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Adams SK, Ducharme GE, Loveday EK. All the single cells: if you like it then you should put some virus on it. J Virol 2024; 98:e0127323. [PMID: 38904395 DOI: 10.1128/jvi.01273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Across a rich 70-year history, single-cell virology has revealed the impact of host and pathogen heterogeneity during virus infections. Recent technological innovations have enabled higher-resolution analyses of cellular and viral heterogeneity. Furthermore, single-cell analysis has revealed extreme phenotypes and provided additional insights into host-pathogen dynamics. Using a single-cell approach to explore fundamental virology questions, contemporary researchers have contributed to a revival of interest in single-cell virology with increased insights and enthusiasm.
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Affiliation(s)
- Sophia K Adams
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Grace E Ducharme
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Emma K Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
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2
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Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM. Local genetic adaptation to habitat in wild chimpanzees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.601734. [PMID: 39026872 PMCID: PMC11257515 DOI: 10.1101/2024.07.09.601734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.
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Affiliation(s)
- Harrison J Ostridge
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Claudia Fontsere
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Daniela C Soto
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Joshua M Schmidt
- Flinders Health and Medical Research Institute (FHMRI), Department of Ophthalmology, Flinders University Sturt Rd, Bedford Park South Australia 5042 Australia
| | - Vrishti Saxena
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Alvarez-Estape
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Christopher D Barratt
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Paolo Gratton
- University of Rome "Tor Vergata" Department of Biology Via Cracovia, 1, Roma, Italia
| | - Gaëlle Bocksberger
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage, 60325 Frankfurt am Main, Germany
| | - Jack D Lester
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alfred Kwabena Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Donatienne Barubiyo
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- University of Konstanz, Centre for the Advanced Study of Collective Behaviour, Universitätsstraße 10, 78464, Konstanz, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rebecca Chancellor
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Heather Cohen
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Charlotte Coupland
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Institute of Cognitive Science, University of Osnabrück, Artilleriestrasse 34, 49076 Osnabrück, Germany
| | - Laia Dotras
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Jef Dupain
- Antwerp Zoo Foundation, RZSA, Kon.Astridplein 26, 2018 Antwerp, Belgium
| | - Villard Ebot Egbe
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Anne-Céline Granjon
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Josephine Head
- The Biodiversity Consultancy, 3E Kings Parade, Cambridge, CB2 1SJ, UK
| | - Daniela Hedwig
- Elephant Listening Project, K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Veerle Hermans
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - R Adriana Hernandez-Aguilar
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Kathryn J Jeffery
- School of Natural Sciences, University of Stirling, UK
- Agence National des Parcs Nationaux (ANPN) Batterie 4, BP20379, Libreville, Gabon
| | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Puschstrasse 4, 04103 Leipzig, Germany
| | - Parag Kadam
- Greater Mahale Ecosystem Research and Conservation Project
| | - Michael Kaiser
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ammie K Kalan
- Department of Anthropology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada
| | - Mbangi Kambere
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Ivonne Kienast
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY 14850, USA
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Deo Kujirakwinja
- Wildlife Conservation Society (WCS), 2300 Southern Boulevard. Bronx, New York 10460, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Institute of Human Origins, Arizona State University, 777 East University Drive, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
- Institute of Human Origins, Arizona State University, 900 Cady Mall, Tempe, AZ 85287 Arizona State University, PO Box 872402, Tempe, AZ 85287-2402 USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | | | - Kevin C Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA
| | - Manuel Llana
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Rumen Martín
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Amelia Meier
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
- Hawai'i Insititute of Marine Biology, University of Hawai'i at Manoa, 46-007 Lilipuna Place, Kaneohe, HI, 96744, USA
| | - David Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark Street, Chicago, Illinois 60614 USA
| | - Emily Neil
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Sonia Nicholl
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Stuart Nixon
- North of England Zoological Society, Chester Zoo, Upton by Chester, CH2 1LH, United Kingdom
| | | | - Christopher Orbell
- Panthera, 8 W 40TH ST, New York, NY 10018, USA
- School of Natural Sciences, University of Stirling, UK
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Robinson Orume
- Korup Rainforest Conservation Society, c/o Korup National Park, P.O. Box 36 Mundemba, South West Region, Cameroon
| | - Liliana Pacheco
- Save the Dogs and Other Animals, DJ 223 Km 3, 905200 Cernavoda CT, Romania
| | - Jodie Preece
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | | | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
| | - Aaron Rundus
- West Chester University, Depts of Anthropology & Sociology and Psychology, West Chester, PA, 19382 USA
| | - Crickette Sanz
- Washington University in Saint Louis, Department of Anthropology, One Brookings Drive, St. Louis, MO 63130, USA
- Congo Program, Wildlife Conservation Society, 151 Avenue Charles de Gaulle, Brazzaville, Republic of Congo
| | - Lilah Sciaky
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Volker Sommer
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | - Fiona A Stewart
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
- Department of Human Origins, Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Nikki Tagg
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Born Free Foundation, Floor 2 Frazer House, 14 Carfax, Horsham, RH12 1ER, UK
| | - Luc Roscelin Tédonzong
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
| | - Joost van Schijndel
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Elleni Vendras
- Frankfurt Zoological Society, Bernhard-Grzimek-Allee 1, 60316 Frankfurt, Germany
| | - Erin G Wessling
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen,Göttingen, Germany
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jacob Willie
- KMDA, Centre for Research and Conservation, Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, B-2018 Antwerp, Belgium
- Terrestrial Ecology Unit (TEREC), Department of Biology, Ghent University (UGent), K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Roman M Wittig
- Ape Social Mind Lab, Institute for Cognitive Sciences Marc Jeannerod, CNRS UMR 5229 CNRS, 67 bd Pinel, 69675 Bron CEDEX, France
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, BP 1301, Abidjan 01, CI
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Kyle Yurkiw
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology (MPI EVAN), Deutscher Platz 6, 04103 Leipzig
| | - Alex Piel
- University College London, Department of Anthropology, 14 Taviton Street, London WC1H 0BW, UK
| | | | - Hjalmar S Kühl
- Senckenberg Museum for Natural History Görlitz, Senckenberg - Member of the Leibniz Association Am Museum 1, 02826 Görlitz, Germany
- International Institute Zittau, Technische Universität Dresden, Markt 23, 02763 Zittau, Germany
| | - Megan Y Dennis
- University of California, Davis, Genome Center, MIND Institute, Department of Biochemistry & Molecular Medicine, One Shields Drive, Davis, CA, 95616, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Department of Primate Behavior and Evolution, Deutscher Platz 6, 04103 Leipzig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103
| | - Aida M Andrés
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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SoRelle ED, Haynes LE, Willard KA, Chang B, Ch’ng J, Christofk H, Luftig MA. Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598975. [PMID: 38915538 PMCID: PMC11195279 DOI: 10.1101/2024.06.14.598975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Viral infection leads to heterogeneous cellular outcomes ranging from refractory to abortive and fully productive states. Single cell transcriptomics enables a high resolution view of these distinct post-infection states. Here, we have interrogated the host-pathogen dynamics following reactivation of Epstein-Barr virus (EBV). While benign in most people, EBV is responsible for infectious mononucleosis, up to 2% of human cancers, and is a trigger for the development of multiple sclerosis. Following latency establishment in B cells, EBV reactivates and is shed in saliva to enable infection of new hosts. Beyond its importance for transmission, the lytic cycle is also implicated in EBV-associated oncogenesis. Conversely, induction of lytic reactivation in latent EBV-positive tumors presents a novel therapeutic opportunity. Therefore, defining the dynamics and heterogeneity of EBV lytic reactivation is a high priority to better understand pathogenesis and therapeutic potential. In this study, we applied single-cell techniques to analyze diverse fate trajectories during lytic reactivation in two B cell models. Consistent with prior work, we find that cell cycle and MYC expression correlate with cells refractory to lytic reactivation. We further found that lytic induction yields a continuum from abortive to complete reactivation. Abortive lytic cells upregulate NFκB and IRF3 pathway target genes, while cells that proceed through the full lytic cycle exhibit unexpected expression of genes associated with cellular reprogramming. Distinct subpopulations of lytic cells further displayed variable profiles for transcripts known to escape virus-mediated host shutoff. These data reveal previously unknown and promiscuous outcomes of lytic reactivation with broad implications for viral replication and EBV-associated oncogenesis.
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Affiliation(s)
- Elliott D. SoRelle
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Lauren E. Haynes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Katherine A. Willard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
| | - Beth Chang
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - James Ch’ng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Heather Christofk
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Center for Virology, Durham, NC 27710, USA
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Genoyer E, Wilson J, Ames JM, Stokes C, Moreno D, Etzyon N, Oberst A, Gale M. Exposure of negative-sense viral RNA in the cytoplasm initiates innate immunity to West Nile virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597966. [PMID: 38895355 PMCID: PMC11185705 DOI: 10.1101/2024.06.07.597966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
For many RNA viruses, immunity is triggered when RIG-I-like receptors (RLRs) detect viral RNA. However, only a minority of infected cells undergo innate immune activation. By examining these "first responder" cells during West Nile virus infection, we found that specific accumulation of anti- genomic negative-sense viral RNA (-vRNA) underlies innate immune activation and that RIG-I preferentially interacts with -vRNA. However, flaviviruses sequester -vRNA into membrane-bound replication compartments away from cytosolic sensors. We found that single-stranded -vRNA accumulates outside of replication compartments in "first responder" cells, rendering it accessible to RLRs. Exposure of this -vRNA occurs at late timepoints of infection, is linked to viral assembly, and depends on the expression of viral structural proteins. These findings reveal that while most infected cells replicate high levels of vRNA, release of -vRNA from replication compartments during assembly occurs at low frequency and is critical for initiation of innate immunity during flavivirus infection.
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Doratt BM, Malherbe DC, Messaoudi I. Transcriptional and functional remodeling of lung-resident T cells and macrophages by Simian varicella virus infection. Front Immunol 2024; 15:1408212. [PMID: 38887303 PMCID: PMC11180879 DOI: 10.3389/fimmu.2024.1408212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/08/2024] [Indexed: 06/20/2024] Open
Abstract
Introduction Varicella zoster virus (VZV) causes varicella and can reactivate as herpes zoster, and both diseases present a significant burden worldwide. However, the mechanisms by which VZV establishes latency in the sensory ganglia and disseminates to these sites remain unclear. Methods We combined a single-cell sequencing approach and a well-established rhesus macaque experimental model using Simian varicella virus (SVV), which recapitulates the VZV infection in humans, to define the acute immune response to SVV in the lung as well as compare the transcriptome of infected and bystander lung-resident T cells and macrophages. Results and discussion Our analysis showed a decrease in the frequency of alveolar macrophages concomitant with an increase in that of infiltrating macrophages expressing antiviral genes as well as proliferating T cells, effector CD8 T cells, and T cells expressing granzyme A (GZMA) shortly after infection. Moreover, infected T cells harbored higher numbers of viral transcripts compared to infected macrophages. Furthermore, genes associated with cellular metabolism (glycolysis and oxidative phosphorylation) showed differential expression in infected cells, suggesting adaptations to support viral replication. Overall, these data suggest that SVV infection remodels the transcriptome of bystander and infected lung-resident T cells and macrophages.
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Affiliation(s)
| | | | - Ilhem Messaoudi
- Department of Microbiology, Immunology, and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, United States
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Flores Cortes E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active and replicating HSV-1 lytic chromatin. J Virol 2024; 98:e0201523. [PMID: 38451083 PMCID: PMC11019955 DOI: 10.1128/jvi.02015-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections but the precise mechanisms are not fully defined. Nucleosomes are dynamic: they slide, breathe, assemble, and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent, whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X, and macroH2A were enhanced in infected cells, whereas those of H2A.B were uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, as well as ectopic and endogenous H2B were assembled into HSV-1 chromatin evenly throughout the genome but canonical H2A was relatively depleted whereas H2A.B was enriched, particularly in the most dynamic viral chromatin. When viral transcription and DNA replication were restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. IMPORTANCE Herpes simplex virus 1 (HSV-1) transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed epigenetic mechanisms of regulation of HSV-1 transcription have not been fully characterized and may differ from those regulating cellular transcription. Whereas lytic HSV-1 chromatin is unusually dynamic, latent silenced HSV-1 chromatin is not. The mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment of the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding of its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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Affiliation(s)
- Esteban Flores Cortes
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Sarah M. Saddoris
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arryn K. Owens
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Rebecca Gibeault
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Daniel P. Depledge
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, Hannover, Germany
| | - Luis M. Schang
- Baker Institute for Animal Health and Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. mBio 2024; 15:e0327823. [PMID: 38411116 PMCID: PMC11005365 DOI: 10.1128/mbio.03278-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. By contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity. IMPORTANCE Investigating the potential mechanisms of gene silencing for DNA viruses in different cell types is important to understand the differential outcomes of infection, particularly for viruses like herpesviruses that can undergo distinct types of infection in different cell types. In addition, investigating chromatin association with viral genomes informs on the mechanisms of epigenetic regulation of DNA processes. However, there is a growing appreciation for heterogeneity in the outcome of infection at the single cell, and even single viral genome, level. Here we describe a novel assay for quantifying viral genome foci with chromatin proteins and show that a portion of genomes are targeted for silencing by H3K27me2 and associate with the reader protein PHF20L1. This study raises important questions regarding the mechanism of H3K27me2-specific targeting to viral genomes, the contribution of epigenetic heterogeneity to herpesvirus infection, and the role of PHF20L1 in regulating the outcome of DNA virus infection.
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Affiliation(s)
- Alison K. Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, USA
| | - Steven McFarlane
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Chris Boutell
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | | | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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Van Eyndhoven LC, Chouri E, Matos CI, Pandit A, Radstake TRDJ, Broen JCA, Singh A, Tel J. Unraveling IFN-I response dynamics and TNF crosstalk in the pathophysiology of systemic lupus erythematosus. Front Immunol 2024; 15:1322814. [PMID: 38596672 PMCID: PMC11002168 DOI: 10.3389/fimmu.2024.1322814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024] Open
Abstract
Introduction The innate immune system serves the crucial first line of defense against a wide variety of potential threats, during which the production of pro-inflammatory cytokines IFN-I and TNFα are key. This astonishing power to fight invaders, however, comes at the cost of risking IFN-I-related pathologies, such as observed during autoimmune diseases, during which IFN-I and TNFα response dynamics are dysregulated. Therefore, these response dynamics must be tightly regulated, and precisely matched with the potential threat. This regulation is currently far from understood. Methods Using droplet-based microfluidics and ODE modeling, we studied the fundamentals of single-cell decision-making upon TLR signaling in human primary immune cells (n = 23). Next, using biologicals used for treating autoimmune diseases [i.e., anti-TNFα, and JAK inhibitors], we unraveled the crosstalk between IFN-I and TNFα signaling dynamics. Finally, we studied primary immune cells isolated from SLE patients (n = 8) to provide insights into SLE pathophysiology. Results single-cell IFN-I and TNFα response dynamics display remarkable differences, yet both being highly heterogeneous. Blocking TNFα signaling increases the percentage of IFN-I-producing cells, while blocking IFN-I signaling decreases the percentage of TNFα-producing cells. Single-cell decision-making in SLE patients is dysregulated, pointing towards a dysregulated crosstalk between IFN-I and TNFα response dynamics. Discussion We provide a solid droplet-based microfluidic platform to study inherent immune secretory behaviors, substantiated by ODE modeling, which can challenge the conceptualization within and between different immune signaling systems. These insights will build towards an improved fundamental understanding on single-cell decision-making in health and disease.
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Affiliation(s)
- Laura C. Van Eyndhoven
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Eleni Chouri
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Catarina I. Matos
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Timothy R. D. J. Radstake
- Center for Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Jasper C. A. Broen
- Regional Rheumatology Center, Máxima Medical Center, Eindhoven and Veldhoven, Eindhoven, Netherlands
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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9
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Yin XT, Hartman A, Sirajuddin N, Shukla D, Leger AS, Keadle TL, Stuart PM. UVB induced reactivation leads to HSV1 in the corneas of virtually all latently infected mice and requires STING to develop corneal disease. Sci Rep 2024; 14:6859. [PMID: 38514671 PMCID: PMC10957950 DOI: 10.1038/s41598-024-52597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/21/2024] [Indexed: 03/23/2024] Open
Abstract
Reactivation of latent herpes simplex type 1 results in virus returning to the cornea leading to recurrent herpetic stromal keratitis (rHSK). We compare two competing models to reactivate viruses from latency, UV-B irradiation and cyclophosphamide (CP). Results revealed that while both result in corneal recrudescence, only UV-B irradiation results in rHSK. To better understand the dynamics of reactivation, we analyzed corneas for both the presence of infectious viruses and the dynamics of exposure to multiple reactivations using UV-B. We noted that multiple reactivations result in progressively worse corneal disease. We also noted that expression of IFNα and STING, surragate markers for the presence of virus, are induced by the presence of reactivated virus. Studies to determine the importance of STING to the development of HSK revealed that in the absence of STING, mice do not develop significant HSK and the magnitude of the infiltrate of CD45+ cells in these corneas is significantly reduced. The resulting paucity of CD45+CD11b+GR-1+F4/80-neutrophils, and to a lesser extent CD45+CD11b+GR-1-F4/80+ macrophages in B6-STING KO mice following reactivation is likely the underlying cause for lack of rHSK as has been noted by ourselves and others. These results underscore the critical importance of STING's role in developing rHSK.
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Affiliation(s)
- Xiao-Tang Yin
- Department of Ophthalmology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alexis Hartman
- Department of Ophthalmology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Nadia Sirajuddin
- Department of Ophthalmology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Deepak Shukla
- Department of Ophthalmology & Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL, USA
| | - Anthony St Leger
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tammie L Keadle
- Department of Biology, Washington University, St. Louis, MO, USA
| | - Patrick M Stuart
- Department of Ophthalmology, Saint Louis University School of Medicine, St. Louis, MO, USA.
- Washington University, 7569 Amherst Avenue, University City, MO, 63130-2805, USA.
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10
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Fredrikson JP, Domanico LF, Pratt SL, Loveday EK, Taylor MP, Chang CB. Single-cell herpes simplex virus type 1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics. SCIENCE ADVANCES 2024; 10:eadk9185. [PMID: 38416818 PMCID: PMC10901367 DOI: 10.1126/sciadv.adk9185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Single-cell analyses of viral infections reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of herpes simplex virus type 1 (HSV-1) infection of neurons at the single-cell level. We used micrometer-scale Matrigel beads, termed microgels, to culture individual murine superior cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are encapsulated in individual media-in-oil droplets with a dual-fluorescent reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. These techniques for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
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Affiliation(s)
- Jacob P. Fredrikson
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Luke F. Domanico
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Shawna L. Pratt
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Emma K. Loveday
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology and Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Connie B. Chang
- Department of Chemical and Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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11
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Chen J, Yin D, Wong HYH, Duan X, Yu KHO, Ho JWK. Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data. Gigascience 2024; 13:giad117. [PMID: 38195165 PMCID: PMC10776309 DOI: 10.1093/gigascience/giad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/17/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
The rapidly growing collection of public single-cell sequencing data has become a valuable resource for molecular, cellular, and microbial discovery. Previous studies mostly overlooked detecting pathogens in human single-cell sequencing data. Moreover, existing bioinformatics tools lack the scalability to deal with big public data. We introduce Vulture, a scalable cloud-based pipeline that performs microbial calling for single-cell RNA sequencing (scRNA-seq) data, enabling meta-analysis of host-microbial studies from the public domain. In our benchmarking experiments, Vulture is 66% to 88% faster than local tools (PathogenTrack and Venus) and 41% faster than the state-of-the-art cloud-based tool Cumulus, while achieving comparable microbial read identification. In terms of the cost on cloud computing systems, Vulture also shows a cost reduction of 83% ($12 vs. ${\$}$70). We applied Vulture to 2 coronavirus disease 2019, 3 hepatocellular carcinoma (HCC), and 2 gastric cancer human patient cohorts with public sequencing reads data from scRNA-seq experiments and discovered cell type-specific enrichment of severe acute respiratory syndrome coronavirus 2, hepatitis B virus (HBV), and Helicobacter pylori-positive cells, respectively. In the HCC analysis, all cohorts showed hepatocyte-only enrichment of HBV, with cell subtype-associated HBV enrichment based on inferred copy number variations. In summary, Vulture presents a scalable and economical framework to mine unknown host-microbial interactions from large-scale public scRNA-seq data. Vulture is available via an open-source license at https://github.com/holab-hku/Vulture.
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Affiliation(s)
- Junyi Chen
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Danqing Yin
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Harris Y H Wong
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
| | - Xin Duan
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
| | - Ken H O Yu
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Joshua W K Ho
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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12
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Wang E, Yang QJ, Xu XX, Zou QC, Long Y, Ma G, Deng ZH, Zhao JB, Li MH, Zeng J. Differential pathogenic and molecular features in neurological infection of SARS-CoV-2 Omicron BA.5.2 and BA.2.75 and Delta. J Med Virol 2024; 96:e29357. [PMID: 38235532 DOI: 10.1002/jmv.29357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/07/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a global threat, exacerbated by the emergence of viral variants. Two variants of SARS-CoV-2, Omicron BA.2.75 and BA.5, led to global infection peaks between May 2022 and May 2023, yet their precise characteristics in pathogenesis are not well understood. In this study, we compared these two Omicron sublineages with the previously dominant Delta variant using a human angiotensin-converting enzyme 2 knock-in mouse model. As expected, Delta exhibited higher viral replication in the lung and brain than both Omicron sublineages which induced less severe lung damage and immune activation. In contrast, the Omicron variants especially BA.5.2 showed a propensity for cellular proliferation and developmental pathways. Both Delta and BA.5.2 variants, but not BA.2.75, led to decreased pulmonary lymphocytes, indicating differential adaptive immune response. Neuroinvasiveness was shared with all strains, accompanied by vascular abnormalities, synaptic injury, and loss of astrocytes. However, Immunostaining assays and transcriptomic analysis showed that BA.5.2 displayed stronger immune suppression and neurodegeneration, while BA.2.75 exhibited more similar characteristics to Delta in the cortex. Such differentially infectious features could be partially attributed to the weakened interaction between Omicron Spike protein and host proteomes decoded via co-immunoprecipitation followed by mass spectrometry in neuronal cells. Our present study supports attenuated replication and pathogenicity of Omicron variants but also highlights their newly infectious characteristics in the lung and brain, especially with BA.5.2 demonstrating enhanced immune evasion and neural damage that could exacerbate neurological sequelae.
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Affiliation(s)
- Erlin Wang
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qiao-Jiang Yang
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiang-Xiong Xu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qing-Cui Zou
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yanghaopeng Long
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Guanqin Ma
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhong-Hua Deng
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie-Bin Zhao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming-Hua Li
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianxiong Zeng
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming National High-level Biosafety Research Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Biodiversity Information, Kunming, Yunnan, China
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13
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Wyler E. Single-Cell RNA-Sequencing of RVFV Infection. Methods Mol Biol 2024; 2824:361-372. [PMID: 39039423 DOI: 10.1007/978-1-0716-3926-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
On the RNA level, viral infections are characterized by perturbations in the host cell transcriptome as well as the development of viral genetic information. Investigating the abundance and dynamic of RNA molecules can provide ample information to understand many aspects of the infection, from viral replication to pathogenesis. A key aspect therein is the resolution of the data, as infections are generally highly heterogeneous. Even in simple model systems such as cell lines, viral infections happen in a very asynchronous way. Quantifying RNAs at single-cell resolution can therefore substantially increase our understanding of these processes.Whereas measuring the RNA in bulk, that is, in samples containing thousands to hundreds of thousands of cells, is established and widely used since many years, methods for studying not only just a few different RNAs in individual cells became widely available only recently. Here, I outline and compare current concepts and methodologies for using single-cell RNA-sequencing to study virus infections. This covers sample preparation, cell preservation, biosafety considerations, and various experimental methods, with a special focus on the aspects that are important for studying virus infections. Since there is not "the one" method for doing single-cell RNA-sequencing, I will not provide a detailed protocol. Rather, this chapter should serve as a primer for getting started with single-cell RNA-sequencing experiments of virus infections and discusses the criteria that allow readers to choose the best procedures for their specific research question.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Helmholtz Association, Berlin, Germany.
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14
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Swaminath S, Russell AB. The use of single-cell RNA-seq to study heterogeneity at varying levels of virus-host interactions. PLoS Pathog 2024; 20:e1011898. [PMID: 38236826 PMCID: PMC10796064 DOI: 10.1371/journal.ppat.1011898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Abstract
The outcome of viral infection depends on the diversity of the infecting viral population and the heterogeneity of the cell population that is infected. Until almost a decade ago, the study of these dynamic processes during viral infection was challenging and limited to certain targeted measurements. Presently, with the use of single-cell sequencing technology, the complex interface defined by the interactions of cells with infecting virus can now be studied across the breadth of the transcriptome in thousands of individual cells simultaneously. In this review, we will describe the use of single-cell RNA sequencing (scRNA-seq) to study the heterogeneity of viral infections, ranging from individual virions to the immune response between infected individuals. In addition, we highlight certain key experimental limitations and methodological decisions that are critical to analyzing scRNA-seq data at each scale.
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Affiliation(s)
- Sharmada Swaminath
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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15
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Flores E, Saddoris SM, Owens AK, Gibeault R, Depledge DP, Schang LM. Histone H2A variant H2A.B is enriched in transcriptionally active HSV-1 lytic chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573075. [PMID: 38187672 PMCID: PMC10769327 DOI: 10.1101/2023.12.22.573075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections, but the precise mechanisms are not fully defined. Nucleosomes are dynamic; they slide, breathe, assemble and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X and macroH2A were enhanced in infected cells, whereas those of H2A.B uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, ectopic, and endogenous H2B, were assembled into HSV-1 chromatin evenly throughout the genome, but canonical H2A was relatively depleted from the viral chromatin whereas H2A.B was enriched in the most dynamic viral chromatin. When viral transcription was restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency, and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants. Importance HSV-1 transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed mechanisms of regulation of HSV-1 transcription by epigenetics have not been fully characterized and may differ from those regulating cellular transcription. In particular, the lytic HSV-1 chromatin is unusually dynamic, whereas the latent silenced one is not, but the mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment on the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding for its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.
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16
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.03.569766. [PMID: 38076966 PMCID: PMC10705572 DOI: 10.1101/2023.12.03.569766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. In contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. This was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity.
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Affiliation(s)
- Alison K Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna R Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
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17
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Bost P, Drayman N. Dissecting viral infections, one cell at a time, by single-cell technologies. Microbes Infect 2023:105268. [PMID: 38008398 PMCID: PMC11161131 DOI: 10.1016/j.micinf.2023.105268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/22/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
The meteoric rise of single-cell genomic technologies, especially of single-cell RNA-sequencing (scRNA-seq), has revolutionized several fields of cellular biology, especially immunology, oncology, neuroscience and developmental biology. While the field of virology has been relatively slow to adopt these technological advances, many works have shed new light on the fascinating interactions of viruses with their hosts using single cell technologies. One clear example is the multitude of studies dissecting viral infections by single-cell sequencing technologies during the recent COVID-19 pandemic. In this review we will detail the advantages of studying viral infections at a single-cell level, how scRNA-seq technologies can be used to achieve this goal and the associated technical limitations, challenges and solutions. We will highlight recent biological discoveries and breakthroughs in virology enabled by single-cell analyses and will end by discussing possible future directions of the field. Given the rate of publications in this exciting new frontier of virology, we have likely missed some important works and we apologize in advance to the researchers whose work we have failed to cite.
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Affiliation(s)
- Pierre Bost
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland; ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093 Switzerland.
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, The Center for Virus Research and The Center for Complex Biological Systems, The University of California, Irvine, CA, 92697, USA
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18
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Bruurs LJM, Müller M, Schipper JG, Rabouw HH, Boersma S, van Kuppeveld FJM, Tanenbaum ME. Antiviral responses are shaped by heterogeneity in viral replication dynamics. Nat Microbiol 2023; 8:2115-2129. [PMID: 37814072 PMCID: PMC10627821 DOI: 10.1038/s41564-023-01501-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/01/2023] [Indexed: 10/11/2023]
Abstract
Antiviral signalling, which can be activated in host cells upon virus infection, restricts virus replication and communicates infection status to neighbouring cells. The antiviral response is heterogeneous, both quantitatively (efficiency of response activation) and qualitatively (transcribed antiviral gene set). To investigate the basis of this heterogeneity, we combined Virus Infection Real-time IMaging (VIRIM), a live-cell single-molecule imaging method, with real-time readouts of the dsRNA sensing pathway to analyse the response of human cells to encephalomyocarditis virus (EMCV) infection. We find that cell-to-cell heterogeneity in viral replication rates early in infection affect the efficiency of antiviral response activation, with lower replication rates leading to more antiviral response activation. Furthermore, we show that qualitatively distinct antiviral responses can be linked to the strength of the antiviral signalling pathway. Our analyses identify variation in early viral replication rates as an important parameter contributing to heterogeneity in antiviral response activation.
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Grants
- ERC starting grant (EU/ERC-677936 RNAREG), NWO klein-2 grant (OCENW.KLEIN.344), Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
- ERC starting grant (EU/ERC-677936 RNAREG), NWO klein-2 grant (OCENW.KLEIN.344), Oncode Institute
- NWO klein-2 grant (OCENW.KLEIN.344), NWO VICI (91812628)
- NWO VICI (91812628), ERC starting grant (EU/ERC-677936 RNAREG), Oncode Institute
- ERC starting grant (EU/ERC-677936 RNAREG), Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
- Howard Hughes Medical Institute international research scholar grant (HHMI/IRS 55008747), Oncode Institute
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Affiliation(s)
- Lucas J M Bruurs
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Micha Müller
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jelle G Schipper
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Huib H Rabouw
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Sanne Boersma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Marvin E Tanenbaum
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.
- Department of Bionanoscience, Delft University of Technology, Delft, the Netherlands.
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19
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Drayman N. mSphere of Influence: Virology in the noise-how cell-to-cell variability impacts viral infection outcomes. mSphere 2023; 8:e0043823. [PMID: 37747254 PMCID: PMC10597340 DOI: 10.1128/msphere.00438-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Nir Drayman works at the intersection of virology and single-cell biology, studying how cellular heterogeneity shapes the outcome of viral infections (and specifically that of HSV-1). In this mSphere of Influence article, he reflects on how two papers, "Remote activation of host cell DNA synthesis in uninfected cells signaled by infected cells in advance of virus transmission" (N. Schmidt, T. Hennig, R. A. Serwa, M. Marchetti, and P. O'Hare, J Virol 89:11107-11115, 2015, https://doi.org/10.1128/jvi.01950-15) and "Extreme heterogeneity of influenza virus infection in single cells" (A. B. Russell, C. Trapnell, and J. D. Bloom, Elife 7:e32303, 2018, https://doi.org/10.7554/eLife.32303), impacted his research by trail blazing the analysis of viral infections in single cells, as well as by illuminating what is yet left to discover.
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Affiliation(s)
- Nir Drayman
- The Department of Molecular Biology and Biochemistry, The Center for Virus Research and The Center for Complex Biological Systems, The University of California, Irvine, Irvine, California, USA
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20
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Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Nat Commun 2023; 14:6245. [PMID: 37803001 PMCID: PMC10558542 DOI: 10.1038/s41467-023-41788-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/15/2023] [Indexed: 10/08/2023] Open
Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
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Affiliation(s)
- Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | | | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California, Berkeley-UCSF Joint Graduate Program in Bioengineering, San Francisco, CA, USA
| | - Beth Shoshana Zha
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - James K Nuñez
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juliane Winkler
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oren S Rosenberg
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
| | - Marco Y Hein
- Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Center for Medical Biochemistry, Vienna, Austria.
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21
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Perumal N, White B, Sanchez-Valdez F, Tarleton RL. cGAS-STING Pathway Activation during Trypanosoma cruzi Infection Leads to Tissue-Dependent Parasite Control. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1123-1133. [PMID: 37603014 PMCID: PMC10783805 DOI: 10.4049/jimmunol.2300373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 08/22/2023]
Abstract
Host cell invasion by Trypanosoma cruzi is a markedly silent process, with limited host transcriptional changes indicative of innate immune recognition, except for a modest type I IFN (IFN-I) response. In this study, we show that T. cruzi-induced IFN-β production was nearly abolished in primary murine cGAS-/- or stimulator of IFN genes (STING)-deficient (STINGGt) macrophages and fibroblasts. T. cruzi infection did not impact the ability of IFN-regulatory factor reporter macrophages to respond to classical cGAS-STING agonists, indicating that the limited IFN-β induction is not due to active parasite suppression. cGAS-/-, STINGGt, and IFN-α/β receptor-/- (IFNAR-/-) macrophages infected with T. cruzi yielded significantly higher numbers of amastigotes compared with wild-type macrophages; however, the impact of the STING pathway during infection in vivo is more complex. Despite an initial increase in parasite growth, STINGGt and IFNAR-/- mice ultimately had lower parasite burden in footpads as compared with wild-type mice, demonstrating a role for IFN-I expression in potentiating parasite growth at the infection site. STING pathway activation had little impact on parasite levels in the skeletal muscle; however, in the heart, cGAS-/- and STINGGt mice, but not IFNAR-/- mice, accumulated higher acute parasite loads, suggesting a protective role of STING sensing of T. cruzi in this organ that was independent of IFN-I. Together, these results demonstrate that host cGAS-STING senses T. cruzi infection, enhancing parasite growth at the site of entry, and contributes to acute-phase parasite restriction in the heart, a major site of tissue damage in chronic T. cruzi infection.
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Affiliation(s)
- Natasha Perumal
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
- Department of Cellular Biology, University of Georgia, Athens, GA
| | - Brooke White
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | | | - Rick L Tarleton
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
- Department of Cellular Biology, University of Georgia, Athens, GA
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22
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Fredrikson JP, Domanico LF, Pratt SL, Loveday EK, Taylor MP, Chang CB. Single-cell Herpes Simplex Virus type-1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558333. [PMID: 37790515 PMCID: PMC10542126 DOI: 10.1101/2023.09.18.558333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Single-cell analyses of viral infections often reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of HSV-1 infection of neurons at the single-cell level. We used micron-scale Matrigel beads, termed microgels, to culture individual murine Superior Cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are subsequently enclosed in individual media-in-oil droplets with a dual fluorescent-reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. The innovative techniques presented here for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
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Affiliation(s)
- Jacob P. Fredrikson
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Luke F. Domanico
- Department of Microbiology & Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Shawna L. Pratt
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Emma K. Loveday
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
| | - Matthew P. Taylor
- Department of Microbiology & Cell Biology, Montana State University, P.O. Box 173520, Bozeman, MT 59717, USA
| | - Connie B. Chang
- Department of Chemical & Biological Engineering, Montana State University, P.O. Box 173920, Bozeman, MT 59717, USA
- Center for Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT 59717, USA
- Department of Physiology & Biomedical Engineering, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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23
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Bacsik DJ, Dadonaite B, Butler A, Greaney AJ, Heaton NS, Bloom JD. Influenza virus transcription and progeny production are poorly correlated in single cells. eLife 2023; 12:RP86852. [PMID: 37675839 PMCID: PMC10484525 DOI: 10.7554/elife.86852] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
The ultimate success of a viral infection at the cellular level is determined by the number of progeny virions produced. However, most single-cell studies of infection quantify the expression of viral transcripts and proteins, rather than the amount of progeny virions released from infected cells. Here, we overcome this limitation by simultaneously measuring transcription and progeny production from single influenza virus-infected cells by embedding nucleotide barcodes in the viral genome. We find that viral transcription and progeny production are poorly correlated in single cells. The cells that transcribe the most viral mRNA do not produce the most viral progeny and often represent aberrant infections that fail to express the influenza NS gene. However, only some of the discrepancy between transcription and progeny production can be explained by viral gene absence or mutations: there is also a wide range of progeny production among cells infected by complete unmutated virions. Overall, our results show that viral transcription is a relatively poor predictor of an infected cell's contribution to the progeny population.
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Affiliation(s)
- David J Bacsik
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences & Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Andrew Butler
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Allison J Greaney
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences & Medical Scientist Training Program, University of WashingtonSeattleUnited States
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of MedicineDurhamUnited States
- Duke Human Vaccine Institute, Duke University School of MedicineDurhamUnited States
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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24
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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] [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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25
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Grabowski F, Kochańczyk M, Korwek Z, Czerkies M, Prus W, Lipniacki T. Antagonism between viral infection and innate immunity at the single-cell level. PLoS Pathog 2023; 19:e1011597. [PMID: 37669278 PMCID: PMC10503725 DOI: 10.1371/journal.ppat.1011597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/15/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
When infected with a virus, cells may secrete interferons (IFNs) that prompt nearby cells to prepare for upcoming infection. Reciprocally, viral proteins often interfere with IFN synthesis and IFN-induced signaling. We modeled the crosstalk between the propagating virus and the innate immune response using an agent-based stochastic approach. By analyzing immunofluorescence microscopy images we observed that the mutual antagonism between the respiratory syncytial virus (RSV) and infected A549 cells leads to dichotomous responses at the single-cell level and complex spatial patterns of cell signaling states. Our analysis indicates that RSV blocks innate responses at three levels: by inhibition of IRF3 activation, inhibition of IFN synthesis, and inhibition of STAT1/2 activation. In turn, proteins coded by IFN-stimulated (STAT1/2-activated) genes inhibit the synthesis of viral RNA and viral proteins. The striking consequence of these inhibitions is a lack of coincidence of viral proteins and IFN expression within single cells. The model enables investigation of the impact of immunostimulatory defective viral particles and signaling network perturbations that could potentially facilitate containment or clearance of the viral infection.
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Affiliation(s)
- Frederic Grabowski
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Korwek
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Maciej Czerkies
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Prus
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
- Department of Statistics, Rice University, Houston, Texas, United States of America
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26
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Pietilä MK, Bachmann JJ, Ravantti J, Pelkmans L, Fraefel C. Cellular state landscape and herpes simplex virus type 1 infection progression are connected. Nat Commun 2023; 14:4515. [PMID: 37500668 PMCID: PMC10374626 DOI: 10.1038/s41467-023-40148-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
Prediction, prevention and treatment of virus infections require understanding of cell-to-cell variability that leads to heterogenous disease outcomes, but the source of this heterogeneity has yet to be clarified. To study the multimodal response of single human cells to herpes simplex virus type 1 (HSV-1) infection, we mapped high-dimensional viral and cellular state spaces throughout the infection using multiplexed imaging and quantitative single-cell measurements of viral and cellular mRNAs and proteins. Here we show that the high-dimensional cellular state scape can predict heterogenous infections, and cells move through the cellular state landscape according to infection progression. Spatial information reveals that infection changes the cellular state of both infected cells and of their neighbors. The multiplexed imaging of HSV-1-induced cellular modifications links infection progression to changes in signaling responses, transcriptional activity, and processing bodies. Our data show that multiplexed quantification of responses at the single-cell level, across thousands of cells helps predict infections and identify new targets for antivirals.
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Affiliation(s)
- Maija K Pietilä
- Institute of Virology, University of Zurich, Zurich, Switzerland.
| | - Jana J Bachmann
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Janne Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland.
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27
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Yin XT, Hartman A, Sirajuddin N, Shukla D, St Leger A, Keadle TL, Stuart PM. UV-B induced HSV-1 reactivation leads to infectious virus in the corneas of virtually all latently infected mice and requires an intact STING to develop herpetic stromal keratitis. RESEARCH SQUARE 2023:rs.3.rs-3097720. [PMID: 37502845 PMCID: PMC10371093 DOI: 10.21203/rs.3.rs-3097720/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Reactivation of latent herpes simplex type 1 results in virus returning to the cornea leading to recurrent herpetic stromal keratitis (rHSK). We compare two competing models to reactivate viruses from latency, UV-B irradiation and cyclophosphamide. Results revealed that while both result in corneal recrudescence, only UV-B irradiation results in rHSK. To better understand the dynamics of reactivation, we analyzed corneas for both the presence of infectious viruses and the dynamics of exposure to multiple reactivations using UV-B. We noted that multiple reactivations result in progressively worse corneal disease. We also noted that expression of IFNα and STING, surragate markers for the presence of virus, are induced by the presence of reactivated virus. Studies to determine the importance of STING to the development of HSK revealed that in the absence of STING, mice do not develop significant HSK and the magnitude of the infiltrate of CD45 + cells in these corneas is significantly reduced. The resulting paucity of CD45 + CD11b + GR-1 + F4/80-neutrophils, and to a lesser extent CD45 + CD11b + GR-1-F4/80 + macrophages in B6-STING KO mice following reactivation is likely the underlying cause for lack of rHSK as has been noted by ourselves and others. These results underscore the critical importance of STING's role in developing rHSK.
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28
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Zhang B, Ding J, Ma Z. ICP4-Associated Activation of Rap1b Facilitates Herpes Simplex Virus Type I (HSV-1) Infection in Human Corneal Epithelial Cells. Viruses 2023; 15:1457. [PMID: 37515145 PMCID: PMC10385634 DOI: 10.3390/v15071457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The strong contribution of RAS-related protein 1b (Rap1b) to cytoskeleton remodeling determines intracellular and extracellular physiological activities, including the successful infection of viruses in permissive cells, but its role in the HSV-1 life cycle is still unclear. Here, we demonstrated that the HSV-1 immediate early (IE) gene ICP4 inhibits protein kinase A (PKA) phosphorylation to induce Rap1b-activation-mediated viral infection. Rap1b activation and membrane enrichment begin at the early stage of HSV-1 infection and remain active during the proliferation period of the virus. Treating the cells with Rap1b small interfering RNA (siRNA) showed a dose-dependent decrease in viral infection levels, but no dose-dependent increase was observed after Rap1b overexpression. Further investigation indicated that the suppression of Rap1b activation derives from phosphorylated PKA and Rap1b mutants with partial or complete prenylation instead of phosphorylation, which promoted viral infection in a dose-dependent manner. Furthermore, the PKA agonist Forskolin disturbed Rap1b activation in a dose-dependent manner, accompanied by a decreasing trend in viral infection. Moreover, the HSV-1 IE gene ICP4 induced PKA dephosphorylation, leading to continuous Rap1b activation, followed by cytoskeleton rearrangement induced by cell division control protein 42 (CDC42) and Ras-related C3 botulinum toxin substrate 1 (RAC1). These further stimulated membrane-triggered physiological processes favoring virus infection. Altogether, we show the significance of Rap1b during HSV-1 infection and uncover the viral infection mechanism determined by the posttranslational regulation of the viral ICP4 gene and Rap1b host protein.
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Affiliation(s)
- Beibei Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Juntao Ding
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Zhenghai Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
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29
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Molecular characterization of human cytomegalovirus infection with single-cell transcriptomics. Nat Microbiol 2023; 8:455-468. [PMID: 36732471 DOI: 10.1038/s41564-023-01325-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023]
Abstract
Human cytomegalovirus (HCMV) can result in either productive or non-productive infection, with the latter potentially leading to viral latency. The molecular factors dictating these outcomes are poorly understood. Here we used single-cell transcriptomics to analyse HCMV infection progression in monocytes, which are latently infected, and macrophages, considered to be permissive for productive infection. We show that early viral gene expression levels, specifically of those encoding immediate early proteins IE1 and IE2, are a major factor dictating productive infection. We also revealed that intrinsic, not induced, host cell interferon-stimulated gene expression level is a main determinant of infection outcome. Intrinsic interferon-stimulated gene expression is downregulated with monocyte to macrophage differentiation, partially explaining increased macrophage susceptibility to productive HCMV infection. Furthermore, non-productive macrophages could reactivate, making them potential latent virus reservoirs. Overall, we decipher molecular features underlying HCMV infection outcomes and propose macrophages as a potential HCMV reservoir.
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30
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Rozman B, Fisher T, Stern-Ginossar N. Translation-A tug of war during viral infection. Mol Cell 2023; 83:481-495. [PMID: 36334591 DOI: 10.1016/j.molcel.2022.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
Abstract
Viral reproduction is contingent on viral protein synthesis that relies on the host ribosomes. As such, viruses have evolved remarkable strategies to hijack the host translational apparatus in order to favor viral protein production and to interfere with cellular innate defenses. Here, we describe the approaches viruses use to exploit the translation machinery, focusing on commonalities across diverse viral families, and discuss the functional relevance of this process. We illustrate the complementary strategies host cells utilize to block viral protein production and consider how cells ensure an efficient antiviral response that relies on translation during this tug of war over the ribosome. Finally, we highlight potential roles mRNA modifications and ribosome quality control play in translational regulation and innate immunity. We address these topics in the context of the COVID-19 pandemic and focus on the gaps in our current knowledge of these mechanisms, specifically in viruses with pandemic potential.
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Affiliation(s)
- Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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31
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Van Eyndhoven LC, Verberne VPG, Bouten CVC, Singh A, Tel J. Transiently heritable fates and quorum sensing drive early IFN-I response dynamics. eLife 2023; 12:83055. [PMID: 36629318 PMCID: PMC9910831 DOI: 10.7554/elife.83055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/10/2023] [Indexed: 01/12/2023] Open
Abstract
Type I interferon (IFN-I)-mediated antiviral responses are central to host defense against viral infections. Crucial is the tight and well-orchestrated control of cellular decision-making leading to the production of IFN-Is. Innovative single-cell approaches revealed that the initiation of IFN-I production is limited to only fractions of 1-3% of the total population, both found in vitro, in vivo, and across cell types, which were thought to be stochastically regulated. To challenge this dogma, we addressed the influence of various stochastic and deterministic host-intrinsic factors on dictating early IFN-I responses, using a murine fibroblast reporter model. Epigenetic drugs influenced the percentage of responding cells. Next, with the classical Luria-Delbrück fluctuation test, we provided evidence for transient heritability driving responder fates, which was verified with mathematical modeling. Finally, while studying varying cell densities, we substantiated an important role for cell density in dictating responsiveness, similar to the phenomenon of quorum sensing. Together, this systems immunology approach opens up new avenues to progress the fundamental understanding on cellular decision-making during early IFN-I responses, which can be translated to other (immune) signaling systems.
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Affiliation(s)
- Laura C Van Eyndhoven
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of TechnologyEindhovenNetherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of TechnologyEindhovenNetherlands
| | - Vincent PG Verberne
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of TechnologyEindhovenNetherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of TechnologyEindhovenNetherlands
| | - Carlijn VC Bouten
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of TechnologyEindhovenNetherlands
- Department of Biomedical Engineering, Eindhoven University of TechnologyEindhovenNetherlands
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of DelawareNewarkUnited States
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of TechnologyEindhovenNetherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of TechnologyEindhovenNetherlands
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32
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Wang T, Wang C, Han J, Hou X, Hu R, Chang W, Wang L, Qi X, Wang J. β-catenin facilitates fowl adenovirus serotype 4 replication through enhancing virus-induced autophagy. Vet Microbiol 2023; 276:109617. [PMID: 36469999 DOI: 10.1016/j.vetmic.2022.109617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
β-catenin is a key component of the Wnt/β-catenin signal transduction cascade which is a highly conserved signaling pathway in eukaryotes. Increasing evidence suggests that the Wnt/β-catenin signaling pathway is involved in the infection of many viruses. However, its role in fowl adenovirus serotype 4 (FAdV-4) replication remains unclear. In the present study, we showed that FAdV-4 infection increased the expression of β-catenin and promoted the nuclear translocation of β-catenin. Overexpression of β-catenin and LiCl treatment stimulated the accumulation of β-catenin in the nucleus, and then facilitated FAdV-4 replication. Conversely, repression of β-catenin by inhibitors and siRNA significantly inhibited FAdV-4 replication. Furthermore, inhibition of autophagy by 3-Methyladenine (3-MA) suppressed the FAdV-4 replication, and repression of β-catenin inhibited the FAdV-4-triggered autophagy. In conclusion, the nuclear translocation of β-catenin benefits FAdV-4 replication, and suppression of β-catenin limits FAdV-4 production by inhibiting FAdV-4-induced autophagy. These findings indicated that β-catenin is an important regulator of FAdV-4 replication which can serve as a potential target for anti-FAdV-4 agents.
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Affiliation(s)
- Ting Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chongyang Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinjie Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaolan Hou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruochen Hu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenchi Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Lizhen Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuefeng Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jingyu Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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33
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Tabtieng T, Lent RC, Kaku M, Monago Sanchez A, Gaglia MM. Caspase-Mediated Regulation and Cellular Heterogeneity of the cGAS/STING Pathway in Kaposi's Sarcoma-Associated Herpesvirus Infection. mBio 2022; 13:e0244622. [PMID: 36255240 PMCID: PMC9765453 DOI: 10.1128/mbio.02446-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
As a result of the ongoing virus-host arms race, viruses have evolved numerous immune subversion strategies, many of which are aimed at suppressing the production of type I interferons (IFNs). Apoptotic caspases have recently emerged as important regulators of type I IFN signaling both in noninfectious contexts and during viral infection. Despite being widely considered antiviral factors since they can trigger cell death, several apoptotic caspases promote viral replication by suppressing innate immune response. Indeed, we previously discovered that the AIDS-associated oncogenic gammaherpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) exploits caspase activity to suppress the antiviral type I IFN response and promote viral replication. However, the mechanism of this novel viral immune evasion strategy is poorly understood, particularly with regard to how caspases antagonize IFN signaling during KSHV infection. Here, we show that caspase activity inhibits the DNA sensor cGAS during KSHV lytic replication to block type I IFN induction. Furthermore, we used single-cell RNA sequencing to reveal that the potent antiviral state conferred by caspase inhibition is mediated by an exceptionally small percentage of IFN-β-producing cells, thus uncovering further complexity of IFN regulation during viral infection. Collectively, these results provide insight into multiple levels of cellular type I IFN regulation that viruses co-opt for immune evasion. Unraveling these mechanisms can inform targeted therapeutic strategies for viral infections and reveal cellular mechanisms of regulating interferon signaling in the context of cancer and chronic inflammatory diseases. IMPORTANCE Type I interferons are key factors that dictate the outcome of infectious and inflammatory diseases. Thus, intricate cellular regulatory mechanisms are in place to control IFN responses. While viruses encode their own immune-regulatory proteins, they can also usurp existing cellular interferon regulatory functions. We found that caspase activity during lytic infection with the AIDS-associated oncogenic gammaherpesvirus Kaposi's sarcoma-associated herpesvirus inhibits the DNA sensor cGAS to block the antiviral type I IFN response. Moreover, single-cell RNA sequencing analyses unexpectedly revealed that an exceptionally small subset of infected cells (<5%) produce IFN, yet this is sufficient to confer a potent antiviral state. These findings reveal new aspects of type I IFN regulation and highlight caspases as a druggable target to modulate cGAS activity.
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Affiliation(s)
- Tate Tabtieng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Biochemistry, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
| | - Rachel C. Lent
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
| | - Machika Kaku
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Immunology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
| | - Alvaro Monago Sanchez
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
| | - Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Program in Biochemistry, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
- Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
- Program in Immunology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts, USA
- Institute for Molecular Virology and Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Wisconsin, USA
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34
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Loveday EK, Sanchez HS, Thomas MM, Chang CB. Single-Cell Infection of Influenza A Virus Using Drop-Based Microfluidics. Microbiol Spectr 2022; 10:e0099322. [PMID: 36125315 PMCID: PMC9603537 DOI: 10.1128/spectrum.00993-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/22/2022] [Indexed: 12/30/2022] Open
Abstract
Drop-based microfluidics has revolutionized single-cell studies and can be applied toward analyzing tens of thousands to millions of single cells and their products contained within picoliter-sized drops. Drop-based microfluidics can shed insight into single-cell virology, enabling higher-resolution analysis of cellular and viral heterogeneity during viral infection. In this work, individual A549, MDCK, and siat7e cells were infected with influenza A virus (IAV) and encapsulated into 100-μm-size drops. Initial studies of uninfected cells encapsulated in drops demonstrated high cell viability and drop stability. Cell viability of uninfected cells in the drops remained above 75%, and the average drop radii changed by less than 3% following cell encapsulation and incubation over 24 h. Infection parameters were analyzed over 24 h from individually infected cells in drops. The number of IAV viral genomes and infectious viruses released from A549 and MDCK cells in drops was not significantly different from bulk infection as measured by reverse transcriptase quantitative PCR (RT-qPCR) and plaque assay. The application of drop-based microfluidics in this work expands the capacity to propagate IAV viruses and perform high-throughput analyses of individually infected cells. IMPORTANCE Drop-based microfluidics is a cutting-edge tool in single-cell research. Here, we used drop-based microfluidics to encapsulate thousands of individual cells infected with influenza A virus within picoliter-sized drops. Drop stability, cell loading, and cell viability were quantified from three different cell lines that support influenza A virus propagation. Similar levels of viral progeny as determined by RT-qPCR and plaque assay were observed from encapsulated cells in drops compared to bulk culture. This approach enables the ability to propagate influenza A virus from encapsulated cells, allowing for future high-throughput analysis of single host cell interactions in isolated microenvironments over the course of the viral life cycle.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Humberto S. Sanchez
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Connie B. Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
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35
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Bocharova OV, Fisher A, Pandit NP, Molesworth K, Mychko O, Scott AJ, Makarava N, Ritzel R, Baskakov IV. Aβ plaques do not protect against HSV-1 infection in a mouse model of familial Alzheimer's disease, and HSV-1 does not induce Aβ pathology in a model of late onset Alzheimer's disease. Brain Pathol 2022; 33:e13116. [PMID: 36064300 PMCID: PMC9836376 DOI: 10.1111/bpa.13116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/11/2022] [Indexed: 01/21/2023] Open
Abstract
The possibility that the etiology of late onset Alzheimer's disease is linked to viral infections of the CNS has been actively debated in recent years. According to the antiviral protection hypothesis, viral pathogens trigger aggregation of Aβ peptides that are produced as a defense mechanism in response to infection to entrap and neutralize pathogens. To test the causative relationship between viral infection and Aβ aggregation, the current study examined whether Aβ plaques protect the mouse brain against Herpes Simplex Virus 1 (HSV-1) infection introduced via a physiological route and whether HSV-1 infection triggers formation of Aβ plaques in a mouse model of late-onset AD that does not develop Aβ pathology spontaneously. In aged 5XFAD mice infected via eye scarification, high density of Aβ aggregates did not improve survival time or rate when compared with wild type controls. In 5XFADs, viral replication sites were found in brain areas with a high density of extracellular Aβ deposits, however, no association between HSV-1 and Aβ aggregates could be found. To test whether HSV-1 triggers Aβ aggregation in a mouse model that lacks spontaneous Aβ pathology, 13-month-old hAβ/APOE4/Trem2*R47H mice were infected with HSV-1 via eye scarification with the McKrae HSV-1 strain, intracranial inoculation with McKrae, intracranial inoculation after priming with LPS for 6 weeks, or intracranial inoculation with high doses of McKrae or 17syn + strains that represent different degrees of neurovirulence. No signs of Aβ aggregation were found in any of the experimental groups. Instead, extensive infiltration of peripheral leukocytes was observed during the acute stage of HSV-1 infection, and phagocytic activity of myeloid cells was identified as the primary defense mechanism against HSV-1. The current results argue against a direct causative relationship between HSV-1 infection and Aβ pathology.
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Affiliation(s)
- Olga V. Bocharova
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Aidan Fisher
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Narayan P. Pandit
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Kara Molesworth
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Olga Mychko
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Alison J. Scott
- Department of Microbial PathogenesisUniversity of Maryland School of DentistryBaltimoreMarylandUSA
| | - Natallia Makarava
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Rodney Ritzel
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR)University of Maryland School of MedicineBaltimoreMarylandUSA
| | - Ilia V. Baskakov
- Center for Biomedical Engineering and TechnologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA,Department of Anatomy and NeurobiologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
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36
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Nguyen TD, Lan Y, Kane SS, Haffner JJ, Liu R, McCall LI, Yang Z. Single-Cell Mass Spectrometry Enables Insight into Heterogeneity in Infectious Disease. Anal Chem 2022; 94:10567-10572. [PMID: 35863111 PMCID: PMC10064790 DOI: 10.1021/acs.analchem.2c02279] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular heterogeneity is generally overlooked in infectious diseases. In this study, we investigated host cell heterogeneity during infection with Trypanosoma cruzi (T. cruzi) parasites, causative agents of Chagas disease (CD). In chronic-stage CD, only a few host cells are infected with a large load of parasites and symptoms may appear at sites distal to parasite colonization. Furthermore, recent work has revealed T. cruzi heterogeneity with regard to replication rates and drug susceptibility. However, the role of cellular-level metabolic heterogeneity in these processes has yet to be assessed. To fill this knowledge gap, we developed a Single-probe SCMS (single-cell mass spectrometry) method compatible with biosafety protocols, to acquire metabolomics data from individual cells during T. cruzi infection. This study revealed heterogeneity in the metabolic response of the host cells to T. cruzi infection in vitro. Our results showed that parasite-infected cells possessed divergent metabolism compared to control cells. Strikingly, some uninfected cells adjacent to infected cells showed metabolic impacts as well. Specific metabolic changes include increases in glycerophospholipids with infection. These results provide novel insight into the pathogenesis of CD. Furthermore, they represent the first application of bioanalytical SCMS to the study of mammalian-infectious agents, with the potential for broad applications to study infectious diseases.
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Affiliation(s)
- Tra D Nguyen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yunpeng Lan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shelley S Kane
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jacob J Haffner
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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37
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Wang C, Hu R, Duan L, Hou Q, Yang M, Wang T, Liu H, Xiao S, Dang R, Wang J, Wang X, Zhang S, Yang Z. The canonical Wnt/β-catenin signaling pathway facilitates pseudorabies virus proliferation and enhances virus-induced autophagy. Vet Microbiol 2022; 272:109502. [PMID: 35841697 DOI: 10.1016/j.vetmic.2022.109502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
Abstract
Pseudorabies virus (PRV) is a swine herpesvirus with a broad host range that causes significant economic losses worldwide. The Wnt/β-catenin signaling pathway is reportedly involved in multiple viruses' proliferation. In this study, we demonstrated that PRV infection significantly activated the Wnt/β-catenin signaling and promoted the nuclear translocation of β-catenin. Applying specific chemical inhibitors (FH535 and iCRT14) caused a remarkable decrease in PRV titers in various cell lines. Knockdown of β-catenin by siRNA also reduced the proliferation of PRV. On the contrary, treatment with lithium chloride (LiCl), an inhibitor of GSK3β, stimulated the Wnt/β-catenin signaling pathway and enhanced the PRV proliferation. Similarly, overexpression of β-catenin promoted PRV proliferation and reversed the antiviral effect of FH535. Moreover, LiCl promoted PRV-induced autophagy, whereas FH535 and iCRT14 showed converse effects. These findings suggest that PRV infection stimulates the canonical Wnt/β-catenin signaling pathway, facilitating PRV proliferation and regulating virus-induced autophagy. These data also provide potential targets for developing antiviral agents against PRV.
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Affiliation(s)
- Chongyang Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruochen Hu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Liuyuan Duan
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Qili Hou
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Mengqing Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ting Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Haijin Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Sa Xiao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruyi Dang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuxia Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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38
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Nahas KL, Connor V, Scherer KM, Kaminski CF, Harkiolaki M, Crump CM, Graham SC. Near-native state imaging by cryo-soft-X-ray tomography reveals remodelling of multiple cellular organelles during HSV-1 infection. PLoS Pathog 2022; 18:e1010629. [PMID: 35797345 PMCID: PMC9262197 DOI: 10.1371/journal.ppat.1010629] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
Herpes simplex virus-1 (HSV-1) is a large, enveloped DNA virus and its assembly in the cell is a complex multi-step process during which viral particles interact with numerous cellular compartments such as the nucleus and organelles of the secretory pathway. Transmission electron microscopy and fluorescence microscopy are commonly used to study HSV-1 infection. However, 2D imaging limits our understanding of the 3D geometric changes to cellular compartments that accompany infection and sample processing can introduce morphological artefacts that complicate interpretation. In this study, we used soft X-ray tomography to observe differences in whole-cell architecture between HSV-1 infected and uninfected cells. To protect the near-native structure of cellular compartments we used a non-disruptive sample preparation technique involving rapid cryopreservation, and a fluorescent reporter virus was used to facilitate correlation of structural changes with the stage of infection in individual cells. We observed viral capsids and assembly intermediates interacting with nuclear and cytoplasmic membranes. Additionally, we observed differences in the morphology of specific organelles between uninfected and infected cells. The local concentration of cytoplasmic vesicles at the juxtanuclear compartment increased and their mean width decreased as infection proceeded, and lipid droplets transiently increased in size. Furthermore, mitochondria in infected cells were elongated and highly branched, suggesting that HSV-1 infection alters the dynamics of mitochondrial fission/fusion. Our results demonstrate that high-resolution 3D images of cellular compartments can be captured in a near-native state using soft X-ray tomography and have revealed that infection causes striking changes to the morphology of intracellular organelles.
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Affiliation(s)
- Kamal L. Nahas
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Beamline B24, Diamond Light Source, Didcot, United Kingdom
| | - Viv Connor
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katharina M. Scherer
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | | | - Colin M. Crump
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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39
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Hertzog J, Zhou W, Fowler G, Rigby RE, Bridgeman A, Blest HTW, Cursi C, Chauveau L, Davenne T, Warner BE, Kinchington PR, Kranzusch PJ, Rehwinkel J. Varicella-Zoster virus ORF9 is an antagonist of the DNA sensor cGAS. EMBO J 2022; 41:e109217. [PMID: 35670106 PMCID: PMC9289529 DOI: 10.15252/embj.2021109217] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 12/25/2022] Open
Abstract
Varicella-Zoster virus (VZV) causes chickenpox and shingles. Although the infection is associated with severe morbidity in some individuals, molecular mechanisms that determine innate immune responses remain poorly defined. We found that the cGAS/STING DNA sensing pathway was required for type I interferon (IFN) induction during VZV infection and that recognition of VZV by cGAS restricted its replication. Screening of a VZV ORF expression library identified the essential VZV tegument protein ORF9 as a cGAS antagonist. Ectopically or virally expressed ORF9 bound to endogenous cGAS leading to reduced type I IFN responses to transfected DNA. Confocal microscopy revealed co-localisation of cGAS and ORF9. ORF9 and cGAS also interacted directly in a cell-free system and phase-separated together with DNA. Furthermore, ORF9 inhibited cGAMP production by cGAS. Taken together, these results reveal the importance of the cGAS/STING DNA sensing pathway for VZV recognition and identify a VZV immune antagonist that partially but directly interferes with DNA sensing via cGAS.
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Affiliation(s)
- Jonny Hertzog
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK,Present address:
Clinical Cooperation Unit VirotherapyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Wen Zhou
- Department of MicrobiologyHarvard Medical SchoolBostonMAUSA,Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMAUSA,Present address:
School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
| | - Gerissa Fowler
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Rachel E Rigby
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Anne Bridgeman
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Henry TW Blest
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Chiara Cursi
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Lise Chauveau
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Tamara Davenne
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | | | - Paul R Kinchington
- Department of OphthalmologyUniversity of PittsburghPittsburghPAUSA,Department of Microbiology and Molecular GeneticsUniversity of PittsburghPittsburghPAUSA
| | - Philip J Kranzusch
- Department of MicrobiologyHarvard Medical SchoolBostonMAUSA,Department of Cancer Immunology and VirologyDana‐Farber Cancer InstituteBostonMAUSA,Parker Institute for Cancer ImmunotherapyDana‐Farber Cancer InstituteBostonMAUSA
| | - Jan Rehwinkel
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
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40
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Harrison KS, Jones C. Regulation of herpes simplex virus type 1 latency-reactivation cycle and ocular disease by cellular signaling pathways. Exp Eye Res 2022; 218:109017. [PMID: 35240194 PMCID: PMC9191828 DOI: 10.1016/j.exer.2022.109017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/04/2022]
Abstract
Following acute infection, herpes simplex virus type 1 (HSV-1) establishes life-long latency in sensory and other neurons. Recurrent ocular HSV-1 outbreaks are generally due to reactivation from latency. The HSV-1 latency-reactivation cycle is a complex virus-host relationship. The viral encoded latency-associated transcript (LAT) is abundantly expressed in latency and encodes several micro-RNAs and other small non-coding RNAs, which may regulate expression of key viral and cellular genes. Certain cellular signaling pathways, including Wnt/β-catenin and mTOR pathway, mediate certain aspect of the latency-reactivation cycle. Stress, via activation of the glucocorticoid receptor and other stress induced cellular transcription factors, are predicted to trigger reactivation from latency by stimulating viral gene expression and impairing immune responses and inflammation. These observations suggest stress and certain cellular signaling pathways play key roles in regulating the latency-reactivation cycle and recurrent ocular disease.
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Affiliation(s)
- Kelly S Harrison
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Rm 250 McElroy Hall, Stillwater, OK, 74078, USA.
| | - Clinton Jones
- Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Rm 250 McElroy Hall, Stillwater, OK, 74078, USA.
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41
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Exploring COVID-19 at the single-cell level: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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42
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Functional single-cell genomics of human cytomegalovirus infection. Nat Biotechnol 2022; 40:391-401. [PMID: 34697476 DOI: 10.1038/s41587-021-01059-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022]
Abstract
Understanding how viral and host factors interact and how perturbations impact infection is the basis for designing antiviral interventions. Here we define the functional contribution of each viral and host factor involved in human cytomegalovirus infection in primary human fibroblasts through pooled CRISPR interference and nuclease screening. To determine how genetic perturbation of critical host and viral factors alters the timing, course and progression of infection, we applied Perturb-seq to record the transcriptomes of tens of thousands of CRISPR-modified single cells and found that, normally, most cells follow a stereotypical transcriptional trajectory. Perturbing critical host factors does not change the stereotypical transcriptional trajectory per se but can stall, delay or accelerate progression along the trajectory, allowing one to pinpoint the stage of infection at which host factors act. Conversely, perturbation of viral factors can create distinct, abortive trajectories. Our results reveal the roles of host and viral factors and provide a roadmap for the dissection of host-pathogen interactions.
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43
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Schlafens Can Put Viruses to Sleep. Viruses 2022; 14:v14020442. [PMID: 35216035 PMCID: PMC8875196 DOI: 10.3390/v14020442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
The Schlafen gene family encodes for proteins involved in various biological tasks, including cell proliferation, differentiation, and T cell development. Schlafens were initially discovered in mice, and have been studied in the context of cancer biology, as well as their role in protecting cells during viral infection. This protein family provides antiviral barriers via direct and indirect effects on virus infection. Schlafens can inhibit the replication of viruses with both RNA and DNA genomes. In this review, we summarize the cellular functions and the emerging relationship between Schlafens and innate immunity. We also discuss the functions and distinctions of this emerging family of proteins as host restriction factors against viral infection. Further research into Schlafen protein function will provide insight into their mechanisms that contribute to intrinsic and innate host immunity.
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44
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Hu H, Srinivas KP, Wang S, Chao MV, Lionnet T, Mohr I, Wilson AC, Depledge DP, Huang TT. Single-cell transcriptomics identifies Gadd45b as a regulator of herpesvirus-reactivating neurons. EMBO Rep 2022; 23:e53543. [PMID: 34842321 PMCID: PMC8811635 DOI: 10.15252/embr.202153543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 02/05/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technique for dissecting the complexity of normal and diseased tissues, enabling characterization of cell diversity and heterogeneous phenotypic states in unprecedented detail. However, this technology has been underutilized for exploring the interactions between the host cell and viral pathogens in latently infected cells. Herein, we use scRNA-seq and single-molecule sensitivity fluorescent in situ hybridization (smFISH) technologies to investigate host single-cell transcriptome changes upon the reactivation of a human neurotropic virus, herpes simplex virus-1 (HSV-1). We identify the stress sensor growth arrest and DNA damage-inducible 45 beta (Gadd45b) as a critical antiviral host factor that regulates HSV-1 reactivation events in a subpopulation of latently infected primary neurons. We show that distinct subcellular localization of Gadd45b correlates with the viral late gene expression program, as well as the expression of the viral transcription factor, ICP4. We propose that a hallmark of a "successful" or "aborted" HSV-1 reactivation state in primary neurons is determined by a unique subcellular localization signature of the stress sensor Gadd45b.
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Affiliation(s)
- Hui‐Lan Hu
- Department of Biochemistry & Molecular PharmacologyNew York University School of MedicineNew YorkNYUSA
| | | | - Shuoshuo Wang
- Department of Cell BiologyInstitute for Systems GeneticsNew York University School of MedicineNew YorkNYUSA
| | - Moses V Chao
- Departments of Cell Biology, Physiology & Neuroscience, and PsychiatrySkirball Institute of Biomolecular MedicineNew York University School of MedicineNew YorkNYUSA
| | - Timothee Lionnet
- Department of Cell BiologyInstitute for Systems GeneticsNew York University School of MedicineNew YorkNYUSA
| | - Ian Mohr
- Department of MicrobiologyNew York University School of MedicineNew YorkNYUSA
| | - Angus C Wilson
- Department of MicrobiologyNew York University School of MedicineNew YorkNYUSA
| | - Daniel P Depledge
- Department of MedicineNew York University School of MedicineNew YorkNYUSA,Present address:
Institute of VirologyHannover Medical SchoolHannoverGermany
| | - Tony T Huang
- Department of Biochemistry & Molecular PharmacologyNew York University School of MedicineNew YorkNYUSA
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45
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Barrozo ER, Aagaard KM. Human placental biology at single-cell resolution: a contemporaneous review. BJOG 2022; 129:208-220. [PMID: 34651399 PMCID: PMC8688323 DOI: 10.1111/1471-0528.16970] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 01/03/2023]
Abstract
Single-cell technologies capture cellular heterogeneity to focus on previously poorly described subpopulations of cells. Work by our laboratory and many others has metagenomically characterised a low biomass intrauterine microbial community, alongside microbial transcripts, antigens and metabolites, but the functional importance of low biomass microbial communities in placental immuno-microenvironments is still being elucidated. Given their hypothesised role in modulating inflammation and immune ontogeny to enable tolerance of beneficial microbes while warding off pathogens, there is a need for single-cell resolution. Herein, we summarise the potential for mechanistic understanding of these and other key fundamental early developmental processes by applying single-cell approaches.
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Affiliation(s)
- Enrico R. Barrozo
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Kjersti M. Aagaard
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
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46
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Ravirala D, Pei G, Zhao Z, Zhang X. Single-cell RNA sequencing reveals a strong connection between Gadd45g upregulation and oncolytic HSV infection in tumor tissue. Mol Ther Oncolytics 2021; 23:330-341. [PMID: 34786476 PMCID: PMC8573104 DOI: 10.1016/j.omto.2021.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
The oncolytic effect of virotherapy derives from the intrinsic capability of the applied virus in selectively infecting and killing tumor cells. Although oncolytic viruses of various constructions have been shown to efficiently infect and kill tumor cells in vitro, the efficiency of these viruses to exert the same effect on tumor cells within tumor tissues in vivo has not been extensively investigated. Here we report our studies using single-cell RNA sequencing to comprehensively analyze the gene expression profile of tumor tissues following herpes simplex virus 2-based oncolytic virotherapy. Our data revealed the extent and cell types within the tumor microenvironment that could be infected by the virus. Moreover, we observed changes in the expression of cellular genes, including antiviral genes, in response to viral infection. One notable gene found to be upregulated significantly in oncolytic virus-infected tumor cells was Gadd45g, which is desirable for optimal virus replication. These results not only help reveal the precise infection status of the oncolytic virus in vivo but also provide insight that may lead to the development of new strategies to further enhance the therapeutic efficacy of oncolytic virotherapy.
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Affiliation(s)
- Divya Ravirala
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoliu Zhang
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
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47
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Aho V, Salminen S, Mattola S, Gupta A, Flomm F, Sodeik B, Bosse JB, Vihinen-Ranta M. Infection-induced chromatin modifications facilitate translocation of herpes simplex virus capsids to the inner nuclear membrane. PLoS Pathog 2021; 17:e1010132. [PMID: 34910768 PMCID: PMC8673650 DOI: 10.1371/journal.ppat.1010132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Herpes simplex virus capsids are assembled and packaged in the nucleus and move by diffusion through the nucleoplasm to the nuclear envelope for egress. Analyzing their motion provides conclusions not only on capsid transport but also on the properties of the nuclear environment during infection. We utilized live-cell imaging and single-particle tracking to characterize capsid motion relative to the host chromatin. The data indicate that as the chromatin was marginalized toward the nuclear envelope it presented a restrictive barrier to the capsids. However, later in infection this barrier became more permissive and the probability of capsids to enter the chromatin increased. Thus, although chromatin marginalization initially restricted capsid transport to the nuclear envelope, a structural reorganization of the chromatin counteracted that to promote capsid transport later. Analyses of capsid motion revealed that it was subdiffusive, and that the diffusion coefficients were lower in the chromatin than in regions lacking chromatin. In addition, the diffusion coefficient in both regions increased during infection. Throughout the infection, the capsids were never enriched at the nuclear envelope, which suggests that instead of nuclear export the transport through the chromatin is the rate-limiting step for the nuclear egress of capsids. This provides motivation for further studies by validating the importance of intranuclear transport to the life cycle of HSV-1.
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Affiliation(s)
- Vesa Aho
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Sami Salminen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Salla Mattola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Alka Gupta
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Felix Flomm
- HPI, Leibniz-Institute for Experimental Virology, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Beate Sodeik
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Jens B. Bosse
- HPI, Leibniz-Institute for Experimental Virology, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Hannover Medical School, Institute of Virology, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Maija Vihinen-Ranta
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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48
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Heparanase-Induced Activation of AKT Stabilizes β-Catenin and Modulates Wnt/β-Catenin Signaling during Herpes Simplex Virus 1 Infection. mBio 2021; 12:e0279221. [PMID: 34749529 PMCID: PMC8576534 DOI: 10.1128/mbio.02792-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Under pathological conditions like herpes simplex virus 1 (HSV-1) infection, host-pathogen interactions lead to major reconstruction of the host protein network, which contributes to the dysregulation of signaling pathways and disease onset. Of note is the upregulation of a multifunctional host protein, heparanase (HPSE), following infection, which serves as a mediator in HSV-1 replication. In this study, we identify a novel function of HPSE and highlight it as a key regulator of β-catenin signal transduction. The regulatory role of HPSE on the activation, nuclear translocation, and signal transduction of β-catenin disrupts cellular homeostasis and establishes a pathogenic environment that promotes viral replication. Under normal physiological conditions, β-catenin is bound to a group of proteins, referred to as the destruction complex, and targeted for ubiquitination and, ultimately, degradation. We show that virus-induced upregulation of HPSE leads to the activation of Akt and subsequent stabilization and activation of β-catenin through (i) the release of β-catenin from the destruction complex, and (ii) direct phosphorylation of β-catenin at Ser552. This study also provides an in-depth characterization of the proviral role of β-catenin signaling during HSV-1 replication using physiologically relevant cell lines and in vivo models of ocular infection. Furthermore, pharmacological inhibitors of this pathway generated a robust antiviral state against multiple laboratory and clinical strains of HSV-1. Collectively, our findings assign a novel regulatory role to HPSE as a driver of β-catenin signaling in HSV-1 infection. IMPORTANCE Heparanase (HPSE) and β-catenin have independently been implicated in regulating key pathophysiological processes, including neovascularization, angiogenesis, and inflammation; however, the relationship between the two proteins has remained elusive thus far. For that reason, characterizing this relationship is crucial and can lead to the development of novel therapeutics. For HSV-1 specifically, current antivirals are not able to abolish the virus from the host, leaving patients susceptible to episodes of viral reactivation. Identifying a host-based intervention can provide a better alternative with enhanced efficacy and sustained relief.
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49
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Patel P, Drayman N, Liu P, Bilgic M, Tay S. Computer vision reveals hidden variables underlying NF-κB activation in single cells. SCIENCE ADVANCES 2021; 7:eabg4135. [PMID: 34678061 PMCID: PMC8535821 DOI: 10.1126/sciadv.abg4135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/02/2021] [Indexed: 05/31/2023]
Abstract
Individual cells are heterogeneous when responding to environmental cues. Under an external signal, certain cells activate gene regulatory pathways, while others completely ignore that signal. Mechanisms underlying cellular heterogeneity are often inaccessible because experiments needed to study molecular states destroy the very states that we need to examine. Here, we developed an image-based support vector machine learning model to uncover variables controlling activation of the immune pathway nuclear factor κB (NF-κB). Computer vision analysis predicts the identity of cells that will respond to cytokine stimulation and shows that activation is predetermined by minute amounts of “leaky” NF-κB (p65:p50) localization to the nucleus. Mechanistic modeling revealed that the ratio of NF-κB to inhibitor of NF-κB predetermines leakiness and activation probability of cells. While cells transition between molecular states, they maintain their overall probabilities for NF-κB activation. Our results demonstrate how computer vision can find mechanisms behind heterogeneous single-cell activation under proinflammatory stimuli.
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Affiliation(s)
- Parthiv Patel
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Ping Liu
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - Mustafa Bilgic
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
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50
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Packard JE, Dembowski JA. HSV-1 DNA Replication-Coordinated Regulation by Viral and Cellular Factors. Viruses 2021; 13:v13102015. [PMID: 34696446 PMCID: PMC8539067 DOI: 10.3390/v13102015] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
DNA replication is an integral step in the herpes simplex virus type 1 (HSV-1) life cycle that is coordinated with the cellular DNA damage response, repair and recombination of the viral genome, and viral gene transcription. HSV-1 encodes its own DNA replication machinery, including an origin binding protein (UL9), single-stranded DNA binding protein (ICP8), DNA polymerase (UL30), processivity factor (UL42), and a helicase/primase complex (UL5/UL8/UL52). In addition, HSV-1 utilizes a combination of accessory viral and cellular factors to coordinate viral DNA replication with other viral and cellular processes. The purpose of this review is to outline the roles of viral and cellular proteins in HSV-1 DNA replication and replication-coupled processes, and to highlight how HSV-1 may modify and adapt cellular proteins to facilitate productive infection.
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