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Shaw AB, Tse HN, Byford O, Plahe G, Moon-Walker A, Hover SE, Saphire EO, Whelan SPJ, Mankouri J, Fontana J, Barr JN. Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry. mBio 2024; 15:e0168423. [PMID: 38874413 PMCID: PMC11253613 DOI: 10.1128/mbio.01684-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/21/2024] [Indexed: 06/15/2024] Open
Abstract
Lymphocytic choriomeningitis virus (LCMV) is an enveloped and segmented negative-sense RNA virus classified within the Arenaviridae family of the Bunyavirales order. LCMV is associated with fatal disease in immunocompromised populations and, as the prototypical arenavirus member, acts as a model for the many highly pathogenic members of the Arenaviridae family, such as Junín, Lassa, and Lujo viruses, all of which are associated with devastating hemorrhagic fevers. To enter cells, the LCMV envelope fuses with late endosomal membranes, for which two established requirements are low pH and interaction between the LCMV glycoprotein (GP) spike and secondary receptor CD164. LCMV subsequently uncoats, where the RNA genome-associated nucleoprotein (NP) separates from the Z protein matrix layer, releasing the viral genome into the cytosol. To further examine LCMV endosome escape, we performed an siRNA screen which identified host cell potassium ion (K+) channels as important for LCMV infection, with pharmacological inhibition confirming K+ channel involvement during the LCMV entry phase completely abrogating productive infection. To better understand the K+-mediated block in infection, we tracked incoming virions along their entry pathway under physiological conditions, where uncoating was signified by separation of NP and Z proteins. In contrast, K+ channel blockade prevented uncoating, trapping virions within Rab7 and CD164-positive endosomes, identifying K+ as a third LCMV entry requirement. K+ did not increase GP-CD164 binding or alter GP-CD164-dependent fusion. Thus, we propose that K+ mediates uncoating by modulating NP-Z interactions within the virion interior. These results suggest K+ channels represent a potential anti-arenaviral target.IMPORTANCEArenaviruses can cause fatal human disease for which approved preventative or therapeutic options are not available. Here, using the prototypical LCMV, we identified K+ channels as critical for arenavirus infection, playing a vital role during the entry phase of the infection cycle. We showed that blocking K+ channel function resulted in entrapment of LCMV particles within late endosomal compartments, thus preventing productive replication. Our data suggest K+ is required for LCMV uncoating and genome release by modulating interactions between the viral nucleoprotein and the matrix protein layer inside the virus particle.
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Affiliation(s)
- Amelia B. Shaw
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Hiu Nam Tse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Owen Byford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Grace Plahe
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex Moon-Walker
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Samantha E. Hover
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jamel Mankouri
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Juan Fontana
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - John N. Barr
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
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Johnson DM, Khakhum N, Wang M, Warner NL, Jokinen JD, Comer JE, Lukashevich IS. Pathogenic and Apathogenic Strains of Lymphocytic Choriomeningitis Virus Have Distinct Entry and Innate Immune Activation Pathways. Viruses 2024; 16:635. [PMID: 38675975 PMCID: PMC11053560 DOI: 10.3390/v16040635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Lymphocytic choriomeningitis virus (LCMV) and Lassa virus (LASV) share many genetic and biological features including subtle differences between pathogenic and apathogenic strains. Despite remarkable genetic similarity, the viscerotropic WE strain of LCMV causes a fatal LASV fever-like hepatitis in non-human primates (NHPs) while the mouse-adapted Armstrong (ARM) strain of LCMV is deeply attenuated in NHPs and can vaccinate against LCMV-WE challenge. Here, we demonstrate that internalization of WE is more sensitive to the depletion of membrane cholesterol than ARM infection while ARM infection is more reliant on endosomal acidification. LCMV-ARM induces robust NF-κB and interferon response factor (IRF) activation while LCMV-WE seems to avoid early innate sensing and failed to induce strong NF-κB and IRF responses in dual-reporter monocyte and epithelial cells. Toll-like receptor 2 (TLR-2) signaling appears to play a critical role in NF-κB activation and the silencing of TLR-2 shuts down IL-6 production in ARM but not in WE-infected cells. Pathogenic LCMV-WE infection is poorly recognized in early endosomes and failed to induce TLR-2/Mal-dependent pro-inflammatory cytokines. Following infection, Interleukin-1 receptor-associated kinase 1 (IRAK-1) expression is diminished in LCMV-ARM- but not LCMV-WE-infected cells, which indicates it is likely involved in the LCMV-ARM NF-κB activation. By confocal microscopy, ARM and WE strains have similar intracellular trafficking although LCMV-ARM infection appears to coincide with greater co-localization of early endosome marker EEA1 with TLR-2. Both strains co-localize with Rab-7, a late endosome marker, but the interaction with LCMV-WE seems to be more prolonged. These findings suggest that LCMV-ARM's intracellular trafficking pathway may facilitate interaction with innate immune sensors, which promotes the induction of effective innate and adaptive immune responses.
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Affiliation(s)
- Dylan M. Johnson
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, Louisville, KY 94202, USA (I.S.L.)
- Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY 94202, USA
- Galveston National Laboratory, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA; (N.K.); (J.E.C.)
- Sandia National Laboratories, Department of Biotechnology & Bioengineering, Livermore, CA 94550, USA
| | - Nittaya Khakhum
- Galveston National Laboratory, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA; (N.K.); (J.E.C.)
| | - Min Wang
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY 94202, USA;
| | - Nikole L. Warner
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, Louisville, KY 94202, USA (I.S.L.)
- Department of Microbiology and Immunology, University of Louisville Health Sciences Center, Louisville, KY 94202, USA
| | - Jenny D. Jokinen
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, Louisville, KY 94202, USA (I.S.L.)
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY 94202, USA;
| | - Jason E. Comer
- Galveston National Laboratory, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA; (N.K.); (J.E.C.)
| | - Igor S. Lukashevich
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, Louisville, KY 94202, USA (I.S.L.)
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY 94202, USA;
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Mei H, Zha Z, Wang W, Xie Y, Huang Y, Li W, Wei D, Zhang X, Qu J, Liu J. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Genome Biol 2021; 22:297. [PMID: 34686207 PMCID: PMC8532573 DOI: 10.1186/s13059-021-02513-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02513-w.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Yusang Xie
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuege Huang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Shanghai Clinical Research and Trial Center, 201210, Shanghai, People's Republic of China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510182, Guangdong Province, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, People's Republic of China. .,Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou Interntional Bio Island, Guangdong Province, 510005, Guangzhou, China.
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Identification of COVID-19 prognostic markers and therapeutic targets through meta-analysis and validation of Omics data from nasopharyngeal samples. EBioMedicine 2021; 70:103525. [PMID: 34392148 PMCID: PMC8358265 DOI: 10.1016/j.ebiom.2021.103525] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background While our battle with the COVID-19 pandemic continues, a multitude of Omics data have been generated from patient samples in various studies. Translation of these data into clinical interventions against COVID-19 remains to be accomplished. Exploring host response to COVID-19 in the upper respiratory tract can unveil prognostic markers and therapeutic targets. Methods We conducted a meta-analysis of published transcriptome and proteome profiles of respiratory samples of COVID-19 patients to shortlist high confidence upregulated host factors. Subsequently, mRNA overexpression of selected genes was validated in nasal swabs from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. Guided by this analysis, we sought to check for potential drug targets. An FDA-approved drug, Auranofin, was tested against SARS-CoV-2 replication in cell culture and Syrian hamster challenge model. Findings The meta-analysis and validation in the COVID-19 cohort revealed S100 family genes (S100A6, S100A8, S100A9, and S100P) as prognostic markers of severe COVID-19. Furthermore, Thioredoxin (TXN) was found to be consistently upregulated. Auranofin, which targets Thioredoxin reductase, was found to mitigate SARS-CoV-2 replication in vitro. Furthermore, oral administration of Auranofin in Syrian hamsters in therapeutic as well as prophylactic regimen reduced viral replication, IL-6 production, and inflammation in the lungs. Interpretation Elevated mRNA level of S100s in the nasal swabs indicate severe COVID-19 disease, and FDA-approved drug Auranofin mitigated SARS-CoV-2 replication in preclinical hamster model. Funding This study was supported by the DBT-IISc partnership program (DBT (IED/4/2020-MED/DBT)), the Infosys Young Investigator award (YI/2019/1106), DBT-BIRAC grant (BT/CS0007/CS/02/20) and the DBT-Wellcome Trust India Alliance Intermediate Fellowship (IA/I/18/1/503613) to ST lab.
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Yan J, Zheng Y, Yuan P, Wang S, Han S, Yin J, Peng B, Li Z, Sun Y, He X, Liu W. Novel Host Protein TBC1D16, a GTPase Activating Protein of Rab5C, Inhibits Prototype Foamy Virus Replication. Front Immunol 2021; 12:658660. [PMID: 34367131 PMCID: PMC8339588 DOI: 10.3389/fimmu.2021.658660] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Prototype foamy virus (PFV) is a member of the oldest family of retroviruses and maintains lifelong latent infection in the host. The lifelong latent infection of PFV may be maintained by the restriction factors of viral replication in the host. However, the mechanisms involved in PFV latent infection are poorly understood. Here, we found that TBC1D16, a TBC domain-containing protein, is significantly down-regulated after PFV infection. Tre2/Bub2/Cdc16 (TBC) domain-containing proteins function as Rab GTPase-activating proteins (GAPs) and are participates in the progression of some diseases and many signaling pathways. However, whether TBC proteins are involved in PFV replication has not been determined. Here, we found that TBC1D16 is a novel antiviral protein that targets Rab5C to suppress PFV replication. Overexpression TBC1D16 inhibited the transcription and expression of Tas and Gag, and silencing TBC1D16 enhanced the PFV replication. Moreover, the highly conserved amino acid residues R494 and Q531 in the TBC domain of TBC1D16 were essential for inhibiting PFV replication. We also found that TBC1D16 promoted the production of PFV-induced IFN-β and the transcription of downstream genes. These results suggest that TBC1D16 might be the first identified TBC proteins that inhibited PFV replication and the mechanism by which TBC1D16 inhibited PFV replication could provide new insights for PFV latency.
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Affiliation(s)
- Jun Yan
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Peipei Yuan
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, China
| | - Shanshan Wang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Song Han
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jun Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Biwen Peng
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhi Li
- College of Life Sciences, Shanxi Normal University, Xi’an, China
| | - Yan Sun
- College of Life Sciences, Shanxi Normal University, Xi’an, China
| | - Xiaohua He
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wanhong Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Shenzhen Research Institute, Wuhan University, Shenzhen, China
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