation of type I interferon signaling pathway is dynamic sequential processes and must be tightly regulated to keep balance between antiviral immune and hyper-inflammatory responses. The precise regulation mechanisms of the innate immune signaling pathway are still worth studying. Here, we found a novel role of the interferon-inducible p200 family protein IFI204 that specifically inhibits the IRF7-mediated type I interferon production by negative control of the transcriptional activity of IRF7 in the nucleus at the late stage of RNA virus infection. Previous studies showed that IFI204 is involved in DNA sensing during DNA virus infection to initiate antiviral immune responses. We demonstrate that IFI204 can inhibit IRF7-mediated activation of type I IFN responses induced by RNA virus infection, which is in contrast with its role in IRF3 activation in cGAS-STING DNA sensing pathway during DNA virus infection. Such negative regulation may help to avoid hyper-inflammatory responses induced by the over-activated IRF7-mediated type I interferons at late stage of the viral infection. Thus, the current study sheds light on the regulation roles of p200 family proteins and the accurate regulation system of type I interferons signaling pathway.
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Affiliation(s)
- Liu Cao
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yanxi Ji
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lanyi Zeng
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qianyun Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhen Zhang
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
| | - Shuting Guo
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xiaolong Guo
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yongjia Tong
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaolu Zhao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Chun-Mei Li
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (YC); (DG)
| | - Deyin Guo
- School of Medicine, Sun Yat-sen University, Guangzhou, China
- * E-mail: (YC); (DG)
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23
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Riedl W, Acharya D, Lee JH, Liu G, Serman T, Chiang C, Chan YK, Diamond MS, Gack MU. Zika Virus NS3 Mimics a Cellular 14-3-3-Binding Motif to Antagonize RIG-I- and MDA5-Mediated Innate Immunity. Cell Host Microbe 2019; 26:493-503.e6. [PMID: 31600501 PMCID: PMC6922055 DOI: 10.1016/j.chom.2019.09.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/29/2019] [Accepted: 09/17/2019] [Indexed: 12/21/2022]
Abstract
14-3-3 protein family members facilitate the translocation of RIG-I-like receptors (RLRs) to organelles that mediate downstream RLR signaling, leading to interferon production. 14-3-3ϵ promotes the cytosolic-to-mitochondrial translocation of RIG-I, while 14-3-3η facilitates MDA5 translocation to mitochondria. We show that the NS3 protein of Zika virus (ZIKV) antagonizes antiviral gene induction by RIG-I and MDA5 by binding to and sequestering the scaffold proteins 14-3-3ϵ and 14-3-3η. 14-3-3-binding is mediated by a negatively charged RLDP motif in NS3 that is conserved in ZIKV strains of African and Asian lineages and is similar to the one found in dengue and West Nile viruses. ZIKV NS3 is sufficient to inhibit the RLR-14-3-3ϵ/η interaction and to suppress antiviral signaling. Mutational perturbation of 14-3-3ϵ/η binding in a recombinant ZIKV leads to enhanced innate immune responses and impaired growth kinetics. Our study provides molecular understanding of immune evasion functions of ZIKV, which may guide vaccine and anti-flaviviral therapy development.
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Affiliation(s)
- William Riedl
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhiraj Acharya
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jung-Hyun Lee
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Guanqun Liu
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Taryn Serman
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Cindy Chiang
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Ying Kai Chan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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24
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Sanchez David RY, Combredet C, Najburg V, Millot GA, Beauclair G, Schwikowski B, Léger T, Camadro JM, Jacob Y, Bellalou J, Jouvenet N, Tangy F, Komarova AV. LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses. Sci Signal 2019; 12:eaar3993. [PMID: 31575732 DOI: 10.1126/scisignal.aar3993] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) RIG-I, MDA5, and LGP2 stimulate inflammatory and antiviral responses by sensing nonself RNA molecules produced during viral replication. Here, we investigated how LGP2 regulates the RIG-I- and MDA5-dependent induction of type I interferon (IFN) signaling and showed that LGP2 interacted with different components of the RNA-silencing machinery. We identified a direct protein-protein interaction between LGP2 and the IFN-inducible, double-stranded RNA binding protein PACT. The LGP2-PACT interaction was mediated by the regulatory C-terminal domain of LGP2 and was necessary for inhibiting RIG-I-dependent responses and for amplifying MDA5-dependent responses. We described a point mutation within LGP2 that disrupted the LGP2-PACT interaction and led to the loss of LGP2-mediated regulation of RIG-I and MDA5 signaling. These results suggest a model in which the LGP2-PACT interaction regulates the inflammatory responses mediated by RIG-I and MDA5 and enables the cellular RNA-silencing machinery to coordinate with the innate immune response.
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Affiliation(s)
- Raul Y Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Ecole doctorale B3MI/Paris7, Paris, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Valérie Najburg
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Gael A Millot
- Hub de Bioinformatique et Biostatistique-C3BI, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Guillaume Beauclair
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Benno Schwikowski
- Systems Biology Laboratory and USR 3756, Institut Pasteur and CNRS, Paris, France
| | - Thibaut Léger
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jean-Michel Camadro
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Université Paris Diderot, CNRS, Sorbonne Paris Cité, F-75205 Paris, France
| | - Yves Jacob
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
| | - Jacques Bellalou
- Platform of Recombinant Proteins in Prokaryotic Cells, Institut Pasteur, 75015, CNRS UMR 3528, Paris, France
| | - Nolwenn Jouvenet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France.
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25
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Characterization of Novel Splice Variants of Zinc Finger Antiviral Protein (ZAP). J Virol 2019; 93:JVI.00715-19. [PMID: 31118263 DOI: 10.1128/jvi.00715-19] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/20/2019] [Indexed: 01/01/2023] Open
Abstract
Given the unprecedented scale of the recent Ebola and Zika viral epidemics, it is crucial to understand the biology of host factors with broad antiviral action in order to develop novel therapeutic approaches. Here, we look into one such factor: zinc finger antiviral protein (ZAP) inhibits a variety of RNA and DNA viruses. Alternative splicing results in two isoforms that differ at their C termini: ZAPL (long) encodes a poly(ADP-ribose) polymerase (PARP)-like domain that is missing in ZAPS (short). Previously, it has been shown that ZAPL is more antiviral than ZAPS, while the latter is more induced by interferon (IFN). In this study, we discovered and confirmed the expression of two additional splice variants of human ZAP: ZAPXL (extralong) and ZAPM (medium). We also found two haplotypes of human ZAP. Since ZAPL and ZAPS have differential activities, we hypothesize that all four ZAP isoforms have evolved to mediate distinct antiviral and/or cellular functions. By taking a gene-knockout-and-reconstitution approach, we have characterized the antiviral, translational inhibition, and IFN activation activities of individual ZAP isoforms. Our work demonstrates that ZAPL and ZAPXL are more active against alphaviruses and hepatitis B virus (HBV) than ZAPS and ZAPM and elucidates the effects of splice variants on the action of a broad-spectrum antiviral factor.IMPORTANCE ZAP is an IFN-induced host factor that can inhibit a wide range of viruses, and there is great interest in fully characterizing its antiviral mechanism. This is the first study that defines the antiviral capacities of individual ZAP isoforms in the absence of endogenous ZAP expression and, hence, cross talk with other isoforms. Our data demonstrate that ZAP is expressed as four different forms: ZAPS, ZAPM, ZAPL, and ZAPXL. The longer ZAP isoforms better inhibit alphaviruses and HBV, while all isoforms equally inhibit Ebola virus transcription and replication. In addition, there is no difference in the abilities of ZAP isoforms to enhance the induction of type I IFN expression. Our results show that the full spectrum of ZAP activities can change depending on the virus target and the relative levels of basal expression and induction by IFN or infection.
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26
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Type I interferon response impairs differentiation potential of pluripotent stem cells. Proc Natl Acad Sci U S A 2019; 116:1384-1393. [PMID: 30606801 PMCID: PMC6347712 DOI: 10.1073/pnas.1812449116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Unlike all differentiated cells, pluripotent stem cells do not elicit a productive antiviral response when infected by a pathogen. This observation seems at odds with the importance of pluripotent stem cells given their absolute requirement for the development of life. Here we investigate why this antiviral response is not utilized in these unique cells. We find that the factors required to maintain pluripotency are incompatible with those involved in eliciting the canonical interferon-based response to virus infection. Upon virus infection, pluripotent stem cells neither induce nor respond to canonical type I interferons (IFN-I). To better understand this biology, we characterized induced pluripotent stem cells (iPSCs) as well as their differentiated parental or rederived counterparts. We confirmed that only iPSCs failed to respond to viral RNA, IFN-I, or viral infection. This lack of response could be phenocopied in fibroblasts with the expression of a reprogramming factor which repressed the capacity to induce canonical antiviral pathways. To ascertain the consequences of restoring the antiviral response in the context of pluripotency, we engineered a system to engage these defenses in iPSCs. Inducible expression of a recombinant virus-activated transcription factor resulted in the successful reconstitution of antiviral defenses through the direct up-regulation of IFN-I–stimulated genes. Induction of the antiviral signature in iPSCs, even for a short duration, resulted in the dysregulation of genes associated with all three germ layers despite maintaining pluripotency markers. Trilineage differentiation of these same cells showed that engagement of the antiviral defenses compromised ectoderm and endoderm formation and dysregulated the development of mesodermal sublineages. In all, these data suggest that the temporal induction of the antiviral response primes iPSCs away from pluripotency and induces numerous aberrant gene products upon differentiation. Together these results suggest that the IFN-I system and pluripotency may be incompatible with each other and thus explain why stem cells do not utilize the canonical antiviral system.
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27
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Au-Yeung N, Horvath CM. Transcriptional and chromatin regulation in interferon and innate antiviral gene expression. Cytokine Growth Factor Rev 2018; 44:11-17. [PMID: 30509403 DOI: 10.1016/j.cytogfr.2018.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022]
Abstract
In response to virus infections, a cell-autonomous, transcription-based antiviral program is engaged to create resistance, impair pathogen replication, and alert professional cells in innate and adaptive immunity. This dual phase antiviral program consists of type I interferon (IFN) production followed by the response to IFN signaling. Pathogen recognition leads to activation of IRF and NFκB factors that function independently and together to recruit cellular coactivators that remodel chromatin, modify histones and activate RNA polymerase II (Pol II) at target gene loci, including the well-characterized IFNβ enhanceosome. In the subsequent response to IFN, a receptor-mediated JAK-STAT signaling cascade directs the assembly of the IRF9-STAT1-STAT2 transcription factor complex called ISGF3, which recruits its own cohort of remodelers, coactivators, and Pol II machinery to activate transcription of a wide range of IFN-stimulated genes. Regulation of the IFN and antiviral gene regulatory networks is not only important for driving innate immune responses to infections, but also may inform treatment of a growing list of chronic diseases that are characterized by hyperactive and constitutive IFN and IFN-stimulated gene (ISG) expression. Here, gene-specific and genome-wide investigations of the chromatin landscape at IFN and ISGs is discussed in parallel with IRF- and STAT- dependent regulation of Pol II transcription.
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Affiliation(s)
- Nancy Au-Yeung
- Department of Molecular Biosciences, Northwestern University, 2200 Campus Drive, Evanston, IL 60208, USA
| | - Curt M Horvath
- Department of Molecular Biosciences, Northwestern University, 2200 Campus Drive, Evanston, IL 60208, USA.
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28
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Chen S, Yang C, Zhang W, Mahalingam S, Wang M, Cheng A. Flaviviridae virus nonstructural proteins 5 and 5A mediate viral immune evasion and are promising targets in drug development. Pharmacol Ther 2018; 190:1-14. [PMID: 29742479 DOI: 10.1016/j.pharmthera.2018.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Infections with viruses in the Flaviviridae family have a vast global and economic impact because of the high morbidity and mortality. The pathogenesis of Flaviviridae infections is very complex and not fully understood because these viruses can inhibit multiple immune pathways including the complement system, NK cells, and IFN induction and signalling pathways. The non-structural (NS) 5 and 5A proteins of Flaviviridae viruses are highly conserved and play an important role in resisting host immunity through various evasion mechanisms. This review summarizes the strategies used by the NS5 and 5A proteins of Flaviviridae viruses for evading the innate immune response by inhibiting pattern recognition receptor (PRR) signalling pathways (TLR/MyD88, IRF7), suppressing interferon (IFN) signalling pathways (IFN-γRs, STAT1, STAT2), and impairing the function of IFN-stimulated genes (ISGs) (e.g. protein kinase R [PKR], oligoadenylate synthase [OAS]). All of these immune evasion mechanisms depend on the interaction of NS5 or NS5A with cellular proteins, such as MyD88 and IRF7, IFN-αRs, IFN-γRs, STAT1, STAT2, PKR and OAS. NS5 is the most attractive target for the discovery of broad spectrum compounds against Flaviviridae virus infection. The methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) activities of NS5 are the main therapeutic targets for antiviral drugs against Flaviviridae virus infection. Based on our site mapping, the sites involved in immune evasion provide some potential and promising targets for further novel antiviral therapeutics.
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Affiliation(s)
- Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China.
| | - Chao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Wei Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Suresh Mahalingam
- Emerging Viruses and Inflammation Research Group, Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Research Center of Avian Disease, College of Veterinary Medicine of Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan 611130, China.
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Marsili G, Perrotti E, Remoli AL, Acchioni C, Sgarbanti M, Battistini A. IFN Regulatory Factors and Antiviral Innate Immunity: How Viruses Can Get Better. J Interferon Cytokine Res 2018; 36:414-32. [PMID: 27379864 DOI: 10.1089/jir.2016.0002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interferon regulatory factor (IRF) family consists of transcriptional regulators that exert multifaceted and versatile functions in multiple biological processes. Their crucial role as central mediators in the establishment and execution of host immunity in response to pathogen-derived signals downstream pattern recognition receptors (PRRs) makes IRFs a hallmark of the host antiviral response. They function as hub molecules at the crossroad of different signaling pathways for the induction of interferon (IFN) and inflammatory cytokines, as well as of antiviral and immunomodulatory genes even in an IFN-independent manner. By regulating the development and activity of immune cells, IRFs also function as a bridge between innate and adaptive responses. As such, IRFs represent attractive and compulsive targets in viral strategies to subvert antiviral signaling. In this study, we discuss current knowledge on the wide array of strategies put in place by pathogenic viruses to evade, subvert, and/or hijack these essential components of host antiviral immunity.
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Affiliation(s)
- Giulia Marsili
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
| | - Edvige Perrotti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
| | - Anna Lisa Remoli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
| | - Chiara Acchioni
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
| | - Marco Sgarbanti
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
| | - Angela Battistini
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità , Rome, Italy
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Moskwa S, Piotrowski W, Marczak J, Pawełczyk M, Lewandowska-Polak A, Jarzębska M, Brauncajs M, Głobińska A, Górski P, Papadopoulos NG, Edwards MR, Johnston SL, Kowalski ML. Innate Immune Response to Viral Infections in Primary Bronchial Epithelial Cells is Modified by the Atopic Status of Asthmatic Patients. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2018; 10:144-154. [PMID: 29411555 PMCID: PMC5809763 DOI: 10.4168/aair.2018.10.2.144] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/10/2017] [Accepted: 09/24/2017] [Indexed: 12/18/2022]
Abstract
Purpose In order to gain an insight into determinants of reported variability in immune responses to respiratory viruses in human bronchial epithelial cells (HBECs) from asthmatics, the responses of HBEC to viral infections were evaluated in HBECs from phenotypically heterogeneous groups of asthmatics and in healthy controls. Methods HBECs were obtained during bronchoscopy from 10 patients with asthma (6 atopic and 4 non-atopic) and from healthy controls (n=9) and grown as undifferentiated cultures. HBECs were infected with parainfluenza virus (PIV)-3 (MOI 0.1) and rhinovirus (RV)-1B (MOI 0.1), or treated with medium alone. The cell supernatants were harvested at 8, 24, and 48 hours. IFN-α, CXCL10 (IP-10), and RANTES (CCL5) were analyzed by using Cytometric Bead Array (CBA), and interferon (IFN)-β and IFN-λ1 by ELISA. Gene expression of IFNs, chemokines, and IFN-regulatory factors (IRF-3 and IRF-7) was determined by using quantitative PCR. Results PIV3 and RV1B infections increased IFN-λ1 mRNA expression in HBECs from asthmatics and healthy controls to a similar extent, and virus-induced IFN-λ1 expression correlated positively with IRF-7 expression. Following PIV3 infection, IP-10 protein release and mRNA expression were significantly higher in asthmatics compared to healthy controls (median 36.03-fold). No differences in the release or expression of RANTES, IFN-λ1 protein and mRNA, or IFN-α and IFN-β mRNA between asthmatics and healthy controls were observed. However, when asthmatics were divided according to their atopic status, HBECs from atopic asthmatics (n=6) generated significantly more IFN-λ1 protein and demonstrated higher IFN-α, IFN-β, and IRF-7 mRNA expressions in response to PIV3 compared to non-atopic asthmatics (n=4) and healthy controls (n=9). In response to RV1B infection, IFN-β mRNA expression was lower (12.39-fold at 24 hours and 19.37-fold at 48 hours) in non-atopic asthmatics compared to atopic asthmatics. Conclusions The immune response of HBECs to virus infections may not be deficient in asthmatics, but seems to be modified by atopic status.
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Affiliation(s)
- Sylwia Moskwa
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland.,Department of Microbiology and Laboratory Medical Immunology, Medical University of Lodz, Lodz, Poland
| | - Wojciech Piotrowski
- Department of Pneumonology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Jerzy Marczak
- Department of Pneumonology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Małgorzata Pawełczyk
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland
| | - Anna Lewandowska-Polak
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland.,Department of Rheumatology, Medical University of Lodz, Lodz, Poland
| | - Marzanna Jarzębska
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland
| | - Małgorzata Brauncajs
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland
| | - Anna Głobińska
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland
| | - Paweł Górski
- Department of Pneumonology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Nikolaos G Papadopoulos
- Allergy Research Centre, 2nd Pediatric Clinic, National Kapodistrian, University of Athens, Athens, Greece
| | - Michael R Edwards
- National Heart and Lung Institute, Imperial College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma
| | - Sebastian L Johnston
- National Heart and Lung Institute, Imperial College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma
| | - Marek L Kowalski
- Department of Immunology, Rheumatology and Allergy; Healthy Ageing Research Centre, Medical University of Lodz, Lodz, Poland.
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Chiang JJ, Sparrer KMJ, van Gent M, Lässig C, Huang T, Osterrieder N, Hopfner KP, Gack MU. Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity. Nat Immunol 2018; 19:53-62. [PMID: 29180807 PMCID: PMC5815369 DOI: 10.1038/s41590-017-0005-y] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
The sensor RIG-I detects double-stranded RNA derived from RNA viruses. Although RIG-I is also known to have a role in the antiviral response to DNA viruses, physiological RNA species recognized by RIG-I during infection with a DNA virus are largely unknown. Using next-generation RNA sequencing (RNAseq), we found that host-derived RNAs, most prominently 5S ribosomal RNA pseudogene 141 (RNA5SP141), bound to RIG-I during infection with herpes simplex virus 1 (HSV-1). Infection with HSV-1 induced relocalization of RNA5SP141 from the nucleus to the cytoplasm, and virus-induced shutoff of host protein synthesis downregulated the abundance of RNA5SP141-interacting proteins, which allowed RNA5SP141 to bind RIG-I and induce the expression of type I interferons. Silencing of RNA5SP141 strongly dampened the antiviral response to HSV-1 and the related virus Epstein-Barr virus (EBV), as well as influenza A virus (IAV). Our findings reveal that antiviral immunity can be triggered by host RNAs that are unshielded following depletion of their respective binding proteins by the virus.
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MESH Headings
- Animals
- Cells, Cultured
- Chlorocebus aethiops
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- Gene Expression/immunology
- HEK293 Cells
- Herpesvirus 1, Human/immunology
- Herpesvirus 1, Human/physiology
- Host-Pathogen Interactions/immunology
- Humans
- Immunity/immunology
- Interferon Type I/genetics
- Interferon Type I/immunology
- Interferon Type I/metabolism
- Mice, Knockout
- Pseudogenes/genetics
- RNA Transport/immunology
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/immunology
- RNA, Ribosomal, 5S/metabolism
- Receptors, Immunologic
- Vero Cells
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Affiliation(s)
- Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | | | - Michiel van Gent
- Department of Microbiology, The University of Chicago, Chicago, IL, USA
| | - Charlotte Lässig
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Teng Huang
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | | | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Michaela U Gack
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.
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32
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Hepatitis C Virus NS5A Targets Nucleosome Assembly Protein NAP1L1 To Control the Innate Cellular Response. J Virol 2017; 91:JVI.00880-17. [PMID: 28659470 DOI: 10.1128/jvi.00880-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis C virus (HCV) is a single-stranded positive-sense RNA hepatotropic virus. Despite cellular defenses, HCV is able to replicate in hepatocytes and to establish a chronic infection that could lead to severe complications and hepatocellular carcinoma. An important player in subverting the host response to HCV infection is the viral nonstructural protein NS5A, which, in addition to its role in replication and assembly, targets several pathways involved in the cellular response to viral infection. Several unbiased screens identified nucleosome assembly protein 1-like 1 (NAP1L1) as an interaction partner of HCV NS5A. Here we confirmed this interaction and mapped it to the C terminus of NS5A of both genotype 1 and 2. NS5A sequesters NAP1L1 in the cytoplasm, blocking its nuclear translocation. However, only NS5A from genotype 2 HCV, and not that from genotype 1, targets NAP1L1 for proteosome-mediated degradation. NAP1L1 is a nuclear chaperone involved in chromatin remodeling, and we demonstrated the NAP1L1-dependent regulation of specific pathways involved in cellular responses to viral infection and cell survival. Among those, we showed that lack of NAP1L1 leads to a decrease of RELA protein levels and a strong defect of IRF3 TBK1/IKKε-mediated phosphorylation, leading to inefficient RIG-I and Toll-like receptor 3 (TLR3) responses. Hence, HCV is able to modulate the host cell environment by targeting NAP1L1 through NS5A.IMPORTANCE Viruses have evolved to replicate and to overcome antiviral countermeasures of the infected cell. Hepatitis C virus is capable of establishing a lifelong chronic infection in the liver, which could develop into cirrhosis and cancer. Chronic viruses are particularly able to interfere with the cellular antiviral pathways by several different mechanisms. In this study, we identified a novel cellular target of the viral nonstructural protein NS5A and demonstrated its role in antiviral signaling. This factor, called nucleosome assembly protein 1-like 1 (NAP1L1), is a nuclear chaperone involved in the remodeling of chromatin during transcription. When it is depleted, specific signaling pathways leading to antiviral effectors are affected. Therefore, we provide evidence for both a novel strategy of virus evasion from cellular immunity and a novel role for a cellular protein, which has not been described to date.
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Lamborn IT, Jing H, Zhang Y, Drutman SB, Abbott JK, Munir S, Bade S, Murdock HM, Santos CP, Brock LG, Masutani E, Fordjour EY, McElwee JJ, Hughes JD, Nichols DP, Belkadi A, Oler AJ, Happel CS, Matthews HF, Abel L, Collins PL, Subbarao K, Gelfand EW, Ciancanelli MJ, Casanova JL, Su HC. Recurrent rhinovirus infections in a child with inherited MDA5 deficiency. J Exp Med 2017; 214:1949-1972. [PMID: 28606988 PMCID: PMC5502429 DOI: 10.1084/jem.20161759] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 04/13/2017] [Accepted: 05/26/2017] [Indexed: 12/15/2022] Open
Abstract
MDA5 is a cytosolic sensor of double-stranded RNA (ds)RNA including viral byproducts and intermediates. We studied a child with life-threatening, recurrent respiratory tract infections, caused by viruses including human rhinovirus (HRV), influenza virus, and respiratory syncytial virus (RSV). We identified in her a homozygous missense mutation in IFIH1 that encodes MDA5. Mutant MDA5 was expressed but did not recognize the synthetic MDA5 agonist/(ds)RNA mimic polyinosinic-polycytidylic acid. When overexpressed, mutant MDA5 failed to drive luciferase activity from the IFNB1 promoter or promoters containing ISRE or NF-κB sequence motifs. In respiratory epithelial cells or fibroblasts, wild-type but not knockdown of MDA5 restricted HRV infection while increasing IFN-stimulated gene expression and IFN-β/λ. However, wild-type MDA5 did not restrict influenza virus or RSV replication. Moreover, nasal epithelial cells from the patient, or fibroblasts gene-edited to express mutant MDA5, showed increased replication of HRV but not influenza or RSV. Thus, human MDA5 deficiency is a novel inborn error of innate and/or intrinsic immunity that causes impaired (ds)RNA sensing, reduced IFN induction, and susceptibility to the common cold virus.
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Affiliation(s)
- Ian T Lamborn
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Huie Jing
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Yu Zhang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Scott B Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Jordan K Abbott
- Immunodeficiency Diagnosis and Treatment Program, Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Shirin Munir
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Heardley M Murdock
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Celia P Santos
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Linda G Brock
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Evan Masutani
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Emmanuel Y Fordjour
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | | | - Dave P Nichols
- Division of Pediatric Pulmonary Medicine, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Corinne S Happel
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Helen F Matthews
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Peter L Collins
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kanta Subbarao
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Erwin W Gelfand
- Immunodeficiency Diagnosis and Treatment Program, Division of Allergy and Immunology, Department of Pediatrics, National Jewish Health, Denver, CO
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale UMR1163, Necker Hospital for Sick Children, Paris, France
- Paris Descartes University, Imagine Institute, Necker Hospital for Sick Children, Paris, France
- Pediatric Immuno-Hematology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, NY
| | - Helen C Su
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Fan YH, Roy S, Mukhopadhyay R, Kapoor A, Duggal P, Wojcik GL, Pass RF, Arav-Boger R. Role of nucleotide-binding oligomerization domain 1 (NOD1) and its variants in human cytomegalovirus control in vitro and in vivo. Proc Natl Acad Sci U S A 2016; 113:E7818-E7827. [PMID: 27856764 PMCID: PMC5137695 DOI: 10.1073/pnas.1611711113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Induction of nucleotide-binding oligomerization domain 2 (NOD2) and downstream receptor-interacting serine/threonine-protein kinase 2 (RIPK2) by human cytomegalovirus (HCMV) is known to up-regulate antiviral responses and suppress virus replication. We investigated the role of nucleotide-binding oligomerization domain 1 (NOD1), which also signals through RIPK2, in HCMV control. NOD1 activation by Tri-DAP (NOD1 agonist) suppressed HCMV and induced IFN-β. Mouse CMV was also inhibited through NOD1 activation. NOD1 knockdown (KD) or inhibition of its activity with small molecule ML130 enhanced HCMV replication in vitro. NOD1 mutations displayed differential effects on HCMV replication and antiviral responses. In cells overexpressing the E56K mutation in the caspase activation and recruitment domain, virus replication was enhanced, but in cells overexpressing the E266K mutation in the nucleotide-binding domain or the wild-type NOD1, HCMV was inhibited, changes that correlated with IFN-β expression. The interaction of NOD1 and RIPK2 determined the outcome of virus replication, as evidenced by enhanced virus growth in NOD1 E56K mutant cells (which failed to interact with RIPK2). NOD1 activities were executed through IFN-β, given that IFN-β KD reduced the inhibitory effect of Tri-DAP on HCMV. Signaling through NOD1 resulting in HCMV suppression was IKKα-dependent and correlated with nuclear translocation and phosphorylation of IRF3. Finally, NOD1 polymorphisms were significantly associated with the risk of HCMV infection in women who were infected with HCMV during participation in a glycoprotein B vaccine trial. Collectively, our data indicate a role for NOD1 in HCMV control via RIPK2- IKKα-IRF3 and suggest that its polymorphisms predict the risk of infection.
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Affiliation(s)
- Yi-Hsin Fan
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Sujayita Roy
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Rupkatha Mukhopadhyay
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Arun Kapoor
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Priya Duggal
- Department of Genetic Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231
| | - Genevieve L Wojcik
- Department of Genetic Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231
| | - Robert F Pass
- Division of Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Ravit Arav-Boger
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287;
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Pestivirus Npro Directly Interacts with Interferon Regulatory Factor 3 Monomer and Dimer. J Virol 2016; 90:7740-7. [PMID: 27334592 DOI: 10.1128/jvi.00318-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Interferon regulatory factor 3 (IRF3) is a transcription factor involved in the activation of type I alpha/beta interferon (IFN-α/β) in response to viral infection. Upon viral infection, the IRF3 monomer is activated into a phosphorylated dimer, which induces the transcription of interferon genes in the nucleus. Viruses have evolved several ways to target IRF3 in order to subvert the innate immune response. Pestiviruses, such as classical swine fever virus (CSFV), target IRF3 for ubiquitination and subsequent proteasomal degradation. This is mediated by the viral protein N(pro) that interacts with IRF3, but the molecular details for this interaction are largely unknown. We used recombinant N(pro) and IRF3 proteins and show that N(pro) interacts with IRF3 directly without additional proteins and forms a soluble 1:1 complex. The full-length IRF3 but not merely either of the individual domains is required for this interaction. The interaction between N(pro) and IRF3 is not dependent on the activation state of IRF3, since N(pro) binds to a constitutively active form of IRF3 in the presence of its transcriptional coactivator, CREB-binding protein (CBP). The results indicate that the N(pro)-binding site on IRF3 encompasses a region that is unperturbed by the phosphorylation and subsequent activation of IRF3 and thus excludes the dimer interface and CBP-binding site. IMPORTANCE The pestivirus N-terminal protease, N(pro), is essential for evading the host's immune system by facilitating the degradation of interferon regulatory factor 3 (IRF3). However, the nature of the N(pro) interaction with IRF3, including the IRF3 species (inactive monomer versus activated dimer) that N(pro) targets for degradation, is largely unknown. We show that classical swine fever virus N(pro) and porcine IRF3 directly interact in solution and that full-length IRF3 is required for interaction with N(pro) Additionally, N(pro) interacts with a constitutively active form of IRF3 bound to its transcriptional cofactor, the CREB-binding protein. This is the first study to demonstrate that N(pro) is able to bind both inactive IRF3 monomer and activated IRF3 dimer and thus likely targets both IRF3 species for ubiquitination and proteasomal degradation.
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Feng H, Zhang QM, Zhang YB, Li Z, Zhang J, Xiong YW, Wu M, Gui JF. Zebrafish IRF1, IRF3, and IRF7 Differentially Regulate IFNΦ1 and IFNΦ3 Expression through Assembly of Homo- or Heteroprotein Complexes. THE JOURNAL OF IMMUNOLOGY 2016; 197:1893-904. [DOI: 10.4049/jimmunol.1600159] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022]
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RIPK4 activates an IRF6-mediated proinflammatory cytokine response in keratinocytes. Cytokine 2016; 83:19-26. [DOI: 10.1016/j.cyto.2016.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 12/12/2022]
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Ren Y, Zhao Y, Lin D, Xu X, Zhu Q, Yao J, Shu HB, Zhong B. The Type I Interferon-IRF7 Axis Mediates Transcriptional Expression of Usp25 Gene. J Biol Chem 2016; 291:13206-15. [PMID: 27129230 PMCID: PMC4933234 DOI: 10.1074/jbc.m116.718080] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Viral infection or lipopolysaccharide (LPS) treatment induces expression of a large array of genes, the products of which play a critical role in host antipathogen immunity and inflammation. We have previously reported that the expression of ubiquitin-specific protease 25 (USP25) is significantly up-regulated after viral infection or LPS treatment, and this is essential for innate immune signaling. However, the mechanism behind this phenomenon is unclear. In this study, we found that viral infection-induced up-regulation of Usp25 is diminished in cells lacking interferon regulatory factor 7 (IRF7) or interferon α receptor 1 (IFNAR1) but not p65. Sendai virus- or type I interferon-induced up-regulation of Usp25 requires de novo protein synthesis of IRF7. Furthermore, IRF7 directly binds to the two conserved IRF binding sites on the USP25 promoter to drive transcription of Usp25, and mutation of these two sites abolished Sendai virus-induced IRF7-mediated activation of the USP25 promoter. Our study has uncovered a previously unknown mechanism by which viral infection or LPS induces up-regulation of USP25.
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Affiliation(s)
- Yujie Ren
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yin Zhao
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dandan Lin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China, and
| | - Ximing Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan 430060, China, and
| | - Qiyun Zhu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Jing Yao
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hong-Bing Shu
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Bo Zhong
- From the State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China,
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Chan YK, Gack MU. A phosphomimetic-based mechanism of dengue virus to antagonize innate immunity. Nat Immunol 2016; 17:523-30. [PMID: 26998762 PMCID: PMC4837045 DOI: 10.1038/ni.3393] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/04/2016] [Indexed: 01/14/2023]
Abstract
14-3-3 proteins regulate biological processes by binding to phosphorylated serine or phosphorylated threonine motifs of cellular proteins. Among the 14-3-3 proteins, 14-3-3ɛ serves a crucial function in antiviral immunity by mediating the cytosol-to-mitochondrial membrane translocation of the pathogen sensor RIG-I. Here we found that the NS3 protein of dengue virus (DV) bound to 14-3-3ɛ and prevented translocation of RIG-I to the adaptor MAVS and thereby blocked antiviral signaling. Intriguingly, a highly conserved phosphomimetic RxEP motif in NS3 was essential for the binding of 14-3-3ɛ. A recombinant mutant DV deficient in binding to 14-3-3ɛ showed impairment in antagonism of RIG-I and elicited a markedly augmented innate immune response and enhanced T cell activation. Our work reveals a novel phosphomimetic-based mechanism for viral antagonism of 14-3-3-mediated immunity, which might guide the rational design of therapeutics.
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Affiliation(s)
- Ying Kai Chan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Michaela U. Gack
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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Sanchez David RY, Combredet C, Sismeiro O, Dillies MA, Jagla B, Coppée JY, Mura M, Guerbois Galla M, Despres P, Tangy F, Komarova AV. Comparative analysis of viral RNA signatures on different RIG-I-like receptors. eLife 2016; 5:e11275. [PMID: 27011352 PMCID: PMC4841775 DOI: 10.7554/elife.11275] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/24/2016] [Indexed: 12/17/2022] Open
Abstract
The RIG-I-like receptors (RLRs) play a major role in sensing RNA virus infection to initiate and modulate antiviral immunity. They interact with particular viral RNAs, most of them being still unknown. To decipher the viral RNA signature on RLRs during viral infection, we tagged RLRs (RIG-I, MDA5, LGP2) and applied tagged protein affinity purification followed by next-generation sequencing (NGS) of associated RNA molecules. Two viruses with negative- and positive-sense RNA genome were used: measles (MV) and chikungunya (CHIKV). NGS analysis revealed that distinct regions of MV genome were specifically recognized by distinct RLRs: RIG-I recognized defective interfering genomes, whereas MDA5 and LGP2 specifically bound MV nucleoprotein-coding region. During CHIKV infection, RIG-I associated specifically to the 3' untranslated region of viral genome. This study provides the first comparative view of the viral RNA ligands for RIG-I, MDA5 and LGP2 in the presence of infection.
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Affiliation(s)
- Raul Y Sanchez David
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Ecole doctorale, Biochimie, Biothérapies, Biologie Moléculaire et Infectiologie (B3MI), Université Paris Diderot - Paris 7, Paris, France
| | - Chantal Combredet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Odile Sismeiro
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Marie-Agnès Dillies
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Bernd Jagla
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and Epigenome, BioMics Pole, Center for Innovation and Technological Research, Institut Pasteur, Paris, France
| | - Marie Mura
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
- Unité Interactions Hôte-Agents Pathogens, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | | | - Philippe Despres
- Technology Platform CYROI, University of Reunion Island, Saint-Clotilde, France
| | - Frédéric Tangy
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS UMR-3569, Paris, France
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Bosco A, Wiehler S, Proud D. Interferon regulatory factor 7 regulates airway epithelial cell responses to human rhinovirus infection. BMC Genomics 2016; 17:76. [PMID: 26810609 PMCID: PMC4727386 DOI: 10.1186/s12864-016-2405-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/18/2016] [Indexed: 12/11/2022] Open
Abstract
Background Human rhinoviruses (HRV) cause the majority of colds and trigger exacerbations of chronic lower airway diseases. Airway epithelial cells are the primary site for HRV infection and replication, and the initiation of host inflammatory responses. At present, the molecular mechanisms that underpin HRV responses in airway epithelial cells are incompletely understood. The aim of this study was to employ microarray profiling, upstream regulator analysis, and siRNA mediated gene silencing to further our understanding of the role of interferon regulatory factor 7 (IRF7) in this response. Methods Primary human bronchial epithelial cells (HBE) where transfected with siRNA that targets IRF7 or a non-silencing control (all-star control) using Lipofectamine. The cells were allowed to recover, and then cultured in the presence or absence of HRV-16 for 24 h. Global patterns of gene expression were profiled on microarrays. A subset of genes identified in the microarray study were validated at the mRNA and/or protein level using real time RT-qPCR, ELISA, and western blots. Results Hundreds of genes were upregulated in HBE during HRV infection. Pathways analysis demonstrated that these genes were mainly involved in type I and II interferon signaling, RIG-I/MDA5 signaling, antigen processing and presentation, and apoptosis. Upstream regulator analysis of these data suggested that IRF7 was a major molecular driver of this response. Knockdown of IRF7 reduced the HRV-driven upregulation of genes involved in antiviral responses (interferon signaling, Toll-like receptor signaling, NOD-like receptor signaling, RIG-I/MDA5 signaling), and increased the expression of genes that promote inflammation (e.g. CXCL5, IL-33, IL1RL1) and the response to oxidative stress. However, the majority of genes that were perturbed by HRV in HBE cells including those that are known to be regulated by IRF7 were insensitive to IRF7 knockdown. Upstream regulator analysis of the part of the response that was insensitive to IRF7 knockdown suggested it was driven by NF-κB, STAT1, STAT3, and IRF1. Conclusions Our findings demonstrate that IRF7 regulates the expression of genes involved in antiviral immunity, inflammation, and the response to oxidative stress during HRV infections in HBE cells, and also suggests that other transcription factors play a major role in this response. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2405-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anthony Bosco
- Telethon Kids Institute, University of Western Australia, PO Box 855, West Perth, WA, 6872, Australia.
| | - Shahina Wiehler
- Airway Inflammation Research Group, Snyder Institute for Chronic Diseases, and the Department of Physiology & Pharmacology, University of Calgary Faculty of Medicine, Calgary, AB, Canada.
| | - David Proud
- Airway Inflammation Research Group, Snyder Institute for Chronic Diseases, and the Department of Physiology & Pharmacology, University of Calgary Faculty of Medicine, Calgary, AB, Canada.
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Moon JS, Lee SH, Kim EJ, Cho H, Lee W, Kim GW, Park HJ, Cho SW, Lee C, Oh JW. Inhibition of Hepatitis C Virus in Mice by a Small Interfering RNA Targeting a Highly Conserved Sequence in Viral IRES Pseudoknot. PLoS One 2016; 11:e0146710. [PMID: 26751678 PMCID: PMC4713436 DOI: 10.1371/journal.pone.0146710] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023] Open
Abstract
The hepatitis C virus (HCV) internal ribosome entry site (IRES) that directs cap-independent viral translation is a primary target for small interfering RNA (siRNA)-based HCV antiviral therapy. However, identification of potent siRNAs against HCV IRES by bioinformatics-based siRNA design is a challenging task given the complexity of HCV IRES secondary and tertiary structures and association with multiple proteins, which can also dynamically change the structure of this cis-acting RNA element. In this work, we utilized siRNA tiling approach whereby siRNAs were tiled with overlapping sequences that were shifted by one or two nucleotides over the HCV IRES stem-loop structures III and IV spanning nucleotides (nts) 277-343. Based on their antiviral activity, we mapped a druggable region (nts 313-343) where the targets of potent siRNAs were enriched. siIE22, which showed the greatest anti-HCV potency, targeted a highly conserved sequence across diverse HCV genotypes, locating within the IRES subdomain IIIf involved in pseudoknot formation. Stepwise target shifting toward the 5' or 3' direction by 1 or 2 nucleotides reduced the antiviral potency of siIE22, demonstrating the importance of siRNA accessibility to this highly structured and sequence-conserved region of HCV IRES for RNA interference. Nanoparticle-mediated systemic delivery of the stability-improved siIE22 derivative gs_PS1 siIE22, which contains a single phosphorothioate linkage on the guide strand, reduced the serum HCV genome titer by more than 4 log10 in a xenograft mouse model for HCV replication without generation of resistant variants. Our results provide a strategy for identifying potent siRNA species against a highly structured RNA target and offer a potential pan-HCV genotypic siRNA therapy that might be beneficial for patients resistant to current treatment regimens.
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Affiliation(s)
- Jae-Su Moon
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Eun-Jung Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Hee Cho
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Wooseong Lee
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Hyun-Ji Park
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Seung-Woo Cho
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
| | - Choongho Lee
- College of Pharmacy, Dongguk University, Goyang 410–820, Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120–749, Korea
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Xu F, Kang Y, Zhuang N, Lu Z, Zhang H, Xu D, Ding Y, Yin H, Shi L. Bcl6 Sets a Threshold for Antiviral Signaling by Restraining IRF7 Transcriptional Program. Sci Rep 2016; 6:18778. [PMID: 26728228 PMCID: PMC4700451 DOI: 10.1038/srep18778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 11/26/2015] [Indexed: 02/04/2023] Open
Abstract
The coordination of restraining and priming of antiviral signaling constitute a fundamental aspect of immunological functions. However, we currently know little about the molecular events that can translate the pathogenic cues into the appropriate code for antiviral defense. Our present study reports a specific role of B cell lymphoma (Bcl)6 as a checkpoint in the initiation of the host response to cytosolic RNA viruses. Remarkably, Bcl6 specifically binds to the interferon-regulatory factor (IRF)7 loci and restrains its transcription, thereby functioning as a negative regulator for interferon (IFN)-β production and antiviral responses. The signal-controlled turnover of the Bcl6, most likely mediated by microRNA-127, coordinates the antiviral response and inflammatory sequelae. Accordingly, de-repression of Bcl6 resulted in a phenotypic conversion of macrophages into highly potent IFN-producing cells and rendered mice more resistant to pathogenic RNA virus infection. The failure to remove the Bcl6 regulator, however, impedes the antiviral signaling and exaggerates viral pneumonia in mice. We thus reveal a novel key molecular checkpoint to orchestrate antiviral innate immunity.
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Affiliation(s)
- Feng Xu
- Department of Infectious Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yanhua Kang
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Ningtong Zhuang
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhe Lu
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hang Zhang
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Dakang Xu
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China.,MIMR-PHI Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Yina Ding
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hongping Yin
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Liyun Shi
- Department of Microbiology and Immunology, Key Lab of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China.,Department of Microbiology and Immunology, Nanjing University of Chinese Medicine, Nanjing 210046, China
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Audsley MD, Marsh GA, Lieu KG, Tachedjian M, Joubert DA, Wang LF, Jans DA, Moseley GW. The immune evasion function of J and Beilong virus V proteins is distinct from that of other paramyxoviruses, consistent with their inclusion in the proposed genus Jeilongvirus. J Gen Virol 2015; 97:581-592. [PMID: 26703878 DOI: 10.1099/jgv.0.000388] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IFN-antagonist function is a major determinant of pathogenicity and cross-species infection by viruses, but remains poorly defined for many potentially zoonotic viruses resident in animal species. The paramyxovirus family contains several zoonotic viruses, including highly pathogenic viruses such as Nipah virus and Hendra virus, and an increasing number of largely uncharacterized animal viruses. Here, we report the characterization of IFN antagonism by the rodent viruses J virus (JPV) and Beilong virus (BeiPV) of the proposed genus Jeilongvirus of the paramyxoviruses. Infection of cells by JPV and BeiPV was found to inhibit IFN-activated nuclear translocation of signal transducer and activator of transcription 1 (STAT1). However, in contrast to most other paramyxoviruses, the JPV and BeiPV V proteins did not interact with or inhibit signalling by STAT1 or STAT2, suggesting that JPV/BeiPV use an atypical V protein-independent strategy to target STATs, consistent with their inclusion in a separate genus. Nevertheless, the V proteins of both viruses interacted with melanoma differentiation-associated protein 5 (MDA5) and robustly inhibited MDA5-dependent activation of the IFN-β promoter. This supports a growing body of evidence that MDA5 is a universal target of paramyxovirus V proteins, such that the V-MDA5 interaction represents a potential target for broad-spectrum antiviral approaches.
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Affiliation(s)
- Michelle D Audsley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Glenn A Marsh
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory (AAHL), Geelong, Victoria 3220, Australia
| | - Kim G Lieu
- Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Mary Tachedjian
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory (AAHL), Geelong, Victoria 3220, Australia
| | - D Albert Joubert
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory (AAHL), Geelong, Victoria 3220, Australia
| | - Lin-Fa Wang
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory (AAHL), Geelong, Victoria 3220, Australia.,Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, 169857Singapore
| | - David A Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Gregory W Moseley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Department of Biochemistry and Molecular Biology, BIO21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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Lissner MM, Thomas BJ, Wee K, Tong AJ, Kollmann TR, Smale ST. Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults. PLoS One 2015; 10:e0132061. [PMID: 26147648 PMCID: PMC4493075 DOI: 10.1371/journal.pone.0132061] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/09/2015] [Indexed: 11/18/2022] Open
Abstract
A variety of age-related differences in the innate and adaptive immune systems have been proposed to contribute to the increased susceptibility to infection of human neonates and older adults. The emergence of RNA sequencing (RNA-seq) provides an opportunity to obtain an unbiased, comprehensive, and quantitative view of gene expression differences in defined cell types from different age groups. An examination of ex vivo human monocyte responses to lipopolysaccharide stimulation or Listeria monocytogenes infection by RNA-seq revealed extensive similarities between neonates, young adults, and older adults, with an unexpectedly small number of genes exhibiting statistically significant age-dependent differences. By examining the differentially induced genes in the context of transcription factor binding motifs and RNA-seq data sets from mutant mouse strains, a previously described deficiency in interferon response factor-3 activity could be implicated in most of the differences between newborns and young adults. Contrary to these observations, older adults exhibited elevated expression of inflammatory genes at baseline, yet the responses following stimulation correlated more closely with those observed in younger adults. Notably, major differences in the expression of constitutively expressed genes were not observed, suggesting that the age-related differences are driven by environmental influences rather than cell-autonomous differences in monocyte development.
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Affiliation(s)
- Michelle M. Lissner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Brandon J. Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kathleen Wee
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ann-Jay Tong
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tobias R. Kollmann
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (TRK); (STS)
| | - Stephen T. Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (TRK); (STS)
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Sun Z, Wang B, Liu Y, Liu X, Mi Y, Gu M, Wang F, Wu C, Hu C. Genome organization and transcriptional regulation of Adenosine Deaminase Acting on RNA gene 1 (ADAR1) in grass carp (Ctenopharyngodon idella). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 50:98-105. [PMID: 25681076 DOI: 10.1016/j.dci.2015.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/07/2015] [Accepted: 02/07/2015] [Indexed: 06/04/2023]
Abstract
ADAR1, involved in A-to-I RNA editing, belongs to adenosine deaminase acting on RNA (ADAR) family. A-to-I RNA editing is the most widespread editing phenomenon in higher eukaryotes. In the present study, we cloned and identified the full-length cDNA, complete genomic sequence and the promoter sequence of grass carp (Ctenopharyngodon idella) ADAR1 (CiADAR1) by homology cloning strategy and genome walking. CiADAR1 full-length cDNA is comprised of a 5'UTR (43 bp), a 3'UTR (229 bp) and a 4179 bp ORF encoding a polypeptide of 1392 amino acids. The deduced amino acid sequence of CiADAR1 contains two Z-DNA binding domains, three dsRNA binding motifs and a conserved catalytic domain. The complete genomic CiADAR1 has 16 exons and 15 introns. Phylogenetic tree analysis revealed that CiADAR1 shared high homology with Danio rerio ADAR1 (DrADAR1). RT-PCR showed that CiADAR1 were ubiquitously expressed and significantly up-regulated after stimulation with poly I:C. In spleen and liver, CiADAR1 mRNA reached the peak at 12 h and maintained the highest level during 12-24 h post-injection. CiADAR1 promoter was found to be 1102 bp in length and divided into two distinct regions, the proximal region containing three putative interferon regulatory factor binding elements (IRF-E) and the distal region containing only one IRF-E. To further study the transcriptional regulatory mechanism of CiADAR1, grass carp IRF1 (CiIRF1) and IRF3 (CiIRF3) were expressed in Escherichia coli BL21 and purified by affinity chromatography with the Ni-NTA His-Bind resin. Then, gel mobility shift assay was employed to analyze the affinity of CiADAR1 promoter sequence with CiIRF1 and CiIRF3 in vitro. The result revealed that CiIRF1 and CiIRF3 bound to CiADAR1 promoter with high affinity, indicating that IRF1 and IRF3 could be the potential transcriptional regulatory factor for CiADAR1. Co-transfection of pcDNA3.1-IRF1 (or pcDNA3.1-IRF3) with pGL3-CiADAR1 into C. idella kidney (CIK) cells showed that both IRF1 and IRF3 played a positive role in CiADAR1 transcription. In addition, the mutant assay revealed that the proximal region of CiADAR1 promoter is the main regulatory region in CiADAR1 transcription.
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Affiliation(s)
- Zhicheng Sun
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Binhua Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yong Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Xiancheng Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yichuan Mi
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Meihui Gu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Fang Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chuxin Wu
- Nanchang Teachers College, Nanchang 330103, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
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Zhu M, Fang T, Li S, Meng K, Guo D. Bipartite Nuclear Localization Signal Controls Nuclear Import and DNA-Binding Activity of IFN Regulatory Factor 3. THE JOURNAL OF IMMUNOLOGY 2015; 195:289-97. [DOI: 10.4049/jimmunol.1500232] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/03/2015] [Indexed: 11/19/2022]
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48
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Ourthiague DR, Birnbaum H, Ortenlöf N, Vargas JD, Wollman R, Hoffmann A. Limited specificity of IRF3 and ISGF3 in the transcriptional innate-immune response to double-stranded RNA. J Leukoc Biol 2015; 98:119-28. [PMID: 25896227 DOI: 10.1189/jlb.4a1014-483rr] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 04/02/2015] [Indexed: 11/24/2022] Open
Abstract
The innate immune response is largely initiated by pathogen-responsive activation of the transcription factor IRF3. Among other target genes, IRF3 controls the expression of IFN-β, which triggers the activation of the transcription factor ISGF3 via the IFNAR. IRF3 and ISGF3 have been reported to control many of the same target genes and together, control the antimicrobial innate-immune program; however, their respective contributions and specificities remain unclear. Here, we used genomic technologies to characterize their specificity in terms of their physical DNA-binding and genetic function. With the use of ChiP-seq and transcriptomic measurements in WT versus ifnar(-/-) versus ifnar(-/-)irf3(-/-) macrophages responding to intracellular dsRNA, we confirmed the known ISGF3 DNA-binding motif and further specified a distinct IRF3 consensus sequence. The functional specificity of IRF3 is particularly pronounced in cytokine/chemokine regulation; yet, even in the control of IFN-β, that specificity is not absolute. By mathematically modeling IFN-β production within an abstracted tissue layer, we find that IRF3 versus ISGF3 specificity may be critical to limiting IFN-β production and ISGF3 activation, temporally and spatially, but that partial overlap in their specificity is tolerable and may enhance the effectiveness of the innate-immune response.
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Affiliation(s)
- Diana R Ourthiague
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Harry Birnbaum
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Niklas Ortenlöf
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Jesse D Vargas
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Roy Wollman
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
| | - Alexander Hoffmann
- *Signaling Systems Laboratory and Department of Chemistry and Biochemistry and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California, USA; and Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, USA
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Iwanaszko M, Kimmel M. NF-κB and IRF pathways: cross-regulation on target genes promoter level. BMC Genomics 2015; 16:307. [PMID: 25888367 PMCID: PMC4430024 DOI: 10.1186/s12864-015-1511-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/31/2015] [Indexed: 12/30/2022] Open
Abstract
Background The NF-κB and IRF transcription factor families are major players in inflammation and antiviral response and act as two major effectors of the innate immune response (IIR). The regulatory mechanisms of activation of these two pathways and their interactions during the IIR are only partially known. Results Our in silico findings report that there is cross-regulation between both pathways at the level of gene transcription regulation, mediated by the presence of binding sites for both factors in promoters of genes essential for these pathways. These findings agree with recent experimental data reporting crosstalk between pathways activated by RIG-I and TLR3 receptors in response to pathogens. Conclusions We present an extended crosstalk diagram of the IRF - NF-κB pathways. We conclude that members of the NF-κB family may directly impact regulation of IRF family, while IRF members impact regulation of NF-κB family rather indirectly, via other transcription factors such as AP-1 and SP1. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1511-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Iwanaszko
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland. .,Department of Statistics, Rice University, Houston, TX, USA. .,Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Marek Kimmel
- Systems Engineering Group, Silesian University of Technology, Gliwice, Poland. .,Department of Statistics, Rice University, Houston, TX, USA.
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Hu S, Hosey KL, Derbigny WA. Analyses of the pathways involved in early- and late-phase induction of IFN-beta during C. muridarum infection of oviduct epithelial cells. PLoS One 2015; 10:e0119235. [PMID: 25798928 PMCID: PMC4370658 DOI: 10.1371/journal.pone.0119235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/26/2015] [Indexed: 11/18/2022] Open
Abstract
We previously reported that the IFN-β secreted by Chlamydia muridarum-infected murine oviduct epithelial cells (OE cells) was mostly dependent on the TLR3 signaling pathway. To further characterize the mechanisms of IFN-β synthesis during Chlamydia infection of OE cells in vitro, we utilized specific inhibitory drugs to clarify the roles of IRF3 and NF-κB on both early- and late-phase C. muridarum infections. Our results showed that the pathways involved in the early-phase of IFN-β production were distinct from that in the late-phase of IFN-β production. Disruption of IRF3 activation using an inhibitor of TBK-1 at early-phase Chlamydia infection had a significant impact on the overall synthesis of IFN-β; however, disruption of IRF3 activation at late times during infection had no effect. Interestingly, inhibition of NF-κB early during Chlamydia infection also had a negative effect on IFN-β production; however, its impact was not significant. Our data show that the transcription factor IRF7 was induced late during Chlamydia infection, which is indicative of a positive feedback mechanism of IFN-β synthesis late during infection. In contrast, IRF7 appears to play little or no role in the early synthesis of IFN-β during Chlamydia infection. Finally, we demonstrate that antibiotics that target chlamydial DNA replication are much more effective at reducing IFN-β synthesis during infection versus antibiotics that target chlamydial transcription. These results provide evidence that early- and late-phase IFN-β production have distinct signaling pathways in Chlamydia-infected OE cells, and suggest that Chlamydia DNA replication might provide a link to the currently unknown chlamydial PAMP for TLR3.
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Affiliation(s)
- Sishun Hu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Kristen L. Hosey
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Wilbert A. Derbigny
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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