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Escalera A, Laporte M, Turner S, Karakus U, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khalil Z, van Bakel H, Smith D, García-Sastre A, Aydillo T. The impact of S2 mutations on Omicron SARS-CoV-2 cell surface expression and fusogenicity. Emerg Microbes Infect 2024; 13:2297553. [PMID: 38112266 PMCID: PMC10866063 DOI: 10.1080/22221751.2023.2297553] [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: 07/06/2023] [Accepted: 12/17/2023] [Indexed: 12/21/2023]
Abstract
SARS-CoV-2 Omicron subvariants are still emerging and spreading worldwide. These variants contain a high number of polymorphisms in the spike (S) glycoprotein that could potentially impact their pathogenicity and transmission. We have previously shown that the S:655Y and P681H mutations enhance S protein cleavage and syncytia formation. Interestingly, these polymorphisms are present in Omicron S protein. Here, we characterized the cleavage efficiency and fusogenicity of the S protein of different Omicron sublineages. Our results showed that Omicron BA.1 subvariant is efficiently cleaved but it is poorly fusogenic compared to previous SARS-CoV-2 strains. To understand the basis of this phenotype, we generated chimeric S protein using combinations of the S1 and S2 domains from WA1, Delta and Omicron BA.1 variants. We found that the S2 domain of Omicron BA.1 hindered efficient cell-cell fusion. Interestingly, this domain only contains six unique polymorphisms never detected before in ancestral SARS-CoV-2 variants. WA1614G S proteins containing the six individuals S2 Omicron mutations were assessed for their fusogenicity and S surface expression after transfection in cells. Results showed that the S:N856K and N969K substitutions decreased syncytia formation and impacted S protein cell surface levels. However, we observed that "first-generation" Omicron sublineages that emerged subsequently, had convergently evolved to an enhanced fusogenic activity and S expression on the surface of infected cells while "second-generation" Omicron variants have highly diverged and showed lineage-specific fusogenic properties. Importantly, our findings could have potential implications in the improvement and redesign of COVID-19 vaccines.
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Affiliation(s)
- Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Umut Karakus
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Cool K, Gaudreault NN, Trujillo JD, Morozov I, McDowell CD, Bold D, Kwon T, Balaraman V, Assato P, Madden DW, Mantlo E, Souza-Neto J, Matias-Ferreyra F, Retallick J, Singh G, Schotsaert M, Carossino M, Balasuriya UBR, Wilson WC, Pogranichniy RM, García-Sastre A, Richt JA. Experimental co-infection of calves with SARS-CoV-2 Delta and Omicron variants of concern. Emerg Microbes Infect 2024; 13:2281356. [PMID: 37938158 PMCID: PMC10763854 DOI: 10.1080/22221751.2023.2281356] [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: 07/30/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023]
Abstract
Since emerging in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has repeatedly crossed the species barrier with natural infections reported in various domestic and wild animal species. The emergence and global spread of SARS-CoV-2 variants of concern (VOCs) has expanded the range of susceptible host species. Previous experimental infection studies in cattle using Wuhan-like SARS-CoV-2 isolates suggested that cattle were not likely amplifying hosts for SARS-CoV-2. However, SARS-CoV-2 sero- and RNA-positive cattle have since been identified in Europe, India, and Africa. Here, we investigated the susceptibility and transmission of the Delta and Omicron SARS-CoV-2 VOCs in cattle. Eight Holstein calves were co-infected orally and intranasally with a mixed inoculum of SARS-CoV-2 VOCs Delta and Omicron BA.2. Twenty-four hours post-challenge, two sentinel calves were introduced to evaluate virus transmission. The co-infection resulted in a high proportion of calves shedding SARS-CoV-2 RNA at 1- and 2-days post-challenge (DPC). Extensive tissue distribution of SARS-CoV-2 RNA was observed at 3 and 7 DPC and infectious virus was recovered from two calves at 3 DPC. Next-generation sequencing revealed that only the SARS-CoV-2 Delta variant was detected in clinical samples and tissues. Similar to previous experimental infection studies in cattle, we observed only limited seroconversion and no clear evidence of transmission to sentinel calves. Together, our findings suggest that cattle are more permissive to infection with SARS-CoV-2 Delta than Omicron BA.2 and Wuhan-like isolates but, in the absence of horizontal transmission, are not likely to be reservoir hosts for currently circulating SARS-CoV-2 variants.
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Affiliation(s)
- Konner Cool
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chester D. McDowell
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Taeyong Kwon
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Velmurugan Balaraman
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Patricia Assato
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Daniel W. Madden
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Emily Mantlo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jayme Souza-Neto
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Franco Matias-Ferreyra
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jaime Retallick
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mariano Carossino
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - William C. Wilson
- Foreign Arthropod-Borne Animal Diseases Research Unit, National Bio and Agro-Defense Facility, United States Department of Agriculture, Manhattan, KS, USA
| | - Roman M. Pogranichniy
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
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3
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Huang C, Yu L, Xu Y, Huang J, Qin Y, Guo X, Zeng Y, Qin Y, Ouyang K, Wei Z, Huang W, García-Sastre A, Chen Y. Long-term co-circulation of multiple influenza A viruses in pigs, Guangxi, China. Emerg Microbes Infect 2024; 13:2337673. [PMID: 38572517 PMCID: PMC11005871 DOI: 10.1080/22221751.2024.2337673] [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: 12/14/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Influenza A viruses (IAVs) pose a persistent potential threat to human health because of the spillover from avian and swine infections. Extensive surveillance was performed in 12 cities of Guangxi, China, during 2018 and 2023. A total of 2540 samples (including 2353 nasal swabs and 187 lung tissues) were collected from 18 pig farms with outbreaks of respiratory disease. From these, 192 IAV-positive samples and 19 genomic sequences were obtained. We found that the H1 and H3 swine influenza A viruses (swIAVs) of multiple lineages and genotypes have continued to co-circulate during that time in this region. Genomic analysis revealed the Eurasian avian-like H1N1 swIAVs (G4) still remained predominant in pig populations. Strikingly, the novel multiple H3N2 genotypes were found to have been generated through the repeated introduction of the early H3N2 North American triple reassortant viruses (TR H3N2 lineage) that emerged in USA and Canada in 1998 and 2005, respectively. Notably, when the matrix gene segment derived from the H9N2 avian influenza virus was introduced into endemic swIAVs, this produced a novel quadruple reassortant H1N2 swIAV that could pose a potential risk for zoonotic infection.
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Affiliation(s)
- Chongqiang Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Liangzheng Yu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Yi Xu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Jiamo Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Yibin Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Institute of Veterinary Medicine, Nanning, People’s Republic of China
| | - Xuan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Nongken Yongxin Animal Husbandry Group Co. Ltd., Nanning, People’s Republic of China
| | - Yongfang Zeng
- Nanning Zhufulai Animal Health Management Co. Ltd., Nanning, People’s Republic of China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, People’s Republic of China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning, People’s Republic of China
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4
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Aydillo T, Balsera-Manzanero M, Rojo-Fernandez A, Escalera A, Salamanca-Rivera C, Pachón J, Del Mar Muñoz-García M, Sánchez-Cordero MJ, Sánchez-Céspedes J, García-Sastre A, Cordero E. Concomitant administration of seasonal influenza and COVID-19 mRNA vaccines. Emerg Microbes Infect 2024; 13:2292068. [PMID: 38054302 PMCID: PMC10798284 DOI: 10.1080/22221751.2023.2292068] [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: 10/03/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Current clinical guidelines support the concomitant administration of seasonal influenza vaccines and COVID-19 mRNA boosters vaccine. Whether dual vaccination may impact vaccine immunogenicity due to an interference between influenza or SARS-CoV-2 antigens is unknown. We aimed to understand the impact of mRNA COVID-19 vaccines administered concomitantly on the immune response to influenza vaccines. For this, 128 volunteers were vaccinated during the 22-23 influenza season. Three groups of vaccination were assembled: FLU vaccine only (46, 35%) versus volunteers that received the mRNA bivalent COVID-19 vaccines concomitantly to seasonal influenza vaccines, FluCOVID vaccine in the same arm (42, 33%) or different arm (40, 31%), respectively. Sera and whole blood were obtained the day of vaccination, +7, and +28 days after for antibody and T cells response quantification. As expected, side effects were increased in individuals who received the FluCOVID vaccine as compared to FLU vaccine only based on the known reactogenicity of mRNA vaccines. In general, antibody levels were high at 4 weeks post-vaccination and differences were found only for the H3N2 virus when administered in different arms compared to the other groups at day 28 post-vaccination. Additionally, our data showed that subjects that received the FluCOVID vaccine in different arm tended to have better antibody induction than those receiving FLU vaccines for H3N2 virus in the absence of pre-existing immunity. Furthermore, no notable differences in the influenza-specific cellular immune response were found for any of the vaccination groups. Our data supports the concomitant administration of seasonal influenza and mRNA COVID-19 vaccines.
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Affiliation(s)
- Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
| | - Maria Balsera-Manzanero
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
| | - Amaya Rojo-Fernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
| | - Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Celia Salamanca-Rivera
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- Department of Preventive Medicine, University of Seville, Spain
| | - Jerónimo Pachón
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Department of Medicine, School of Medicine, University of Sevilla, Sevilla, Spain
| | | | | | - Javier Sánchez-Céspedes
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- CIBERINFEC, CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn School of Medicine at Mount Sinai, The Tisch Cancer Institute, New York, USA
| | - Elisa Cordero
- Viral Diseases and Infections in Immunodeficiencies Research Group, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital/CSIC/University of Seville, Seville, Spain
- Unit of Infectious Diseases, Microbiology and Parasitology, Virgen del Rocío University Hospital, Sevilla, Spain
- CIBERINFEC, CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Medicine, School of Medicine, University of Sevilla, Sevilla, Spain
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5
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Fernández JJ, Marin A, Rosales R, Penrice-Randal R, Mlcochova P, Alvarez Y, Villalon-Letelier F, Yildiz S, Pérez E, Rathnasinghe R, Cupic A, Kehrer T, Uccellini MB, Alonso S, Martínez F, McGovern BL, Clark JJ, Sharma P, Bayón Y, Alonso A, Albrecht RA, White KM, Schotsaert M, Miorin L, Stewart JP, Hiscox JA, Gupta RK, Irigoyen N, García-Sastre A, Crespo MS, Fernández N. The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167193. [PMID: 38648902 DOI: 10.1016/j.bbadis.2024.167193] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.
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Affiliation(s)
- Jose Javier Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- 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
| | - Romel Rosales
- 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
| | - Rebekah Penrice-Randal
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yolanda Alvarez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | | | - Soner Yildiz
- 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
| | - Enrique Pérez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Raveen Rathnasinghe
- 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; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- 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; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- 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; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- 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
| | - Sara Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Fernando Martínez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - Briana Lynn McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jordan J Clark
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Yolanda Bayón
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
| | - Andrés Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain
| | - 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
| | - Kris M White
- 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
| | - Michael Schotsaert
- 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
| | - Lisa Miorin
- 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
| | - James P Stewart
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Infectious Disease, University of Georgia, GA, USA
| | - Julian A Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Infectious Diseases Horizontal Technology Centre (ID HTC), A*STAR, Singapore, Singapore; Department of Preventive Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Adolfo García-Sastre
- 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, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain.
| | - Nieves Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003 Valladolid, Spain; Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003 Valladolid, Spain
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6
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Monzón S, Varona S, Negredo A, Vidal-Freire S, Patiño-Galindo JA, Ferressini-Gerpe N, Zaballos A, Orviz E, Ayerdi O, Muñoz-Gómez A, Delgado-Iribarren A, Estrada V, García C, Molero F, Sánchez-Mora P, Torres M, Vázquez A, Galán JC, Torres I, Causse Del Río M, Merino-Diaz L, López M, Galar A, Cardeñoso L, Gutiérrez A, Loras C, Escribano I, Alvarez-Argüelles ME, Del Río L, Simón M, Meléndez MA, Camacho J, Herrero L, Jiménez P, Navarro-Rico ML, Jado I, Giannetti E, Kuhn JH, Sanchez-Lockhart M, Di Paola N, Kugelman JR, Guerra S, García-Sastre A, Cuesta I, Sánchez-Seco MP, Palacios G. Monkeypox virus genomic accordion strategies. Nat Commun 2024; 15:3059. [PMID: 38637500 PMCID: PMC11026394 DOI: 10.1038/s41467-024-46949-7] [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: 09/06/2023] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. Person-to-person transmission appears higher than for clade I or subclade IIa MPXV, possibly caused by genomic changes in subclade IIb MPXV. Key genomic changes could occur in the genome's low-complexity regions (LCRs), which are challenging to sequence and are often dismissed as uninformative. Here, using a combination of highly sensitive techniques, we determine a high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This reveals significant variation in short tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of single-nucleotide polymorphisms (SNPs) and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs), including OPG153, OPG204, and OPG208, could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. We posit that genomic studies focusing on phenotypic MPXV differences should consider LCR variability.
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Affiliation(s)
- Sara Monzón
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Sarai Varona
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Escuela Internacional de Doctorado de la UNED (EIDUNED), Universidad Nacional de Educación a Distancia (UNED), 2832, Madrid, Spain
| | - Anabel Negredo
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Santiago Vidal-Freire
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | | | - Angel Zaballos
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Eva Orviz
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Oskar Ayerdi
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Ana Muñoz-Gómez
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | | | - Vicente Estrada
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Cristina García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Francisca Molero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Patricia Sánchez-Mora
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Montserrat Torres
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ana Vázquez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Juan-Carlos Galán
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Ignacio Torres
- Servicio de Microbiología, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, 46010, Valencia, Spain
| | - Manuel Causse Del Río
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica de Córdoba, 14004, Córdoba, Spain
| | - Laura Merino-Diaz
- Unidad Clínico de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del Rocío, 41013, Sevilla, Spain
| | - Marcos López
- Servicio de Microbiología y Parasitología, Hospital Universitario Puerta de Hierro Majadahonda, 28222, Madrid, Spain
| | - Alicia Galar
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, 28007, Madrid, Spain
| | - Laura Cardeñoso
- Servicio de Microbiología, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, 28006, Madrid, Spain
| | - Almudena Gutiérrez
- Servicio de Microbiología y Parasitología Clínica, Hospital Universitario La Paz, 28046, Madrid, Spain
| | - Cristina Loras
- Servicio de Microbiología, Hospital General y Universitario, 13005, Ciudad Real, Spain
| | - Isabel Escribano
- Servicio de Microbiología, Hospital General Universitario Dr. Balmis, 03010, Alicante, Spain
| | | | | | - María Simón
- Servicio de Microbiología, Hospital Central de la Defensa "Gómez Ulla", 28947, Madrid, Spain
| | - María Angeles Meléndez
- Servicio de Microbiología y Parasitología, Hospital Universitario 12 de Octubre, 28041, Madrid, Spain
| | - Juan Camacho
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Laura Herrero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Jiménez
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Luisa Navarro-Rico
- Unidad de Genómica, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabel Jado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Elaina Giannetti
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
| | - Mariano Sanchez-Lockhart
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Nicholas Di Paola
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Jeffrey R Kugelman
- United States Army Research Institute for Infectious Disease, Fort Detrick, Frederick, MD, 21702, USA
| | - Susana Guerra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departmento de Medicina Preventiva, Salud Publica y Microbiología, Universidad Autónoma de Madrid, 28029, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Global Health 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
- The Tisch Cancer Institute, 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
| | - Isabel Cuesta
- Unidad de Bioinformática, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maripaz P Sánchez-Seco
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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7
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Losada A, Izquierdo-Useros N, Aviles P, Vergara-Alert J, Latino I, Segalés J, Gonzalez SF, Cuevas C, Raïch-Regué D, Muñoz-Alonso MJ, Perez-Zsolt D, Muñoz-Basagoiti J, Rodon J, Chang LA, Warang P, Singh G, Brustolin M, Cantero G, Roca N, Pérez M, Bustos-Morán E, White K, Schotsaert M, García-Sastre A. Plitidepsin as an Immunomodulator against Respiratory Viral Infections. J Immunol 2024; 212:1307-1318. [PMID: 38416036 PMCID: PMC10984758 DOI: 10.4049/jimmunol.2300426] [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] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
Plitidepsin is a host-targeted compound known for inducing a strong anti-SARS-CoV-2 activity, as well as for having the capacity of reducing lung inflammation. Because IL-6 is one of the main cytokines involved in acute respiratory distress syndrome, the effect of plitidepsin in IL-6 secretion in different in vitro and in vivo experimental models was studied. A strong plitidepsin-mediated reduction of IL-6 was found in human monocyte-derived macrophages exposed to nonproductive SARS-CoV-2. In resiquimod (a ligand of TLR7/8)-stimulated THP1 human monocytes, plitidepsin-mediated reductions of IL-6 mRNA and IL-6 levels were also noticed. Additionally, although resiquimod-induced binding to DNA of NF-κB family members was unaffected by plitidepsin, a decrease in the regulated transcription by NF-κB (a key transcription factor involved in the inflammatory cascade) was observed. Furthermore, the phosphorylation of p65 that is required for full transcriptional NF-κB activity was significantly reduced by plitidepsin. Moreover, decreases of IL-6 levels and other proinflammatory cytokines were also seen in either SARS-CoV-2 or H1N1 influenza virus-infected mice, which were treated at low enough plitidepsin doses to not induce antiviral effects. In summary, plitidepsin is a promising therapeutic agent for the treatment of viral infections, not only because of its host-targeted antiviral effect, but also for its immunomodulatory effect, both of which were evidenced in vitro and in vivo by the decrease of proinflammatory cytokines.
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Affiliation(s)
- Alejandro Losada
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute, Can Ruti Campus, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Aviles
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Júlia Vergara-Alert
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Irene Latino
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Joaquim Segalés
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Santiago F Gonzalez
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Carmen Cuevas
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | | | - María J Muñoz-Alonso
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | | | | | - Jordi Rodon
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Lauren A Chang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marco Brustolin
- Unit of Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Guillermo Cantero
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Núria Roca
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Mònica Pérez
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Eugenio Bustos-Morán
- Department of Research and Development, PharmaMar S.A., Colmenar Viejo, Madrid, Spain
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- The Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY
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8
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Laghlali G, Wiest MJ, Karadag D, Warang P, O'Konek JJ, Chang LA, Park S, Farazuddin M, Landers JJ, Janczak KW, García-Sastre A, Baker JR, Wong PT, Schotsaert M. Enhanced mucosal B- and T-cell responses against SARS-CoV-2 after heterologous intramuscular mRNA prime/intranasal protein boost vaccination with a combination adjuvant. bioRxiv 2024:2024.03.28.587260. [PMID: 38586014 PMCID: PMC10996704 DOI: 10.1101/2024.03.28.587260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Current COVID-19 mRNA vaccines delivered intramuscularly (IM) induce effective systemic immunity, but with suboptimal immunity at mucosal sites, limiting their ability to impart sterilizing immunity. There is strong interest in rerouting immune responses induced in the periphery by parenteral vaccination to the portal entry site of respiratory viruses, such as SARS-CoV-2, by mucosal vaccination. We previously demonstrated the combination adjuvant, NE/IVT, consisting of a nanoemulsion (NE) and an RNA-based RIG-I agonist (IVT) induces potent systemic and mucosal immune responses in protein-based SARS-CoV-2 vaccines administered intranasally (IN). Herein, we demonstrate priming IM with mRNA followed by heterologous IN boosting with NE/IVT adjuvanted recombinant antigen induces strong mucosal and systemic antibody responses and enhances antigen-specific T cell responses in mucosa-draining lymph nodes compared to IM/IM and IN/IN prime/boost regimens. While all regimens induced cross-neutralizing antibodies against divergent variants and sterilizing immunity in the lungs of challenged mice, mucosal vaccination, either as homologous prime/boost or heterologous IN boost after IM mRNA prime was required to impart sterilizing immunity in the upper respiratory tract. Our data demonstrate the benefit of hybrid regimens whereby strong immune responses primed via IM vaccination are rerouted by IN vaccination to mucosal sites to provide optimal protection to SARS-CoV-2.
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9
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Anandakrishnan N, Yi Z, Sun Z, Liu T, Haydak J, Eddy S, Jayaraman P, DeFronzo S, Saha A, Sun Q, Yang D, Mendoza A, Mosoyan G, Wen HH, Schaub JA, Fu J, Kehrer T, Menon R, Otto EA, Godfrey B, Suarez-Farinas M, Leffters S, Twumasi A, Meliambro K, Charney AW, García-Sastre A, Campbell KN, Gusella GL, He JC, Miorin L, Nadkarni GN, Wisnivesky J, Li H, Kretzler M, Coca SG, Chan L, Zhang W, Azeloglu EU. Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury. medRxiv 2024:2024.03.18.24304401. [PMID: 38562892 PMCID: PMC10984064 DOI: 10.1101/2024.03.18.24304401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.
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10
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Escalera A, Rojo-Fernandez A, Rombauts A, Abelenda-Alonso G, Carratalà J, García-Sastre A, Aydillo T. SARS-CoV-2 infection induces robust mucosal antibody responses in the upper respiratory tract. iScience 2024; 27:109210. [PMID: 38433913 PMCID: PMC10906537 DOI: 10.1016/j.isci.2024.109210] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/15/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Despite multiple research efforts to characterize coronavirus disease 2019 (COVID-19) in humans, there is no clear data on the specific role of mucosal immunity on COVID-19 disease. Here, we longitudinally profile the antibody response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal HCoV-OC43 S proteins in serum and nasopharyngeal swabs from COVID-19 patients. Results showed that specific antibody responses against SARS-CoV-2 and HCoV-OC43 S proteins can be detected in the upper respiratory tract. We found that COVID-19 patients mounted a robust mucosal antibody response against SARS-CoV-2 S with specific secretory immunoglobulin A (sIgA), IgA, IgG, and IgM antibody subtypes detected in the nasal swabs. Additionally, COVID-19 patients showed IgG, IgA, and sIgA responses against HCoV-OC43 S in the local mucosa, whereas no specific IgM was detected. Interestingly, mucosal antibody titers against SARS-CoV-2 peaked at day 7, whereas HCoV-OC43 titers peaked earlier at day 3 post-recruitment, suggesting an immune memory recall to conserved epitopes of beta-HCoVs in the upper respiratory tract.
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Affiliation(s)
- Alba Escalera
- 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
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amaya Rojo-Fernandez
- 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
| | - Alexander Rombauts
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Gabriela Abelenda-Alonso
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute (ISCII), 28029 Madrid, Spain
| | - Jordi Carratalà
- Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases (CIBERINFEC), Carlos III Health Institute (ISCII), 28029 Madrid, Spain
| | - Adolfo García-Sastre
- 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
- The Tisch Cancer Institute, 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 Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Teresa Aydillo
- 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
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11
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Lamoot A, Jangra S, Laghlali G, Warang P, Singh G, Chang LA, Park SC, Singh G, De Swarte K, Zhong Z, Louage B, De Lombaerde E, Ye T, Chen Y, Cuadrado-Castano S, Lienenklaus S, Sanders NN, Lambrecht BN, García-Sastre A, Schotsaert M, De Geest BG. Lipid Nanoparticle Encapsulation Empowers Poly(I:C) to Activate Cytoplasmic RLRs and Thereby Increases Its Adjuvanticity. Small 2024; 20:e2306892. [PMID: 37867244 DOI: 10.1002/smll.202306892] [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] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/05/2023] [Indexed: 10/24/2023]
Abstract
Poly(I:C) is a synthetic analogue of dsRNA capable of activating both TLR3 and RLRs, such as MDA-5 and RIG-I, as pathogen recognition receptors. While poly(I:C) is known to provoke a robust type I IFN, type III IFN, and Th1 cytokine response, its therapeutic use as a vaccine adjuvant is limited due to its vulnerability to nucleases and poor uptake by immune cells. is encapsulated poly(I:C) into lipid nanoparticles (LNPs) containing an ionizable cationic lipid that can electrostatically interact with poly(I:C). LNP-formulated poly(I:C) triggered both lysosomal TLR3 and cytoplasmic RLRs, in vitro and in vivo, whereas poly(I:C) in an unformulated soluble form only triggered endosomal-localized TLR3. Administration of LNP-formulated poly(I:C) in mouse models led to efficient translocation to lymphoid tissue and concurrent innate immune activation following intramuscular (IM) administration, resulting in a significant increase in innate immune activation compared to unformulated soluble poly(I:C). When used as an adjuvant for recombinant full-length SARS-CoV-2 spike protein, LNP-formulated poly(I:C) elicited potent anti-spike antibody titers, surpassing those of unformulated soluble poly(I:C) by orders of magnitude and offered complete protection against a SARS-CoV-2 viral challenge in vivo, and serum from these mice are capable of significantly reducing viral infection in vitro.
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Affiliation(s)
- Alexander Lamoot
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
| | - Sonia Jangra
- 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
| | - Gabriel Laghlali
- 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
| | - Prajakta Warang
- 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
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren A Chang
- 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
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Seok-Chan Park
- 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
- Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, South Korea
| | - Gagandeep Singh
- 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
| | - Kim De Swarte
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, 9000, Belgium
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, 9000, Belgium
| | - Zifu Zhong
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
| | - Benoit Louage
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
| | | | - Tingting Ye
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
| | - Yong Chen
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
| | - Sara Cuadrado-Castano
- 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
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Stefan Lienenklaus
- Institute for Laboratory Animal Science and Institute of Immunology, Hannover Medical School, 30625, Hannover, Germany
| | - Niek N Sanders
- Laboratory of Gene Therapy, Ghent University, Merelbeke, 9820, Belgium
| | - Bart N Lambrecht
- Laboratory of Mucosal Immunology, VIB-UGent Center for Inflammation Research, Ghent University, Ghent, 9000, Belgium
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, 9000, Belgium
| | - Adolfo García-Sastre
- 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
- The Tisch Cancer Institute, 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
| | - Michael Schotsaert
- 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
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruno G De Geest
- Department of Pharmaceutics, Ghent University, Ghent, 9000, Belgium
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12
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Muñoz-Alía MÁ, Nace RA, Balakrishnan B, Zhang L, Packiriswamy N, Singh G, Warang P, Mena I, Narjari R, Vandergaast R, Peng KW, García-Sastre A, Schotsaert M, Russell SJ. Surface-modified measles vaccines encoding oligomeric, prefusion-stabilized SARS-CoV-2 spike glycoproteins boost neutralizing antibody responses to Omicron and historical variants, independent of measles seropositivity. mBio 2024; 15:e0292823. [PMID: 38193729 PMCID: PMC10865805 DOI: 10.1128/mbio.02928-23] [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: 11/02/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024] Open
Abstract
Serum titers of SARS-CoV-2-neutralizing antibodies (nAbs) correlate well with protection from symptomatic COVID-19 but decay rapidly in the months following vaccination or infection. In contrast, measles-protective nAb titers are lifelong after measles vaccination, possibly due to persistence of the live-attenuated virus in lymphoid tissues. We, therefore, sought to generate a live recombinant measles vaccine capable of driving high SARS-CoV-2 nAb responses. Since previous clinical testing of a live measles vaccine encoding a SARS-CoV-2 spike glycoprotein resulted in suboptimal anti-spike antibody titers, our new vectors were designed to encode prefusion-stabilized SARS-CoV-2 spike glycoproteins, trimerized via an inserted peptide domain, and displayed on a dodecahedral miniferritin scaffold. Additionally, to circumvent the blunting of vaccine efficacy by preformed anti-measles antibodies, we extensively modified the measles surface glycoproteins. Comprehensive in vivo mouse testing demonstrated the potent induction of high titer nAbs in measles-immune mice and confirmed the significant contributions to overall potency afforded by prefusion stabilization, trimerization, and miniferritin display of the SARS-CoV-2 spike glycoprotein. In animals primed and boosted with a measles virus (MeV) vaccine encoding the ancestral SARS-CoV-2 spike, high-titer nAb responses against ancestral virus strains were only weakly cross-reactive with the Omicron variant. However, in primed animals that were boosted with a MeV vaccine encoding the Omicron BA.1 spike, antibody titers to both ancestral and Omicron strains were robustly elevated, and the passive transfer of serum from these animals protected K18-ACE2 mice from infection and morbidity after exposure to BA.1 and WA1/2020 strains. Our results demonstrate that by engineering the antigen, we can develop potent measles-based vaccine candidates against SARS-CoV-2.IMPORTANCEAlthough the live-attenuated measles virus (MeV) is one of the safest and most efficacious human vaccines, a measles-vectored COVID-19 vaccine candidate expressing the SARS-CoV-2 spike failed to elicit neutralizing antibody (nAb) responses in a phase-1 clinical trial, especially in measles-immune individuals. Here, we constructed a comprehensive panel of MeV-based COVID-19 vaccine candidates using a MeV with extensive modifications on the envelope glycoproteins (MeV-MR). We show that artificial trimerization of the spike is critical for the induction of nAbs and that their magnitude can be significantly augmented when the spike protein is synchronously fused to a dodecahedral scaffold. Furthermore, preexisting measles immunity did not abolish heterologous immunity elicited by our vector. Our results highlight the importance of antigen optimization in the development of spike-based COVID-19 vaccines and therapies.
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Affiliation(s)
- Miguel Á. Muñoz-Alía
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
| | - Rebecca A. Nace
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Lianwen Zhang
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Kah-Whye Peng
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
- Imanis Life Sciences, Rochester, Minnesota, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen J. Russell
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Vyriad Inc, Rochester, Minnesota, USA
- Imanis Life Sciences, Rochester, Minnesota, USA
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
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13
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Pathak R, Eliscovich C, Mena I, Cupic A, Rutkowska M, Chandran K, Jangra RK, García-Sastre A, Singer RH, Kalpana GV. Visualization of Early RNA Replication Kinetics of SARS-CoV-2 by Using Single Molecule RNA-FISH Combined with Immunofluorescence. Viruses 2024; 16:262. [PMID: 38400039 PMCID: PMC10893374 DOI: 10.3390/v16020262] [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: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
SARS-CoV-2 infection remains a global burden. Despite intensive research, the mechanism and dynamics of early viral replication are not completely understood, such as the kinetics of the formation of genomic RNA (gRNA), sub-genomic RNA (sgRNA), and replication centers/organelles (ROs). We employed single-molecule RNA-fluorescence in situ hybridization (smRNA-FISH) to simultaneously detect viral gRNA and sgRNA and immunofluorescence to detect nsp3 protein, a marker for the formation of RO, and carried out a time-course analysis. We found that single molecules of gRNA are visible within the cytoplasm at 30 min post infection (p.i.). Starting from 2 h p.i., most of the viral RNA existed in clusters/speckles, some of which were surrounded by single molecules of sgRNA. These speckles associated with nsp3 protein starting at 3 h p.i., indicating that these were precursors to ROs. Furthermore, RNA replication was asynchronous, as cells with RNA at all stages of replication were found at any given time point. Our probes detected the SARS-CoV-2 variants of concern, and also suggested that the BA.1 strain exhibited a slower rate of replication kinetics than the WA1 strain. Our results provide insights into the kinetics of SARS-CoV-2 early post-entry events, which will facilitate identification of new therapeutic targets for early-stage replication to combat COVID-19.
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Affiliation(s)
- Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.C.); (R.K.J.)
| | - Carolina Eliscovich
- Department of Medicine (Hepatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.M.); (A.C.); (M.R.); (A.G.-S.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.M.); (A.C.); (M.R.); (A.G.-S.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Magdalena Rutkowska
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.M.); (A.C.); (M.R.); (A.G.-S.)
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.C.); (R.K.J.)
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.C.); (R.K.J.)
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (I.M.); (A.C.); (M.R.); (A.G.-S.)
- 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
- The Tisch Cancer Institute, 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
| | - Robert H. Singer
- Departments of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Departments of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ganjam V. Kalpana
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.C.); (R.K.J.)
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14
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Carossino M, Izadmehr S, Trujillo JD, Gaudreault NN, Dittmar W, Morozov I, Balasuriya UBR, Cordon-Cardo C, García-Sastre A, Richt JA. ACE2 and TMPRSS2 distribution in the respiratory tract of different animal species and its correlation with SARS-CoV-2 tissue tropism. Microbiol Spectr 2024; 12:e0327023. [PMID: 38230954 PMCID: PMC10846196 DOI: 10.1128/spectrum.03270-23] [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: 09/07/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024] Open
Abstract
A wide range of animal species show variable susceptibility to SARS-CoV-2; however, host factors associated with varied susceptibility remain to be defined. Here, we examined whether susceptibility to SARS-CoV-2 and virus tropism in different animal species are dependent on the expression and distribution of the virus receptor angiotensin-converting enzyme 2 (ACE2) and the host cell factor transmembrane serine protease 2 (TMPRSS2). We cataloged the upper and lower respiratory tract of multiple animal species and humans in a tissue-specific manner and quantitatively evaluated the distribution and abundance of ACE2 and TMPRSS2 mRNA in situ. Our results show that: (i) ACE2 and TMPRSS2 mRNA are abundant in the conduction portion of the respiratory tract, (ii) ACE2 mRNA occurs at a lower abundance compared to TMPRSS2 mRNA, (iii) co-expression of ACE2-TMPRSS2 mRNAs is highest in those species with the highest susceptibility to SARS-CoV-2 infection (i.e., cats, Syrian hamsters, and white-tailed deer), and (iv) expression of ACE2 and TMPRSS2 mRNA was not altered following SARS-CoV-2 infection. Our results demonstrate that while specific regions of the respiratory tract are enriched in ACE2 and TMPRSS2 mRNAs in different animal species, this is only a partial determinant of susceptibility to SARS-CoV-2 infection.IMPORTANCESARS-CoV-2 infects a wide array of domestic and wild animals, raising concerns regarding its evolutionary dynamics in animals and potential for spillback transmission of emerging variants to humans. Hence, SARS-CoV-2 infection in animals has significant public health relevance. Host factors determining animal susceptibility to SARS-CoV-2 are vastly unknown, and their characterization is critical to further understand susceptibility and viral dynamics in animal populations and anticipate potential spillback transmission. Here, we quantitatively assessed the distribution and abundance of the two most important host factors, angiotensin-converting enzyme 2 and transmembrane serine protease 2, in the respiratory tract of various animal species and humans. Our results demonstrate that while specific regions of the respiratory tract are enriched in these two host factors, they are only partial determinants of susceptibility. Detailed analysis of additional host factors is critical for our understanding of the underlying mechanisms governing viral susceptibility and reservoir hosts.
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Affiliation(s)
- Mariano Carossino
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Sudeh Izadmehr
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessie D. Trujillo
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Wellesley Dittmar
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Igor Morozov
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Udeni B. R. Balasuriya
- Department of Pathobiological Sciences and Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
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15
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Bayrak CS, Forst C, Jones DR, Gresham D, Pushalkar S, Wu S, Vogel C, Mahal L, Ghedin E, Ross T, García-Sastre A, Zhang B. Patient Subtyping Analysis of Baseline Multi-omic Data Reveals Distinct Pre-immune States Predictive of Vaccination Responses. bioRxiv 2024:2024.01.18.576213. [PMID: 38328256 PMCID: PMC10849502 DOI: 10.1101/2024.01.18.576213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Understanding the molecular mechanisms that underpin diverse vaccination responses is a critical step toward developing efficient vaccines. Molecular subtyping approaches can offer valuable insights into the heterogeneous nature of responses and aid in the design of more effective vaccines. In order to explore the molecular signatures associated with the vaccine response, we analyzed baseline transcriptomics data from paired samples of whole blood, proteomics and glycomics data from serum, and metabolomics data from urine, obtained from influenza vaccine recipients (2019-2020 season) prior to vaccination. After integrating the data using a network-based model, we performed a subtyping analysis. The integration of multiple data modalities from 62 samples resulted in five baseline molecular subtypes with distinct molecular signatures. These baseline subtypes differed in the expression of pre-existing adaptive or innate immunity signatures, which were linked to significant variation across subtypes in baseline immunoglobulin A (IgA) and hemagglutination inhibition (HAI) titer levels. It is worth noting that these significant differences persisted through day 28 post-vaccination, indicating the effect of initial immune state on vaccination response. These findings highlight the significance of interpersonal variation in baseline immune status as a crucial factor in determining vaccine response and efficacy. Ultimately, incorporating molecular profiling could enable personalized vaccine optimization.
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16
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Seoane R, Lama-Díaz T, Romero AM, El Motiam A, Martínez-Férriz A, Vidal S, Bouzaher YH, Blanquer M, Tolosa RM, Castillo Mewa J, Rodríguez MS, García-Sastre A, Xirodimas D, Sutherland JD, Barrio R, Alepuz P, Blanco MG, Farràs R, Rivas C. SUMOylation modulates eIF5A activities in both yeast and pancreatic ductal adenocarcinoma cells. Cell Mol Biol Lett 2024; 29:15. [PMID: 38229033 PMCID: PMC10790418 DOI: 10.1186/s11658-024-00533-5] [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: 07/19/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND The eukaryotic translation initiation protein eIF5A is a highly conserved and essential factor that plays a critical role in different physiological and pathological processes including stress response and cancer. Different proteomic studies suggest that eIF5A may be a small ubiquitin-like modifier (SUMO) substrate, but whether eIF5A is indeed SUMOylated and how relevant is this modification for eIF5A activities are still unknown. METHODS SUMOylation was evaluated using in vitro SUMOylation assays, Histidine-tagged proteins purification from His6-SUMO2 transfected cells, and isolation of endogenously SUMOylated proteins using SUMO-binding entities (SUBES). Mutants were engineered by site-directed mutagenesis. Protein stability was measured by a cycloheximide chase assay. Protein localization was determined using immunofluorescence and cellular fractionation assays. The ability of eIF5A1 constructs to complement the growth of Saccharomyces cerevisiae strains harboring thermosensitive mutants of a yeast EIF5A homolog gene (HYP2) was analyzed. The polysome profile and the formation of stress granules in cells expressing Pab1-GFP (a stress granule marker) by immunofluorescence were determined in yeast cells subjected to heat shock. Cell growth and migration of pancreatic ductal adenocarcinoma PANC-1 cells overexpressing different eIF5A1 constructs were evaluated using crystal violet staining and transwell inserts, respectively. Statistical analysis was performed with GraphPad Software, using unpaired Student's t-test, or one-way or two-way analysis of variance (ANOVA). RESULTS We found that eIF5A is modified by SUMO2 in vitro, in transfected cells and under endogenous conditions, revealing its physiological relevance. We identified several SUMO sites in eIF5A and found that SUMOylation modulates both the stability and the localization of eIF5A in mammalian cells. Interestingly, the SUMOylation of eIF5A responds to specific stresses, indicating that it is a regulated process. SUMOylation of eIF5A is conserved in yeast, the eIF5A SUMOylation mutants are unable to completely suppress the defects of HYP2 mutants, and SUMOylation of eIF5A is important for both stress granules formation and disassembly of polysomes induced by heat-shock. Moreover, mutation of the SUMOylation sites in eIF5A abolishes its promigratory and proproliferative activities in PANC-1 cells. CONCLUSIONS SUMO2 conjugation to eIF5A is a stress-induced response implicated in the adaptation of yeast cells to heat-shock stress and required to promote the growth and migration of pancreatic ductal adenocarcinoma cells.
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Affiliation(s)
- Rocío Seoane
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tomás Lama-Díaz
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Antonia María Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, Burjassot, 46100, Valencia, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), C/ Américo Vespucio 24, Edificio Cabimer, 41092, Seville, Spain
| | - Ahmed El Motiam
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | | | - Santiago Vidal
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yanis H Bouzaher
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - María Blanquer
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - Rocío M Tolosa
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
| | - Juan Castillo Mewa
- Research Department in Genomics and Proteomics, Instituto Conmemorativo Gorgas de Estudios de la Salud, 0816-02593, Panamá, Republic of Panama
| | - Manuel S Rodríguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31400, Toulouse, France
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dimitris Xirodimas
- Montpellier Cell Biology Research Center (CRBM), CNRS-UMR 5237 Université de Montpellier, Montpellier, France
| | - James D Sutherland
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Rosa Barrio
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | - Paula Alepuz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, Burjassot, 46100, Valencia, Spain
- Instituto Bio TecMed, Universitat de València, Burjassot, 46100, Valencia, Spain
| | - Miguel G Blanco
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain
- Departamento de Bioquímica e Bioloxía Molecular, Universidade de Santiago de Compostela, 15706, Santiago de Compostela, Spain
| | - Rosa Farràs
- Centro de Investigación Príncipe Felipe, 46012, Valencia, Spain
| | - Carmen Rivas
- Centro de Investigación en Medicina Molecular (CIMUS), IDIS, Universidade de Santiago de Compostela, Avda Barcelona, 15706, Santiago de Compostela, Spain.
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología (CNB), CSIC, Darwin 3, 28049, Madrid, Spain.
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17
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Jangra S, Lamoot A, Singh G, Laghlali G, Chen Y, Yz T, García-Sastre A, De Geest BG, Schotsaert M. Lipid nanoparticle composition for adjuvant formulation modulates disease after influenza virus infection in QIV vaccinated mice. bioRxiv 2024:2024.01.14.575599. [PMID: 38293047 PMCID: PMC10827098 DOI: 10.1101/2024.01.14.575599] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adjuvants can enhance vaccine effectiveness of currently licensed influenza vaccines. We tested influenza vaccination in a mouse model with two adjuvants: Sendai virus derived defective interfering (SDI) RNA, a RIG-I agonist, and an amphiphilic imidazoquinoline (IMDQ-PEG-Chol), TLR7/8 adjuvant. The negatively charged SDI RNA was formulated into lipid nanoparticles (LNPs) facilitating the direct delivery of a RIG-I agonist to the cytosol. We have previously tested SDI and IMDQ-PEG-Chol as standalone and combination adjuvants for influenza and SARS-CoV-2 vaccines. Here we tested two different ionizable lipids, K-Ac7-Dsa and S-Ac7-Dog, for LNP formulations. The adjuvanticity of IMDQ-PEG-Chol with and without empty or SDI-loaded LNPs was validated in a licensed vaccine setting (quadrivalent influenza vaccine or QIV) against H1N1 influenza virus, showing robust induction of antibody titres and T cell responses. Depending on the adjuvant combination and LNP lipid composition (K-Ac7-Dsa or S-Ac7-Dog lipids), humoral and cellular vaccine responses could be tailored towards type 1 or type 2 host responses with specific cytokine profiles that correlated with protection during viral infection. The extent of protection conferred by different vaccine/LNP/adjuvant combinations was examined against challenge with the vaccine-matching strain of H1N1 influenza A virus. Groups that received either LNP formulated with SDI, IMDQ-PEG-Chol or both showed very low levels of viral replication in their lungs at five days post virus infection. LNP ionizable lipid composition as well as loading (empty versus SDI) also skewed host responses to infection, as reflected in the cytokine and chemokine levels in lungs of vaccinated animals upon infection. These studies show the potential of LNPs as adjuvant delivery vehicles for licensed vaccines and illustrate the importance of LNP composition for subsequent host responses to infection, an important point of consideration for vaccine safety.
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Affiliation(s)
- Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | | | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Gabriel Laghlali
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Department of Pharmaceutics, Ghent University, Ghent Belgium
| | - Yong Chen
- Department of Pharmaceutics, Ghent University, Ghent Belgium
| | - Tingting Yz
- Department of Pharmaceutics, Ghent University, Ghent Belgium
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | | | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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18
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Kessler S, García-Sastre A, Schwemmle M, Ciminski K. Reverse Genetics of Bat Influenza A Viruses. Methods Mol Biol 2024; 2733:75-86. [PMID: 38064027 DOI: 10.1007/978-1-0716-3533-9_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
New World fruit bats were recently found to harbor two distinct and previously unknown influenza A viruses (IAVs) of the subtypes H17N10 and H18N11. Although viral genome sequences were detected in the liver, intestine, lung, and kidney of infected bats and the complete genome sequences have been isolated from their rectal swab samples, all attempts to isolate an infectious virus from bats in nature have failed. The lack of an infectious bat IAV isolate was overcome by reverse genetic approaches that led to the generation of an infectious virus in vitro. Using such synthetic bat IAVs enabled the identification of their unconventional cell entry via major histocompatibility complex II (MCH-II) molecules and their ability to replicate in mice, ferrets, and bats. Importantly, we also showed that these synthetic recombinant bat IAVs are not able to reassort with conventional IAVs, preventing the acquisition of enhanced transmission properties in non-bat species by reassortment with conventional IAVs. As authentic viruses are key for understanding the molecular biology of bat IAVs, in this chapter, we describe our recently established reverse genetics protocol for generating H17N10 and H18N11 in vitro. This step-by-step protocol starts with cloning of cDNA copies of the viral RNA segments into reverse genetics plasmids, followed by the generation of a highly concentrated stock and finally a method to determine viral titers.
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Affiliation(s)
- Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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19
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Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, Zubatyuk R, Bosko IP, Furs KV, Karpenko AD, Kornoushenko YV, Shuldau M, Yushkevich A, Benabderrahmane MB, Bousquet-Melou P, Bureau R, Charton B, Cirou BC, Gil G, Allen WJ, Sirimulla S, Watowich S, Antonopoulos N, Epitropakis N, Krasoulis A, Itsikalis V, Theodorakis S, Kozlovskii I, Maliutin A, Medvedev A, Popov P, Zaretckii M, Eghbal-Zadeh H, Halmich C, Hochreiter S, Mayr A, Ruch P, Widrich M, Berenger F, Kumar A, Yamanishi Y, Zhang KYJ, Bengio E, Bengio Y, Jain MJ, Korablyov M, Liu CH, Marcou G, Glaab E, Barnsley K, Iyengar SM, Ondrechen MJ, Haupt VJ, Kaiser F, Schroeder M, Pugliese L, Albani S, Athanasiou C, Beccari A, Carloni P, D'Arrigo G, Gianquinto E, Goßen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Muñiz-Chicharro A, Musiani F, Nunes-Alves A, Paiardi G, Rossetti G, Sadiq SK, Spyrakis F, Talarico C, Tsengenes A, Wade RC, Copeland C, Gaiser J, Olson DR, Roy A, Venkatraman V, Wheeler TJ, Arthanari H, Blaschitz K, Cespugli M, Durmaz V, Fackeldey K, Fischer PD, Gorgulla C, Gruber C, Gruber K, Hetmann M, Kinney JE, Padmanabha Das KM, Pandita S, Singh A, Steinkellner G, Tesseyre G, Wagner G, Wang ZF, Yust RJ, Druzhilovskiy DS, Filimonov DA, Pogodin PV, Poroikov V, Rudik AV, Stolbov LA, Veselovsky AV, De Rosa M, De Simone G, Gulotta MR, Lombino J, Mekni N, Perricone U, Casini A, Embree A, Gordon DB, Lei D, Pratt K, Voigt CA, Chen KY, Jacob Y, Krischuns T, Lafaye P, Zettor A, Rodríguez ML, White KM, Fearon D, Von Delft F, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, García-Sastre A, Yup Lee S, Naffakh N, Varnek A, Klambauer G, Hermans TM. A community effort in SARS-CoV-2 drug discovery. Mol Inform 2024; 43:e202300262. [PMID: 37833243 DOI: 10.1002/minf.202300262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
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20
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Cobela-García A, Mena I, García-Sastre A. Rescue of Recombinant Newcastle Disease Virus Expressing Heterologous Genes. Methods Mol Biol 2024; 2733:37-46. [PMID: 38064025 DOI: 10.1007/978-1-0716-3533-9_3] [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] [Indexed: 12/18/2023]
Abstract
Reverse genetics allows for the generation of recombinant infectious viruses from viral sequences or complete viral genomes cloned into plasmids. Using reverse genetics, it is then possible to introduce changes in the genome of infectious viruses for multiple applications.Newcastle disease virus (NDV) is a non-segmented, negative-sense RNA virus that has been amenable to manipulation by reverse genetics for more than two decades. Since then, recombinant NDVs have been extensively used as viral vectors to express heterologous proteins. We describe the key steps required to design and introduce an additional transcription unit in the genome of the Newcastle disease virus for the efficient expression of a heterologous gene.
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Affiliation(s)
- Arantza Cobela-García
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University Hamburg, Hamburg, Germany
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-BasedMedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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21
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Diego JGB, Singh G, Jangra S, Handrejk K, Laporte M, Chang LA, El Zahed SS, Pache L, Chang MW, Warang P, Aslam S, Mena I, Webb BT, Benner C, García-Sastre A, Schotsaert M. Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian hamsters. PLoS Pathog 2024; 20:e1011805. [PMID: 38198521 PMCID: PMC10805310 DOI: 10.1371/journal.ppat.1011805] [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: 06/03/2023] [Revised: 01/23/2024] [Accepted: 11/06/2023] [Indexed: 01/12/2024] Open
Abstract
Hybrid immunity (vaccination + natural infection) to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. The mRNA vaccine, BNT162b2, was dosed to induce binding antibody titers against ancestral spike, but inefficient serum virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed for T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera, reflected by smaller antigenic cartography distances. Transcriptomics post-infection reflects both vaccination status and disease course and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of high titers of neutralizing antibodies in the serum, correlates with recall of broadly reactive B- and T-cell responses.
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Affiliation(s)
- Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kim Handrejk
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Lauren A. Chang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sara S. El Zahed
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Lars Pache
- NCI Designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, California, United States of America
| | - Max W. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Brett T. Webb
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, United States of America
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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22
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Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, García-Bernalt Diego J, Wu TC, Marches F, Chaussabel D, García-Sastre A, Schotsaert M, Williams A, Palucka K. Protocol for establishing primary human lung organoid-derived air-liquid interface cultures from cryopreserved human lung tissue. STAR Protoc 2023; 4:102735. [PMID: 37991921 PMCID: PMC10696416 DOI: 10.1016/j.xpro.2023.102735] [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: 09/01/2023] [Revised: 10/12/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
Primary human lung organoid-derived air-liquid interface (ALI) cultures serve as a physiologically relevant model to study human airway epithelium in vitro. Here, we present a protocol for establishing these cultures from cryopreserved human lung tissue. We describe steps for lung tissue cryostorage, tissue dissociation, lung epithelial organoid generation, and ALI culture differentiation. We also include quality control steps and technical readouts for monitoring virus response. This protocol demonstrates severe acute respiratory syndrome coronavirus 2 infection in these cultures as an example of their utility. For complete details on the use and execution of this protocol, please refer to Diana Cadena Castaneda et al. (2023).1.
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Affiliation(s)
| | - Sonia Jangra
- 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
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Megan Callender
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew Coxe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Angela Choi
- 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
| | - Juan García-Bernalt Diego
- 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
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adolfo García-Sastre
- 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; The Tisch Cancer Institute, 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
| | - Michael Schotsaert
- 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
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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23
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Patiño LH, Guerra S, Muñoz M, Luna N, Farrugia K, van de Guchte A, Khalil Z, Gonzalez-Reiche AS, Hernandez MM, Banu R, Shrestha P, Liggayu B, Firpo Betancourt A, Reich D, Cordon-Cardo C, Albrecht R, Pearl R, Simon V, Rooker A, Sordillo EM, van Bakel H, García-Sastre A, Bogunovic D, Palacios G, Paniz Mondolfi A, Ramírez JD. Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022. Emerg Microbes Infect 2023; 12:e2192830. [PMID: 36927408 PMCID: PMC10114986 DOI: 10.1080/22221751.2023.2192830] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.
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Affiliation(s)
- Luz H. Patiño
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Muñoz
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernadette Liggayu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Reich
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rebecca Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aria Rooker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- Department of Microbiology, Centre for Inborn Errors of Immunity, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alberto Paniz Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
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24
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Rodilla AM, Valanparambil RM, Mack PC, Hsu CY, Cagan J, Tavolacci SC, Carreño JM, Brody R, Moore A, King JC, Gomez JE, Rohs N, Rolfo C, Bunn PA, Gerber DE, Minna JD, Krammer F, Ramalingam SS, García-Sastre A, Shyr Y, Ahmed R, Hirsch FR. Longitudinal nucleocapsid antibody testing reveals undocumented SARS-CoV-2 infections in patients with lung cancer. Cancer Cell 2023; 41:1838-1840. [PMID: 37863065 DOI: 10.1016/j.ccell.2023.09.017] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023]
Abstract
Patients diagnosed with lung cancer (LC) exhibit increased susceptibility to SARS-CoV-2 infection. Rodilla et al. monitor the levels of plasma anti-nucleocapsid antibodies within a cohort of fully vaccinated LC patients and reveal that the actual infection rate is nearly twice the documented rate, indicating a significant prevalence of unreported cases.
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Affiliation(s)
- Ananda M Rodilla
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajesh M Valanparambil
- Emory Vaccine Center, Emory University, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Philip C Mack
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chih-Yuan Hsu
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - Jazz Cagan
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sooyun C Tavolacci
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachel Brody
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amy Moore
- LUNGevity Foundation, Bethesda, MD, USA
| | | | - Jorge E Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nicholas Rohs
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul A Bunn
- Division of Medical Oncology, University of Colorado Cancer Center, Aurora, CO, USA
| | - David E Gerber
- Hamon Center for Therapeutic Oncology Research, Departments of Internal Medicine and Pharmacology UT Southwestern Medical Center, Dallas, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, Departments of Internal Medicine and Pharmacology UT Southwestern Medical Center, Dallas, TX, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), 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, USA
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Fred R Hirsch
- Center for Thoracic Oncology, Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Kusakabe T, Lin WY, Cheong JG, Singh G, Ravishankar A, Yeung ST, Mesko M, DeCelie MB, Carriche G, Zhao Z, Rand S, Doron I, Putzel GG, Worgall S, Cushing M, Westblade L, Inghirami G, Parkhurst CN, Guo CJ, Schotsaert M, García-Sastre A, Josefowicz SZ, Salvatore M, Iliev ID. Fungal microbiota sustains lasting immune activation of neutrophils and their progenitors in severe COVID-19. Nat Immunol 2023; 24:1879-1889. [PMID: 37872315 PMCID: PMC10805066 DOI: 10.1038/s41590-023-01637-4] [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: 06/15/2023] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Gastrointestinal fungal dysbiosis is a hallmark of several diseases marked by systemic immune activation. Whether persistent pathobiont colonization during immune alterations and impaired gut barrier function has a durable impact on host immunity is unknown. We found that elevated levels of Candida albicans immunoglobulin G (IgG) antibodies marked patients with severe COVID-19 (sCOVID-19) who had intestinal Candida overgrowth, mycobiota dysbiosis and systemic neutrophilia. Analysis of hematopoietic stem cell progenitors in sCOVID-19 revealed transcriptional changes in antifungal immunity pathways and reprogramming of granulocyte myeloid progenitors (GMPs) for up to a year. Mice colonized with C. albicans patient isolates experienced increased lung neutrophilia and pulmonary NETosis during severe acute respiratory syndrome coronavirus-2 infection, which were partially resolved with antifungal treatment or by interleukin-6 receptor blockade. sCOVID-19 patients treated with tocilizumab experienced sustained reductions in C. albicans IgG antibodies titers and GMP transcriptional changes. These findings suggest that gut fungal pathobionts may contribute to immune activation during inflammatory diseases, offering potential mycobiota-immune therapeutic strategies for sCOVID-19 with prolonged symptoms.
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Affiliation(s)
- Takato Kusakabe
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Woan-Yu Lin
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
| | - Jin-Gyu Cheong
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Stephen T Yeung
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Microbiology, New York University, Langone Health, New York City, NY, USA
| | - Marissa Mesko
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Meghan Bialt DeCelie
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Guilhermina Carriche
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Sophie Rand
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Itai Doron
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Gregory G Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
| | - Stefan Worgall
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pediatrics, Weill Cornell Medicine, New York City, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Christopher N Parkhurst
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Chun-Jun Guo
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai New York, New York City, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Steven Z Josefowicz
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Mirella Salvatore
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York City, NY, USA
| | - Iliyan D Iliev
- Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York City, NY, USA.
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease (JRI), Weill Cornell Medicine, New York City, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York City, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York City, NY, USA.
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26
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Tur-Planells V, García-Sastre A, Cuadrado-Castano S, Nistal-Villan E. Engineering Non-Human RNA Viruses for Cancer Therapy. Vaccines (Basel) 2023; 11:1617. [PMID: 37897020 PMCID: PMC10611381 DOI: 10.3390/vaccines11101617] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Alongside the development and progress in cancer immunotherapy, research in oncolytic viruses (OVs) continues advancing novel treatment strategies to the clinic. With almost 50 clinical trials carried out over the last decade, the opportunities for intervention using OVs are expanding beyond the old-fashioned concept of "lytic killers", with promising breakthrough therapeutic strategies focused on leveraging the immunostimulatory potential of different viral platforms. This review presents an overview of non-human-adapted RNA viruses engineered for cancer therapy. Moreover, we describe the diverse strategies employed to manipulate the genomes of these viruses to optimize their therapeutic capabilities. By focusing on different aspects of this particular group of viruses, we describe the insights into the promising advancements in the field of virotherapy and its potential to revolutionize cancer treatment.
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Affiliation(s)
- Vicent Tur-Planells
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Department of Medicine, 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
- The Tisch Cancer Institute, 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
| | - Sara Cuadrado-Castano
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute (IGI), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Estanislao Nistal-Villan
- Microbiology Section, Department of Pharmaceutical Science and Health, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28668 Boadilla del Monte, Spain;
- Departamento de Ciencias Médicas Básicas, Instituto de Medicina Molecular Aplicada (IMMA) Nemesio Díez, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, 28668 Boadilla del Monte, Spain
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27
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe 2023; 31:1668-1684.e12. [PMID: 37738983 PMCID: PMC10750313 DOI: 10.1016/j.chom.2023.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Revised: 07/01/2023] [Accepted: 08/07/2023] [Indexed: 09/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2.
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Affiliation(s)
- Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90024, USA; Institute for Quantitative and Computational Biosciences (OCBio), University of California, Los Angeles, Los Angeles, CA 90024, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Erika A Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Tseng
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Tolga Çağatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Flores
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fahmida Alam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Magdalena Rutkowska
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manisha R Ummadi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | - Giuseppe Pisanelli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy
| | - R Blake Richardson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan C Veit
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | - Baran Ak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, 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; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorena Zuliani-Alvarez
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; 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
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, 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; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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28
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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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29
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Cohen P, DeGrace EJ, Danziger O, Patel RS, Barrall EA, Bobrowski T, Kehrer T, Cupic A, Miorin L, García-Sastre A, Rosenberg BR. Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single-cell RNA sequencing. Microbiol Spectr 2023; 11:e0077623. [PMID: 37676044 PMCID: PMC10580996 DOI: 10.1128/spectrum.00776-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/12/2023] [Indexed: 09/08/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). scRNA-Seq library preparation methods and data processing workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq library preparation methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We show that compared to 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') libraries or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5') libraries sequenced with standard read configurations, 10X 5' libraries sequenced with an extended length read 1 (R1) that covers both cell barcode and transcript sequence (termed "10X 5' with extended R1") increase the number of unambiguous reads spanning leader-sgmRNA junction sites. We further present a data processing workflow, single-cell coronavirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to viral sgmRNAs or viral genomic RNA (gRNA). We find that combining 10X 5' with extended R1 library preparation/sequencing and scCoVseq data processing maximizes the number of viral UMIs per cell quantified by scRNA-Seq. Corresponding sgmRNA expression levels are highly correlated with expression in matched bulk RNA-Seq data sets quantified with established tools for SARS-CoV-2 analysis. Using this scRNA-Seq approach, we find that SARS-CoV-2 gene expression is highly correlated across individual infected cells, which suggests that the proportion of viral sgmRNAs remains generally consistent throughout infection. Taken together, these results and corresponding data processing workflow enable robust quantification of coronavirus sgmRNA expression at single-cell resolution, thereby supporting high-resolution studies of viral RNA processes in individual cells. IMPORTANCE Single-cell RNA sequencing (scRNA-Seq) has emerged as a valuable tool to study host-virus interactions, especially for coronavirus disease 2019 (COVID-19). Here we compare the performance of different scRNA-Seq library preparation methods and sequencing strategies to detect SARS-CoV-2 RNAs and develop a data processing workflow to quantify unambiguous sequence reads derived from SARS-CoV-2 genomic RNA and subgenomic mRNAs. After establishing a workflow that maximizes the detection of SARS-CoV-2 subgenomic mRNAs, we explore patterns of SARS-CoV-2 gene expression across cells with variable levels of total viral RNA, assess host gene expression differences between infected and bystander cells, and identify non-canonical and lowly abundant SARS-CoV-2 RNAs. The sequencing and data processing strategies developed here can enhance studies of coronavirus RNA biology at single-cell resolution and thereby contribute to our understanding of viral pathogenesis.
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Affiliation(s)
- Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emma J. DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roosheel S. Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erika A. Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tesia Bobrowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brad R. Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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30
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Sircy LM, Ramstead AG, Joshi H, Baessler A, Mena I, García-Sastre A, Williams MA, Scott Hale J. Generation of antigen-specific memory CD4 T cells by heterologous immunization enhances the magnitude of the germinal center response upon influenza infection. bioRxiv 2023:2023.08.29.555253. [PMID: 37693425 PMCID: PMC10491174 DOI: 10.1101/2023.08.29.555253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Current influenza vaccine strategies have yet to overcome significant obstacles, including rapid antigenic drift of seasonal influenza viruses, in generating efficacious long-term humoral immunity. Due to the necessity of germinal center formation in generating long-lived high affinity antibodies, the germinal center has increasingly become a target for the development of novel or improvement of less-efficacious vaccines. However, there remains a major gap in current influenza research to effectively target T follicular helper cells during vaccination to alter the germinal center reaction. In this study, we used a heterologous infection or immunization priming strategy to seed an antigen-specific memory CD4+ T cell pool prior to influenza infection in mice to evaluate the effect of recalled memory T follicular helper cells in increased help to influenza-specific primary B cells and enhanced generation of neutralizing antibodies. We found that heterologous priming with intranasal infection with acute lymphocytic choriomeningitis virus (LCMV) or intramuscular immunization with adjuvanted recombinant LCMV glycoprotein induced increased antigen-specific effector CD4+ T and B cellular responses following infection with a recombinant influenza strain that expresses LCMV glycoprotein. Heterologously primed mice had increased expansion of secondary Th1 and Tfh cell subsets, including increased CD4+ TRM cells in the lung. However, the early enhancement of the germinal center cellular response following influenza infection did not impact influenza-specific antibody generation or B cell repertoires compared to primary influenza infection. Overall, our study suggests that while heterologous infection/immunization priming of CD4+ T cells is able to enhance the early germinal center reaction, further studies to understand how to target the germinal center and CD4+ T cells specifically to increase long-lived antiviral humoral immunity are needed.
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Affiliation(s)
- Linda M. Sircy
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Andrew G. Ramstead
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Hemant Joshi
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Andrew Baessler
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Matthew A. Williams
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - J. Scott Hale
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
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31
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Thomas SN, Niemeyer BF, Jimenez-Valdes RJ, Kaiser AJ, Espinosa JM, Sullivan KD, Goodspeed A, Costello JC, Alder JK, Cañas-Arranz R, García-Sastre A, Benam KH. Down syndrome is associated with altered frequency and functioning of tracheal multiciliated cells, and response to influenza virus infection. iScience 2023; 26:107361. [PMID: 37554445 PMCID: PMC10405068 DOI: 10.1016/j.isci.2023.107361] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/01/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
Individuals with Down syndrome (DS) clinically manifest severe respiratory illnesses; however, there is a paucity of data on how DS influences homeostatic physiology of lung airway, and its reactive responses to pulmonary pathogens. We generated well-differentiated ciliated airway epithelia using tracheas from wild-type and Dp(16)1/Yey mice in vitro, and discovered that Dp(16)1/Yey epithelia have significantly lower abundance of ciliated cells, an altered ciliary beating profile, and reduced mucociliary transport. Interestingly, both sets of differentiated epithelia released similar quantities of viral particles after infection with influenza A virus (IAV). However, RNA-sequencing and proteomic analyses revealed an immune hyperreactive phenotype particularly for monocyte-recruiting chemokines in Dp(16)1/Yey epithelia. Importantly, when we challenged mice in vivo with IAV, we observed immune hyper-responsiveness in Dp(16)1/Yey mice, evidenced by higher quantities of lung airway infiltrated monocytes, and elevated levels of pro-inflammatory cytokines in bronchoalveolar lavage fluid. Our findings illuminate mechanisms underlying DS-mediated pathophysiological changes in airway epithelium.
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Affiliation(s)
- Samantha N. Thomas
- Department of Bioengineering, University of Colorado Denver, Aurora, CO 80045, USA
| | - Brian F. Niemeyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rocio J. Jimenez-Valdes
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alexander J. Kaiser
- Department of Bioengineering, University of Colorado Denver, Aurora, CO 80045, USA
| | - Joaquin M. Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kelly D. Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrew Goodspeed
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - James C. Costello
- Linda Crnic Institute for Down Syndrome, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- University of Colorado Comprehensive Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jonathan K. Alder
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rodrigo Cañas-Arranz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, 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
- Global Health and Emerging Pathogens Institute, 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
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kambez H. Benam
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
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32
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Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, García-Bernalt Diego J, Lin J, Wu TC, Marches F, Chaussabel D, Yu P, Salner A, Aucello G, Koff J, Hudson B, Church SE, Gorman K, Anguiano E, García-Sastre A, Williams A, Schotsaert M, Palucka K. Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia. iScience 2023; 26:107374. [PMID: 37520727 PMCID: PMC10374611 DOI: 10.1016/j.isci.2023.107374] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/04/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023] Open
Abstract
The COVID-19 pandemic continues to be a health crisis with major unmet medical needs. The early responses from airway epithelial cells, the first target of the virus regulating the progression toward severe disease, are not fully understood. Primary human air-liquid interface cultures representing the broncho-alveolar epithelia were used to study the kinetics and dynamics of SARS-CoV-2 variants infection. The infection measured by nucleoprotein expression, was a late event appearing between day 4-6 post infection for Wuhan-like virus. Other variants demonstrated increasingly accelerated timelines of infection. All variants triggered similar transcriptional signatures, an "early" inflammatory/immune signature preceding a "late" type I/III IFN, but differences in the quality and kinetics were found, consistent with the timing of nucleoprotein expression. Response to virus was spatially organized: CSF3 expression in basal cells and CCL20 in apical cells. Thus, SARS-CoV-2 virus triggers specific responses modulated over time to engage different arms of immune response.
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Affiliation(s)
| | - Sonia Jangra
- 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
| | - Marina Yurieva
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jan Martinek
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Megan Callender
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew Coxe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Angela Choi
- 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
| | - Juan García-Bernalt Diego
- 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
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Te-Chia Wu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter Yu
- Hartford HealthCare Cancer Institute, Hartford, CT 06102, USA
| | - Andrew Salner
- Hartford HealthCare Cancer Institute, Hartford, CT 06102, USA
| | - Gabrielle Aucello
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jonathan Koff
- Adult Cystic Fibrosis Program, Yale University, New Haven, CT 06519, USA
| | - Briana Hudson
- Nanostring Technologies, Translational Sciences, Seattle, WA 98109, USA
| | - Sarah E. Church
- Nanostring Technologies, Translational Sciences, Seattle, WA 98109, USA
| | - Kara Gorman
- Nanostring Technologies, Translational Sciences, Seattle, WA 98109, USA
| | | | - Adolfo García-Sastre
- 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
- The Tisch Cancer Institute, 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
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Michael Schotsaert
- 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
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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33
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Kuhn JH, Abe J, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Kumar Baranwal V, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Blair CD, Blasdell KR, Blouin AG, Bradfute SB, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Kumar Chaturvedi K, Chooi KM, Crane A, Dal Bó E, Carlos de la Torre J, de Souza WM, de Swart RL, Debat H, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, Laura García M, García-Sastre A, Garrison AR, Gaskin TR, Gong W, Gonzalez JPJ, de Bellocq J, Griffiths A, Groschup MH, Günther I, Günther S, Hammond J, Hasegawa Y, Hayashi K, Hepojoki J, Higgins CM, Hongō S, Horie M, Hughes HR, Hume AJ, Hyndman TH, Ikeda K, Jiāng D, Jonson GB, Junglen S, Klempa B, Klingström J, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Lǐ J, Li JM, Liu R, Lukashevich IS, MacDiarmid RM, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mühlberger E, Nabeshima T, Naidu R, Natsuaki T, Navarro B, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Ochoa-Corona FM, Okada T, Palacios G, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Rabbidge LO, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Rodrigues TCS, Romanowski V, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sadiq S, Salvato MS, Sasaya T, Schwemmle M, Sharpe SR, Shi M, Shimomoto Y, Kavi Sidharthan V, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Takeyama S, Tatara A, Tesh RB, Thornburg NJ, Tian X, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tu C, Turina M, Tzanetakis IE, Maria Vaira A, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Waltzek TB, Whitfield AE, Wolf YI, Xia H, Xylogianni E, Yanagisawa H, Yano K, Ye G, Yuan Z, Zerbini FM, Zhang G, Zhang S, Zhang YZ, Zhao L, Økland AL. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). J Gen Virol 2023; 104:001864. [PMID: 37622664 PMCID: PMC10721048 DOI: 10.1099/jgv.0.001864] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 08/26/2023] Open
Abstract
In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Junya Abe
- Ornamental Plants and Vegetables Research Center, Agricultural Research Department, Hokkaido Research Organization, Takikawa, Hokkaido, Japan
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Sergey V. Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - María A. Ayllón
- Centro de Biotecnología y Genómica de Plantas; Departamento de Biotecnología-Biología Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón; Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State University, Starkville, MS,, Mississippi State, USA
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Carol D. Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Paul A. Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J. Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Bloemfontein, South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N. Charrel
- Unite des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Krishna Kumar Chaturvedi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - William M. de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L. de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina
| | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - J. Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W. Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, PR China
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas R. Gaskin
- Brandenburg State Office of Rural Development, Agriculture and Land Consolidation (LELF), Frankfurt, Germany
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Wenjie Gong
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Jean-Paul J. Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ines Günther
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Yusuke Hasegawa
- Department of Clinical Plant Science, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Kazusa Hayashi
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Colleen M. Higgins
- The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University; International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Timothy H. Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Kenichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Gilda B. Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, PR China
| | - Ran Liu
- Illumina (China), Beijing, PR China
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H. Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Pontificia Universidad Católica de ValparaísoCampus Curauma, Valparaíso, Chile
| | - Shin-Yi L. Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | | | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - José A. Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | | | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Francisco M. Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Tomoyuki Okada
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Colin R. Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Janusz T. Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Daniel R. Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA, USA
| | - Thomas S. Postler
- Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
| | - Lee O. Rabbidge
- The New Zealand Institute for Plant and Food Research Limited; The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Sheli R. Radoshitzky
- Division of Antivirals, Office of Infectious Diseases, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O. Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Thaís C. S. Rodrigues
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Jonathan A. Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, Mississippi State, USA
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Maria S. Salvato
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Stephen R. Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, PR China
| | | | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS “E. Medea”, Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M. Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sawana Takeyama
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Akio Tatara
- Faculty of Agricultural Production and Management, Shizuoka Professional University of Agriculture, Shizuoka, Japan
| | - Robert B. Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | | | - Xin Tian
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Nicole D. Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | - Changchun Tu
- College of Veterinary Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, PR China
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E. Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | | | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, Galveston, TX,, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Thomas B. Waltzek
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Anna E. Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Evanthia Xylogianni
- Plant Pathology Laboratory, Department of Crop Science, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Votanikos, Athens, Greece
| | | | - Kazutaka Yano
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, PR China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Guilin Zhang
- Center for Disease Control and Prevention of Xinjiang Military Command Area, Urumqi, Xinjiang, PR China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, PR China
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, PR China
| | - Lu Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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Kottur J, White KM, Rodriguez ML, Rechkoblit O, Quintana-Feliciano R, Nayar A, García-Sastre A, Aggarwal AK. Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. PLoS Pathog 2023; 19:e1011546. [PMID: 37523415 PMCID: PMC10414583 DOI: 10.1371/journal.ppat.1011546] [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: 03/27/2023] [Revised: 08/10/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
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Affiliation(s)
- Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - M. Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Richard Quintana-Feliciano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ahana Nayar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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Jangra S, Landers JJ, Laghlali G, Rathnasinghe R, Warang P, Park SC, O'Konek JJ, Singh G, Janczak KW, García-Sastre A, Arya N, Karadag D, Baker JR, Schotsaert M, Wong PT. Multicomponent intranasal adjuvant for mucosal and durable systemic SARS-CoV-2 immunity in young and aged mice. NPJ Vaccines 2023; 8:96. [PMID: 37386041 PMCID: PMC10310740 DOI: 10.1038/s41541-023-00691-1] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023] Open
Abstract
Multiple FDA-approved SARS-CoV-2 vaccines currently provide excellent protection against severe disease. Despite this, immunity can wane relatively fast, particularly in the elderly and novel viral variants capable of evading infection- and vaccination-induced immunity continue to emerge. Intranasal (IN) vaccination more effectively induces mucosal immune responses than parenteral vaccines, which would improve protection and reduce viral transmission. Here, we developed a rationally designed IN adjuvant consisting of a combined nanoemulsion (NE)-based adjuvant and an RNA-based RIG-I agonist (IVT DI) to drive more robust, broadly protective antibody and T cell responses. We previously demonstrated this combination adjuvant (NE/IVT) potently induces protective immunity through synergistic activation of an array of innate receptors. We now demonstrate that NE/IVT with the SARS-CoV-2 receptor binding domain (RBD), induces robust and durable humoral, mucosal, and cellular immune responses of equivalent magnitude and quality in young and aged mice. This contrasted with the MF59-like intramuscular adjuvant, Addavax, which showed a decrease in immunogenicity with age. Robust antigen-specific IFN-γ/IL-2/TNF-α was induced in both young and aged NE/IVT-immunized animals, which is significant as their reduced production is associated with suboptimal protective immunity in the elderly. These findings highlight the potential of adjuvanted mucosal vaccines for improving protection against COVID-19.
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Affiliation(s)
- Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey J Landers
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Laghlali
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seok-Chan Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Laboratory of Pathology, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Korea
- Biosafety Research Institute, College of Veterinary Medicine, Jeonbuk National University, Iksan, 54596, Korea
| | - Jessica J O'Konek
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katarzyna W Janczak
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nandini Arya
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dilara Karadag
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - James R Baker
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Pamela T Wong
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA.
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA.
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36
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Singh I, Li F, Fink EA, Chau I, Li A, Rodriguez-Hernández A, Glenn I, Zapatero-Belinchón FJ, Rodriguez ML, Devkota K, Deng Z, White K, Wan X, Tolmachova NA, Moroz YS, Kaniskan HÜ, Ott M, García-Sastre A, Jin J, Fujimori DG, Irwin JJ, Vedadi M, Shoichet BK. Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase. J Med Chem 2023; 66:7785-7803. [PMID: 37294077 PMCID: PMC10374283 DOI: 10.1021/acs.jmedchem.2c02120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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] [Indexed: 06/10/2023]
Abstract
An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5'-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme's SAM site, leading to three inhibitors with IC50 values from 6 to 50 μM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC50 values from 12 to 341 μM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC50 values from 3.5 to 39 μM. Overall, 32 inhibitors encompassing 11 chemotypes had IC50 values < 50 μM and 5 inhibitors in 4 chemotypes had IC50 values < 10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.
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Affiliation(s)
- Isha Singh
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Elissa A Fink
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Graduate Program in Biophysics, University of California San Francisco, San Francisco, California 94143, United States
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alice Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Annía Rodriguez-Hernández
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Isabella Glenn
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | | | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kanchan Devkota
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Zhijie Deng
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xiaobo Wan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
| | - Nataliya A Tolmachova
- Enamine Ltd, Kyïv 02094, Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry, National Ukrainian Academy of Science, Kyïv 02660, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyïv, Kyïv 01601, Ukraine
- Chemspace, Riga LV-1082, Latvia
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Melanie Ott
- Gladstone Institutes, San Francisco, California 94158, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Department of Medicine, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- QBI COVID-19 Research Group (QCRG), San Francisco, California 94158, United States
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Sánchez-de Prada L, Sanz-Muñoz I, Sun W, Palese P, Ortiz de Lejarazu R, Eiros JM, García-Sastre A, Aydillo T. Group 1 and group 2 hemagglutinin stalk antibody response according to age. Front Immunol 2023; 14:1194073. [PMID: 37313413 PMCID: PMC10258341 DOI: 10.3389/fimmu.2023.1194073] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/12/2023] [Indexed: 06/15/2023] Open
Abstract
Objective Antibodies elicited by seasonal influenza vaccines mainly target the head of hemagglutinin (HA). However, antibodies against the stalk domain are cross-reactive and have been proven to play a role in reducing influenza disease severity. We investigated the induction of HA stalk-specific antibodies after seasonal influenza vaccination, considering the age of the cohorts. Methods A total of 166 individuals were recruited during the 2018 influenza vaccine campaign (IVC) and divided into groups: <50 (n = 14), 50-64 (n = 34), 65-79 (n = 61), and ≥80 (n = 57) years old. Stalk-specific antibodies were quantified by ELISA at day 0 and day 28 using recombinant viruses (cH6/1 and cH14/3) containing an HA head domain (H6 or H14) from wild bird origin with a stalk domain from human H1 or H3, respectively. The geometric mean titer (GMT) and the fold rise (GMFR) were calculated, and differences were assessed using ANOVA adjusted by the false discovery rate (FDR) and the Wilcoxon tests (p <0.05). Results All age groups elicited some level of increase in anti-stalk antibodies after receiving the influenza vaccine, except for the ≥80-year-old cohort. Additionally, <65-year-old vaccinees had higher group 1 antibody titers versus group 2 before and after vaccination. Similarly, vaccinees within the <50-year-old group showed a higher increase in anti-stalk antibody titers when compared to older individuals (≥80 years old), especially for group 1 anti-stalk antibodies. Conclusion Seasonal influenza vaccines can the induction of cross-reactive anti-stalk antibodies against group 1 and group 2 HAs. However, low responses were observed in older groups, highlighting the impact of immunosenescence in adequate humoral immune responses.
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Affiliation(s)
- Laura Sánchez-de Prada
- National Influenza Center of Valladolid, Valladolid, Spain
- Department of Microbiology and Immunology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | | | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - José María Eiros
- National Influenza Center of Valladolid, Valladolid, Spain
- Department of Microbiology and Immunology, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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García-Bernalt Diego J, Singh G, Jangra S, Handrejk K, Laporte M, Chang LA, El Zahed SS, Pache L, Chang MW, Warang P, Aslam S, Mena I, Webb BT, Benner C, García-Sastre A, Schotsaert M. Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters. bioRxiv 2023:2023.05.22.541294. [PMID: 37425792 PMCID: PMC10327228 DOI: 10.1101/2023.05.22.541294] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Hybrid immunity to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. mRNA vaccine, BNT162b2, was dosed to induce binding antibody titers against ancestral spike, but inefficient serum virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera. Transcriptomics post-infection reflects both vaccination status and disease course and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of high titers of neutralizing antibodies in the serum, correlates with recall of broadly reactive B- and T-cell responses.
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Affiliation(s)
- Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, Spain
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Kim Handrejk
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Lauren A Chang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara S El Zahed
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Lars Pache
- NCI Designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Prajakta Warang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Brett T Webb
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, NY, USA
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Roytenberg R, García-Sastre A, Li W. Vaccine-induced immune thrombotic thrombocytopenia: what do we know hitherto? Front Med (Lausanne) 2023; 10:1155727. [PMID: 37261122 PMCID: PMC10227460 DOI: 10.3389/fmed.2023.1155727] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT), also known as thrombosis with thrombocytopenia syndrome, is a catastrophic and life-threatening reaction to coronavirus disease 2019 (COVID-19) vaccines, which occurs disproportionately in response to vaccination with non-replicating adenovirus vector (AV) vaccines. The mechanism of VITT is not well defined and it has not been resolved why cases of VITT are predominated by vaccination with AV vaccines. However, virtually all VITT patients have positive platelet-activating anti-platelet factor 4 (PF4) antibody titers. Subsequently, platelets are activated and depleted in an Fcγ-receptor IIa (FcγRIIa or CD32a)-dependent manner, but it is not clear why or how the anti-PF4 response is mounted. This review describes the pathogenesis of VITT and provides insight into possible mechanisms that prompt the formation of a PF4/polyanion complex, which drives VITT pathology, as an amalgam of current experimental data or hypotheses.
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Affiliation(s)
- Renat Roytenberg
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV, United States
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40
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Ponce-de-León S, Torres M, Soto-Ramírez LE, Calva JJ, Santillán-Doherty P, Carranza-Salazar DE, Carreño JM, Carranza C, Juárez E, Carreto-Binaghi LE, Ramírez-Martínez L, Paz De la Rosa G, Vigueras-Moreno R, Ortiz-Stern A, López-Vidal Y, Macías AE, Torres-Flores J, Rojas-Martínez O, Suárez-Martínez A, Peralta-Sánchez G, Kawabata H, González-Domínguez I, Martínez-Guevara JL, Sun W, Sarfati-Mizrahi D, Soto-Priante E, Chagoya-Cortés HE, López-Macías C, Castro-Peralta F, Palese P, García-Sastre A, Krammer F, Lozano-Dubernard B. Interim safety and immunogenicity results from an NDV-based COVID-19 vaccine phase I trial in Mexico. NPJ Vaccines 2023; 8:67. [PMID: 37164959 PMCID: PMC10170424 DOI: 10.1038/s41541-023-00662-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023] Open
Abstract
There is still a need for safe, efficient, and low-cost coronavirus disease 2019 (COVID-19) vaccines that can stop transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we evaluated a vaccine candidate based on a live recombinant Newcastle disease virus (NDV) that expresses a stable version of the spike protein in infected cells as well as on the surface of the viral particle (AVX/COVID-12-HEXAPRO, also known as NDV-HXP-S). This vaccine candidate can be grown in embryonated eggs at a low cost, similar to influenza virus vaccines, and it can also be administered intranasally, potentially to induce mucosal immunity. We evaluated this vaccine candidate in prime-boost regimens via intramuscular, intranasal, or intranasal followed by intramuscular routes in an open-label non-randomized non-placebo-controlled phase I clinical trial in Mexico in 91 volunteers. The primary objective of the trial was to assess vaccine safety, and the secondary objective was to determine the immunogenicity of the different vaccine regimens. In the interim analysis reported here, the vaccine was found to be safe, and the higher doses tested were found to be immunogenic when given intramuscularly or intranasally followed by intramuscular administration, providing the basis for further clinical development of the vaccine candidate. The study is registered under ClinicalTrials.gov identifier NCT04871737.
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Affiliation(s)
- Samuel Ponce-de-León
- Programa Universitario de Investigación en Salud (PUIS), Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Edif. de los Programas Universitarios, Planta Alta. Circuito de la Investigación Científica S/N Ciudad Universitaria, Ciudad de México, C.P. 04510, México
| | - Martha Torres
- Laboratorio de Inmunobiología de la tuberculosis, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cossio Villegas, Calzada de Tlalpan 4502, Sección XVI, CP 14080, Tlalpan, México
| | - Luis Enrique Soto-Ramírez
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Vasco de Quiroga 15, Belisario Dominguez, Sección XVI, 14080, Tlalpan, México
- Departamento de Infectología y Vigilancia Epidemiológica, Hospital Médica Sur, S.A.B. de C. V., Puente de Piedra 150, Toriello Guerra, 14050, Tlalpan, México
| | - Juan José Calva
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Vasco de Quiroga 15, Belisario Dominguez, Sección XVI, 14080, Tlalpan, México
| | - Patricio Santillán-Doherty
- Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cossio Villegas, Calzada de Tlalpan 4502, Sección XVI, CP 14080, Tlalpan, México
| | - Dora Eugenia Carranza-Salazar
- ProcliniQ Investigación Clínica, S. A. de C. V., Renato Leduc 155 (Xontepec 91), Toriello Guerra, 14050, Tlalpan, México
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Claudia Carranza
- Laboratorio de Inmunobiología de la tuberculosis, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cossio Villegas, Calzada de Tlalpan 4502, Sección XVI, CP 14080, Tlalpan, México
| | - Esmeralda Juárez
- Departamento de Investigación en Microbiología, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cossio Villegas, Calzada de Tlalpan 4502, Sección XVI, CP 14080, Tlalpan, México
| | - Laura E Carreto-Binaghi
- Laboratorio de Inmunobiología de la tuberculosis, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cossio Villegas, Calzada de Tlalpan 4502, Sección XVI, CP 14080, Tlalpan, México
| | - Luis Ramírez-Martínez
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Georgina Paz De la Rosa
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Rosalía Vigueras-Moreno
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Alejandro Ortiz-Stern
- iLS Clinical Research, S. C. (iLS), Matias Romero 102 - 205 Del Valle, Benito Juárez, CP 03100, CDMX, México
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 3000, Circuito Interior S/N. Ciudad Universitaria, Coyoacán, CP.04510, México
| | - Alejandro E Macías
- Departamento de Medicina, Universidad de Guanajuato, 20 de Enero 929, C.P 37000, León Guanajuato, México
| | - Jesús Torres-Flores
- Dirección Adjunta de Desarrollo Tecnológico, Vinculación e Innovación, Consejo Nacional de Ciencia y Tecnología (CONACYT), Insurgentes Sur 1582, Crédito Constructor, CP 03940, Benito Juárez, CDMX, México
| | - Oscar Rojas-Martínez
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Alejandro Suárez-Martínez
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Gustavo Peralta-Sánchez
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Hisaaki Kawabata
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Irene González-Domínguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - José Luis Martínez-Guevara
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Weina Sun
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - David Sarfati-Mizrahi
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Ernesto Soto-Priante
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Héctor Elías Chagoya-Cortés
- Consultora Mextrategy, S.A.S. de C. V. (Mextrategy), Insurgentes Sur 1079 P7-127, Nochebuena, CP 03720, CDMX, Mexico
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica. Hospital de Especialidades del Centro Médico Nacional Siglo XXI. Instituto Mexicano del Seguro Social (IMSS), Av. Cuauhtémoc 330, Doctores, C.P. 06720, Benito Juárez, CDMX, México
| | - Felipa Castro-Peralta
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
- Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA.
| | - Bernardo Lozano-Dubernard
- Laboratorio Avi-Mex, S. A. de C. V. (Avimex), Maíz 18, Granjas Esmeralda, CP 09810, Iztapalapa, CDMX, Mexico.
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Pillai TK, Johnson KE, Song T, Gregianini TS, Tatiana G. B, Wang G, Medina RA, Van Bakel H, García-Sastre A, Nelson MI, Ghedin E, Veiga ABG. Tracking the emergence of antigenic variants in influenza A virus epidemics in Brazil. Virus Evol 2023; 9:vead027. [PMID: 37207002 PMCID: PMC10191192 DOI: 10.1093/ve/vead027] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/04/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
Influenza A virus (IAV) circulation patterns differ in North America and South America, with influenza seasons often characterized by different subtypes and strains. However, South America is relatively undersampled considering the size of its population. To address this gap, we sequenced the complete genomes of 220 IAVs collected between 2009 and 2016 from hospitalized patients in southern Brazil. New genetic drift variants were introduced into southern Brazil each season from a global gene pool, including four H3N2 clades (3c, 3c2, 3c3, and 3c2a) and five H1N1pdm clades (clades 6, 7, 6b, 6c, and 6b1). In 2016, H1N1pdm viruses belonging to a new 6b1 clade caused a severe influenza epidemic in southern Brazil that arrived early and spread rapidly, peaking mid-autumn. Inhibition assays showed that the A/California/07/2009(H1N1) vaccine strain did not protect well against 6b1 viruses. Phylogenetically, most 6b1 sequences that circulated in southern Brazil belong to a single transmission cluster that rapidly diffused across susceptible populations, leading to the highest levels of influenza hospitalization and mortality seen since the 2009 pandemic. Continuous genomic surveillance is needed to monitor rapidly evolving IAVs for vaccine strain selection and understand their epidemiological impact in understudied regions.
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Affiliation(s)
- Tara K Pillai
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
| | - Katherine E Johnson
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Timothy Song
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul—LACEN/CEVS/SES‐RS, Av. Ipiranga, 5400, Porto Alegre, RS 90450-190, Brazil
| | - Baccin Tatiana G.
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Rio Grande do Sul, RS 90050-170, Brazil
- Department of Pediatric Infectious Diseases and Immunology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, RM 8330024, Chile
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, RM 8330024, Chile
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology and Experimental Medicine, School of Medicine, Emory University, 1462 Clifton Road, Office 429, Atlanta, GA 30322, USA
| | - Harm Van Bakel
- Laboratory of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Martha I Nelson
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Elodie Ghedin
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, 50 South Drive, Bethesda, MD 20894, USA
- Department of Biology, Center for Genomics & Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Ana B G Veiga
- Graduate Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Rio Grande do Sul, RS 90050-170, Brazil
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai Hospital, 1 Gustave L. Levy Place, New York, NY 10029, USA
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42
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Bhat P, Aksenova V, Gazzara M, Rex EA, Aslam S, Haddad C, Gao S, Esparza M, Cagatay T, Batten K, El Zahed SS, Arnaoutov A, Zhong H, Shay JW, Tolbert BS, Dasso M, Lynch KW, García-Sastre A, Fontoura BMA. Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex. Nat Commun 2023; 14:2304. [PMID: 37085480 PMCID: PMC10121598 DOI: 10.1038/s41467-023-37911-0] [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: 09/06/2022] [Accepted: 04/05/2023] [Indexed: 04/23/2023] Open
Abstract
Nuclear export of influenza A virus (IAV) mRNAs occurs through the nuclear pore complex (NPC). Using the Auxin-Induced Degron (AID) system to rapidly degrade proteins, we show that among the nucleoporins localized at the nucleoplasmic side of the NPC, TPR is the key nucleoporin required for nuclear export of influenza virus mRNAs. TPR recruits the TRanscription and EXport complex (TREX)-2 to the NPC for exporting a subset of cellular mRNAs. By degrading components of the TREX-2 complex (GANP, Germinal-center Associated Nuclear Protein; PCID2, PCI domain containing 2), we show that influenza mRNAs require the TREX-2 complex for nuclear export and replication. Furthermore, we found that cellular mRNAs whose export is dependent on GANP have a small number of exons, a high mean exon length, long 3' UTR, and low GC content. Some of these features are shared by influenza virus mRNAs. Additionally, we identified a 45 nucleotide RNA signal from influenza virus HA mRNA that is sufficient to mediate GANP-dependent mRNA export. Thus, we report a role for the TREX-2 complex in nuclear export of influenza mRNAs and identified RNA determinants associated with the TREX-2-dependent mRNA export.
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Affiliation(s)
- Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emily A Rex
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sadaf Aslam
- 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
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Matthew Esparza
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tolga Cagatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sara S El Zahed
- 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
| | - Alexei Arnaoutov
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hualin Zhong
- Department of Biological Sciences, Hunter College, New York, NY, 10065, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Adolfo García-Sastre
- 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
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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43
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mSphere 2023; 8:e0003423. [PMID: 36700653 PMCID: PMC10117089 DOI: 10.1128/msphere.00034-23] [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] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | - W Paul Duprex
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-Hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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44
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Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, Diego JGB, Lin J, Wu TC, Marches F, Chaussabel D, Yu P, Salner A, Aucello G, Koff J, Hudson B, Church SE, Gorman K, Anguiano E, García-Sastre A, Williams A, Schotsaert M, Palucka K. Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia. bioRxiv 2023:2023.03.30.534980. [PMID: 37034597 PMCID: PMC10081226 DOI: 10.1101/2023.03.30.534980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The COVID-19 pandemic continues to be a health crisis with major unmet medical needs. The early responses from airway epithelial cells, the first target of the virus regulating the progression towards severe disease, are not fully understood. Primary human air-liquid interface cultures representing the broncho-alveolar epithelia were used to study the kinetics and dynamics of SARS-CoV-2 variants infection. The infection measured by nucleoprotein expression, was a late event appearing between day 4-6 post infection for Wuhan-like virus. Other variants demonstrated increasingly accelerated timelines of infection. All variants triggered similar transcriptional signatures, an "early" inflammatory/immune signature preceding a "late" type I/III IFN, but differences in the quality and kinetics were found, consistent with the timing of nucleoprotein expression. Response to virus was spatially organized: CSF3 expression in basal cells and CCL20 in apical cells. Thus, SARS-CoV-2 virus triggers specific responses modulated over time to engage different arms of immune response.
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45
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Hemann EA, Knoll ML, Wilkins CR, Subra C, Green R, García-Sastre A, Thomas PG, Trautmann L, Ireton RC, Loo YM, Gale M. A Small Molecule RIG-I Agonist Serves as an Adjuvant to Induce Broad Multifaceted Influenza Virus Vaccine Immunity. J Immunol 2023; 210:1247-1256. [PMID: 36939421 PMCID: PMC10149148 DOI: 10.4049/jimmunol.2300026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/10/2023] [Indexed: 03/21/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I) is essential for activating host cell innate immunity to regulate the immune response against many RNA viruses. We previously identified that a small molecule compound, KIN1148, led to the activation of IFN regulatory factor 3 (IRF3) and served to enhance protection against influenza A virus (IAV) A/California/04/2009 infection. We have now determined direct binding of KIN1148 to RIG-I to drive expression of IFN regulatory factor 3 and NF-κB target genes, including specific immunomodulatory cytokines and chemokines. Intriguingly, KIN1148 does not lead to ATPase activity or compete with ATP for binding but activates RIG-I to induce antiviral gene expression programs distinct from type I IFN treatment. When administered in combination with a vaccine against IAV, KIN1148 induces both neutralizing Ab and IAV-specific T cell responses compared with vaccination alone, which induces comparatively poor responses. This robust KIN1148-adjuvanted immune response protects mice from lethal A/California/04/2009 and H5N1 IAV challenge. Importantly, KIN1148 also augments human CD8+ T cell activation. Thus, we have identified a small molecule RIG-I agonist that serves as an effective adjuvant in inducing noncanonical RIG-I activation for induction of innate immune programs that enhance adaptive immune protection of antiviral vaccination.
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Affiliation(s)
- Emily A Hemann
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH
| | - Megan L Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Courtney R Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Caroline Subra
- The Henry M. Jackson Foundation for the Advancement of Military Medicine and the U.S. Military HIV Research Program, Bethesda, MD
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Adolfo García-Sastre
- Department of Microbiology, The Tisch Cancer Institute, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Infectious Diseases, Department of Medicine, The Tisch Cancer Institute, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Pathology, Molecular and Cell-Based Medicine, The Tisch Cancer Institute, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN
| | - Lydie Trautmann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine and the U.S. Military HIV Research Program, Bethesda, MD
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR
| | - Renee C Ireton
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
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46
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Déjosez M, Marin A, Hughes GM, Morales AE, Godoy-Parejo C, Gray JL, Qin Y, Singh AA, Xu H, Juste J, Ibáñez C, White KM, Rosales R, Francoeur NJ, Sebra RP, Alcock D, Volkert TL, Puechmaille SJ, Pastusiak A, Frost SDW, Hiller M, Young RA, Teeling EC, García-Sastre A, Zwaka TP. Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell 2023; 186:957-974.e28. [PMID: 36812912 PMCID: PMC10085545 DOI: 10.1016/j.cell.2023.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 09/23/2022] [Revised: 12/06/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
Bats are distinctive among mammals due to their ability to fly, use laryngeal echolocation, and tolerate viruses. However, there are currently no reliable cellular models for studying bat biology or their response to viral infections. Here, we created induced pluripotent stem cells (iPSCs) from two species of bats: the wild greater horseshoe bat (Rhinolophus ferrumequinum) and the greater mouse-eared bat (Myotis myotis). The iPSCs from both bat species showed similar characteristics and had a gene expression profile resembling that of cells attacked by viruses. They also had a high number of endogenous viral sequences, particularly retroviruses. These results suggest that bats have evolved mechanisms to tolerate a large load of viral sequences and may have a more intertwined relationship with viruses than previously thought. Further study of bat iPSCs and their differentiated progeny will provide insights into bat biology, virus host relationships, and the molecular basis of bats' special traits.
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Affiliation(s)
- Marion Déjosez
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariadna E Morales
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Carlos Godoy-Parejo
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jonathan L Gray
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Yiren Qin
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Arun A Singh
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Hui Xu
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Javier Juste
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain; CIBER Epidemiology and Public Health, CIBERESP, Madrid, Spain
| | - Carlos Ibáñez
- Estación biológica de doñana (CSIC), Avda. Américo Vespucio 26, Seville 41092, Spain
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Genomics, New York, NY, USA
| | - Dominic Alcock
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Thomas L Volkert
- Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA
| | | | - Andrzej Pastusiak
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA
| | - Simon D W Frost
- Microsoft Premonition, Microsoft Building 99, 14820 NE 36th Street, Redmond, WA 98052, USA; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany; Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany; Faculty of Biosciences, Goethe University, Max-von-Laue-Str, 60438 Frankfurt, Germany
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, 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; Department of Pathology, Molecular and Cell-Based Medicine and the Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Thomas P Zwaka
- Huffington Center for Cell-Based Research in Parkinson's disease, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Department of Cell, Developmental, and Regenerative Biology, and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA; Paratus Sciences, 430 East 29th Street, Suite 600, New York, NY 10016, USA.
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47
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Wei J, Patil A, Collings CK, Alfajaro MM, Liang Y, Cai WL, Strine MS, Filler RB, DeWeirdt PC, Hanna RE, Menasche BL, Ökten A, Peña-Hernández MA, Klein J, McNamara A, Rosales R, McGovern BL, Luis Rodriguez M, García-Sastre A, White KM, Qin Y, Doench JG, Yan Q, Iwasaki A, Zwaka TP, Qi J, Kadoch C, Wilen CB. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nat Genet 2023; 55:471-483. [PMID: 36894709 PMCID: PMC10011139 DOI: 10.1038/s41588-023-01307-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 08/11/2022] [Accepted: 01/23/2023] [Indexed: 03/11/2023]
Abstract
Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and can provide new drug targets. Here we demonstrate that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes, specifically canonical BRG1/BRM-associated factor (cBAF) complexes, promote severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and represent host-directed therapeutic targets. The catalytic activity of SMARCA4 is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, ACE2 expression and virus susceptibility. The transcription factors HNF1A/B interact with and recruit mSWI/SNF complexes to ACE2 enhancers, which contain high HNF1A motif density. Notably, small-molecule mSWI/SNF ATPase inhibitors or degraders abrogate angiotensin-converting enzyme 2 (ACE2) expression and confer resistance to SARS-CoV-2 variants and a remdesivir-resistant virus in three cell lines and three primary human cell types, including airway epithelial cells, by up to 5 logs. These data highlight the role of mSWI/SNF complex activities in conferring SARS-CoV-2 susceptibility and identify a potential class of broad-acting antivirals to combat emerging coronaviruses and drug-resistant variants.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wesley L Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bridget L Menasche
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arya Ökten
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew McNamara
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yiren Qin
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Thomas P Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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48
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. mBio 2023; 14:e0018823. [PMID: 36700642 PMCID: PMC9973315 DOI: 10.1128/mbio.00188-23] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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49
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Goodrum F, Lowen AC, Lakdawala S, Alwine J, Casadevall A, Imperiale MJ, Atwood W, Avgousti D, Baines J, Banfield B, Banks L, Bhaduri-McIntosh S, Bhattacharya D, Blanco-Melo D, Bloom D, Boon A, Boulant S, Brandt C, Broadbent A, Brooke C, Cameron C, Campos S, Caposio P, Chan G, Cliffe A, Coffin J, Collins K, Damania B, Daugherty M, Debbink K, DeCaprio J, Dermody T, Dikeakos J, DiMaio D, Dinglasan R, Duprex WP, Dutch R, Elde N, Emerman M, Enquist L, Fane B, Fernandez-Sesma A, Flenniken M, Frappier L, Frieman M, Frueh K, Gack M, Gaglia M, Gallagher T, Galloway D, García-Sastre A, Geballe A, Glaunsinger B, Goff S, Greninger A, Hancock M, Harris E, Heaton N, Heise M, Heldwein E, Hogue B, Horner S, Hutchinson E, Hyser J, Jackson W, Kalejta R, Kamil J, Karst S, Kirchhoff F, Knipe D, Kowalik T, Lagunoff M, Laimins L, Langlois R, Lauring A, Lee B, Leib D, Liu SL, Longnecker R, Lopez C, Luftig M, Lund J, Manicassamy B, McFadden G, McIntosh M, Mehle A, Miller WA, Mohr I, Moody C, Moorman N, Moscona A, Mounce B, Munger J, Münger K, Murphy E, Naghavi M, Nelson J, Neufeldt C, Nikolich J, O'Connor C, Ono A, Orenstein W, Ornelles D, Ou JH, Parker J, Parrish C, Pekosz A, Pellett P, Pfeiffer J, Plemper R, Polyak S, Purdy J, Pyeon D, Quinones-Mateu M, Renne R, Rice C, Schoggins J, Roller R, Russell C, Sandri-Goldin R, Sapp M, Schang L, Schmid S, Schultz-Cherry S, Semler B, Shenk T, Silvestri G, Simon V, Smith G, Smith J, Spindler K, Stanifer M, Subbarao K, Sundquist W, Suthar M, Sutton T, Tai A, Tarakanova V, tenOever B, Tibbetts S, Tompkins S, Toth Z, van Doorslaer K, Vignuzzi M, Wallace N, Walsh D, Weekes M, Weinberg J, Weitzman M, Weller S, Whelan S, White E, Williams B, Wobus C, Wong S, Yurochko A. Virology under the Microscope-a Call for Rational Discourse. J Virol 2023; 97:e0008923. [PMID: 36700640 PMCID: PMC9972907 DOI: 10.1128/jvi.00089-23] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.
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Affiliation(s)
- Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - James Alwine
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Daphne Avgousti
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lawrence Banks
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | | - David Bloom
- University of Florida, Gainesville, Florida, USA
| | - Adrianus Boon
- University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Curtis Brandt
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | | | - Craig Cameron
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | - Gary Chan
- SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna Cliffe
- University of Virginia, Charlottesville, Virginia, USA
| | - John Coffin
- Tufts University, Boston, Massachusetts, USA
| | | | - Blossom Damania
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Kari Debbink
- Johns Hopkins University, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | - Nels Elde
- University of Utah, Salt Lake City, Utah, USA
| | - Michael Emerman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynn Enquist
- Princeton University, Princeton, New Jersey, USA
| | | | | | | | | | | | - Klaus Frueh
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michaela Gack
- Florida Research and Innovation Center, Port Saint Lucie, Florida, USA
| | - Marta Gaglia
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Denise Galloway
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Adam Geballe
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Meaghan Hancock
- Oregon Health and Science University, Beaverton, Oregon, USA
| | - Eva Harris
- University of California, Berkeley, Berkeley, California, USA
| | | | - Mark Heise
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | | | | | | | - Jeremy Kamil
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | - David Knipe
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ryan Langlois
- University of Minnesota, Minneapolis, Minnesota, USA
| | - Adam Lauring
- University of Michigan, Ann Arbor, Michigan, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Leib
- Dartmouth College, Lebanon, New Hampshire, USA
| | - Shan-Lu Liu
- The Ohio State University, Columbus, Ohio, USA
| | | | | | | | - Jennifer Lund
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | - Andrew Mehle
- University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Ian Mohr
- New York University, New York, New York, USA
| | - Cary Moody
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | | | | | | | - Karl Münger
- Tufts University, Boston, Massachusetts, USA
| | - Eain Murphy
- SUNY Upstate Medical University, Syracuse, New York, USA
| | | | - Jay Nelson
- Oregon Health and Science University, Beaverton, Oregon, USA
| | | | | | | | - Akira Ono
- University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Ornelles
- Wake Forest University, Winston-Salem, North Carolina, USA
| | - Jing-hsiung Ou
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | | | - John Purdy
- University of Arizona, Tucson, Arizona, USA
| | - Dohun Pyeon
- Michigan State University, East Lansing, Michigan, USA
| | | | - Rolf Renne
- University of Florida, Gainesville, Florida, USA
| | - Charles Rice
- The Rockefeller University, New York, New York, USA
| | | | | | - Charles Russell
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Martin Sapp
- Louisiana State University, Shreveport, Louisiana, USA
| | | | | | | | - Bert Semler
- University of California, Irvine, Irvine, California, USA
| | - Thomas Shenk
- Princeton University, Princeton, New Jersey, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jason Smith
- University of Washington, Seattle, Washington, USA
| | | | | | - Kanta Subbarao
- The Peter Doherty Institute, Melbourne, Victoria, Australia
| | | | | | - Troy Sutton
- The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Tai
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | - Zsolt Toth
- University of Florida, Gainesville, Florida, USA
| | | | | | | | - Derek Walsh
- Northwestern University, Chicago, Illinois, USA
| | | | | | | | - Sandra Weller
- University of Connecticut, Farmington, Connecticut, USA
| | - Sean Whelan
- Washington University, St. Louis, Missouri, USA
| | | | | | | | - Scott Wong
- Oregon Health and Science University, Beaverton, Oregon, USA
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Cohen P, DeGrace EJ, Danziger O, Patel RS, Barrall EA, Bobrowski T, Kehrer T, Cupic A, Miorin L, García-Sastre A, Rosenberg BR. Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing. bioRxiv 2023:2021.11.22.469642. [PMID: 34845443 PMCID: PMC8629185 DOI: 10.1101/2021.11.22.469642] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single cell RNA sequencing (scRNA-Seq) studies have provided critical insight into the pathogenesis of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), the causative agent of COronaVIrus Disease 2019 (COVID-19). scRNA-Seq workflows are generally designed for the detection and quantification of eukaryotic host mRNAs and not viral RNAs. Here, we compare different scRNA-Seq methods for their ability to quantify and detect SARS-CoV-2 RNAs with a focus on subgenomic mRNAs (sgmRNAs). We present a data processing strategy, single cell CoronaVirus sequencing (scCoVseq), which quantifies reads unambiguously assigned to sgmRNAs or genomic RNA (gRNA). Compared to standard 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') and Chromium Next GEM Single Cell V(D)J (10X 5') sequencing, we find that 10X 5' with an extended read 1 (R1) sequencing strategy maximizes the detection of sgmRNAs by increasing the number of unambiguous reads spanning leader-sgmRNA junction sites. Using this method, we show that viral gene expression is highly correlated across cells suggesting a relatively consistent proportion of viral sgmRNA production throughout infection. Our method allows for quantification of coronavirus sgmRNA expression at single-cell resolution, and thereby supports high resolution studies of the dynamics of coronavirus RNA synthesis.
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Affiliation(s)
- Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Emma J DeGrace
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Roosheel S Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Erika A Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Tesia Bobrowski
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10035
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