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Chivé C, Martίn-Faivre L, Eon-Bertho A, Alwardini C, Degrouard J, Albinet A, Noyalet G, Chevaillier S, Maisonneuve F, Sallenave JM, Devineau S, Michoud V, Garcia-Verdugo I, Baeza-Squiban A. Exposure to PM 2.5 modulate the pro-inflammatory and interferon responses against influenza virus infection in a human 3D bronchial epithelium model. Environ Pollut 2024; 348:123781. [PMID: 38492752 DOI: 10.1016/j.envpol.2024.123781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/29/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Epidemiological studies showed a positive association between exposure to PM2.5 and the severity of influenza virus infection. However, the mechanisms by which PM2.5 can disrupt antiviral defence are still unclear. From this perspective, the objective of this study was to evaluate the effects of PM2.5 on antiviral signalling in the respiratory epithelium using the bronchial Calu-3 cell line grown at the air-liquid interface. Pre-exposure to PM2.5 before infection with the influenza virus was investigated, as well as a co-exposure. Although a physical interaction between the virus and the particles seems possible, no effect of PM2.5 on viral replication was observed during co-exposure, although a downregulation of IFN-β release was associated to PM2.5 exposure. However, pre-exposure slightly increased the viral nucleoprotein production and the pro-inflammatory response. Conversely, the level of the myxovirus resistance protein A (MxA), an interferon-stimulated gene (ISG) induced by IFN-β, was reduced. Therefore, these results suggest that pre-exposure to PM2.5 could alter the antiviral response of bronchial epithelial cells, increasing their susceptibility to viral infection.
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Affiliation(s)
- Chloé Chivé
- Université Paris Cité, Functional and Adaptive Biology Unit, UMR8251-CNRS, Paris, France; French Environment and Energy Management Agency 20, Avenue Du Grésillé - BP, 90406 49004, Angers, France
| | - Lydie Martίn-Faivre
- Université Paris Cité, Inflamex Excellence Laboratory, INSERM UMR-1152-PHERE, F-75018, Paris, France
| | - Alice Eon-Bertho
- Université Paris Cité, Functional and Adaptive Biology Unit, UMR8251-CNRS, Paris, France
| | - Christelle Alwardini
- Université Paris Cité, Functional and Adaptive Biology Unit, UMR8251-CNRS, Paris, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405, Orsay, France
| | - Alexandre Albinet
- Institut National de L'Environnement Industriel et des Risques (INERIS), Parc Technologique Alata BP2, 60550, Verneuil en Halatte, France
| | - Gael Noyalet
- Université Paris Cité and Université Paris Est Créteil, CNRS, LISA, F-75013, Paris, France
| | - Servanne Chevaillier
- Université Paris Cité and Université Paris Est Créteil, CNRS, LISA, F-75013, Paris, France
| | - Franck Maisonneuve
- Université Paris Est Créteil and Université Paris Cité, CNRS, LISA, F-94010, Créteil, France
| | - Jean-Michel Sallenave
- Université Paris Cité, Inflamex Excellence Laboratory, INSERM UMR-1152-PHERE, F-75018, Paris, France
| | - Stéphanie Devineau
- Université Paris Cité, Functional and Adaptive Biology Unit, UMR8251-CNRS, Paris, France
| | - Vincent Michoud
- Université Paris Cité and Université Paris Est Créteil, CNRS, LISA, F-75013, Paris, France
| | - Ignacio Garcia-Verdugo
- Université Paris Cité, Inflamex Excellence Laboratory, INSERM UMR-1152-PHERE, F-75018, Paris, France.
| | - Armelle Baeza-Squiban
- Université Paris Cité, Functional and Adaptive Biology Unit, UMR8251-CNRS, Paris, France
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Cohn O, Yankovitz G, Mandelboim M, Peshes-Yaloz N, Brandes R, Bacharach E, Gat-Viks I. The host transcriptional response to superinfection by influenza A virus and Streptococcus pneumoniae. mSystems 2024; 9:e0104823. [PMID: 38446104 PMCID: PMC11019783 DOI: 10.1128/msystems.01048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Secondary bacterial challenges during influenza virus infection "superinfection") cause excessive mortality and hospitalization. Here, we present a longitudinal study of bulk gene expression changes in murine lungs during superinfection, with an initial influenza A virus infection and a subsequent Streptococcus pneumoniae infection. In addition to the well-characterized impairment of the host response, we identified superinfection-specific alterations in the global transcriptional program that are linked to the host's ability to resist the pathogens. Particularly, whereas superinfected mice manifested an excessive rapid induction of the resistance-to-infection program, there was a substantial tissue-level rewiring of this program: upon superinfection, interferon-regulated genes were switched from positive to negative correlations with the host's resistance state, whereas genes of fatty acid metabolism switched from negative to positive correlations with resistance states. Thus, the transcriptional resistance state in superinfection is reprogrammed toward repressed interferon signaling and induced fatty acid metabolism. Our findings suggest new insights into a tissue-level remodeling of the host defense upon superinfection, providing promising targets for future therapeutic interventions. IMPORTANCE Secondary bacterial infections are the most frequent complications during influenza A virus (IAV) pandemic outbreaks, contributing to excessive morbidity and mortality in the human population. Most IAV-related deaths are attributed to Streptococcus pneumoniae (SP) infections, which usually begin within the first week of IAV infection in the respiratory tracts. Here, we focused on longitudinal transcriptional responses during a superinfection model consisting of an SP infection that follows an initial IAV infection, comparing superinfection to an IAV-only infection, an SP-only infection, and control treatments. Our longitudinal data allowed a fine analysis of gene expression changes during superinfection. For instance, we found that superinfected mice exhibited rapid gene expression induction or reduction within the first 12 h after encountering the second pathogen. Cell proliferation and immune response activation processes were upregulated, while endothelial processes, vasculogenesis, and angiogenesis were downregulated, providing promising targets for future therapeutic interventions. We further analyzed the longitudinal transcriptional responses in the context of a previously defined spectrum of the host's resistance state, revealing superinfection-specific reprogramming of resistance states, such as reprogramming of fatty acid metabolism and interferon signaling. The reprogrammed functions are compelling new targets for switching the pathogenic superinfection state into a single-infection state.
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Affiliation(s)
- Ofir Cohn
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Gal Yankovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- Department of Epidemiology and Preventive Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naama Peshes-Yaloz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rachel Brandes
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Zhang S, Li B, Zeng L, Yang K, Jiang J, Lu F, Li L, Li W. Exploring the immune-inflammatory mechanism of Maxing Shigan Decoction in treating influenza virus A-induced pneumonia based on an integrated strategy of single-cell transcriptomics and systems biology. Eur J Med Res 2024; 29:234. [PMID: 38622728 PMCID: PMC11017673 DOI: 10.1186/s40001-024-01777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Influenza is an acute respiratory infection caused by influenza virus. Maxing Shigan Decoction (MXSGD) is a commonly used traditional Chinese medicine prescription for the prevention and treatment of influenza. However, its mechanism remains unclear. METHOD The mice model of influenza A virus pneumonia was established by nasal inoculation. After 3 days of intervention, the lung index was calculated, and the pathological changes of lung tissue were detected by HE staining. Firstly, transcriptomics technology was used to analyze the differential genes and important pathways in mouse lung tissue regulated by MXSGD. Then, real-time fluorescent quantitative PCR (RT-PCR) was used to verify the changes in mRNA expression in lung tissues. Finally, intestinal microbiome and intestinal metabolomics were performed to explore the effect of MXSGD on gut microbiota. RESULTS The lung inflammatory cell infiltration in the MXSGD group was significantly reduced (p < 0.05). The results of bioinformatics analysis for transcriptomics results show that these genes are mainly involved in inflammatory factors and inflammation-related signal pathways mediated inflammation biological modules, etc. Intestinal microbiome showed that the intestinal flora Actinobacteriota level and Desulfobacterota level increased in MXSGD group, while Planctomycetota in MXSGD group decreased. Metabolites were mainly involved in primary bile acid biosynthesis, thiamine metabolism, etc. This suggests that MXSGD has a microbial-gut-lung axis regulation effect on mice with influenza A virus pneumonia. CONCLUSION MXSGD may play an anti-inflammatory and immunoregulatory role by regulating intestinal microbiome and intestinal metabolic small molecules, and ultimately play a role in the treatment of influenza A virus pneumonia.
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Affiliation(s)
- Shiying Zhang
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
- Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Bei Li
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Shenzhen Luohu People's Hospital, Shenzhen, China
- The Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Liuting Zeng
- Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Kailin Yang
- Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Junyao Jiang
- School of Life Science, Westlake University, Hangzhou, China
| | - Fangguo Lu
- Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Ling Li
- Hunan University of Chinese Medicine, Changsha, Hunan, China.
| | - Weiqing Li
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China.
- Shenzhen Luohu People's Hospital, Shenzhen, China.
- The Third Affiliated Hospital of Shenzhen University, Shenzhen, China.
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Wu W, Arunagiri V, Do-Umehara HC, Chen C, Gu S, Biswas I, Ridge KM, Budinger GRS, Liu S, Liu J. Miz1 represses type I interferon production and limits viral clearance during influenza A virus infection. Sci Signal 2024; 17:eadg7867. [PMID: 38593156 DOI: 10.1126/scisignal.adg7867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Type I interferons (IFNs) are critical for the antiviral immune response, and fine-tuning type I IFN production is critical to effectively clearing viruses without causing harmful immunopathology. We showed that the transcription factor Miz1 epigenetically repressed the expression of genes encoding type I IFNs in mouse lung epithelial cells by recruiting histone deacetylase 1 (HDAC1) to the promoters of Ifna and Ifnb. Loss of function of Miz1 resulted in augmented production of these type I IFNs during influenza A virus (IAV) infection, leading to improved viral clearance in vitro and in vivo. IAV infection induced Miz1 accumulation by promoting the cullin-4B (CUL4B)-mediated ubiquitylation and degradation of the E3 ubiquitin ligase Mule (Mcl-1 ubiquitin ligase E3; also known as Huwe1 or Arf-BP1), which targets Miz1 for degradation. As a result, Miz1 accumulation limited type I IFN production and favored viral replication. This study reveals a previously unrecognized function of Miz1 in regulating antiviral defense and a potential mechanism for influenza viruses to evade host immune defense.
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Affiliation(s)
- Wenjiao Wu
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- Department of Pharmacy, Guangdong Second Provincial General Hospital, 466 Middle Xingang Road, Guangzhou 510317, Guangdong, China
| | - Vinothini Arunagiri
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hanh Chi Do-Umehara
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Cong Chen
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shuyin Gu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Indrani Biswas
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Jing Liu
- Department of Surgery, College of Medicine, Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
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5
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Zhang Z, Jin H, Zhang X, Bai M, Zheng K, Tian J, Deng B, Mao L, Qiu P, Huang B. Bioinformatics and system biology approach to identify the influences among COVID-19, influenza, and HIV on the regulation of gene expression. Front Immunol 2024; 15:1369311. [PMID: 38601162 PMCID: PMC11004287 DOI: 10.3389/fimmu.2024.1369311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Background Coronavirus disease (COVID-19), caused by SARS-CoV-2, has emerged as a infectious disease, coexisting with widespread seasonal and sporadic influenza epidemics globally. Individuals living with HIV, characterized by compromised immune systems, face an elevated risk of severe outcomes and increased mortality when affected by COVID-19. Despite this connection, the molecular intricacies linking COVID-19, influenza, and HIV remain unclear. Our research endeavors to elucidate the shared pathways and molecular markers in individuals with HIV concurrently infected with COVID-19 and influenza. Furthermore, we aim to identify potential medications that may prove beneficial in managing these three interconnected illnesses. Methods Sequencing data for COVID-19 (GSE157103), influenza (GSE185576), and HIV (GSE195434) were retrieved from the GEO database. Commonly expressed differentially expressed genes (DEGs) were identified across the three datasets, followed by immune infiltration analysis and diagnostic ROC analysis on the DEGs. Functional enrichment analysis was performed using GO/KEGG and Gene Set Enrichment Analysis (GSEA). Hub genes were screened through a Protein-Protein Interaction networks (PPIs) analysis among DEGs. Analysis of miRNAs, transcription factors, drug chemicals, diseases, and RNA-binding proteins was conducted based on the identified hub genes. Finally, quantitative PCR (qPCR) expression verification was undertaken for selected hub genes. Results The analysis of the three datasets revealed a total of 22 shared DEGs, with the majority exhibiting an area under the curve value exceeding 0.7. Functional enrichment analysis with GO/KEGG and GSEA primarily highlighted signaling pathways associated with ribosomes and tumors. The ten identified hub genes included IFI44L, IFI44, RSAD2, ISG15, IFIT3, OAS1, EIF2AK2, IFI27, OASL, and EPSTI1. Additionally, five crucial miRNAs (hsa-miR-8060, hsa-miR-6890-5p, hsa-miR-5003-3p, hsa-miR-6893-3p, and hsa-miR-6069), five essential transcription factors (CREB1, CEBPB, EGR1, EP300, and IRF1), and the top ten significant drug chemicals (estradiol, progesterone, tretinoin, calcitriol, fluorouracil, methotrexate, lipopolysaccharide, valproic acid, silicon dioxide, cyclosporine) were identified. Conclusion This research provides valuable insights into shared molecular targets, signaling pathways, drug chemicals, and potential biomarkers for individuals facing the complex intersection of COVID-19, influenza, and HIV. These findings hold promise for enhancing the precision of diagnosis and treatment for individuals with HIV co-infected with COVID-19 and influenza.
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Affiliation(s)
- Zhen Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Hao Jin
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Xu Zhang
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Mei Bai
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Kexin Zheng
- Microbiology Laboratory Department, Jinzhou Center for Disease Control and Prevention, Jinzhou, Liaoning, China
| | - Jing Tian
- Department of Immunology, School of Basic Medical Science, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bin Deng
- Laboratory Department, Jinzhou Central Hospital, Jinzhou, Liaoning, China
| | - Lingling Mao
- Institute for Prevention and Control of Infection and Infectious Diseases, Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Pengcheng Qiu
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Bo Huang
- Thoracic Surgery Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning, China
- Thoracic Surgery Department, Yingkou Central Hospital, Yingkou, Liaoning, China
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Yang R, Pan M, Guo J, Huang Y, Zhang QC, Deng T, Wang J. Mapping of the influenza A virus genome RNA structure and interactions reveals essential elements of viral replication. Cell Rep 2024; 43:113833. [PMID: 38416642 DOI: 10.1016/j.celrep.2024.113833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024] Open
Abstract
Influenza A virus (IAV) represents a constant public health threat. The single-stranded, segmented RNA genome of IAV is replicated in host cell nuclei as a series of 8 ribonucleoprotein complexes (vRNPs) with RNA structures known to exert essential function to support viral replication. Here, we investigate RNA secondary structures and RNA interactions networks of the IAV genome and construct an in vivo structure model for each of the 8 IAV genome segments. Our analyses reveal an overall in vivo and in virio resemblance of the IAV genome conformation but also wide disparities among long-range and intersegment interactions. Moreover, we identify a long-range RNA interaction that exerts an essential role in genome packaging. Disrupting this structure displays reduced infectivity, attenuating virus pathogenicity in mice. Our findings characterize the in vivo RNA structural landscape of the IAV genome and reveal viral RNA structures that can be targeted to develop antiviral interventions.
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Affiliation(s)
- Rui Yang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minglei Pan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Huang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- The State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Tao Deng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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7
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Zou Y, Sun X, Wang Y, Wang Y, Ye X, Tu J, Yu R, Huang P. Integrating single-cell RNA sequencing data to genome-wide association analysis data identifies significant cell types in influenza A virus infection and COVID-19. Brief Funct Genomics 2024; 23:110-117. [PMID: 37340787 DOI: 10.1093/bfgp/elad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 02/23/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
With the global pandemic of COVID-19, the research on influenza virus has entered a new stage, but it is difficult to elucidate the pathogenesis of influenza disease. Genome-wide association studies (GWASs) have greatly shed light on the role of host genetic background in influenza pathogenesis and prognosis, whereas single-cell RNA sequencing (scRNA-seq) has enabled unprecedented resolution of cellular diversity and in vivo following influenza disease. Here, we performed a comprehensive analysis of influenza GWAS and scRNA-seq data to reveal cell types associated with influenza disease and provide clues to understanding pathogenesis. We downloaded two GWAS summary data, two scRNA-seq data on influenza disease. After defining cell types for each scRNA-seq data, we used RolyPoly and LDSC-cts to integrate GWAS and scRNA-seq. Furthermore, we analyzed scRNA-seq data from the peripheral blood mononuclear cells (PBMCs) of a healthy population to validate and compare our results. After processing the scRNA-seq data, we obtained approximately 70 000 cells and identified up to 13 cell types. For the European population analysis, we determined an association between neutrophils and influenza disease. For the East Asian population analysis, we identified an association between monocytes and influenza disease. In addition, we also identified monocytes as a significantly related cell type in a dataset of healthy human PBMCs. In this comprehensive analysis, we identified neutrophils and monocytes as influenza disease-associated cell types. More attention and validation should be given in future studies.
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Affiliation(s)
- Yixin Zou
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xifang Sun
- Department of Mathematics, School of Science, Xi'an Shiyou University, Xi'an, China
| | - Yifan Wang
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Yidi Wang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiangyu Ye
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junlan Tu
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rongbin Yu
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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8
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Buttrini M, De Conto F. Host Cell-dependent Modulatory Role of Ras Homolog Enriched in Brain-Like-1 (RhebL1) Protein in Influenza A/NWS/33 Virus-infected Mammalian Cells. FRONT BIOSCI-LANDMRK 2024; 29:116. [PMID: 38538289 DOI: 10.31083/j.fbl2903116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The Mammalian Target of Rapamycin (mTOR) signaling pathway regulates protein phosphorylation and exerts control over major cellular processes. mTOR is activated by the small G-protein Ras Homolog Enriched in Brain (Rheb), which is encoded by the Rheb1 and Rheb-like-1 (RhebL1) genes. There is currently a paucity of information on the role of RhebL1, and specifically its involvement in viral infection. In the present study we investigated the role of RhebL1 during human influenza A/NWS/33 (NWS/33) (H1N1) virus infection of rhesus monkey-kidney (LLC-MK2) cells and human type II alveolar epithelial (A549) cells. METHODS To assess the efficiency of NWS/33 virus replication, the expression of viral nucleoprotein was examined by indirect immunofluorescence (IIF) and the viral yield by fifty percent tissue culture infectious dose assay. An RNA-mediated RNA interference approach was used to investigate the role of RhebL1 during NWS/33 infection. RhebL1 expression was evaluated by IIF, Western blotting, and enzyme-linked immunosorbent assays. A two-tailed Student's t-test was applied to evaluate differences between groups. RESULTS RhebL1 was differentially expressed in the cell models used in this study. Silencing of the RhebL1 gene led to increased NWS/33 virus infection in A549 cells, but not in LLC-MK2 cells. Moreover, the expression of hyperphosphorylated cytokeratin 8, a marker of NWS/33 virus infection efficiency, increased in A549 cells depleted of RhebL1 but remained almost unchanged in LLC-MK2 cells. CONCLUSIONS These are the first results showing involvement of the endogenous RhebL1 protein during viral infection. Our data suggests that RhebL1 exerts a host cell-dependent modulatory role during influenza virus infection. RhebL1 appears to be a restrictive factor against NWS/33 virus replication in A549 cells, but not in LLC-MK2.
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Affiliation(s)
- Mirko Buttrini
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Flora De Conto
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
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9
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Yuan J, Pan J, Zhang X, Gao R. TRIM21 reduces H1N1-induced inflammation and apoptosis by regulating the TBK1-IRF3 signaling pathway in A549 cells. Arch Virol 2024; 169:74. [PMID: 38480558 DOI: 10.1007/s00705-024-05989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/29/2023] [Indexed: 04/10/2024]
Abstract
Triple motif protein 21 (TRIM21) has an antiviral function that inhibits various viral infections. However, its role in the progress of influenza A virus (IAV) infection is unclear. In this study, we investigated the role and molecular mechanism of TRIM21 in IAV infection. RT-qPCR was used to determine the level of TRIM21 mRNA, and ELISA was used to measure the levels of IFN-α, IFN-β, IL-6, and TNF-α. The levels of the TRIM21, NP, TBK1, IRF3, p-TBK1, and p-IRF3 proteins were estimated by Western blot. The results showed that, after IAV infection, TRIM21 was upregulated in clinical patient serum and A549 cells, and this was correlated with the IFN response. Overexpression of TRIM21 reduced IAV replication and transcription in in vitro cell experiments. TRIM21 also increased IFN-α and IFN-β levels and decreased IL-6 and TNF-α levels in A549 cells. In addition, overexpression of TRIM21 inhibited IAV-induced apoptosis. Further experiments demonstrated that TBK1-IRF3 signaling was activated by TRIM21 and was involved in the inhibitory effect of TRIM21 on virus replication. In summary, our study suggests that TRIM21 inhibits viral replication by activating the TBK1-IRF3 signaling pathway, further inhibiting the infection process of IAV.
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Affiliation(s)
- Juan Yuan
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China
| | - Jianli Pan
- The Special Department, Xi'an Children's Hospital, Xi'an, 710003, Shaanxi, China
| | - Xiaofang Zhang
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China
| | - Rui Gao
- Outpatient of Infectious Diseases, Xi'an Children's Hospital, No 69, Xiju Yuan Lane, Lianhu District, Xi'an, 710003, Shaanxi, China.
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10
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Merz MP, Seal SV, Grova N, Mériaux S, Guebels P, Kanli G, Mommaerts E, Nicot N, Kaoma T, Keunen O, Nazarov PV, Turner JD. Early-life influenza A (H1N1) infection independently programs brain connectivity, HPA AXIS and tissue-specific gene expression profiles. Sci Rep 2024; 14:5898. [PMID: 38467724 PMCID: PMC10928197 DOI: 10.1038/s41598-024-56601-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Early-life adversity covers a range of physical, social and environmental stressors. Acute viral infections in early life are a major source of such adversity and have been associated with a broad spectrum of later-life effects outside the immune system or "off-target". These include an altered hypothalamus-pituitary-adrenal (HPA) axis and metabolic reactions. Here, we used a murine post-natal day 14 (PND 14) Influenza A (H1N1) infection model and applied a semi-holistic approach including phenotypic measurements, gene expression arrays and diffusion neuroimaging techniques to investigate HPA axis dysregulation, energy metabolism and brain connectivity. By PND 56 the H1N1 infection had been resolved, and there was no residual gene expression signature of immune cell infiltration into the liver, adrenal gland or brain tissues examined nor of immune-related signalling. A resolved early-life H1N1 infection had sex-specific effects. We observed retarded growth of males and altered pre-stress (baseline) blood glucose and corticosterone levels at PND42 after the infection was resolved. Cerebral MRI scans identified reduced connectivity in the cortex, midbrain and cerebellum that were accompanied by tissue-specific gene expression signatures. Gene set enrichment analysis confirmed that these were tissue-specific changes with few common pathways. Early-life infection independently affected each of the systems and this was independent of HPA axis or immune perturbations.
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Affiliation(s)
- Myriam P Merz
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
- Central Biobank Charité, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Snehaa V Seal
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de Université, L-4365, Esch-Sur-Alzette, Luxembourg
| | - Nathalie Grova
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
- Inserm U1256, NGERE, Nutrition-Génétique Et Exposition Aux Risques Environnementaux, Université de Lorraine, 54000, Nancy, France
| | - Sophie Mériaux
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Pauline Guebels
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg
| | - Georgia Kanli
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Elise Mommaerts
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Nathalie Nicot
- LuxGen Genome Center, Laboratoire National de Santé, Luxembourg Institute of Health, 3555, Dudelange, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Olivier Keunen
- In Vivo Imaging Platform, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Translational Radiomics, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Bioinformatics Platform, Data Integration and Analysis Unit, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
- Multiomics Data Science Research Group, Department of Cancer Research, Luxembourg Institute of Health, 1445, Strassen, Luxembourg
| | - Jonathan D Turner
- Immune Endocrine and Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), 29 Rue Henri Koch, 4354, Esch-Sur-Alzette, Luxembourg.
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11
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Chen L, Hua J, He X. Bioinformatics analysis identifies a key gene HLA_DPA1 in severe influenza-associated immune infiltration. BMC Genomics 2024; 25:257. [PMID: 38454348 PMCID: PMC10918912 DOI: 10.1186/s12864-024-10184-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Severe influenza is a serious global health issue that leads to prolonged hospitalization and mortality on a significant scale. The pathogenesis of this infectious disease is poorly understood. Therefore, this study aimed to identify the key genes associated with severe influenza patients necessitating invasive mechanical ventilation. METHODS The current study utilized two publicly accessible gene expression profiles (GSE111368 and GSE21802) from the Gene Expression Omnibus database. The research focused on identifying the genes exhibiting differential expression between severe and non-severe influenza patients. We employed three machine learning algorithms, namely the Least Absolute Shrinkage and Selection Operator regression model, Random Forest, and Support Vector Machine-Recursive Feature Elimination, to detect potential key genes. The key gene was further selected based on the diagnostic performance of the target genes substantiated in the dataset GSE101702. A single-sample gene set enrichment analysis algorithm was applied to evaluate the participation of immune cell infiltration and their associations with key genes. RESULTS A total of 44 differentially expressed genes were recognized; among them, we focused on 10 common genes, namely PCOLCE2, HLA_DPA1, LOC653061, TDRD9, MPO, HLA_DQA1, MAOA, S100P, RAP1GAP, and CA1. To ensure the robustness of our findings, we employed overlapping LASSO regression, Random Forest, and SVM-RFE algorithms. By utilizing these algorithms, we were able to pinpoint the aforementioned 10 genes as potential biomarkers for distinguishing between both cases of influenza (severe and non-severe). However, the gene HLA_DPA1 has been recognized as a crucial factor in the pathological condition of severe influenza. Notably, the validation dataset revealed that this gene exhibited the highest area under the receiver operating characteristic curve, with a value of 0.891. The use of single-sample gene set enrichment analysis has provided valuable insights into the immune responses of patients afflicted with severe influenza that have further revealed a categorical correlation between the expression of HLA_DPA1 and lymphocytes. CONCLUSION The findings indicated that the HLA_DPA1 gene may play a crucial role in the immune-pathological condition of severe influenza and could serve as a promising therapeutic target for patients infected with severe influenza.
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Affiliation(s)
- Liang Chen
- Department of Infectious Diseases, Taikang Xianlin Drum Tower Hospital, Affiliated Hospital of Medical College of Nanjing University, No 188, Lingshan North Road, Qixia District, Nanjing, 210046, China.
| | - Jie Hua
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaopu He
- Department of Geriatric Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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12
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Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nat Genet 2024; 56:408-419. [PMID: 38424460 DOI: 10.1038/s41588-024-01668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
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Affiliation(s)
| | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Saideep Gona
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zepeng Mu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Vania Yotova
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Renata Sindeaux
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | | | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, Quebec, Canada
| | - David Lougheed
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Romain Gregoire
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - David Brownlee
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Yang Li
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - David Bujold
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- McGill Genome Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Genomic Medicine Center, Children's Mercy, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada.
- McGill Genome Centre, Montreal, Quebec, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
| | - Luis B Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
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13
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Hu Y, Jiang L, Wang G, Song Y, Shan Z, Wang X, Deng G, Shi J, Tian G, Zeng X, Liu L, Chen H, Li C. M6PR interacts with the HA2 subunit of influenza A virus to facilitate the fusion of viral and endosomal membranes. Sci China Life Sci 2024; 67:579-595. [PMID: 38038885 DOI: 10.1007/s11427-023-2471-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
Influenza A virus (IAV) commandeers numerous host cellular factors for successful replication. However, very few host factors have been revealed to be involved in the fusion of viral envelope and late endosomal membranes. In this study, we identified cation-dependent mannose-6-phosphate receptor (M6PR) as a crucial host factor for the replication of IAV. We found that siRNA knockdown of M6PR expression significantly reduced the growth titers of different subtypes of IAV, and that the inhibitory effect of M6PR siRNA treatment on IAV growth was overcome by the complement of exogenously expressed M6PR. When A549 cells were treated with siRNA targeting M6PR, the nuclear accumulation of viral nucleoprotein (NP) was dramatically inhibited at early timepoints post-infection, indicating that M6PR engages in the early stage of the IAV replication cycle. By investigating the role of M6PR in the individual entry and post-entry steps of IAV replication, we found that the downregulation of M6PR expression had no effect on attachment, internalization, early endosome trafficking, or late endosome acidification. However, we found that M6PR expression was critical for the fusion of viral envelope and late endosomal membranes. Of note, M6PR interacted with the hemagglutinin (HA) protein of IAV, and further studies showed that the lumenal domain of M6PR and the ectodomain of HA2 mediated the interaction and directly promoted the fusion of the viral and late endosomal membranes, thereby facilitating IAV replication. Together, our findings highlight the importance of the M6PR-HA interaction in the fusion of viral and late endosomal membranes during IAV replication.
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Affiliation(s)
- Yuzhen Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Li Jiang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guangwen Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Yangming Song
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Zhibo Shan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xuyuan Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guohua Deng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Jianzhong Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Guobin Tian
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xianying Zeng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Liling Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Hualan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Chengjun Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
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14
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Zhang L, Shao Y, Wang Y, Yang Q, Guo J, Gao GF, Deng T. Twenty natural amino acid substitution screening at the last residue 121 of influenza A virus NS2 protein reveals the critical role of NS2 in promoting virus genome replication by coordinating with viral polymerase. J Virol 2024; 98:e0116623. [PMID: 38054704 PMCID: PMC10804943 DOI: 10.1128/jvi.01166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023] Open
Abstract
Both influenza A virus genome transcription (vRNA→mRNA) and replication (vRNA→cRNA→vRNA), catalyzed by the influenza RNA polymerase (FluPol), are dynamically regulated across the virus life cycle. It has been reported that the last amino acid I121 of the viral NS2 protein plays a critical role in promoting viral genome replication in influenza mini-replicon systems. Here, we performed a 20 natural amino acid substitution screening at residue NS2-I121 in the context of virus infection. We found that the hydrophobicity of the residue 121 is essential for virus survival. Interestingly, through serial passage of the rescued mutant viruses, we further identified adaptive mutations PA-K19E and PB1-S713N on FluPol which could effectively compensate for the replication-promoting defect caused by NS2-I121 mutation in the both mini-replicon and virus infection systems. Structural analysis of different functional states of FluPol indicates that PA-K19E and PB1-S713N could stabilize the replicase conformation of FluPol. By using a cell-based NanoBiT complementary reporter assay, we further demonstrate that both wild-type NS2 and PA-K19E/PB1-S713N could enhance FluPol dimerization, which is necessary for genome replication. These results reveal the critical role NS2 plays in promoting viral genome replication by coordinating with FluPol.IMPORTANCEThe intrinsic mechanisms of influenza RNA polymerase (FluPol) in catalyzing viral genome transcription and replication have been largely resolved. However, the mechanisms of how transcription and replication are dynamically regulated remain elusive. We recently reported that the last amino acid of the viral NS2 protein plays a critical role in promoting viral genome replication in an influenza mini-replicon system. Here, we conducted a 20 amino acid substitution screening at the last residue 121 in virus rescue and serial passage. Our results demonstrate that the replication-promoting function of NS2 is important for virus survival and efficient multiplication. We further show evidence that NS2 and NS2-I121 adaptive mutations PA-K19E/PB1-S713N regulate virus genome replication by promoting FluPol dimerization. This work highlights the coordination between NS2 and FluPol in fulfilling efficient genome replication. It further advances our understanding of the regulation of viral RNA synthesis for influenza A virus.
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Affiliation(s)
- Lei Zhang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- />Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, China
| | - Yuekun Shao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qiuxian Yang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiamei Guo
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Deng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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15
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Li X, Ye Z, Plant EP. 5' copyback defective viral genomes are major component in clinical and non-clinical influenza samples. Virus Res 2024; 339:199274. [PMID: 37981214 PMCID: PMC10701078 DOI: 10.1016/j.virusres.2023.199274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Clinical samples from people with influenza disease have been analyzed to assess the presence and abundance of Defective Viral Genomes (DVGs), but these have not been assessed using the same bioinformatic pipeline. The type of DVG most described for influenza infections (deletion DVGs) differs from the most commonly described DVGs from non-segmented negative stranded viruses (5' copyback). This could be attributed to either differences between viruses or the tools used to detect and characterize DVGs. Here we analyze several NGS datasets from people infected with different types of influenza virus using the same bioinformatic pipeline. We observe that 5' copyback DVGs are prevalent in all human clinical samples but not in the cultured samples. To address this discrepancy between clinical and laboratory cultures, we infected cell culture and ferrets with an H5N8 influenza A virus (FLUAV) and analyzed the DVG composition. The results demonstrate that the DVG population is skewed toward 5' copyback DVGs in the in vivo infections and deletion DVGs in the in vitro infections. This demonstrates that there are differences in vivo genome production and in vitro genome production, and this has implications for how the role of DVGs in clinical disease is studied. We also investigate the role the host cofactor ANP32B has in DVG production.
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Affiliation(s)
- Xing Li
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA
| | - Ewan P Plant
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccine Research and Review, CBER, FDA, Silver Spring, MD, USA.
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16
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Stumpff JP, Kim SY, McFadden MI, Nishida A, Shirazi R, Steuerman Y, Gat-Viks I, Forero A, Nair MG, Morrison J. Pleural macrophages translocate to the lung during infection to promote improved influenza outcomes. Proc Natl Acad Sci U S A 2023; 120:e2300474120. [PMID: 38100417 PMCID: PMC10743374 DOI: 10.1073/pnas.2300474120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Seasonal influenza results in 3 to 5 million cases of severe disease and 250,000 to 500,000 deaths annually. Macrophages have been implicated in both the resolution and progression of the disease, but the drivers of these outcomes are poorly understood. We probed mouse lung transcriptomic datasets using the Digital Cell Quantifier algorithm to predict immune cell subsets that correlated with mild or severe influenza A virus (IAV) infection outcomes. We identified a unique lung macrophage population that transcriptionally resembled small serosal cavity macrophages and whose presence correlated with mild disease. Until now, the study of serosal macrophage translocation in the context of viral infections has been neglected. Here, we show that pleural macrophages (PMs) migrate from the pleural cavity to the lung after infection with IAV. We found that the depletion of PMs increased morbidity and pulmonary inflammation. There were increased proinflammatory cytokines in the pleural cavity and an influx of neutrophils within the lung. Our results show that PMs are recruited to the lung during IAV infection and contribute to recovery from influenza. This study expands our knowledge of PM plasticity and identifies a source of lung macrophages independent of monocyte recruitment and local proliferation.
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Affiliation(s)
- James P. Stumpff
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
| | - Sang Yong Kim
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA92521
| | - Matthew I. McFadden
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
| | - Andrew Nishida
- Department of Microbiology, University of Washington, Seattle, WA98109
| | - Roksana Shirazi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
| | - Yael Steuerman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
| | - Meera G. Nair
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA92521
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA92521
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17
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Probst L, Laloli L, Licheri MF, Licheri M, Gultom M, Holwerda M, V’kovski P, Dijkman R. Generation and Characterization of an Influenza D Reporter Virus. Viruses 2023; 15:2444. [PMID: 38140686 PMCID: PMC10747006 DOI: 10.3390/v15122444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Influenza D virus (IDV) can infect various livestock animals, such as cattle, swine, and small ruminants, and was shown to have zoonotic potential. Therefore, it is important to identify viral factors involved in the broad host tropism and identify potential antiviral compounds that can inhibit IDV infection. Recombinant reporter viruses provide powerful tools for studying viral infections and antiviral drug discovery. Here we present the generation of a fluorescent reporter IDV using our previously established reverse genetic system for IDV. The mNeonGreen (mNG) fluorescent reporter gene was incorporated into the IDV non-structural gene segment as a fusion protein with the viral NS1 or NS2 proteins, or as a separate protein flanked by two autoproteolytic cleavage sites. We demonstrate that only recombinant reporter viruses expressing mNG as an additional separate protein or as an N-terminal fusion protein with NS1 could be rescued, albeit attenuated, compared to the parental reverse genetic clone. Serial passaging experiments demonstrated that the mNG gene is stably integrated for up to three passages, after which internal deletions accumulate. We conducted a proof-of-principle antiviral screening with the established fluorescent reporter viruses and identified two compounds influencing IDV infection. These results demonstrate that the newly established recombinant IDV reporter virus can be applied for antiviral drug discovery and monitoring viral replication, adding a new molecular tool for investigating IDV.
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Affiliation(s)
- Lukas Probst
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Laura Laloli
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Manon Flore Licheri
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Matthias Licheri
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Mitra Gultom
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Melle Holwerda
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Philip V’kovski
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
| | - Ronald Dijkman
- Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
- European Virus Bioinformatics Center, 07743 Jena, Germany
- Microscope Imaging Center, University of Bern, 3012 Bern, Switzerland
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18
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Mai G, Zhang C, Lan C, Zhang J, Wang Y, Tang K, Tang J, Zeng J, Chen Y, Cheng P, Liu S, Long H, Wen Q, Li A, Liu X, Zhang R, Xu S, Liu L, Niu Y, Yang L, Wang Y, Yin D, Sun C, Chen YQ, Shen W, Zhang Z, Du X. Characterizing the dynamics of BCR repertoire from repeated influenza vaccination. Emerg Microbes Infect 2023; 12:2245931. [PMID: 37542407 PMCID: PMC10438862 DOI: 10.1080/22221751.2023.2245931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/12/2023] [Accepted: 08/03/2023] [Indexed: 08/06/2023]
Abstract
Yearly epidemics of seasonal influenza cause an enormous disease burden around the globe. An understanding of the rules behind the immune response with repeated vaccination still presents a significant challenge, which would be helpful for optimizing the vaccination strategy. In this study, 34 healthy volunteers with 16 vaccinated were recruited, and the dynamics of the BCR repertoire for consecutive vaccinations in two seasons were tracked. In terms of diversity, length, network, V and J gene segments usage, somatic hypermutation (SHM) rate and isotype, it was found that the overall changes were stronger in the acute phase of the first vaccination than the second vaccination. However, the V gene segments of IGHV4-39, IGHV3-9, IGHV3-7 and IGHV1-69 were amplified in the acute phase of the first vaccination, with IGHV3-7 dominant. On the other hand, for the second vaccination, the changes were dominated by IGHV1-69, with potential for coding broad neutralizing antibody. Additional analysis indicates that the application of V gene segment for IGHV3-7 in the acute phase of the first vaccination was due to the elevated usage of isotypes IgM and IgG3. While for IGHV1-69 in the second vaccination, it was contributed by isotypes IgG1 and IgG2. Finally, 41 public BCR clusters were identified in the vaccine group, with both IGHV3-7 and IGHV1-69 were involved and representative complementarity determining region 3 (CDR3) motifs were characterized. This study provides insights into the immune response dynamics following repeated influenza vaccination in humans and can inform universal vaccine design and vaccine strategies in the future.
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Affiliation(s)
- Guoqin Mai
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Center for Precision Medicine, Guangdong Academy of Medical Sciences, Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
| | - Jie Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Kang Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jing Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yilin Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Peiwen Cheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shuning Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Qilan Wen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Aqin Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xuan Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Ruitong Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shuyang Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lin Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yanlan Niu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Lan Yang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yihan Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Di Yin
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Caijun Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Wei Shen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Zhenhai Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Center for Precision Medicine, Guangdong Academy of Medical Sciences, Medical Research Institute, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, People’s Republic of China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, People’s Republic of China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People’s Republic of China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, People’s Republic of China
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19
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Liang Y, Huang P. Associations of telomere length with risk of mortality from influenza and pneumonia in US adults: a prospective cohort study of NHANES 1999-2002. Aging Clin Exp Res 2023; 35:3115-3125. [PMID: 37962763 DOI: 10.1007/s40520-023-02607-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Due to the ongoing Coronavirus disease 2019 (COVID-19) pandemic, interest has arisen to realize the relationship between telomere length (TL) and influenza and pneumonia mortality. AIM Our study attempted to investigate this correlation by analyzing information gathered from the National Health and Nutrition Examination Survey (NHANES) 1999-2002. METHODS A total of 7229 participants were involved in the conducted research. We utilized Cox proportional risk model analysis to determine the hazard ratio (HR) and 95% confidence interval (CI) for TL and influenza and pneumonia mortality. RESULTS During the average follow-up time of 204.10 ± 51.26 months, 33 (0.45%) participants died from influenza and pneumonia. After adjusting for multiple variables, shorter TL was associated with higher influenza-pneumonia mortality. In subgroup analyses stratified by sex, men exhibited stronger associations with influenza-pneumonia mortality than women (Model 1: HRmale: 0.014 vs HRfemale: 0.054; Model 2: HRmale: 0.082 vs HRfemale: 0.890; Model 3: HRmale: 0.072 vs HRfemale: 0.776). For subgroup analyses by visceral adiposity index (VAI), all statistically significant (P < 0.05) models displayed an inverse relationship between TL and influenza and pneumonia mortality. CONCLUSIONS Our research provides further proof for the connection between shorter telomeres and higher influenza-pneumonia mortality. Larger prospective researches are essential to support our results and explain the underlying mechanisms.
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Affiliation(s)
- Yingshan Liang
- Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, 510800, China.
| | - Peipei Huang
- Southern Medical University, Guangzhou, 510000, Guangdong, China
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20
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Ogasawara S. Replication-competent influenza virus with a protein-responsive multiplication ability. N Biotechnol 2023; 77:100-110. [PMID: 37586547 DOI: 10.1016/j.nbt.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 07/30/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Applications of influenza A viruses (IAV) for virotherapy and biotechnology have accelerated substantially with the development of reverse genetic technology and advances in the understanding of packaging signals. While the use of a replication-competent IAV is particularly promising, owing to its efficient transmission to organ depths with high infectivity, there is also a risk that its multiplication cannot be controlled in a cell-type-specific manner, causing an infectious disease. Therefore, here a simple and effective replication-competent IAV-based cell-targeting system has been developed. It was demonstrated that the activity of the ribonucleoprotein complex (RNP) of IAV could be regulated by the interaction between the endogenous protein and a nanobody fused to the subunit of RNA-dependent RNA polymerase (RdRp). To validate the feasibility of the method, it was demonstrated that RNP containing RdRp fused with Nb139, a nanobody against p53, is inactive in HEK293T cells expressing endogenous p53, but active in p53-defective Saos-2 cells. Finally, a replication-competent IAV was successfully generated that multiplies only in p53-defective tumor cells and an IAV vector was developed that can deliver a foreign gene in cell type-specific manner. The method is flexible because the nanobody can be easily altered to target a different cell type, offering a valuable platform for virotherapy and biotechnology.
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Affiliation(s)
- Shinzi Ogasawara
- Department of Biology, Faculty of Science, Shinshu University, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan.
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21
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Rosli S, Harpur CM, Lam M, West AC, Hodges C, Mansell A, Lawlor KE, Tate MD. Gasdermin D promotes hyperinflammation and immunopathology during severe influenza A virus infection. Cell Death Dis 2023; 14:727. [PMID: 37945599 PMCID: PMC10636052 DOI: 10.1038/s41419-023-06258-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/20/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
Excessive inflammation and tissue damage during severe influenza A virus (IAV) infection can lead to the development of fatal pulmonary disease. Pyroptosis is a lytic and pro-inflammatory form of cell death executed by the pore-forming protein gasdermin D (GSDMD). In this study, we investigated a potential role for GSDMD in promoting the development of severe IAV disease. IAV infection resulted in cleavage of GSDMD in vivo and in vitro in lung epithelial cells. Mice genetically deficient in GSDMD (Gsdmd-/-) developed less severe IAV disease than wildtype mice and displayed improved survival outcomes. GSDMD deficiency significantly reduced neutrophil infiltration into the airways as well as the levels of pro-inflammatory cytokines TNF, IL-6, MCP-1, and IL-1α and neutrophil-attracting chemokines CXCL1 and CXCL2. In contrast, IL-1β and IL-18 responses were not largely impacted by GSDMD deficiency. In addition, Gsdmd-/- mice displayed significantly improved influenza disease resistance with reduced viral burden and less severe pulmonary pathology, including decreased epithelial damage and cell death. These findings indicate a major role for GSDMD in promoting damaging inflammation and the development of severe IAV disease.
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Affiliation(s)
- Sarah Rosli
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Christopher M Harpur
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Maggie Lam
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Alison C West
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Christopher Hodges
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Ashley Mansell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
- Adiso Therapeutics, Concord, MA, USA
| | - Kate E Lawlor
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Vic, Australia.
- Department of Molecular and Translational Sciences, Monash University, Clayton, Vic, Australia.
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22
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Liu Y, Wang Y, Zhang R, Wang S, Li J, An Z, Song J, Wu W. Transcriptomics profile of human bronchial epithelial cells exposed to ambient fine particles and influenza virus (H3N2). Sci Rep 2023; 13:19259. [PMID: 37935887 PMCID: PMC10630401 DOI: 10.1038/s41598-023-46724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023] Open
Abstract
Fine particulate matter (PM2.5) pollution remains a major threat to public health. As the physical barrier against inhaled air pollutants, airway epithelium is a primary target for PM2.5 and influenza viruses, two major environmental insults. Recent studies have shown that PM2.5 and influenza viruses may interact to aggravate airway inflammation, an essential event in the pathogenesis of diverse pulmonary diseases. Airway epithelium plays a critical role in lung health and disorders. Thus far, the mechanisms for the interactive effect of PM2.5 and the influenza virus on gene transcription of airway epithelial cells have not been fully uncovered. In this present pilot study, the transcriptome sequencing approach was introduced to identify responsive genes following individual and co-exposure to PM2.5 and influenza A (H3N2) viruses in a human bronchial epithelial cell line (BEAS-2B). Enrichment analysis revealed the function of differentially expressed genes (DEGs). Specifically, the DEGs enriched in the xenobiotic metabolism by the cytochrome P450 pathway were linked to PM2.5 exposure. In contrast, the DEGs enriched in environmental information processing and human diseases, such as viral protein interaction with cytokines and cytokine receptors and epithelial cell signaling in bacterial infection, were significantly related to H3N2 exposure. Meanwhile, co-exposure to PM2.5 and H3N2 affected G protein-coupled receptors on the cell surface. Thus, the results from this study provides insights into PM2.5- and influenza virus-induced airway inflammation and potential mechanisms.
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Affiliation(s)
- Yuan Liu
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Yinbiao Wang
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Rui Zhang
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Shaolan Wang
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Juan Li
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Zhen An
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Jie Song
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China
| | - Weidong Wu
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, Henan Province, China.
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23
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Zhu Z, Fan H, Fodor E. Defining the minimal components of the influenza A virus replication machinery via an in vitro reconstitution system. PLoS Biol 2023; 21:e3002370. [PMID: 37943954 PMCID: PMC10662765 DOI: 10.1371/journal.pbio.3002370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 10/09/2023] [Indexed: 11/12/2023] Open
Abstract
During influenza A virus infection, the viral RNA polymerase transcribes the viral negative-sense segmented RNA genome and replicates it in a two-step process via complementary RNA within viral ribonucleoprotein (vRNP) complexes. While numerous viral and host factors involved in vRNP functions have been identified, dissecting the roles of individual factors remains challenging due to the complex cellular environment in which vRNP activity has been studied. To overcome this challenge, we reconstituted viral transcription and a full cycle of replication in a test tube using vRNPs isolated from virions and recombinant factors essential for these processes. This novel system uncovers the minimal components required for influenza virus replication and also reveals new roles of regulatory factors in viral replication. Moreover, it sheds light on the molecular interplay underlying the temporal regulation of viral transcription and replication. Our highly robust in vitro system enables systematic functional analysis of factors modulating influenza virus vRNP activity and paves the way for imaging key steps of viral transcription and replication.
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Affiliation(s)
- Zihan Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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24
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Gao J, Wei J, Qin S, Liu S, Mo S, Long Q, Tan S, Lu N, Xie Z, Lin J. Exploring the global immune landscape of peripheral blood mononuclear cells in H5N6-infected patient with single-cell transcriptomics. BMC Med Genomics 2023; 16:249. [PMID: 37853397 PMCID: PMC10585775 DOI: 10.1186/s12920-023-01693-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
BACKGROUND Avian influenza viruses (AIV), particularly H5N6, have risen in infection frequency, prompting major concerns. Single-cell RNA sequencing (scRNA-seq) can illustrate the immune cell landscape present in the peripheral circulation of influenza H5N6-infected individuals at the single-cell level. This study attempted to employ scRNA-seq technology to map the potentially hidden single cell landscape of influenza H5N6. METHODS High-quality transcriptomes were generated from scRNA-seq data of peripheral blood mononuclear cells (PBMCs), which were taken from a critically-ill child diagnosed with H5N6 avian influenza infection and one healthy control donor. Cluster analysis was then performed on the scRNA-seq data to identify the different cell types. The pathways, pseudotime developmental trajectories and gene regulatory networks involved in different cell subpopulations were also explored. RESULTS In total, 3,248 single cell transcriptomes were captured by scRNA-seq from PBMC of the child infected with H5N6 avian influenza and the healthy control donor and further identified seven immune microenvironment cell types. In addition, a subsequent subpopulation analysis of innate lymphoid cells (ILC) and CD4+ T cells revealed that subpopulations of ILC and CD4+ T cells were involved in cytokine and inflammation-related pathways and had significant involvement in the biological processes of oxidative stress and cell death. CONCLUSION In conclusion, characterizing the overall immune cell composition of H5N6-infected individuals by assessing the immune cell landscape in the peripheral circulation of H5N6 avian influenza-infected and healthy control donors at single-cell resolution provides key information for understanding H5N6 pathogenesis.
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Affiliation(s)
- Jiamin Gao
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Jing Wei
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Simei Qin
- Department of Pediatrics, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Sheng Liu
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Shuangyan Mo
- Department of Pediatrics, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China
| | - Qian Long
- Department of Clinical Laboratory, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Shiji Tan
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Ning Lu
- Department of Intensive Care Unit, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning) and The Fourth People's Hospital of Nanning, Nanning, 530023, Guangxi Zhuang Autonomous Region, China
| | - Zhouhua Xie
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
- Department of Tuberculosis, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
| | - Jianyan Lin
- Laboratory of Infectious Disease, HIV/AIDS Clinical Treatment Center of Guangxi (Nanning), The Fourth People's Hospital of Nanning, Guangxi Zhuang Autonomous Region, Nanning, 530023, China.
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25
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Xu F, Gan X, Tao Y, Li D, Xie P, Liu F, Yang F, Ma Y. Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study. BMC Infect Dis 2023; 23:692. [PMID: 37848822 PMCID: PMC10580584 DOI: 10.1186/s12879-023-08706-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Previous observational studies have indicated a correlation between the gut microbiota and influenza; however, the exact nature of the bidirectional causal connection remains uncertain. METHOD A two-way, two-sample Mendelian randomization (MR) study was conducted to evaluate the possible causal connection between the gut microbiota and the two outcomes of influenza (pneumonia without influenza and influenza pneumonia). The statistical analysis of gut microbiota is derived from the information of the most extensive meta-analysis (GWAS) conducted by the MiBioGen Alliance, encompassing a sample size of 18,340.The summary statistical data for influenza (not pneumonia, n = 291,090) and influenza pneumonia (n = 342,499) are from GWAS data published by FinnGen consortium R8.Estimate and summarize Single-nucleotide polymorphisms (SNPs) using Inverse variance weighted (IVW), MR Egger, and Weighted median (WM) in bidirectional MR analysis. To assess the heterogeneity, horizontal pleiotropy, and stability of SNPs, we employed Cochran's Q test, MR Egger intercept test, and sensitivity analysis. RESULT The IVW analysis indicated that there was a significant association between influenza infection and five bacterial taxa. Additionally, the abundance changes of seven gut microbiota were found to be causally related to influenza infection. In addition, seven bacterial taxa showed a significant association with the occurrence of influenza pneumonia. The findings from the WM analysis largely support the outcomes of IVW, however, the results of MR egger analysis do not align with IVW. Furthermore, there is no proof to substantiate the cause-and-effect relationship between influenza pneumonia and the composition of gut microbiota. CONCLUSION This analysis demonstrates a possible bidirectional causal connection between the prevalence of particular gut microbiota and the occurrence of influenza infection. The presence of certain gut microbiota may potentially contribute to the development of pneumonia caused by influenza. Additional investigation into the interaction between particular bacterial communities and influenza can enhance efforts in preventing, monitoring, and treating influenza.
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Affiliation(s)
- Fan Xu
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Xiuyuan Gan
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Yang Tao
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Dongling Li
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Puguang Xie
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Fangying Liu
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China
| | - Fan Yang
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China.
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China.
| | - Yu Ma
- Chongqing Key Laboratory of Emergency Medicine, Chongqing Emergency Medical Center, School of Medicine, Chongqing University Central Hospital, Chongqing University, Chongqing, 400014, China.
- Central laboratory of Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing, 400014, China.
- Department of Critical Care Medicine, Chongqing University Central Hospital, Chongqing, 400014, China.
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26
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Sheppard CM, Goldhill DH, Swann OC, Staller E, Penn R, Platt OK, Sukhova K, Baillon L, Frise R, Peacock TP, Fodor E, Barclay WS. An Influenza A virus can evolve to use human ANP32E through altering polymerase dimerization. Nat Commun 2023; 14:6135. [PMID: 37816726 PMCID: PMC10564888 DOI: 10.1038/s41467-023-41308-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/09/2023] [Indexed: 10/12/2023] Open
Abstract
Human ANP32A and ANP32B are essential but redundant host factors for influenza virus genome replication. While most influenza viruses cannot replicate in edited human cells lacking both ANP32A and ANP32B, some strains exhibit limited growth. Here, we experimentally evolve such an influenza A virus in these edited cells and unexpectedly, after 2 passages, we observe robust viral growth. We find two mutations in different subunits of the influenza polymerase that enable the mutant virus to use a novel host factor, ANP32E, an alternative family member, which is unable to support the wild type polymerase. Both mutations reside in the symmetric dimer interface between two polymerase complexes and reduce polymerase dimerization. These mutations have previously been identified as adapting influenza viruses to mice. Indeed, the evolved virus gains the ability to use suboptimal mouse ANP32 proteins and becomes more virulent in mice. We identify further mutations in the symmetric dimer interface which we predict allow influenza to adapt to use suboptimal ANP32 proteins through a similar mechanism. Overall, our results suggest a balance between asymmetric and symmetric dimers of influenza virus polymerase that is influenced by the interaction between polymerase and ANP32 host proteins.
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Affiliation(s)
- Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK.
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Olivia C Swann
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ecco Staller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca Penn
- Department of Infectious Disease, Imperial College London, London, UK
| | - Olivia K Platt
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, UK
| | - Laury Baillon
- Department of Infectious Disease, Imperial College London, London, UK
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK.
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27
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Zhu Z, You R, Li H, Feng S, Ma H, Tuo C, Meng X, Feng S, Peng Y. Multi-omics data integration reveals the complexity and diversity of host factors associated with influenza virus infection. PeerJ 2023; 11:e16194. [PMID: 37842064 PMCID: PMC10569165 DOI: 10.7717/peerj.16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023] Open
Abstract
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes. Further analysis showed that the dynamic response of human cells to virus infection, cell type and strain specificity contribute significantly to the diversity of DEGs. Additionally, large heterogeneity was also observed in protein-protein interactions between humans and different types or subtypes of influenza viruses. Overall, the study deepens our understanding of the diversity and complexity of interactions between influenza viruses and humans, and provides a valuable resource for further studies on such interactions.
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Affiliation(s)
- Zhaozhong Zhu
- College of Biology, Hunan University, Changsha, China
- School of Public Health, University of South China, Hengyang, China
| | - Ruina You
- College of Biology, Hunan University, Changsha, China
| | - Huiru Li
- College of Biology, Hunan University, Changsha, China
| | - Shuidong Feng
- School of Public Health, University of South China, Hengyang, China
| | - Huan Ma
- College of Biology, Hunan University, Changsha, China
| | - Chaohao Tuo
- College of Biology, Hunan University, Changsha, China
| | | | - Song Feng
- Xiangya Hospital, Central South University, Changsha, China
| | - Yousong Peng
- College of Biology, Hunan University, Changsha, China
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28
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Yin Y, Qiu Z, Lei Y, Huang J, Sun Y, Liu H, Wu W, Wang X, Shu Y, Zheng Q, Fang S. Screening and identification of specific cluster miRNAs in N2a cells infected by H7N9 virus. Virus Genes 2023; 59:716-722. [PMID: 37395889 DOI: 10.1007/s11262-023-01996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/10/2023] [Indexed: 07/04/2023]
Abstract
This study aims to screen and identify specific cluster miRNAs of H7N9 virus-infected N2a cells and explore the possible pathogenesis of these miRNAs. The N2a cells are infected with H7N9 and H1N1 influenza viruses, and the cells are collected at 12, 24 and 48 h to extract total RNA. To sequence miRNAs and identify different virus-specific miRNAs, high-throughput sequencing technology is used. Fifteen H7N9 virus-specific cluster miRNAs are screened, and eight of them are included in the miRBase database. These cluster-specific miRNAs regulate many signaling pathways, such as the PI3K-Akt signaling pathway, the RAS signaling pathway, the cAMP signaling pathway, actin cytoskeleton regulation and cancer-related genes. The study provides a scientific basis for the pathogenesis of H7N9 avian influenza, which is regulated by miRNAs.
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Affiliation(s)
- Yitong Yin
- Jinan University, College of Pharmacy, Guangzhou, 510632, China
| | - Zengzhao Qiu
- National Sun yat-sen University, Public Health Hospital (Shenzhen), Shenzhen, 518107, China
| | - Yuxuan Lei
- National Sun yat-sen University, Public Health Hospital (Shenzhen), Shenzhen, 518107, China
| | - Jia Huang
- Guangdong Pharmaceutical University, Public Health College, Guangzhou, 510006, China
| | - Ying Sun
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Hui Liu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Weihua Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xin Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuelong Shu
- National Sun yat-sen University, Public Health Hospital (Shenzhen), Shenzhen, 518107, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College CN, Beijing, 102206, China
| | - Qing Zheng
- Jinan University, College of Pharmacy, Guangzhou, 510632, China.
| | - Shisong Fang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China.
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29
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Haas KM, McGregor MJ, Bouhaddou M, Polacco BJ, Kim EY, Nguyen TT, Newton BW, Urbanowski M, Kim H, Williams MAP, Rezelj VV, Hardy A, Fossati A, Stevenson EJ, Sukerman E, Kim T, Penugonda S, Moreno E, Braberg H, Zhou Y, Metreveli G, Harjai B, Tummino TA, Melnyk JE, Soucheray M, Batra J, Pache L, Martin-Sancho L, Carlson-Stevermer J, Jureka AS, Basler CF, Shokat KM, Shoichet BK, Shriver LP, Johnson JR, Shaw ML, Chanda SK, Roden DM, Carter TC, Kottyan LC, Chisholm RL, Pacheco JA, Smith ME, Schrodi SJ, Albrecht RA, Vignuzzi M, Zuliani-Alvarez L, Swaney DL, Eckhardt M, Wolinsky SM, White KM, Hultquist JF, Kaake RM, García-Sastre A, Krogan NJ. Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets. Nat Commun 2023; 14:6030. [PMID: 37758692 PMCID: PMC10533562 DOI: 10.1038/s41467-023-41442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.
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Affiliation(s)
- Kelsey M Haas
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Michael J McGregor
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Thong T Nguyen
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Billy W Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Matthew Urbanowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Heejin Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Michael A P Williams
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Alexandra Hardy
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Andrea Fossati
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Erica J Stevenson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Ellie Sukerman
- Division of Infectious Diseases, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Tiffany Kim
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sudhir Penugonda
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal and IRYCIS, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Yuan Zhou
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bhavya Harjai
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
- Graduate Program in Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - James E Melnyk
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Jyoti Batra
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Laura Martin-Sancho
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Infectious Disease, Imperial College London, London, SW7 2BX, UK
| | - Jared Carlson-Stevermer
- Synthego Corporation, Redwood City, CA, 94063, USA
- Serotiny Inc., South San Francisco, CA, 94080, USA
| | - Alexander S Jureka
- Molecular Virology and Vaccine Team, Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization & Respiratory Diseases, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA
- General Dynamics Information Technology, Federal Civilian Division, Atlanta, GA, 30329, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Brian K Shoichet
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Leah P Shriver
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63105, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Jeffrey R Johnson
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Megan L Shaw
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medical Biosciences, University of the Western Cape, Bellville, 7535, Western Cape, South Africa
| | - Sumit K Chanda
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Leah C Kottyan
- Center of Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin Madison, Madison, WI, 53706, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco Vignuzzi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Paris, France
| | - Lorena Zuliani-Alvarez
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Kris M White
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judd F Hultquist
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, 60611, USA.
| | - Robyn M Kaake
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
| | - Adolfo García-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA, 94158, USA.
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30
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Lotfi B, Mebarka O, Alhatlani BY, Abdallah EM, Kawsar SMA. Pharmacoinformatics and Breed-Based De Novo Hybridization Studies to Develop New Neuraminidase Inhibitors as Potential Anti-Influenza Agents. Molecules 2023; 28:6678. [PMID: 37764457 PMCID: PMC10534564 DOI: 10.3390/molecules28186678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/09/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Influenza represents a profoundly transmissible viral ailment primarily afflicting the respiratory system. Neuraminidase inhibitors constitute a class of antiviral therapeutics employed in the management of influenza. These inhibitors impede the liberation of the viral neuraminidase protein, thereby impeding viral dissemination from the infected cell to host cells. As such, neuraminidase has emerged as a pivotal target for mitigating influenza and its associated complications. Here, we apply a de novo hybridization approach based on a breed-centric methodology to elucidate novel neuraminidase inhibitors. The breed technique amalgamates established ligand frameworks with the shared target, neuraminidase, resulting in innovative inhibitor constructs. Molecular docking analysis revealed that the seven synthesized breed molecules (designated Breeds 1-7) formed more robust complexes with the neuraminidase receptor than conventional clinical neuraminidase inhibitors such as zanamivir, oseltamivir, and peramivir. Pharmacokinetic evaluations of the seven breed molecules (Breeds 1-7) demonstrated favorable bioavailability and optimal permeability, all falling within the specified parameters for human application. Molecular dynamics simulations spanning 100 nanoseconds corroborated the stability of these breed molecules within the active site of neuraminidase, shedding light on their structural dynamics. Binding energy assessments, which were conducted through MM-PBSA analysis, substantiated the enduring complexes formed by the seven types of molecules and the neuraminidase receptor. Last, the investigation employed a reaction-based enumeration technique to ascertain the synthetic pathways for the synthesis of the seven breed molecules.
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Affiliation(s)
- Bourougaa Lotfi
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Ouassaf Mebarka
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, BP 145, Biskra 70700, Algeria;
| | - Bader Y. Alhatlani
- Unit of Scientific Research, Applied College, Qassim University, Buraydah 52571, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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King CR, Liu Y, Amato KA, Schaack GA, Mickelson C, Sanders AE, Hu T, Gupta S, Langlois RA, Smith JA, Mehle A. Pathogen-driven CRISPR screens identify TREX1 as a regulator of DNA self-sensing during influenza virus infection. Cell Host Microbe 2023; 31:1552-1567.e8. [PMID: 37652009 PMCID: PMC10528757 DOI: 10.1016/j.chom.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Host:pathogen interactions dictate the outcome of infection, yet the limitations of current approaches leave large regions of this interface unexplored. Here, we develop a novel fitness-based screen that queries factors important during the middle to late stages of infection. This is achieved by engineering influenza virus to direct the screen by programming dCas9 to modulate host gene expression. Our genome-wide screen for pro-viral factors identifies the cytoplasmic DNA exonuclease TREX1. TREX1 degrades cytoplasmic DNA to prevent inappropriate innate immune activation by self-DNA. We reveal that this same process aids influenza virus replication. Infection triggers release of mitochondrial DNA into the cytoplasm, activating antiviral signaling via cGAS and STING. TREX1 metabolizes the DNA, preventing its sensing. Collectively, these data show that self-DNA is deployed to amplify innate immunity, a process tempered by TREX1. Moreover, they demonstrate the power and generality of pathogen-driven fitness-based screens to pinpoint key host regulators of infection.
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Affiliation(s)
- Cason R King
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yiping Liu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A Amato
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Grace A Schaack
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Clayton Mickelson
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Autumn E Sanders
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Tony Hu
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srishti Gupta
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ryan A Langlois
- Department of Microbiology and Immunology and the Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Judith A Smith
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Vaswani CM, Varkouhi AK, Gupta S, Ektesabi AM, Tsoporis JN, Yousef S, Plant PJ, da Silva AL, Cen Y, Tseng YC, Batah SS, Fabro AT, Advani SL, Advani A, Leong-Poi H, Marshall JC, Garcia CC, Rocco PRM, Albaiceta GM, Sebastian-Bolz S, Watts TH, Moraes TJ, Capelozzi VL, Dos Santos CC. Preventing occludin tight-junction disruption via inhibition of microRNA-193b-5p attenuates viral load and influenza-induced lung injury. Mol Ther 2023; 31:2681-2701. [PMID: 37340634 PMCID: PMC10491994 DOI: 10.1016/j.ymthe.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/02/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023] Open
Abstract
Virus-induced lung injury is associated with loss of pulmonary epithelial-endothelial tight junction integrity. While the alveolar-capillary membrane may be an indirect target of injury, viruses may interact directly and/or indirectly with miRs to augment their replication potential and evade the host antiviral defense system. Here, we expose how the influenza virus (H1N1) capitalizes on host-derived interferon-induced, microRNA (miR)-193b-5p to target occludin and compromise antiviral defenses. Lung biopsies from patients infected with H1N1 revealed increased miR-193b-5p levels, marked reduction in occludin protein, and disruption of the alveolar-capillary barrier. In C57BL/6 mice, the expression of miR-193b-5p increased, and occludin decreased, 5-6 days post-infection with influenza (PR8). Inhibition of miR-193b-5p in primary human bronchial, pulmonary microvascular, and nasal epithelial cells enhanced antiviral responses. miR-193b-deficient mice were resistant to PR8. Knockdown of occludin, both in vitro and in vivo, and overexpression of miR-193b-5p reconstituted susceptibility to viral infection. miR-193b-5p inhibitor mitigated loss of occludin, improved viral clearance, reduced lung edema, and augmented survival in infected mice. Our results elucidate how the innate immune system may be exploited by the influenza virus and how strategies that prevent loss of occludin and preserve tight junction function may limit susceptibility to virus-induced lung injury.
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Affiliation(s)
- Chirag M Vaswani
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Amir K Varkouhi
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Sahil Gupta
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Faculty of Medicine, School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Amin M Ektesabi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James N Tsoporis
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Sadiya Yousef
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Pamela J Plant
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Adriana L da Silva
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Yuchen Cen
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Yi-Chieh Tseng
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada
| | - Sabrina S Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Alexandre T Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Suzanne L Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Andrew Advani
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada
| | - Howard Leong-Poi
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Cristiana C Garcia
- Laboratory of Respiratory, Exanthematic Viruses, Enterovirus and Viral Emergencies, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Integrated Research Group on Biomarkers. René Rachou Institute, FIOCRUZ Minas, Belo Horizonte, Brazil
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Brazil
| | - Guillermo M Albaiceta
- Departamento de Biología Funcional, Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain; Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Spain; CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Steffen Sebastian-Bolz
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tania H Watts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Theo J Moraes
- Program in Translational Medicine, SickKids Research Institute, Toronto, ON, Canada; Department of Pediatrics University of Toronto and Respirology, Hospital for Sick Children, Toronto, ON, Canada
| | - Vera L Capelozzi
- Department of Pathology, University of São Paulo, São Paulo, Brazil
| | - Claudia C Dos Santos
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, ON, Canada; Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Interdepartmental Division of Critical Care, St Michael's Hospital, University of Toronto, Toronto, ON, Canada.
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Jitobaom K, Sirihongthong T, Boonarkart C, Phakaratsakul S, Suptawiwat O, Auewarakul P. Human Schlafen 11 inhibits influenza A virus production. Virus Res 2023; 334:199162. [PMID: 37356582 PMCID: PMC10410578 DOI: 10.1016/j.virusres.2023.199162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Schlafen (SLFN) proteins are a subset of interferon-stimulated early response genes with antiviral properties. An antiviral mechanism of SLFN11 was previously demonstrated in human immunodeficiency virus type 1 (HIV-1)-infected cells, and it was shown that SLFN11 inhibited HIV-1 virus production in a codon usage-specific manner. The codon usage patterns of many viruses are vastly different from those of their hosts. The codon usage-specific inhibition of HIV-1 expression by SLFN11 suggests that SLFN11 may be able to inhibit other viruses with a suboptimal codon usage pattern. However, the effect of SLFN11 on the replication of influenza A virus (IAV) has never been reported. The induction of SLFN11 expression was observed upon IAV infection. The reduction of SLFN11 expression also promotes influenza virus replication. Moreover, we found that overexpression of SLFN11 could reduce the expression of a reporter gene with a viral codon usage pattern, and the inhibition of viral hemagglutinin (HA) gene was codon-specific as the expression of codon optimized HA was not affected. These results indicate that SLFN11 inhibits the influenza A virus in a codon-specific manner and that SLFN11 may contribute to innate defense against influenza A viruses.
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Affiliation(s)
- Kunlakanya Jitobaom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Thanyaporn Sirihongthong
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Chompunuch Boonarkart
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Supinya Phakaratsakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand
| | - Ornpreya Suptawiwat
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkoknoi, Bangkok 10700, Thailand.
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Bamunuarachchi G, Vaddadi K, Yang X, Dang Q, Zhu Z, Hewawasam S, Huang C, Liang Y, Guo Y, Liu L. MicroRNA-9-1 Attenuates Influenza A Virus Replication via Targeting Tankyrase 1. J Innate Immun 2023; 15:647-664. [PMID: 37607510 PMCID: PMC10601686 DOI: 10.1159/000532063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 07/11/2023] [Indexed: 08/24/2023] Open
Abstract
An unstable influenza genome leads to the virus resistance to antiviral drugs that target viral proteins. Thus, identification of host factors essential for virus replication may pave the way to develop novel antiviral therapies. In this study, we investigated the roles of the poly(ADP-ribose) polymerase enzyme, tankyrase 1 (TNKS1), and the endogenous small noncoding RNA, miR-9-1, in influenza A virus (IAV) infection. Increased expression of TNKS1 was observed in IAV-infected human lung epithelial cells and mouse lungs. TNKS1 knockdown by RNA interference repressed influenza viral replication. A screen using TNKS1 3'-untranslation region (3'-UTR) reporter assays and predicted microRNAs identified that miR-9-1 targeted TNKS1. Overexpression of miR-9-1 reduced influenza viral replication in lung epithelial cells as measured by viral mRNA and protein levels as well as virus production. miR-9-1 induced type I interferon production and enhanced the phosphorylation of STAT1 in cell culture. The ectopic expression of miR-9-1 in the lungs of mice by using an adenoviral viral vector enhanced type I interferon response, inhibited viral replication, and reduced susceptibility to IAV infection. Our results indicate that miR-9-1 is an anti-influenza microRNA that targets TNKS1 and enhances cellular antiviral state.
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Affiliation(s)
- Gayan Bamunuarachchi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Kishore Vaddadi
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Xiaoyun Yang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Quanjin Dang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Zhengyu Zhu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Sankha Hewawasam
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Chaoqun Huang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yurong Liang
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Yujie Guo
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Lin Liu
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, USA
- Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK, USA
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Quach HQ, Goergen KM, Grill DE, Haralambieva IH, Ovsyannikova IG, Poland GA, Kennedy RB. Virus-specific and shared gene expression signatures in immune cells after vaccination in response to influenza and vaccinia stimulation. Front Immunol 2023; 14:1168784. [PMID: 37600811 PMCID: PMC10436507 DOI: 10.3389/fimmu.2023.1168784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background In the vaccine era, individuals receive multiple vaccines in their lifetime. Host gene expression in response to antigenic stimulation is usually virus-specific; however, identifying shared pathways of host response across a wide spectrum of vaccine pathogens can shed light on the molecular mechanisms/components which can be targeted for the development of broad/universal therapeutics and vaccines. Method We isolated PBMCs, monocytes, B cells, and CD8+ T cells from the peripheral blood of healthy donors, who received both seasonal influenza vaccine (within <1 year) and smallpox vaccine (within 1 - 4 years). Each of the purified cell populations was stimulated with either influenza virus or vaccinia virus. Differentially expressed genes (DEGs) relative to unstimulated controls were identified for each in vitro viral infection, as well as for both viral infections (shared DEGs). Pathway enrichment analysis was performed to associate identified DEGs with KEGG/biological pathways. Results We identified 2,906, 3,888, 681, and 446 DEGs in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, in response to influenza stimulation. Meanwhile, 97, 120, 20, and 10 DEGs were identified as gene signatures in PBMCs, monocytes, B cells, and CD8+ T cells, respectively, upon vaccinia stimulation. The majority of DEGs identified in PBMCs were also found in monocytes after either viral stimulation. Of the virus-specific DEGs, 55, 63, and 9 DEGs occurred in common in PBMCs, monocytes, and B cells, respectively, while no DEGs were shared in infected CD8+ T cells after influenza and vaccinia. Gene set enrichment analysis demonstrated that these shared DEGs were over-represented in innate signaling pathways, including cytokine-cytokine receptor interaction, viral protein interaction with cytokine and cytokine receptor, Toll-like receptor signaling, RIG-I-like receptor signaling pathways, cytosolic DNA-sensing pathways, and natural killer cell mediated cytotoxicity. Conclusion Our results provide insights into virus-host interactions in different immune cells, as well as host defense mechanisms against viral stimulation. Our data also highlights the role of monocytes as a major cell population driving gene expression in ex vivo PBMCs in response to viral stimulation. The immune response signaling pathways identified in this study may provide specific targets for the development of novel virus-specific therapeutics and improved vaccines for vaccinia and influenza. Although influenza and vaccinia viruses have been selected in this study as pathogen models, this approach could be applicable to other pathogens.
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Affiliation(s)
- Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Diane E. Grill
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
| | - Iana H. Haralambieva
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States
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Min J, Li Y, Li X, Wang M, Li H, Bi Y, Xu P, Liu W, Ye X, Li J. The circRNA circVAMP3 restricts influenza A virus replication by interfering with NP and NS1 proteins. PLoS Pathog 2023; 19:e1011577. [PMID: 37603540 PMCID: PMC10441791 DOI: 10.1371/journal.ppat.1011577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Circular RNAs (circRNAs) are involved in various biological roles, including viral infection and antiviral immune responses. To identify influenza A virus (IAV) infection-related circRNAs, we compared the circRNA profiles of A549 cells upon IAV infection. We found that circVAMP3 is substantially upregulated after IAV infection or interferon (IFN) stimulation. Furthermore, IAV and IFN-β induced the expression of QKI-5, which promoted the biogenesis of circVAMP3. Overexpression of circVAMP3 inhibited IAV replication, while circVAMP3 knockdown promoted viral replication, suggesting that circVAMP3 restricts IAV replication. We verified the effect of circVAMP3 on viral infection in mice and found that circVAMP3 restricted IAV replication and pathogenesis in vivo. We also found that circVAMP3 functions as a decoy to the viral proteins nucleoprotein (NP) and nonstructural protein 1 (NS1). Mechanistically, circVAMP3 interfered with viral ribonucleoprotein complex activity by reducing the interaction of NP with polymerase basic 1, polymerase basic 2, or vRNA and restored the activation of IFN-β by alleviating the inhibitory effect of NS1 to RIG-I or TRIM25. Our study provides new insights into the roles of circRNAs, both in directly inhibiting virus replication and in restoring innate immunity against IAV infection.
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Affiliation(s)
- Jie Min
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yucen Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xinda Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingge Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Huizi Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Xin Ye
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Zhao Z, Li J, Feng Y, Kang X, Li Y, Chen Y, Li W, Yang W, Zhao L, Huang S, Zhang S, Jiang T. Host DNA Demethylation Induced by DNMT1 Inhibition Up-Regulates Antiviral OASL Protein during Influenza a Virus Infection. Viruses 2023; 15:1646. [PMID: 37631988 PMCID: PMC10459088 DOI: 10.3390/v15081646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Influenza A virus (IAV) is a leading cause of human respiratory infections and poses a major public health concern. IAV replication can affect the expression of DNA methyltransferases (DNMTs), and the subsequent changes in DNA methylation regulate gene expression and may lead to abnormal gene transcription and translation, yet the underlying mechanisms of virus-induced epigenetic changes from DNA methylation and its role in virus-host interactions remain elusive. Here in this paper, we showed that DNMT1 expression could be suppressed following the inhibition of miR-142-5p or the PI3K/AKT signaling pathway during IAV infection, resulting in demethylation of the promotor region of the 2'-5'-oligoadenylate synthetase-like (OASL) protein and promotion of its expression in A549 cells. OASL expression enhanced RIG-I-mediated interferon induction and then suppressed replication of IAV. Our study elucidated an innate immunity mechanism by which up-regulation of OASL contributes to host antiviral responses via epigenetic modifications in IAV infection, which could provide important insights into the understanding of viral pathogenesis and host antiviral defense.
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Affiliation(s)
- Zhiyan Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.Z.); (S.H.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Ye Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Xiaoping Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Yuchang Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Yuehong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Wei Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Wenguang Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Lu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Shenghai Huang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.Z.); (S.H.)
| | - Sen Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
| | - Tao Jiang
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.Z.); (S.H.)
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China; (J.L.); (Y.F.); (X.K.); (Y.L.); (Y.C.); (W.L.); (W.Y.); (L.Z.)
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Diefenbach-Elstob TR, Chanthalavanh P, Bobbitt ME, Brown SK, Rynehart C, Spirason N, Peck H, Deng YM, Dapat C, Subbarao K, Barr IG. Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza during 2022. Commun Dis Intell (2018) 2023; 47. [PMID: 37817300 DOI: 10.33321/cdi.2023.47.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Indexed: 10/12/2023]
Abstract
As part of its role in the World Health Organization's (WHO) Global Influenza Surveillance and Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza in Melbourne received a record total of 12,073 human influenza positive samples during 2022. Viruses were analysed for their antigenic, genetic and antiviral susceptibility properties. Selected viruses were propagated in qualified cells or embryonated hen's eggs for potential use in seasonal influenza virus vaccines. In 2022, influenza A(H3N2) viruses predominated over influenza A(H1N1)pdm09 and B viruses, accounting for 77% of all viruses analysed. The majority of A(H1N1)pdm09, A(H3N2) and influenza B viruses analysed at the Centre were found to be antigenically and genetically similar to the respective WHO recommended vaccine strains for the southern hemisphere in 2022. Of 3,372 samples tested for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, two A(H1N1)pdm09 viruses showed highly reduced inhibition against oseltamivir.
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Affiliation(s)
| | | | - Monica E Bobbitt
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Sook Kwan Brown
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Cleve Rynehart
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Heidi Peck
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Clyde Dapat
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza
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Yang ZS, Lin CY, Khan MB, Hsu MC, Assavalapsakul W, Thitithanyanont A, Wang SF. Understanding the role of galectins toward influenza A virus infection. Expert Opin Ther Targets 2023; 27:927-937. [PMID: 37747065 DOI: 10.1080/14728222.2023.2263912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/24/2023] [Indexed: 09/26/2023]
Abstract
INTRODUCTION Influenza A virus (IAV) is highly contagious and causes respiratory diseases in birds, mammals, and humans. Some strains of IAV, whether from human or avian sources, have developed resistance to existing antiviral drugs. Therefore, the discovery of new influenza antiviral drugs and therapeutic approaches is crucial. Recent studies have shown that galectins (Gal), a group of β-galactose-binding lectins, play a role in regulating various viral infections, including IAVs. AREAS COVERED This review provides an overview of the roles of different galectins in IAV infection. We discuss the characteristics of galectins, their impact on IAV infection and spread, and highlight their positive or negative regulatory functions and potential mechanisms during IAV infection. Furthermore, we explore the potential application of galectins in IAV therapy. EXPERT OPINION Galectins were first identified in the mid-1970s, and currently, 15 mammalian galectins have been identified. While all galectin members possess the carbohydrate recognition domain (CRD) that interacts with β-galactoside, their regulatory functions vary in different DNA or RNA virus infections. Certain galectin members have been found to regulate IAV infection through diverse mechanisms. Therefore, a comprehensive understanding of their roles in IAV infection is essential, as it may pave the way for novel therapeutic strategies.
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Affiliation(s)
- Zih-Syuan Yang
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Yen Lin
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Muhammad Bilal Khan
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Cheng Hsu
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Program in Tropical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Peacock TP, Sheppard CM, Lister MG, Staller E, Frise R, Swann OC, Goldhill DH, Long JS, Barclay WS. Mammalian ANP32A and ANP32B Proteins Drive Differential Polymerase Adaptations in Avian Influenza Virus. J Virol 2023; 97:e0021323. [PMID: 37074204 PMCID: PMC10231198 DOI: 10.1128/jvi.00213-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/14/2023] [Indexed: 04/20/2023] Open
Abstract
ANP32 proteins, which act as influenza polymerase cofactors, vary between birds and mammals. In mammals, ANP32A and ANP32B have been reported to serve essential but redundant roles to support influenza polymerase activity. The well-known mammalian adaptation PB2-E627K enables influenza polymerase to use mammalian ANP32 proteins. However, some mammalian-adapted influenza viruses do not harbor this substitution. Here, we show that alternative PB2 adaptations, Q591R and D701N, also allow influenza polymerase to use mammalian ANP32 proteins, whereas other PB2 mutations, G158E, T271A, and D740N, increase polymerase activity in the presence of avian ANP32 proteins as well. Furthermore, PB2-E627K strongly favors use of mammalian ANP32B proteins, whereas D701N shows no such bias. Accordingly, PB2-E627K adaptation emerges in species with strong pro-viral ANP32B proteins, such as humans and mice, while D701N is more commonly seen in isolates from swine, dogs, and horses, where ANP32A proteins are the preferred cofactor. Using an experimental evolution approach, we show that the passage of viruses containing avian polymerases in human cells drove acquisition of PB2-E627K, but not in the absence of ANP32B. Finally, we show that the strong pro-viral support of ANP32B for PB2-E627K maps to the low-complexity acidic region (LCAR) tail of ANP32B. IMPORTANCE Influenza viruses naturally reside in wild aquatic birds. However, the high mutation rate of influenza viruses allows them to rapidly and frequently adapt to new hosts, including mammals. Viruses that succeed in these zoonotic jumps pose a pandemic threat whereby the virus adapts sufficiently to efficiently transmit human-to-human. The influenza virus polymerase is central to viral replication and restriction of polymerase activity is a major barrier to species jumps. ANP32 proteins are essential for influenza polymerase activity. In this study, we describe how avian influenza viruses can adapt in several different ways to use mammalian ANP32 proteins. We further show that differences between mammalian ANP32 proteins can select different adaptive changes and are responsible for some of the typical mutations that arise in mammalian-adapted influenza polymerases. These different adaptive mutations may determine the relative zoonotic potential of influenza viruses and thus help assess their pandemic risk.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Carol M. Sheppard
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Margaret G. Lister
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ecco Staller
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Olivia C. Swann
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Daniel H. Goldhill
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jason S. Long
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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Kim S, Carrel M, Kitchen A. Spatial genetic structure of 2009 H1N1 pandemic influenza established as a result of interaction with human populations in mainland China. PLoS One 2023; 18:e0284716. [PMID: 37196010 PMCID: PMC10191359 DOI: 10.1371/journal.pone.0284716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/06/2023] [Indexed: 05/19/2023] Open
Abstract
Identifying the spatial patterns of genetic structure of influenza A viruses is a key factor for understanding their spread and evolutionary dynamics. In this study, we used phylogenetic and Bayesian clustering analyses of genetic sequences of the A/H1N1pdm09 virus with district-level locations in mainland China to investigate the spatial genetic structure of the A/H1N1pdm09 virus across human population landscapes. Positive correlation between geographic and genetic distances indicates high degrees of genetic similarity among viruses within small geographic regions but broad-scale genetic differentiation, implying that local viral circulation was a more important driver in the formation of the spatial genetic structure of the A/H1N1pdm09 virus than even, countrywide viral mixing and gene flow. Geographic heterogeneity in the distribution of genetic subpopulations of A/H1N1pdm09 virus in mainland China indicates both local to local transmission as well as broad-range viral migration. This combination of both local and global structure suggests that both small-scale and large-scale population circulation in China is responsible for viral genetic structure. Our study provides implications for understanding the evolution and spread of A/H1N1pdm09 virus across the population landscape of mainland China, which can inform disease control strategies for future pandemics.
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Affiliation(s)
- Seungwon Kim
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
| | - Margaret Carrel
- Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa, United States of America
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, Iowa, United States of America
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Vo V, Harrington A, Chang CL, Baker H, Moshi MA, Ghani N, Itorralba JY, Tillett RL, Dahlmann E, Basazinew N, Gu R, Familara TD, Boss S, Vanderford F, Ghani M, Tang AJ, Matthews A, Papp K, Khan E, Koutras C, Kan HY, Lockett C, Gerrity D, Oh EC. Identification and genome sequencing of an influenza H3N2 variant in wastewater from elementary schools during a surge of influenza A cases in Las Vegas, Nevada. Sci Total Environ 2023; 872:162058. [PMID: 36758698 PMCID: PMC9909754 DOI: 10.1016/j.scitotenv.2023.162058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 05/25/2023]
Abstract
Real-time surveillance of infectious diseases at schools or in communities is often hampered by delays in reporting due to resource limitations and infrastructure issues. By incorporating quantitative PCR and genome sequencing, wastewater surveillance has been an effective complement to public health surveillance at the community and building-scale for pathogens such as poliovirus, SARS-CoV-2, and even the monkeypox virus. In this study, we asked whether wastewater surveillance programs at elementary schools could be leveraged to detect RNA from influenza viruses shed in wastewater. We monitored for influenza A and B viral RNA in wastewater from six elementary schools from January to May 2022. Quantitative PCR led to the identification of influenza A viral RNA at three schools, which coincided with the lifting of COVID-19 restrictions and a surge in influenza A infections in Las Vegas, Nevada, USA. We performed genome sequencing of wastewater RNA, leading to the identification of a 2021-2022 vaccine-resistant influenza A (H3N2) 3C.2a1b.2a.2 subclade. We next tested wastewater samples from a treatment plant that serviced the elementary schools, but we were unable to detect the presence of influenza A/B RNA. Together, our results demonstrate the utility of near-source wastewater surveillance for the detection of local influenza transmission in schools, which has the potential to be investigated further with paired school-level influenza incidence data.
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Affiliation(s)
- Van Vo
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Anthony Harrington
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Ching-Lan Chang
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Hayley Baker
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Michael A Moshi
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Nabih Ghani
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Jose Yani Itorralba
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Elizabeth Dahlmann
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Natnael Basazinew
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Richard Gu
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Tiffany D Familara
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Sage Boss
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Fritz Vanderford
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Moonis Ghani
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Austin J Tang
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Alice Matthews
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Katerina Papp
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Eakalak Khan
- Department of Civil and Environmental Engineering and Construction, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Carolina Koutras
- R-Zero Systems, Inc., 345 W Bearcat Dr Suite #100, South Salt Lake, UT 84115, USA
| | - Horng-Yuan Kan
- Southern Nevada Health District, Las Vegas, NV 89106, USA
| | | | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Edwin C Oh
- Laboratory of Neurogenetics and Precision Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Nevada Institute of Personalized Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; Department of Internal Medicine, UNLV School of Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.
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Tessema MB, Tuipulotu DE, Oates CV, Brooks AG, Man SM, Londrigan SL, Reading PC. Mouse guanylate-binding protein 1 does not mediate antiviral activity against influenza virus in vitro or in vivo. Immunol Cell Biol 2023; 101:383-396. [PMID: 36744765 PMCID: PMC10952839 DOI: 10.1111/imcb.12627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 02/07/2023]
Abstract
Many interferon (IFN)-stimulated genes are upregulated within host cells following infection with influenza and other viruses. While the antiviral activity of some IFN-stimulated genes, such as the IFN-inducible GTPase myxoma resistance (Mx)1 protein 1, has been well defined, less is known regarding the antiviral activities of related IFN-inducible GTPases of the guanylate-binding protein (GBP) family, particularly mouse GBPs, where mouse models can be used to assess their antiviral properties in vivo. Herein, we demonstrate that mouse GBP1 (mGBP1) was upregulated in a mouse airway epithelial cell line (LA-4 cells) following pretreatment with mouse IFNα or infection by influenza A virus (IAV). Whereas doxycycline-inducible expression of mouse Mx1 (mMx1) in LA-4 cells resulted in reduced susceptibility to IAV infection and reduced viral growth, inducible mGBP1 did not. Moreover, primary cells isolated from mGBP1-deficient mice (mGBP1-/- ) showed no difference in susceptibility to IAV and mGBP1-/- macrophages showed no defect in IAV-induced NLRP3 (NLR family pyrin domain containing 3) inflammasome activation. After intranasal IAV infection, mGBP1-/- mice also showed no differences in virus replication or induction of inflammatory responses in the airways during infection. Thus, using complementary approaches such as mGBP1 overexpression, cells from mGBP1-/- mice and intranasal infection of mGBP1-/- we demonstrate that mGBP1 does not play a major role in modulating IAV infection in vitro or in vivo.
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Affiliation(s)
- Melkamu B Tessema
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Daniel Enosi Tuipulotu
- Division of Immunology and Infectious Disease, The John Curtin School of Medical ResearchThe Australian National UniversityCanberraACTAustralia
| | - Clare V Oates
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Andrew G Brooks
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Si Ming Man
- Division of Immunology and Infectious Disease, The John Curtin School of Medical ResearchThe Australian National UniversityCanberraACTAustralia
| | - Sarah L Londrigan
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
| | - Patrick C Reading
- Department of Microbiology and ImmunologyThe Peter Doherty Institute for Infection and Immunity, University of MelbourneMelbourneVICAustralia
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference LaboratoryThe Peter Doherty Institute for Infection and ImmunityMelbourneVICAustralia
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Lee CY, Raghunathan V, Caceres C, Geiger G, Seibert B, Cargnin Faccin F, Gay L, Ferreri L, Kaul D, Wrammert J, Tan G, Perez D, Lowen A. Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies. Proc Natl Acad Sci U S A 2023; 120:e2208718120. [PMID: 37068231 PMCID: PMC10151473 DOI: 10.1073/pnas.2208718120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 02/15/2023] [Indexed: 04/19/2023] Open
Abstract
The hemagglutinin (HA) stem region is a major target of universal influenza vaccine efforts owing to the presence of highly conserved epitopes across multiple influenza A virus (IAV) strains and subtypes. To explore the potential impact of vaccine-induced immunity targeting the HA stem, we examined the fitness effects of viral escape from stem-binding broadly neutralizing antibodies (stem-bnAbs). Recombinant viruses containing each individual antibody escape substitution showed diminished replication compared to wild-type virus, indicating that stem-bnAb escape incurred fitness costs. A second-site mutation in the HA head domain (N129D; H1 numbering) reduced the fitness effects observed in primary cell cultures and likely enabled the selection of escape mutations. Functionally, this putative permissive mutation increased HA avidity for its receptor. These results suggest a mechanism of epistasis in IAV, wherein modulating the efficiency of attachment eases evolutionary constraints imposed by the requirement for membrane fusion. Taken together, the data indicate that viral escape from stem-bnAbs is costly but highlights the potential for epistatic interactions to enable evolution within the functionally constrained HA stem domain.
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Affiliation(s)
- Chung-Young Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, The Republic of Korea
| | - Vedhika Raghunathan
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | - C. Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Flavio Cargnin Faccin
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Lucas M. Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Jens Wrammert
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, CA 92037
- Division of Infectious Disease, Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322
- Emory-University of Georgia Center of Excellence for Influenza Research and Surveillance, Atlanta, GA 30322
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Vicary AC, Mendes M, Swaminath S, Lekbua A, Reddan J, Rodriguez ZK, Russell AB. Maximal interferon induction by influenza lacking NS1 is infrequent owing to requirements for replication and export. PLoS Pathog 2023; 19:e1010943. [PMID: 37068114 PMCID: PMC10138204 DOI: 10.1371/journal.ppat.1010943] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/27/2023] [Accepted: 03/31/2023] [Indexed: 04/18/2023] Open
Abstract
Influenza A virus exhibits high rates of replicative failure due to a variety of genetic defects. Most influenza virions cannot, when acting as individual particles, complete the entire viral life cycle. Nevertheless influenza is incredibly successful in the suppression of innate immune detection and the production of interferons, remaining undetected in >99% of cells in tissue-culture models of infection. Notably, the same variation that leads to replication failure can, by chance, inactivate the major innate immune antagonist in influenza A virus, NS1. What explains the observed rarity of interferon production in spite of the frequent loss of this, critical, antagonist? By studying how genetic and phenotypic variation in a viral population lacking NS1 correlates with interferon production, we have built a model of the "worst-case" failure from an improved understanding of the steps at which NS1 acts in the viral life cycle to prevent the triggering of an innate immune response. In doing so, we find that NS1 prevents the detection of de novo innate immune ligands, defective viral genomes, and viral export from the nucleus, although only generation of de novo ligands appears absolutely required for enhanced detection of virus in the absence of NS1. Due to this, the highest frequency of interferon production we observe (97% of infected cells) requires a high level of replication in the presence of defective viral genomes with NS1 bearing an inactivating mutation that does not impact its partner encoded on the same segment, NEP. This is incredibly unlikely to occur given the standard variation found within a viral population, and would generally require direct, artificial, intervention to achieve at an appreciable rate. Thus from our study, we procure at least a partial explanation for the seeming contradiction between high rates of replicative failure and the rarity of the interferon response to influenza infection.
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Affiliation(s)
- Alison C. Vicary
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marisa Mendes
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Asama Lekbua
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jack Reddan
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Zaida K. Rodriguez
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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Scheibner D, Salaheldin AH, Bagato O, Zaeck LM, Mostafa A, Blohm U, Müller C, Eweas AF, Franzke K, Karger A, Schäfer A, Gischke M, Hoffmann D, Lerolle S, Li X, Abd El-Hamid HS, Veits J, Breithaupt A, Boons GJ, Matrosovich M, Finke S, Pleschka S, Mettenleiter TC, de Vries RP, Abdelwhab EM. Phenotypic effects of mutations observed in the neuraminidase of human origin H5N1 influenza A viruses. PLoS Pathog 2023; 19:e1011135. [PMID: 36745654 PMCID: PMC9934401 DOI: 10.1371/journal.ppat.1011135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
Global spread and regional endemicity of H5Nx Goose/Guangdong avian influenza viruses (AIV) pose a continuous threat for poultry production and zoonotic, potentially pre-pandemic, transmission to humans. Little is known about the role of mutations in the viral neuraminidase (NA) that accompanied bird-to-human transmission to support AIV infection of mammals. Here, after detailed analysis of the NA sequence of human H5N1 viruses, we studied the role of A46D, L204M, S319F and S430G mutations in virus fitness in vitro and in vivo. Although H5N1 AIV carrying avian- or human-like NAs had similar replication efficiency in avian cells, human-like NA enhanced virus replication in human airway epithelia. The L204M substitution consistently reduced NA activity of H5N1 and nine other influenza viruses carrying NA of groups 1 and 2, indicating a universal effect. Compared to the avian ancestor, human-like H5N1 virus has less NA incorporated in the virion, reduced levels of viral NA RNA replication and NA expression. We also demonstrate increased accumulation of NA at the plasma membrane, reduced virus release and enhanced cell-to-cell spread. Furthermore, NA mutations increased virus binding to human-type receptors. While not affecting high virulence of H5N1 in chickens, the studied NA mutations modulated virulence and replication of H5N1 AIV in mice and to a lesser extent in ferrets. Together, mutations in the NA of human H5N1 viruses play different roles in infection of mammals without affecting virulence or transmission in chickens. These results are important to understand the genetic determinants for replication of AIV in mammals and should assist in the prediction of AIV with zoonotic potential.
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Affiliation(s)
- David Scheibner
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Ahmed H. Salaheldin
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Alexandria University, El-Beheira, Egypt
| | - Ola Bagato
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Water Pollution Research Department, Dokki, Giza, Egypt
| | - Luca M. Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Water Pollution Research Department, Dokki, Giza, Egypt
| | - Ulrike Blohm
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Ahmed F. Eweas
- Department of Medicinal Chemistry, National Research Center, Dokki, Giza, Egypt; Department of Science, University of Technology and Applied Sciences-Rustaq, Rustaq, Sultanate of Oman
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Alexander Schäfer
- Institute of Immunology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Marcel Gischke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Solène Lerolle
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON, Canada; Department of Biochemistry, Microbiology and Immunology and Emerging Pathogens Research Centre, University of Ottawa, Ottawa, Ontario, Canada
| | - Hatem S. Abd El-Hamid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Damanhur University, Al-Buheira, Egypt
| | - Jutta Veits
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Geert-Jan Boons
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Science, the Netherlands
| | | | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF) partner site Giessen-Marburg-Langen, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Robert P. de Vries
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Science, the Netherlands
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- * E-mail:
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Chen Y, Shen J, Wu Y, Ni M, Deng Y, Sun X, Wang X, Zhang T, Pan F, Tang Z. Tea consumption and risk of lower respiratory tract infections: a two-sample mendelian randomization study. Eur J Nutr 2023; 62:385-393. [PMID: 36042048 PMCID: PMC9427168 DOI: 10.1007/s00394-022-02994-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/24/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Observational studies have reported the association between tea consumption and the risk of lower respiratory tract infections (LRTIs). However, a consensus has yet to be reached, and whether the observed association is driven by confounding factors or reverse causality remains unclear. METHOD A two-sample Mendelian randomization (MR) analysis was conducted to determine whether genetically predicted tea intake is causally associated with the risk of common LRTI subtypes. Genome-wide association study (GWAS) from UK Biobank was used to identify single-nucleotide polymorphisms (SNPs) associated with an extra cup of tea intake each day. The summary statistics for acute bronchitis, acute bronchiolitis, bronchiectasis, pneumonia, and influenza and pneumonia were derived from the FinnGen project. RESULTS We found that genetically predicted an extra daily cup of tea intake was causally associated with the decreased risk of bronchiectasis [odds ratio (OR) = 0.61, 95% confidence interval (CI) = 0.47-0.78, P < 0.001], pneumonia (OR = 0.90, 95% CI = 0.85-0.96, P = 0.002), influenza and pneumonia (OR = 0.91, 95% CI = 0.85-0.97, P = 0.002), but not with acute bronchitis (OR = 0.91, 95% CI = 0.82-1.01, P = 0.067) and acute bronchiolitis (OR = 0.79, 95% CI = 0.60-1.05, P = 0.100). Sensitivity analyses showed that no heterogeneity and pleiotropy could bias the results. CONCLUSIONS Our findings provided new evidence that genetically predicted an extra daily cup of tea intake may causally associated with a decreased risk of bronchiectasis, pneumonia, and influenza and pneumonia.
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Affiliation(s)
- Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jiran Shen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ye Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Man Ni
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Yujie Deng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xiaoya Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xinqi Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Tao Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
- The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Zhiru Tang
- School of Health Service and Management, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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48
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Lei R, Hernandez Garcia A, Tan TJC, Teo QW, Wang Y, Zhang X, Luo S, Nair SK, Peng J, Wu NC. Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Rep 2023; 42:111951. [PMID: 36640354 PMCID: PMC9931530 DOI: 10.1016/j.celrep.2022.111951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
Influenza neuraminidase (NA) has received increasing attention as an effective vaccine target. However, its mutational tolerance is not well characterized. Here, the fitness effects of >6,000 mutations in human H3N2 NA are probed using deep mutational scanning. Our result shows that while its antigenic regions have high mutational tolerance, there are solvent-exposed regions with low mutational tolerance. We also find that protein stability is a major determinant of NA mutational fitness. The deep mutational scanning result correlates well with mutational fitness inferred from natural sequences using a protein language model, substantiating the relevance of our findings to the natural evolution of circulating strains. Additional analysis further suggests that human H3N2 NA is far from running out of mutations despite already evolving for >50 years. Overall, this study advances our understanding of the evolutionary potential of NA and the underlying biophysical constraints, which in turn provide insights into NA-based vaccine design.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrea Hernandez Garcia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Peng
- HeliXon Limited, Beijing 100084, China; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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49
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Larkin H, Larkin H. Twenty-Strain "Universal" mRNA Flu Vaccine Effective in Animal Studies. JAMA 2023; 329:114. [PMID: 36625826 DOI: 10.1001/jama.2022.23512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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50
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Lozhkov AA, Yolshin ND, Baranovskaya IL, Plotnikova MA, Sergeeva MV, Gyulikhandanova NE, Klotchenko SA, Vasin AV. Kinetics of interferon-λ and receptor expression in response to in vitro respiratory viral infection. Acta Virol 2023; 67:99-108. [PMID: 36950890 DOI: 10.4149/av_2023_110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The major protective immune response against viruses is the production of type I and III interferons (IFNs). IFNs induce the expression of hundreds of IFN-stimulated genes (ISGs) that block viral replication and further viral spread. In this report, we analyzed the expression of IFNs and some ISGs (MxA, PKR, OAS-1, IFIT-1, RIG-1, MDA5, SOCS-1) in alveolar epithelial cells (A549) in response to infection with influenza A viruses (A/California/07/09 (H1N1pdm); A/Texas/50/12 (H3N2)); influenza B virus (B/Phuket/3073/13); adenovirus type 5 and 6; or respiratory syncytial virus (strain A2). Influenza B virus had the ability to most rapidly induce IFNs and ISGs as well as to stimulate excessive IFN-α, IFN-β and IFN-λ secretion. It seems curious that IAV H1N1pdm did not induce IFN-λ secretion, but enhanced type I IFN and interleukin (IL)-6 production. We emphasized the importance of the negative regulation of virus-triggered signaling and cellular IFN response. We showed a decrease in IFNLR1 mRNA in the case of IBV infection. The attenuation of SOCS-1 expression in IAV H1N1pdm can be considered as the inability of the system to restore the immune status. Presumably, the lack of negative feedback loop regulation of proinflammatory immune response may be a factor contributing to the particular pathogenicity of several strains of influenza. Keywords: lambda interferons; MxA; influenza; respiratory syncytial virus; A549 cells.
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