1
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Moore KM, Pelletier AN, Lapp S, Metz A, Tharp GK, Lee M, Bhasin SS, Bhasin M, Sékaly RP, Bosinger SE, Suthar MS. Single-cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells. J Virol 2024; 98:e0019424. [PMID: 38567950 PMCID: PMC11092337 DOI: 10.1128/jvi.00194-24] [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: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10× Genomics Chromium single-cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human monocyte-derived dendritic cells infected with ZIKV at the single-cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN-dependent and -independent genes (the antiviral module). We modeled the ZIKV-specific antiviral state at the protein level, leveraging experimentally derived protein interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per-cell basis with experimental protein interaction data. IMPORTANCE Zika virus (ZIKV) remains a public health threat given its potential for re-emergence and the detrimental fetal outcomes associated with infection during pregnancy. Understanding the dynamics between ZIKV and its host is critical to understanding ZIKV pathogenesis. Through ZIKV-inclusive single-cell RNA sequencing (scRNA-seq), we demonstrate on the single-cell level the dynamic interplay between ZIKV and the host: the transcriptional program that restricts viral infection and ZIKV-mediated inhibition of that response. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool for gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.
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Affiliation(s)
- Kathryn M. Moore
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | | | - Stacey Lapp
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Amanda Metz
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Gregory K. Tharp
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Laboratory, Atlanta, Georgia, USA
| | - Michelle Lee
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Swati Sharma Bhasin
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Manoj Bhasin
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Rafick-Pierre Sékaly
- Emory Vaccine Center, Atlanta, Georgia, USA
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Laboratory, Atlanta, Georgia, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
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2
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Metz-Zumaran C, Uckeley ZM, Doldan P, Muraca F, Keser Y, Lukas P, Kuropka B, Küchenhoff L, Rastgou Talemi S, Höfer T, Freund C, Cavalcanti-Adam EA, Graw F, Stanifer M, Boulant S. The population context is a driver of the heterogeneous response of epithelial cells to interferons. Mol Syst Biol 2024; 20:242-275. [PMID: 38273161 PMCID: PMC10912784 DOI: 10.1038/s44320-024-00011-2] [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: 05/19/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
Isogenic cells respond in a heterogeneous manner to interferon. Using a micropatterning approach combined with high-content imaging and spatial analyses, we characterized how the population context (position of a cell with respect to neighboring cells) of epithelial cells affects their response to interferons. We identified that cells at the edge of cellular colonies are more responsive than cells embedded within colonies. We determined that this spatial heterogeneity in interferon response resulted from the polarized basolateral interferon receptor distribution, making cells located in the center of cellular colonies less responsive to ectopic interferon stimulation. This was conserved across cell lines and primary cells originating from epithelial tissues. Importantly, cells embedded within cellular colonies were not protected from viral infection by apical interferon treatment, demonstrating that the population context-driven heterogeneous response to interferon influences the outcome of viral infection. Our data highlights that the behavior of isolated cells does not directly translate to their behavior in a population, placing the population context as one important factor influencing heterogeneity during interferon response in epithelial cells.
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Affiliation(s)
- Camila Metz-Zumaran
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, 1200 Newell Drive, 32610, Gainesville, FL, USA
- Department of Infectious Disease, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 60120, Heidelberg, Germany
| | - Zina M Uckeley
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, 1200 Newell Drive, 32610, Gainesville, FL, USA
| | - Patricio Doldan
- Department of Infectious Disease, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 60120, Heidelberg, Germany
| | - Francesco Muraca
- Department of Infectious Disease, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 344, 60120, Heidelberg, Germany
| | - Yagmur Keser
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, 1200 Newell Drive, 32610, Gainesville, FL, USA
| | - Pascal Lukas
- BioQuant-Center for Quantitative Biology, Heidelberg University, 60120, Heidelberg, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Leonie Küchenhoff
- BioQuant-Center for Quantitative Biology, Heidelberg University, 60120, Heidelberg, Germany
| | - Soheil Rastgou Talemi
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Freund
- Institute of Chemistry and Biochemistry, Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Elisabetta Ada Cavalcanti-Adam
- Max Planck Institute for Medical Research, Heidelberg, Germany
- Cellular Biomechanics, University of Bayreuth, Bayreuth, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Frederik Graw
- BioQuant-Center for Quantitative Biology, Heidelberg University, 60120, Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
- Department of Medicine 5, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Megan Stanifer
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, 1200 Newell Drive, 32610, Gainesville, FL, USA.
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, 1200 Newell Drive, 32610, Gainesville, FL, USA.
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3
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Yeh M, Salazar-Cavazos E, Krishnan A, Altan-Bonnet G, DeVoe DL. Probing T-cell activation in nanoliter tumor co-cultures using membrane displacement trap arrays. Integr Biol (Camb) 2024; 16:zyae014. [PMID: 39074471 PMCID: PMC11286267 DOI: 10.1093/intbio/zyae014] [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: 01/31/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
Immune responses against cancer are inherently stochastic, with small numbers of individual T cells within a larger ensemble of lymphocytes initiating the molecular cascades that lead to tumor cytotoxicity. A potential source of this intra-tumor variability is the differential ability of immune cells to respond to tumor cells. Classical microwell co-cultures of T cells and tumor cells are inadequate for reliably culturing and analyzing low cell numbers needed to probe this variability, and have failed in recapitulating the heterogeneous small domains observed in tumors. Here we leverage a membrane displacement trap array technology that overcomes limitations of conventional microwell plates for immunodynamic studies. The microfluidic platform supports on-demand formation of dense nanowell cultures under continuous perfusion reflecting the tumor microenvironment, with real-time monitoring of T cell proliferation and activation within each nanowell. The system enables selective ejection of cells for profiling by fluorescence activated cell sorting, allowing observed on-chip variability in immune response to be correlated with off-chip quantification of T cell activation. The technology offers new potential for probing the molecular origins of T cell heterogeneity and identifying specific cell phenotypes responsible for initiating and propagating immune cascades within tumors. Insight Box Variability in T cell activation plays a critical role in the immune response against cancer. New tools are needed to unravel the mechanisms that drive successful anti-tumor immune response, and to support the development of novel immunotherapies utilizing rare T cell phenotypes that promote effective immune surveillance. To this end, we present a microfluidic cell culture platform capable of probing differential T cell activation in an array of nanoliter-scale wells coupled with off-chip cell analysis, enabling a high resolution view of variable immune response within tumor / T cell co-cultures containing cell ensembles orders of magnitude smaller than conventional well plate studies.
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Affiliation(s)
- Michael Yeh
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, United States
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | | | - Anagha Krishnan
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Grégoire Altan-Bonnet
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Don L DeVoe
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, United States
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4
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Moore KM, Pelletier AN, Lapp S, Metz A, Tharp GK, Lee M, Bhasin SS, Bhasin M, Sékaly RP, Bosinger SE, Suthar MS. Single cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.19.576293. [PMID: 38293140 PMCID: PMC10827181 DOI: 10.1101/2024.01.19.576293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN dependent and independent genes (antiviral module). We modeled the ZIKV specific antiviral state at the protein level leveraging experimentally derived protein-interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per cell basis with experimental protein interaction data. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool to gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.
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5
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Kotov DI, Lee OV, Fattinger SA, Langner CA, Guillen JV, Peters JM, Moon A, Burd EM, Witt KC, Stetson DB, Jaye DL, Bryson BD, Vance RE. Early cellular mechanisms of type I interferon-driven susceptibility to tuberculosis. Cell 2023; 186:5536-5553.e22. [PMID: 38029747 PMCID: PMC10757650 DOI: 10.1016/j.cell.2023.11.002] [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: 10/18/2022] [Revised: 06/16/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
Mycobacterium tuberculosis (Mtb) causes 1.6 million deaths annually. Active tuberculosis correlates with a neutrophil-driven type I interferon (IFN) signature, but the cellular mechanisms underlying tuberculosis pathogenesis remain poorly understood. We found that interstitial macrophages (IMs) and plasmacytoid dendritic cells (pDCs) are dominant producers of type I IFN during Mtb infection in mice and non-human primates, and pDCs localize near human Mtb granulomas. Depletion of pDCs reduces Mtb burdens, implicating pDCs in tuberculosis pathogenesis. During IFN-driven disease, we observe abundant DNA-containing neutrophil extracellular traps (NETs) described to activate pDCs. Cell-type-specific disruption of the type I IFN receptor suggests that IFNs act on IMs to inhibit Mtb control. Single-cell RNA sequencing (scRNA-seq) indicates that type I IFN-responsive cells are defective in their response to IFNγ, a cytokine critical for Mtb control. We propose that pDC-derived type I IFNs act on IMs to permit bacterial replication, driving further neutrophil recruitment and active tuberculosis disease.
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Affiliation(s)
- Dmitri I Kotov
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Ophelia V Lee
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan A Fattinger
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Charlotte A Langner
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jaresley V Guillen
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joshua M Peters
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Andres Moon
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Eileen M Burd
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Kristen C Witt
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel B Stetson
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - David L Jaye
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Bryan D Bryson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Russell E Vance
- Division of Immunology and Molecular Medicine, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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6
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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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7
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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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8
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Schneor L, Kaltenbach S, Friedman S, Tussia-Cohen D, Nissan Y, Shuler G, Fraimovitch E, Kolodziejczyk AA, Weinberg M, Donati G, Teeling EC, Yovel Y, Hagai T. Comparison of antiviral responses in two bat species reveals conserved and divergent innate immune pathways. iScience 2023; 26:107435. [PMID: 37575178 PMCID: PMC10415932 DOI: 10.1016/j.isci.2023.107435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/28/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
Bats host a range of disease-causing viruses without displaying clinical symptoms. The mechanisms behind this are a continuous source of interest. Here, we studied the antiviral response in the Egyptian fruit bat and Kuhl's pipistrelle, representing two subordinal clades. We profiled the antiviral response in fibroblasts using RNA sequencing and compared bat with primate and rodent responses. Both bats upregulate similar genes; however, a subset of these genes is transcriptionally divergent between them. These divergent genes also evolve rapidly in sequence, have specific promoter architectures, and are associated with programs underlying tolerance and resistance. Finally, we characterized antiviral genes that expanded in bats, with duplicates diverging in sequence and expression. Our study reveals a largely conserved antiviral program across bats and points to a set of genes that rapidly evolve through multiple mechanisms. These can contribute to bat adaptation to viral infection and provide directions to understanding the mechanisms behind it.
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Affiliation(s)
- Lilach Schneor
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stefan Kaltenbach
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sivan Friedman
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dafna Tussia-Cohen
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yomiran Nissan
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gal Shuler
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evgeny Fraimovitch
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | | | - Maya Weinberg
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Giacomo Donati
- Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
- Molecular Biotechnology Center, University of Turin, Torino, Italy
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Yossi Yovel
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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9
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Chandwani R, Fang TC, Dewell S, Tarakhovsky A. Control of enhancer and promoter activation in the type I interferon response by the histone demethylase Kdm4d/JMJD2d. Front Immunol 2023; 14:1146699. [PMID: 37275914 PMCID: PMC10236313 DOI: 10.3389/fimmu.2023.1146699] [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: 01/17/2023] [Accepted: 04/13/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Transcriptional activation depends on the interplay of chromatin modifiers to establish a permissive epigenetic landscape. While histone 3 lysine 9 (H3K9) methylation has long been associated with gene repression, there is limited evidence to support a role for H3K9 demethylases in gene activation. Methods We leveraged knockdown and overexpression of JMJD2d / Kdm4d in mouse embryonic fibroblasts, coupled with extensive epigenomic analysesm to decipher the role of histone 3 lysine 9 demethylases in the innate immune response. Results Here we describe the H3K9 demethylase Kdm4d/JMJD2d as a positive regulator of type I interferon responses. In mouse embryonic fibroblasts (MEFs), depletion of JMJD2d attenuates the transcriptional response, conferring increased viral susceptibility, while overexpression of the demethylase results in more robust IFN activation. We find that the underlying mechanism of JMJD2d in type I interferon responses consists of an effect both on the transcription of enhancer RNAs (eRNAs) and on dynamic H3K9me2 at associated promoters. In support of these findings, we establish that JMJD2d is associated with enhancer regions throughout the genome prior to stimulation but is redistributed to inducible promoters in conjunction with transcriptional activation. Discussion Taken together, our data reveal JMJD2d as a chromatin modifier that connects enhancer transcription with promoter demethylation to modulate transcriptional responses.
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Affiliation(s)
- Rohit Chandwani
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY, United States
| | - Terry C. Fang
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY, United States
| | - Scott Dewell
- Genomics Resource Facility, The Rockefeller University, New York, NY, United States
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY, United States
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10
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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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11
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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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12
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Van Eyndhoven LC, Tel J. Revising immune cell coordination: Origins and importance of single-cell variation. Eur J Immunol 2022; 52:1889-1897. [PMID: 36250412 PMCID: PMC10092580 DOI: 10.1002/eji.202250073] [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: 06/29/2022] [Revised: 08/15/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Moving from the optimalization of single-cell technologies to the interpretation of the multi-complex single-cell data, the field of immunoengineering is granted with numerous important insights into the coordination of immune cell activation and how to modulate it for therapeutic purposes. However, insights come with additional follow-up questions that challenge our perception on how immune responses are generated and fine-tuned to fight a wide array of pathogens in ever-changing and often unpredictable microenvironments. Are immune responses really either being tightly regulated by molecular determinants, or highly flexible attributed to stochasticity? What exactly makes up the basic rules by which single cells cooperate to establish tissue-level immunity? Taking the type I IFN system and its newest insights as a main example throughout this review, we revise the basic concepts of (single) immune cell coordination, redefine the concepts of noise, stochasticity and determinism, and highlight the importance of single-cell variation in immunology and beyond.
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Affiliation(s)
- Laura C Van Eyndhoven
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
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13
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Mendes M, Russell AB. Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes. PLoS Pathog 2021; 17:e1010125. [PMID: 34882752 PMCID: PMC8691639 DOI: 10.1371/journal.ppat.1010125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/21/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Found in a diverse set of viral populations, defective interfering particles are parasitic variants that are unable to replicate on their own yet rise to relatively high frequencies. Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity. For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase. Using a library-based approach, we comprehensively profile the growth and replication of defective influenza species, demonstrating that they possess an advantage during genome replication, and that exclusion during population expansion reshapes population composition in a manner consistent with their final, observed, distribution in natural populations. We find that an innate immune response is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties. Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.
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Affiliation(s)
- Marisa Mendes
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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14
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Alexander AF, Kelsey I, Forbes H, Miller-Jensen K. Single-cell secretion analysis reveals a dual role for IL-10 in restraining and resolving the TLR4-induced inflammatory response. Cell Rep 2021; 36:109728. [PMID: 34551303 DOI: 10.1016/j.celrep.2021.109728] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/18/2021] [Accepted: 08/26/2021] [Indexed: 01/22/2023] Open
Abstract
Following Toll-like receptor 4 (TLR4) stimulation of macrophages, negative feedback mediated by the anti-inflammatory cytokine interleukin-10 (IL-10) limits the inflammatory response. However, extensive cell-to-cell variability in TLR4-stimulated cytokine secretion raises questions about how negative feedback is robustly implemented. To explore this, we characterize the TLR4-stimulated secretion program in primary murine macrophages using a single-cell microwell assay that enables evaluation of functional autocrine IL-10 signaling. High-dimensional analysis of single-cell data reveals three tiers of TLR4-induced proinflammatory activation based on levels of cytokine secretion. Surprisingly, while IL-10 inhibits TLR4-induced activation in the highest tier, it also contributes to the TLR4-induced activation threshold by regulating which cells transition from non-secreting to secreting states. This role for IL-10 in restraining TLR4 inflammatory activation is largely mediated by intermediate interferon (IFN)-β signaling, while TNF likely mediates response resolution by IL-10. Thus, cell-to-cell variability in cytokine regulatory motifs provides a means to tailor the TLR4-induced inflammatory response.
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Affiliation(s)
- Amanda F Alexander
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Ilana Kelsey
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Hannah Forbes
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, New Haven, CT 06511, USA.
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15
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Suomalainen M, Greber UF. Virus Infection Variability by Single-Cell Profiling. Viruses 2021; 13:1568. [PMID: 34452433 PMCID: PMC8402812 DOI: 10.3390/v13081568] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cell-to-cell variability of infection has long been known, yet it has remained one of the least understood phenomena in infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell RNA sequencing (scRNA-seq), single-molecule RNA-fluorescence in situ hybridization (FISH), and copper(I)-catalyzed azide-alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect infection variability in human and mouse cells. We show how the combined use of scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how scRNA-seq profiling and scRNA-FISH of coxsackie, influenza, dengue, zika, and herpes simplex virus infections uncover transcriptional variability, and how the host interferon response tunes influenza and sendai virus infections. We introduce the concept of "cell state" in infection variability, and conclude with advances by single-cell simultaneous measurements of chromatin accessibility and mRNA counts at high-throughput. Such technology will further dissect the sequence of events in virus infection and pathology, and better characterize the genetic and genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.
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Affiliation(s)
- Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Urs F. Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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16
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Krenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A, Salata C, Rilo Christoff R, Pestana Garcez P, Mirazimi A, Knoblich JA. Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Cell Stem Cell 2021; 28:1362-1379.e7. [PMID: 33838105 PMCID: PMC7611471 DOI: 10.1016/j.stem.2021.03.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 12/07/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Viral infection in early pregnancy is a major cause of microcephaly. However, how distinct viruses impair human brain development remains poorly understood. Here we use human brain organoids to study the mechanisms underlying microcephaly caused by Zika virus (ZIKV) and herpes simplex virus (HSV-1). We find that both viruses efficiently replicate in brain organoids and attenuate their growth by causing cell death. However, transcriptional profiling reveals that ZIKV and HSV-1 elicit distinct cellular responses and that HSV-1 uniquely impairs neuroepithelial identity. Furthermore, we demonstrate that, although both viruses fail to potently induce the type I interferon system, the organoid defects caused by their infection can be rescued by distinct type I interferons. These phenotypes are not seen in 2D cultures, highlighting the superiority of brain organoids in modeling viral infections. These results uncover virus-specific mechanisms and complex cellular immune defenses associated with virus-induced microcephaly.
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Affiliation(s)
- Veronica Krenn
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Camilla Bosone
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Helmholtz Centre for Infection Research, Braunschweig, and the Hanover Medical School, Hanover 30625, Germany; Cluster of Excellence - Resolving Infection Susceptibility (RESIST), Hanover Medical School, Hanover 30625, Germany
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Raissa Rilo Christoff
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Patricia Pestana Garcez
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Ali Mirazimi
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm 17177, Sweden; National Veterinary Institute, Uppsala 75189, Sweden
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria; Medical University of Vienna, Vienna 1030, Austria.
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17
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Van Eyndhoven LC, Singh A, Tel J. Decoding the dynamics of multilayered stochastic antiviral IFN-I responses. Trends Immunol 2021; 42:824-839. [PMID: 34364820 DOI: 10.1016/j.it.2021.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/11/2021] [Accepted: 07/11/2021] [Indexed: 12/11/2022]
Abstract
Type I Interferon (IFN-I) responses were first recognized for their role in antiviral immunity, but it is now widely appreciated that IFN-Is have many immunomodulatory functions, influencing antitumor responses, autoimmune manifestations, and antimicrobial defenses. Given these pivotal roles, it may be surprising that multilayered stochastic events create highly heterogeneous, but tightly regulated, all-or-nothing cellular decisions. Recently, mathematical models have provided crucial insights into the stochastic nature of antiviral IFN-I responses, which we critically evaluate in this review. In this context, we emphasize the need for innovative single-cell technologies combined with mathematical models to further reveal, understand, and predict the complexity of the IFN-I system in physiological and pathological conditions that may be relevant to a plethora of diseases.
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Affiliation(s)
- Laura C Van Eyndhoven
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands; Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
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18
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Gregg RW, Shabnam F, Shoemaker JE. Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production. Bioinformatics 2021; 37:1428-1434. [PMID: 33196784 DOI: 10.1093/bioinformatics/btaa969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION The cGAS pathway is a component of the innate immune system responsible for the detection of pathogenic DNA and upregulation of interferon beta (IFNβ). Experimental evidence shows that IFNβ signaling occurs in highly heterogeneous cells and is stochastic in nature; however, the benefits of these attributes remain unclear. To investigate how stochasticity and heterogeneity affect IFNβ production, an agent-based model is developed to simulate both DNA transfection and viral infection. RESULTS We show that heterogeneity can enhance IFNβ responses during infection. Furthermore, by varying the degree of IFNβ stochasticity, we find that only a percentage of cells (20-30%) need to respond during infection. Going beyond this range provides no additional protection against cell death or reduction of viral load. Overall, these simulations suggest that heterogeneity and stochasticity are important for moderating immune potency while minimizing cell death during infection. AVAILABILITY AND IMPLEMENTATION Model repository is available at: https://github.com/ImmuSystems-Lab/AgentBasedModel-cGASPathway. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Robert W Gregg
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA
| | - Fathima Shabnam
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA
| | - Jason E Shoemaker
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA.,McGowan Institute for Regenerative Medicine, 15219, Pittsburgh, PA 15260, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
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19
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Agelopoulos M, Foutadakis S, Thanos D. The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression. Front Immunol 2021; 12:682397. [PMID: 34149720 PMCID: PMC8212036 DOI: 10.3389/fimmu.2021.682397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 01/05/2023] Open
Abstract
Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.
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Affiliation(s)
| | | | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
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20
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Van Eyndhoven LC, Chouri E, Subedi N, Tel J. Phenotypical Diversification of Early IFNα-Producing Human Plasmacytoid Dendritic Cells Using Droplet-Based Microfluidics. Front Immunol 2021; 12:672729. [PMID: 33995415 PMCID: PMC8117785 DOI: 10.3389/fimmu.2021.672729] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
Plasmacytoid dendritic cells (pDCs) are a rare type of highly versatile immune cells that besides their specialized function of massive type I interferon (IFN-I) production are able to exert cytotoxic effector functions. However, diversification upon toll like receptor (TLR)-induced activation leads to highly heterogeneous responses that have not been fully characterized yet. Using droplet-based microfluidics, we showed that upon TLR7/8 and TLR9-induced single-cell activation only 1-3% secretes IFNα, and only small fractions upregulate cytotoxicity markers. Interestingly, this 1-3% of early IFN-producing pDCs, also known as first responders, express high levels of programmed death-ligand 1 (PD-L1) and TNF-related apoptosis-inducing ligand (TRAIL), which makes these hybrid cells similar to earlier described IFN-I producing killer pDCs (IKpDCs). IFN-I priming increases the numbers of IFNα producing cells up to 40%, but does not significantly upregulate the cytotoxicity markers. Besides, these so-called second responders do not show a cytotoxic phenotype as potent as observed for the first responders. Overall, our results indicate that the first responders are the key drivers orchestrating population wide IFN-I responses and possess high cytotoxic potential.
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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
| | - Nikita Subedi
- 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
| | - 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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21
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Hare DN, Subapanditha MK, Mossman KL. Detecting single cell interferon-beta production using a fluorescent reporter telomerase-immortalized human fibroblast cell line. STAR Protoc 2021; 2:100436. [PMID: 33912845 PMCID: PMC8063907 DOI: 10.1016/j.xpro.2021.100436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recent data suggest that cells respond to infection by upregulating the antiviral cytokine interferon-beta (IFN-ß) in a fraction of infected cells. Approaches are thus needed to study these responses on a single-cell level rather than bulk population. Here, we describe a protocol to analyze the IFN-ß response of individual cells using flow cytometry and immunofluorescence microscopy. We show the heterogeneous IFN-ß response to inactivated Sendai virus and human cytomegalovirus, but this protocol can be adapted to other viruses. For complete details on the use and execution of this protocol, please refer to Hare et al. (2020). Single-cell assays are needed to measure IFN production in virus-infected cells Immortalized THF cells with IFN-b reporter are used to measure IFN production Individual cells are analyzed via flow cytometry and fluorescence microscopy Simple single-cell assays can uncover data obscured in bulk population measurements
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Affiliation(s)
- David N Hare
- Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Minomi K Subapanditha
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Karen L Mossman
- Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.,Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
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22
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Shapiro M, Krug LT, MacCarthy T. Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection. PLoS Pathog 2021; 17:e1009560. [PMID: 33930088 PMCID: PMC8115780 DOI: 10.1371/journal.ppat.1009560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 01/22/2023] Open
Abstract
Herpes-Simplex Virus 1 (HSV-1) infects most humans when they are young, sometimes with fatal consequences. Gene expression occurs in a temporal order upon lytic HSV-1 infection: immediate early (IE) genes are expressed, then early (E) genes, followed by late (L) genes. During this infection cycle, the HSV-1 genome has the potential for exposure to APOBEC3 (A3) proteins, a family of cytidine deaminases that cause C>U mutations on single-stranded DNA (ssDNA), often resulting in a C>T transition. We developed a computational model for the mutational pressure of A3 on the lytic cycle of HSV-1 to determine which viral kinetic gene class is most vulnerable to A3 mutations. Using in silico stochastic methods, we simulated the infectious cycle under varying intensities of A3 mutational pressure. We found that the IE and E genes are more vulnerable to A3 than L genes. We validated this model by analyzing the A3 evolutionary footprints in 25 HSV-1 isolates. We find that IE and E genes have evolved to underrepresent A3 hotspot motifs more so than L genes, consistent with greater selection pressure on IE and E genes. We extend this model to two-step infections, such as those of polyomavirus, and find that the same pattern holds for over 25 human Polyomavirus (HPyVs) genomes. Genes expressed earlier during infection are more vulnerable to mutations than those expressed later.
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Affiliation(s)
- Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, United States of America
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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24
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Stanifer ML, Guo C, Doldan P, Boulant S. Importance of Type I and III Interferons at Respiratory and Intestinal Barrier Surfaces. Front Immunol 2020; 11:608645. [PMID: 33362795 PMCID: PMC7759678 DOI: 10.3389/fimmu.2020.608645] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/11/2020] [Indexed: 12/23/2022] Open
Abstract
Interferons (IFNs) constitute the first line of defense against microbial infections particularly against viruses. They provide antiviral properties to cells by inducing the expression of hundreds of genes known as interferon-stimulated genes (ISGs). The two most important IFNs that can be produced by virtually all cells in the body during intrinsic innate immune response belong to two distinct families: the type I and type III IFNs. The type I IFN receptor is ubiquitously expressed whereas the type III IFN receptor's expression is limited to epithelial cells and a subset of immune cells. While originally considered to be redundant, type III IFNs have now been shown to play a unique role in protecting mucosal surfaces against pathogen challenges. The mucosal specific functions of type III IFN do not solely rely on the restricted epithelial expression of its receptor but also on the distinct means by which type III IFN mediates its anti-pathogen functions compared to the type I IFN. In this review we first provide a general overview on IFNs and present the similarities and differences in the signal transduction pathways leading to the expression of either type I or type III IFNs. By highlighting the current state-of-knowledge of the two archetypical mucosal surfaces (e.g. the respiratory and intestinal epitheliums), we present the differences in the signaling cascades used by type I and type III IFNs to uniquely induce the expression of ISGs. We then discuss in detail the role of each IFN in controlling pathogen infections in intestinal and respiratory epithelial cells. Finally, we provide our perspective on novel concepts in the field of IFN (stochasticity, response heterogeneity, cellular polarization/differentiation and tissue microenvironment) that we believe have implications in driving the differences between type I and III IFNs and could explain the preferences for type III IFNs at mucosal surfaces.
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Affiliation(s)
- Megan L. Stanifer
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Cuncai Guo
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Patricio Doldan
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Steeve Boulant
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
- Research Group “Cellular polarity and viral infection”, German Cancer Research Center (DKFZ), Heidelberg, Germany
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25
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Hare DN, Baid K, Dvorkin-Gheva A, Mossman KL. Virus-Intrinsic Differences and Heterogeneous IRF3 Activation Influence IFN-Independent Antiviral Protection. iScience 2020; 23:101864. [PMID: 33319181 PMCID: PMC7726339 DOI: 10.1016/j.isci.2020.101864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/04/2020] [Accepted: 11/20/2020] [Indexed: 02/09/2023] Open
Abstract
Type 1 interferon (IFN) plays a critical role in early antiviral defense and priming of adaptive immunity by signaling upregulation of host antiviral IFN-stimulated genes (ISGs). Certain stimuli trigger strong activation of IFN regulatory factor 3 (IRF3) and direct upregulation of ISGs in addition to IFN. It remains unclear why some stimuli are stronger activators of IRF3 and how this leads to IFN-independent antiviral protection. We found that UV-inactivated human cytomegalovirus (HCMV) particles triggered an IFN-independent ISG signature that was absent in cells infected with UV-inactivated Sendai virus particles. HCMV particles triggered mostly uniform activation of IRF3 and low-level IFN-β production within the population while SeV particles triggered a small fraction of cells producing abundant IFN-β. These findings suggest that population-level activation of IRF3 and antiviral protection emerges from a diversity of responses occurring simultaneously in single cells. Moreover, this occurs in the absence of virus replication. The antiviral response to virus particles requires low levels of interferon Cells respond differently to HCMV or SeV particles Heterogeneous IRF3 activation influences the response to virus
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Affiliation(s)
- David N Hare
- Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Kaushal Baid
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Anna Dvorkin-Gheva
- Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
| | - Karen L Mossman
- Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S4L8, Canada.,Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4L8, Canada
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Vats A, Gautam D, Maharana J, Singh Chera J, Kumar S, Rout PK, Werling D, De S. Poly I:C stimulation in-vitro as a marker for an antiviral response in different cell types generated from Buffalo (Bubalus bubalis). Mol Immunol 2020; 121:136-143. [PMID: 32200171 DOI: 10.1016/j.molimm.2020.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/06/2020] [Accepted: 03/09/2020] [Indexed: 01/17/2023]
Abstract
The innate immune system is activated upon virus invasion of a host cell by recognizing viral component, such as dsRNA through specific receptors, resulting in the production of type- I IFNs, which confer an antiviral state within the invaded as well as surrounding cells. In the present study, fibroblast, monocyte and macrophage cells derived from water Buffalo (Bubalus bubalis) were exposed to a synthetic dsRNA analogue, poly I:C to mimic viral invasion in each cell type. Recognition of poly I:C through cytosolic helicase receptors RIG-I and MDA5 molecule lead to the activation of the RLR pathway, subsequently activating the MAVS-IRF3/7 cascade and the production of antiviral effector molecule like IFNβ and ISGs. Within the different cell types, we identified variability in RLR receptor and IFNβ expression after poly I:C administration. Fibroblasts responded quickly and strongly with IFNβ production, followed by macrophages and monocytes. Despite absolute expression variability among different cell types the expression trend of RLRs pathway genes were similar. Length of poly I:C molecule also influence IFNβ expression in response of RLR pathway. Short (LMW) poly I:C induce stronger IFN-β expression in myeloid (macrophage and monocyte) cells. In contrast long (HMW) poly I:C preferably elicit higher IFNβ expression in non-myeloid (fibroblast) cell. Therefore, MDA5 and RIG-1 plays an indispensable role in eliciting antiviral response in non- immune (fibroblast) host cell. Thus, stimulation of RLR pathway with suitable and potentially cell-type specific agonist molecules successfully elicit antiviral state in the host animal, with fibroblasts conferring a stronger antiviral state compared with the monocytes and macrophages.
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Affiliation(s)
- Ashutosh Vats
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Devika Gautam
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Jitendra Maharana
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jatinder Singh Chera
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sushil Kumar
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Pramod K Rout
- ICAR-Central Institute for Research on Goats, Mathura, Uttar Pradesh, India
| | - Dirk Werling
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield, AL9 7TA, UK
| | - Sachinandan De
- Animal Genomics Lab., Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, Haryana, India.
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27
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Single-Cell Expression Variability Implies Cell Function. Cells 2019; 9:cells9010014. [PMID: 31861624 PMCID: PMC7017299 DOI: 10.3390/cells9010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) data becomes widely available, cell-to-cell variability in gene expression, or single-cell expression variability (scEV), has been increasingly appreciated. However, it remains unclear whether this variability is functionally important and, if so, what are its implications for multi-cellular organisms. Here, we analyzed multiple scRNA-seq data sets from lymphoblastoid cell lines (LCLs), lung airway epithelial cells (LAECs), and dermal fibroblasts (DFs) and, for each cell type, selected a group of homogenous cells with highly similar expression profiles. We estimated the scEV levels for genes after correcting the mean-variance dependency in that data and identified 465, 466, and 364 highly variable genes (HVGs) in LCLs, LAECs, and DFs, respectively. Functions of these HVGs were found to be enriched with those biological processes precisely relevant to the corresponding cell type’s function, from which the scRNA-seq data used to identify HVGs were generated—e.g., cytokine signaling pathways were enriched in HVGs identified in LCLs, collagen formation in LAECs, and keratinization in DFs. We repeated the same analysis with scRNA-seq data from induced pluripotent stem cells (iPSCs) and identified only 79 HVGs with no statistically significant enriched functions; the overall scEV in iPSCs was of negligible magnitude. Our results support the “variation is function” hypothesis, arguing that scEV is required for cell type-specific, higher-level system function. Thus, quantifying and characterizing scEV are of importance for our understating of normal and pathological cellular processes.
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Abadie K, Pease NA, Wither MJ, Kueh HY. Order by chance: origins and benefits of stochasticity in immune cell fate control. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 18:95-103. [PMID: 33791444 PMCID: PMC8009491 DOI: 10.1016/j.coisb.2019.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To protect against diverse challenges, the immune system must continuously generate an arsenal of specialized cell types, each of which can mount a myriad of effector responses upon detection of potential threats. To do so, it must generate multiple differentiated cell populations with defined sizes and proportions, often from rare starting precursor cells. Here, we discuss the emerging view that inherently probabilistic mechanisms, involving rare, rate-limiting regulatory events in single cells, control fate decisions and population sizes and fractions during immune development and function. We first review growing evidence that key fate control points are gated by stochastic signaling and gene regulatory events that occur infrequently over decision-making timescales, such that initially homogeneous cells can adopt variable outcomes in response to uniform signals. We next discuss how such stochastic control can provide functional capabilities that are harder to achieve with deterministic control strategies, and may be central to robust immune system function.
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Affiliation(s)
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington
- Molecular and Cellular Biology Program, University of Washington
| | | | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington
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29
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Leviyang S, Strawn N, Griva I. Regulation of interferon stimulated gene expression levels at homeostasis. Cytokine 2019; 126:154870. [PMID: 31629105 DOI: 10.1016/j.cyto.2019.154870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 01/12/2023]
Abstract
Interferon stimulated genes (ISGs), a collection of genes important in the early innate immune response, are upregulated in response to stimulation by extracellular type I interferons. The regulation of ISGs has been extensively studied in cells exposed to significant interferon stimulation, but less is known about ISG regulation in homeostatic regimes in which extracellular interferon levels are low. Using a collection of pre-existing, publicly available microarray datasets, we investigated ISG regulation at homeostasis in CD4, pulmonary epithelial, fibroblast and macrophage cells. We used a linear regression model to predict ISG expression levels from regulator expression levels. Our results suggest significant regulation of ISG expression at homeostasis, both through the ISGF3 molecule and through IRF7 and IRF8 associated pathways. We find that roughly 50% of ISGs have expression levels significantly correlated with ISGF3 expression levels at homeostasis, supporting previous results suggesting that homeostatic IFN levels have broad functional consequences. We find that ISG expression levels varied in their correlation with ISGF3, with epithelial and macrophage cells showing more correlation than CD4 and fibroblast cells. Our analysis provides a novel approach for decomposing and quantifying ISG regulation.
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Affiliation(s)
- Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, District of Columbia 20057, USA.
| | - Nate Strawn
- Department of Mathematics and Statistics, Georgetown University, District of Columbia 20057, USA
| | - Igor Griva
- Department of Mathematical Sciences, George Mason University, Fairfax, VA 22030, USA
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30
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Abstract
Experimental studies of the innate immune response of mammalian cells to viruses reveal pervasive heterogeneity at the level of single cells. Interferons are induced only in a fraction of virus-infected cells; subsequently a fraction of cells exposed to interferons upregulate interferon-stimulated genes. Nevertheless, quantitative experiments and linked mathematical models show that the interferon response can be effective in curbing viral spread through two distinct mechanisms. First, paracrine interferon signals from scattered source cells can protect many uninfected cells, and the self-amplification of interferon production might serve to calibrate response amplitude to strength of viral infection. Second, models of the tug-of-war between viral replication and the innate interferon response imply a pivotal role of interferon action on already infected cells in curbing viral spread, through effectively lowering virus replication rate. This finding is in line with the observation that several pathogenic viruses selectively abrogate interferon action on infected cells. Thus, interferons may delay viral spread in acute infections by acting as sentinels, warning uninfected cells of imminent danger, or as negative feedback regulators of virus replication in infected cells. The timing of the interferon response relative to the onset of viral replication is critical for its effectiveness in curbing viral spread.
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Affiliation(s)
- Soheil Rastgou Talemi
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ) and Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ) and Bioquant Center, University of Heidelberg, Heidelberg, Germany
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31
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Jennings J, Sang Y. Porcine Interferon Complex and Co-Evolution with Increasing Viral Pressure after Domestication. Viruses 2019; 11:v11060555. [PMID: 31208045 PMCID: PMC6631851 DOI: 10.3390/v11060555] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/16/2022] Open
Abstract
Consisting of nearly 60 functional genes, porcine interferon (IFN)-complex represents an evolutionary surge of IFN evolution in domestic ungulate species. To compare with humans and mice, each of these species contains about 20 IFN functional genes, which are better characterized using the conventional IFN-α/β subtypes as examples. Porcine IFN-complex thus represents an optimal model for studying IFN evolution that resulted from increasing viral pressure during domestication and industrialization. We hypothesize and justify that porcine IFN-complex may extend its functionality in antiviral and immunomodulatory activity due to its superior molecular diversity. Furthermore, these unconventional IFNs could even confer some functional and signaling novelty beyond that of the well-studied IFN-α/β subtypes. Investigations into porcine IFN-complex will further our understanding of IFN biology and promote IFN-based therapeutic designs to confront swine viral diseases.
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Affiliation(s)
- Jordan Jennings
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN 37209, USA.
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Drayman N, Patel P, Vistain L, Tay S. HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 2019; 8:e46339. [PMID: 31090537 PMCID: PMC6570482 DOI: 10.7554/elife.46339] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022] Open
Abstract
Viral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous, with most infected cells giving rise to no or few viral progeny while some cells produce thousands. Analysis of Herpes Simplex virus 1 (HSV-1) infection by population-averaged measurements has taught us a lot about the course of viral infection, but has also produced contradictory results, such as the concurrent activation and inhibition of type I interferon signaling during infection. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that these cells cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming involves the recruitment of β-catenin to the host nucleus and viral replication compartments, and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.
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Affiliation(s)
- Nir Drayman
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Parthiv Patel
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Luke Vistain
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
| | - Savaş Tay
- Institute for Molecular EngineeringThe University of ChicagoChicagoUnited States
- Institute for Genomics and Systems BiologyThe University of ChicagoChicagoUnited States
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West Nile Virus-Inclusive Single-Cell RNA Sequencing Reveals Heterogeneity in the Type I Interferon Response within Single Cells. J Virol 2019; 93:JVI.01778-18. [PMID: 30626670 DOI: 10.1128/jvi.01778-18] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/20/2018] [Indexed: 02/08/2023] Open
Abstract
West Nile virus (WNV) is a neurotropic mosquito-borne flavivirus of global importance. Neuroinvasive WNV infection results in encephalitis and can lead to prolonged neurological impairment or death. Type I interferon (IFN-I) is crucial for promoting antiviral defenses through the induction of antiviral effectors, which function to restrict viral replication and spread. However, our understanding of the antiviral response to WNV infection is mostly derived from analysis of bulk cell populations. It is becoming increasingly apparent that substantial heterogeneity in cellular processes exists among individual cells, even within a seemingly homogenous cell population. Here, we present WNV-inclusive single-cell RNA sequencing (scRNA-seq), an approach to examine the transcriptional variation and viral RNA burden across single cells. We observed that only a few cells within the bulk population displayed robust transcription of IFN-β mRNA, and this did not appear to depend on viral RNA abundance within the same cell. Furthermore, we observed considerable transcriptional heterogeneity in the IFN-I response, with genes displaying high unimodal and bimodal expression patterns. Broadly, IFN-stimulated genes negatively correlated with viral RNA abundance, corresponding with a precipitous decline in expression in cells with high viral RNA levels. Altogether, we demonstrated the feasibility and utility of WNV-inclusive scRNA-seq as a high-throughput technique for single-cell transcriptomics and WNV RNA detection. This approach can be implemented in other models to provide insights into the cellular features of protective immunity and identify novel therapeutic targets.IMPORTANCE West Nile virus (WNV) is a clinically relevant pathogen responsible for recurrent epidemics of neuroinvasive disease. Type I interferon is essential for promoting an antiviral response against WNV infection; however, it is unclear how heterogeneity in the antiviral response at the single-cell level impacts viral control. Specifically, conventional approaches lack the ability to distinguish differences across cells with varying viral abundance. The significance of our research is to demonstrate a new technique for studying WNV infection at the single-cell level. We discovered extensive variation in antiviral gene expression and viral abundance across cells. This protocol can be applied to primary cells or in vivo models to better understand the underlying cellular heterogeneity following WNV infection for the development of targeted therapeutic strategies.
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Type I interferon response impairs differentiation potential of pluripotent stem cells. Proc Natl Acad Sci U S A 2019; 116:1384-1393. [PMID: 30606801 PMCID: PMC6347712 DOI: 10.1073/pnas.1812449116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Unlike all differentiated cells, pluripotent stem cells do not elicit a productive antiviral response when infected by a pathogen. This observation seems at odds with the importance of pluripotent stem cells given their absolute requirement for the development of life. Here we investigate why this antiviral response is not utilized in these unique cells. We find that the factors required to maintain pluripotency are incompatible with those involved in eliciting the canonical interferon-based response to virus infection. Upon virus infection, pluripotent stem cells neither induce nor respond to canonical type I interferons (IFN-I). To better understand this biology, we characterized induced pluripotent stem cells (iPSCs) as well as their differentiated parental or rederived counterparts. We confirmed that only iPSCs failed to respond to viral RNA, IFN-I, or viral infection. This lack of response could be phenocopied in fibroblasts with the expression of a reprogramming factor which repressed the capacity to induce canonical antiviral pathways. To ascertain the consequences of restoring the antiviral response in the context of pluripotency, we engineered a system to engage these defenses in iPSCs. Inducible expression of a recombinant virus-activated transcription factor resulted in the successful reconstitution of antiviral defenses through the direct up-regulation of IFN-I–stimulated genes. Induction of the antiviral signature in iPSCs, even for a short duration, resulted in the dysregulation of genes associated with all three germ layers despite maintaining pluripotency markers. Trilineage differentiation of these same cells showed that engagement of the antiviral defenses compromised ectoderm and endoderm formation and dysregulated the development of mesodermal sublineages. In all, these data suggest that the temporal induction of the antiviral response primes iPSCs away from pluripotency and induces numerous aberrant gene products upon differentiation. Together these results suggest that the IFN-I system and pluripotency may be incompatible with each other and thus explain why stem cells do not utilize the canonical antiviral system.
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35
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Gene expression variability across cells and species shapes innate immunity. Nature 2018; 563:197-202. [PMID: 30356220 PMCID: PMC6347972 DOI: 10.1038/s41586-018-0657-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
As the first line of defence against pathogens, cells mount an innate immune response, which varies widely from cell to cell. The response must be potent but carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here we characterize the innate immune response's transcriptional divergence between species and variability in expression among cells. Using bulk and single-cell transcriptomics in fibroblasts and mononuclear phagocytes from different species, challenged with immune stimuli, we map the architecture of the innate immune response. Transcriptionally diverging genes, including those that encode cytokines and chemokines, vary across cells and have distinct promoter structures. Conversely, genes that are involved in the regulation of this response, such as those that encode transcription factors and kinases, are conserved between species and display low cell-to-cell variability in expression. We suggest that this expression pattern, which is observed across species and conditions, has evolved as a mechanism for fine-tuned regulation to achieve an effective but balanced response.
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36
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Leviyang S, Griva I. Investigating Functional Roles for Positive Feedback and Cellular Heterogeneity in the Type I Interferon Response to Viral Infection. Viruses 2018; 10:v10100517. [PMID: 30241427 PMCID: PMC6213501 DOI: 10.3390/v10100517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/16/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Secretion of type I interferons (IFN) by infected cells mediates protection against many viruses, but prolonged or excessive type I IFN secretion can lead to immune pathology. A proper type I IFN response must therefore maintain a balance between protection and excessive IFN secretion. It has been widely noted that the type I IFN response is driven by positive feedback and is heterogeneous, with only a fraction of infected cells upregulating IFN expression even in clonal cell lines, but the functional roles of feedback and heterogeneity in balancing protection and excessive IFN secretion are not clear. To investigate the functional roles for feedback and heterogeneity, we constructed a mathematical model coupling IFN and viral dynamics that extends existing mathematical models by accounting for feedback and heterogeneity. We fit our model to five existing datasets, reflecting different experimental systems. Fitting across datasets allowed us to compare the IFN response across the systems and suggested different signatures of feedback and heterogeneity in the different systems. Further, through numerical experiments, we generated hypotheses of functional roles for IFN feedback and heterogeneity consistent with our mathematical model. We hypothesize an inherent tradeoff in the IFN response: a positive feedback loop prevents excessive IFN secretion, but also makes the IFN response vulnerable to viral antagonism. We hypothesize that cellular heterogeneity of the IFN response functions to protect the feedback loop from viral antagonism. Verification of our hypotheses will require further experimental studies. Our work provides a basis for analyzing the type I IFN response across systems.
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Affiliation(s)
- Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC 20057, USA.
| | - Igor Griva
- Department of Mathematical Sciences, George Mason University, Fairfax, VA 22030, USA.
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37
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Wimmers F, Subedi N, van Buuringen N, Heister D, Vivié J, Beeren-Reinieren I, Woestenenk R, Dolstra H, Piruska A, Jacobs JFM, van Oudenaarden A, Figdor CG, Huck WTS, de Vries IJM, Tel J. Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells. Nat Commun 2018; 9:3317. [PMID: 30127440 PMCID: PMC6102223 DOI: 10.1038/s41467-018-05784-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/25/2018] [Indexed: 01/01/2023] Open
Abstract
Type I interferon (IFN) is a key driver of immunity to infections and cancer. Plasmacytoid dendritic cells (pDCs) are uniquely equipped to produce large quantities of type I IFN but the mechanisms that control this process are poorly understood. Here we report on a droplet-based microfluidic platform to investigate type I IFN production in human pDCs at the single-cell level. We show that type I IFN but not TNFα production is limited to a small subpopulation of individually stimulated pDCs and controlled by stochastic gene regulation. Combining single-cell cytokine analysis with single-cell RNA-seq profiling reveals no evidence for a pre-existing subset of type I IFN-producing pDCs. By modulating the droplet microenvironment, we demonstrate that vigorous pDC population responses are driven by a type I IFN amplification loop. Our study highlights the significance of stochastic gene regulation and suggests strategies to dissect the characteristics of immune responses at the single-cell level. Plasmacytoid dendritic cells (pDC) are a pivotal component of the immune system. Here, the authors utilize single-cell microfluidics to interrogate the human pDC compartment and reveal a subset of type I IFN secreting pDCs that is regulated by stochastic gene expression and amplified by microenvironmental cues.
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Affiliation(s)
- Florian Wimmers
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, 94305, CA, USA
| | - Nikita Subedi
- Department of Biomedical Engineering, Laboratory of Immunoengineering, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands
| | - Nicole van Buuringen
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Daan Heister
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Judith Vivié
- Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, 3584 CT, The Netherlands
| | - Inge Beeren-Reinieren
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Rob Woestenenk
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Harry Dolstra
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Aigars Piruska
- Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 HP, The Netherlands
| | - Joannes F M Jacobs
- Department of Laboratory Medicine, Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | | | - Carl G Figdor
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Wilhelm T S Huck
- Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 HP, The Netherlands
| | - I Jolanda M de Vries
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jurjen Tel
- Department of Tumor Immunology, Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands. .,Department of Biomedical Engineering, Laboratory of Immunoengineering, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands. .,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5612 AZ, The Netherlands.
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38
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Nikopoulou C, Panagopoulos G, Sianidis G, Psarra E, Ford E, Thanos D. The Transcription Factor ThPOK Orchestrates Stochastic Interchromosomal Interactions Required for IFNB1 Virus-Inducible Gene Expression. Mol Cell 2018; 71:352-361.e5. [PMID: 30017585 DOI: 10.1016/j.molcel.2018.06.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/30/2018] [Accepted: 06/07/2018] [Indexed: 02/01/2023]
Abstract
Virus infection induces stochastic activation of the interferon-β gene. Three previously identified Alu-like DNA elements called NRCs (NF-κB reception centers) function by capturing and delivering NF-κB to the IFNB1 enhancer via stochastic interchromosomal interactions. We show that the transcription factor ThPOK binds cooperatively with NF-κB to NRCs and mediates their physical proximity with the IFNB1 gene via its ability to oligomerize when bound to DNA. ThPOK knockdown significantly decreased the frequency of interchromosomal interactions, NF-κB DNA binding to the IFNB1 enhancer, and virus-induced IFNB1 gene activation. We also demonstrate that cooperative DNA binding between ThPOK and NF-κB on the same face of the double DNA helix is required for interchromosomal interactions and distinguishes NRCs from various other Alu elements bearing κB sites. These studies show how DNA binding cooperativity of stereospecifically aligned transcription factors provides the necessary ultrasensitivity for the all-or-none stochastic cell responses to virus infection.
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Affiliation(s)
- Chrysa Nikopoulou
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Giorgos Panagopoulos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Georgios Sianidis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Eleni Psarra
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Ethan Ford
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Efessiou Street, Athens 11527, Greece.
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39
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Czerkies M, Korwek Z, Prus W, Kochańczyk M, Jaruszewicz-Błońska J, Tudelska K, Błoński S, Kimmel M, Brasier AR, Lipniacki T. Cell fate in antiviral response arises in the crosstalk of IRF, NF-κB and JAK/STAT pathways. Nat Commun 2018; 9:493. [PMID: 29402958 PMCID: PMC5799375 DOI: 10.1038/s41467-017-02640-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 12/14/2017] [Indexed: 12/24/2022] Open
Abstract
The innate immune system processes pathogen-induced signals into cell fate decisions. How information is turned to decision remains unknown. By combining stochastic mathematical modelling and experimentation, we demonstrate that feedback interactions between the IRF3, NF-κB and STAT pathways lead to switch-like responses to a viral analogue, poly(I:C), in contrast to pulse-like responses to bacterial LPS. Poly(I:C) activates both IRF3 and NF-κB, a requirement for induction of IFNβ expression. Autocrine IFNβ initiates a JAK/STAT-mediated positive-feedback stabilising nuclear IRF3 and NF-κB in first responder cells. Paracrine IFNβ, in turn, sensitises second responder cells through a JAK/STAT-mediated positive feedforward pathway that upregulates the positive-feedback components: RIG-I, PKR and OAS1A. In these sensitised cells, the 'live-or-die' decision phase following poly(I:C) exposure is shorter-they rapidly produce antiviral responses and commit to apoptosis. The interlinked positive feedback and feedforward signalling is key for coordinating cell fate decisions in cellular populations restricting pathogen spread.
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Affiliation(s)
- Maciej Czerkies
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Zbigniew Korwek
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Wiktor Prus
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Marek Kochańczyk
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | | | - Karolina Tudelska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Sławomir Błoński
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Marek Kimmel
- Departments of Statistics and Bioengineering, and Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, 77005, USA
- Systems Engineering Group, Silesian University of Technology, Gliwice, 44-100, Poland
| | - Allan R Brasier
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555-1060, USA
| | - Tomasz Lipniacki
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, 02-106, Poland.
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40
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Doğanay S, Lee MY, Baum A, Peh J, Hwang SY, Yoo JY, Hergenrother PJ, García-Sastre A, Myong S, Ha T. Single-cell analysis of early antiviral gene expression reveals a determinant of stochastic IFNB1 expression. Integr Biol (Camb) 2017; 9:857-867. [PMID: 29098213 PMCID: PMC6201300 DOI: 10.1039/c7ib00146k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RIG-I-like receptors (RLRs) are cytoplasmic sensors of viral RNA that trigger the signaling cascade that leads to type I interferon (IFN) production. Transcriptional induction of RLRs by IFN is believed to play the role of positive feedback to further amplify viral sensing. We found that RLRs and several other IFN-stimulated genes (ISGs) are induced early in viral infection independent of IFN. Expression of these early ISGs requires IRF3/IRF7 and is highly correlated amongst them. Simultaneous detection of mRNA of IFNB1, viral replicase, and ISGs revealed distinct populations of IFNB1 expressing and non-expressing cells which are highly correlated with the levels of early ISGs but are uncorrelated with IFN-dependent ISGs and viral gene expression. Individual expression of RLRs made IFNB1 expression more robust and earlier, suggesting a causal relation between levels of RLR and induction of IFN.
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Affiliation(s)
- Sultan Doğanay
- Center for Computational Biology and Biophysics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Maurice Youzong Lee
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Biophysics Program, Stanford University, CA 94305, USA
| | - Alina Baum
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, New York, NY 10029, USA
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY 10591, USA
| | - Jessie Peh
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Sun-Young Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, KOREA
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 790-784, KOREA
| | - Paul J. Hergenrother
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Taekjip Ha
- Center for Computational Biology and Biophysics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics, and Center for Physics of Living Cells, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland
- Howard Hughes Medical Institute
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41
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Cai C, Zhou J, Sun X, Sun T, Xie W, Cui J. Integrated modeling and analysis of intracellular and intercellular mechanisms in shaping the interferon response to viral infection. PLoS One 2017; 12:e0186105. [PMID: 29020068 PMCID: PMC5636135 DOI: 10.1371/journal.pone.0186105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022] Open
Abstract
The interferons (IFNs) responses to viral infection are heterogeneous, while the underlying mechanisms for variability among cells are still not clear. In this study, we developed a hybrid model to systematically identify the sources of IFN induction heterogeneity. The experiment-integrated simulation demonstrated that the viral dose/type, the diversity in transcriptional factors activation and the intercellular paracrine signaling could strikingly shape the heterogeneity of IFN expression. We further determined that the IFNβ and IFNλ1 induced diverse dynamics of IFN-stimulated genes (ISGs) production. Collectively, our findings revealed the intracellular and intercellular mechanisms contributing to cell-to-cell variation in IFN induction, and further demonstrated the significant effects of IFN heterogeneity on antagonizing viruses.
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Affiliation(s)
- Chunmei Cai
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jie Zhou
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiaoqiang Sun
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | | | - Weihong Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
- Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou, P. R. China
- * E-mail:
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42
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Xu J, Sun Y, Li Y, Ruthel G, Weiss SR, Raj A, Beiting D, López CB. Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence. Nat Commun 2017; 8:799. [PMID: 28986577 PMCID: PMC5630589 DOI: 10.1038/s41467-017-00909-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/02/2017] [Indexed: 12/03/2022] Open
Abstract
Replication defective viral genomes (DVGs) generated during virus replication are the primary triggers of antiviral immunity in many RNA virus infections. However, DVGs can also facilitate viral persistence. Why and how these two opposing functions of DVGs are achieved remain unknown. Here we report that during Sendai and respiratory syncytial virus infections DVGs selectively protect a subpopulation of cells from death, thereby promoting the establishment of persistent infections. We find that during Sendai virus infection this phenotype results from DVGs stimulating a mitochondrial antiviral-signaling (MAVS)-mediated TNF response that drives apoptosis of highly infected cells while extending the survival of cells enriched in DVGs. The pro-survival effect of TNF depends on the activity of the TNFR2/TRAF1 pathway that is regulated by MAVS signaling. These results identify TNF as a pivotal factor in determining cell fate during a viral infection and delineate a MAVS/TNFR2-mediated mechanism that drives the persistence of otherwise acute viruses. Replication defective viral genomes (DVGs) can facilitate persistence of paramyxoviruses, but the underlying mechanisms are unclear. Using FISH, Xu et al. here analyze the cellular response to DVGs on a single cell level and show that a MAVS-mediated TNF response specifically extends survival of cells enriched in DVGs.
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Affiliation(s)
- Jie Xu
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Sun
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Gordon Ruthel
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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43
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Timm AC, Warrick JW, Yin J. Quantitative profiling of innate immune activation by viral infection in single cells. Integr Biol (Camb) 2017; 9:782-791. [PMID: 28831492 PMCID: PMC5603422 DOI: 10.1039/c7ib00082k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cells infected by viruses can exhibit diverse patterns of viral and cellular gene expression. The patterns arise in part from the stochastic or noisy reaction kinetics associated with the small number of genomes, enzymes, and other molecules that typically initiate virus replication and activate cellular anti-viral defenses. It is not known what features, if any, of the early viral or cellular gene expression correlate with later processes of viral replication or cell survival. Here we used two fluorescent reporters to visualize innate immune activation of human prostate cancer (PC3) cells against infection by vesicular stomatitis virus. The cells were engineered to express green-fluorescent protein under control of the promoter for IFIT2, an interferon-sensitive component of the anti-viral response, while red-fluorescent protein was expressed as a byproduct of virus infection. To isolate and quantitatively analyze single-cells, we used a unique microwell array device and open-source image processing software. Kinetic analysis of viral and cellular reporter profiles from hundreds of cells revealed novel relationships between gene expression and the outcome of infection. Specifically, the relative timing rather than the magnitude of the viral gene expression and innate immune activation correlated with the infection outcome. Earlier viral or anti-viral gene expression favored or hindered virus growth, respectively. Further, analysis of kinetic parameters estimated from these data suggests a trade-off between robust antiviral signaling and cell death, as indicated by a higher rate of detectable cell lysis in infected cells with a detectable immune response. In short, cells that activate an immune response lyse at a higher rate. More broadly, we demonstrate how the intrinsic heterogeneity of individual cell behaviors can be exploited to discover features of viral and host gene expression that correlate with single-cell outcomes, which will ultimately impact whether or not infections spread.
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Affiliation(s)
- Andrea C Timm
- Systems Biology Theme, Wisconsin Institute for Discovery, Department of Chemical and Biological Engineering, University of Wisconsin, Madison, WI, USA.
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44
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Aguilera LU, Zimmer C, Kummer U. A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. BMC SYSTEMS BIOLOGY 2017; 11:26. [PMID: 28219373 PMCID: PMC5322793 DOI: 10.1186/s12918-017-0406-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 02/02/2017] [Indexed: 02/05/2023]
Abstract
Background Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts are low, stochastic formalisms like Monte Carlo simulations are more appropriate and well established. However, compared to the wealth of computational methods used to fit and analyze deterministic models, there is only little available to quantify the exactness of the fit of stochastic models compared to experimental data or to analyze different aspects of the modeling results. Results Here, we developed a method to fit stochastic simulations to experimental high-throughput data, meaning data that exhibits distributions. The method uses a comparison of the probability density functions that are computed based on Monte Carlo simulations and the experimental data. Multiple parameter values are iteratively evaluated using optimization routines. The method improves its performance by selecting parameters values after comparing the similitude between the deterministic stability of the system and the modes in the experimental data distribution. As a case study we fitted a model of the IRF7 gene expression circuit to time-course experimental data obtained by flow cytometry. IRF7 shows bimodal dynamics upon IFN stimulation. This dynamics occurs due to the switching between active and basal states of the IRF7 promoter. However, the exact molecular mechanisms responsible for the bimodality of IRF7 is not fully understood. Conclusions Our results allow us to conclude that the activation of the IRF7 promoter by the combination of IRF7 and ISGF3 is sufficient to explain the observed bimodal dynamics. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0406-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis U Aguilera
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Christoph Zimmer
- BIOMS (Center for Modeling and Simulation in the Biosciences), Heidelberg University, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Ursula Kummer
- Department of Modeling of Biological Processes, COS Heidelberg / Bioquant, Heidelberg University, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.
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45
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Dalet A, Argüello RJ, Combes A, Spinelli L, Jaeger S, Fallet M, Vu Manh TP, Mendes A, Perego J, Reverendo M, Camosseto V, Dalod M, Weil T, Santos MA, Gatti E, Pierre P. Protein synthesis inhibition and GADD34 control IFN-β heterogeneous expression in response to dsRNA. EMBO J 2017; 36:761-782. [PMID: 28100675 DOI: 10.15252/embj.201695000] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 02/01/2023] Open
Abstract
In innate immune responses, induction of type-I interferons (IFNs) prevents virus spreading while viral replication is delayed by protein synthesis inhibition. We asked how cells perform these apparently contradictory activities. Using single fibroblast monitoring by flow cytometry and mathematical modeling, we demonstrate that type-I IFN production is linked to cell's ability to enter dsRNA-activated PKR-dependent translational arrest and then overcome this inhibition by decreasing eIF2α phosphorylation through phosphatase 1c cofactor GADD34 (Ppp1r15a) expression. GADD34 expression, shown here to be dependent on the IRF3 transcription factor, is responsible for a biochemical cycle permitting pulse of IFN synthesis to occur in cells undergoing protein synthesis inhibition. Translation arrest is further demonstrated to be key for anti-viral response by acting synergistically with MAVS activation to amplify TBK1 signaling and IFN-β mRNA transcription, while GADD34-dependent protein synthesis recovery contributes to the heterogeneous expression of IFN observed in dsRNA-activated cells.
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Affiliation(s)
- Alexandre Dalet
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | | | - Alexis Combes
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | - Lionel Spinelli
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | | | - Mathieu Fallet
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | | | - Andreia Mendes
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | - Jessica Perego
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | | | - Voahirana Camosseto
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France.,International associated laboratory (LIA) CNRS "Mistra", Marseille, France
| | - Marc Dalod
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | - Tobias Weil
- Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, Aveiro, Portugal
| | - Manuel A Santos
- International associated laboratory (LIA) CNRS "Mistra", Marseille, France.,Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, Aveiro, Portugal
| | - Evelina Gatti
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France .,International associated laboratory (LIA) CNRS "Mistra", Marseille, France.,Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, Aveiro, Portugal
| | - Philippe Pierre
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France .,International associated laboratory (LIA) CNRS "Mistra", Marseille, France.,Institute for Research in Biomedicine - iBiMED and Aveiro Health Sciences Program, University of Aveiro, Aveiro, Portugal
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Cohen EM, Kobiler O. Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells. PLoS Pathog 2016; 12:e1006082. [PMID: 27923068 PMCID: PMC5161387 DOI: 10.1371/journal.ppat.1006082] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 11/21/2016] [Indexed: 12/11/2022] Open
Abstract
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells. Single cell variation is of major interest in understanding key biological processes, like cancer, development and host pathogen interaction. During viral infection, these cell to cell variations can change the outcome of the whole organism infection. We suggested that differences in the number of parental viral genomes that initiate the replication process alter the outcome of infection among single cells. In this work we present a method based on genetically barcoded herpesvirus recombinants to identify the number of viral genomes initiating replication in individual cells. Our results indicate that viral gene expression is tightly linked to the number of viral genomes replicating per cell. Remarkably, we found that high cellular gene expression was an indicator for a lower viral gene expression in a given cell. We suggest that variations among single cells result from preexisting differences among cells, as well as from random viral host interactions.
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Affiliation(s)
- Efrat M. Cohen
- Department of Clinical Microbiology and Immunology,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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Pascutti MF, Erkelens MN, Nolte MA. Impact of Viral Infections on Hematopoiesis: From Beneficial to Detrimental Effects on Bone Marrow Output. Front Immunol 2016; 7:364. [PMID: 27695457 PMCID: PMC5025449 DOI: 10.3389/fimmu.2016.00364] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/02/2016] [Indexed: 01/17/2023] Open
Abstract
The ability of the bone marrow (BM) to generate copious amounts of blood cells required on a daily basis depends on a highly orchestrated process of proliferation and differentiation of hematopoietic stem and progenitor cells (HSPCs). This process can be rapidly adapted under stress conditions, such as infections, to meet the specific cellular needs of the immune response and the ensuing physiological changes. This requires a tight regulation in order to prevent either hematopoietic failure or transformation. Although adaptation to bacterial infections or systemic inflammation has been studied and reviewed in depth, specific alterations of hematopoiesis to viral infections have received less attention so far. Viruses constantly pose a significant health risk and demand an adequate, balanced response from our immune system, which also affects the BM. In fact, both the virus itself and the ensuing immune response can have a tremendous impact on the hematopoietic process. On one hand, this can be beneficial: it helps to boost the cellular response of the body to resolve the viral infection. But on the other hand, when the virus and the resulting antiviral response persist, the inflammatory feedback to the hematopoietic system will become chronic, which can be detrimental for a balanced BM output. Chronic viral infections frequently have clinical manifestations at the level of blood cell formation, and we summarize which viruses can lead to BM pathologies, like aplastic anemia, pancytopenia, hemophagocytic lymphohistiocytosis, lymphoproliferative disorders, and malignancies. Regarding the underlying mechanisms, we address specific effects of acute and chronic viral infections on blood cell production. As such, we distinguish four different levels in which this can occur: (1) direct viral infection of HSPCs, (2) viral recognition by HSPCs, (3) indirect effects on HSPCs by inflammatory mediators, and (4) the role of the BM microenvironment on hematopoiesis upon virus infection. In conclusion, this review provides a comprehensive overview on how viral infections can affect the formation of new blood cells, aiming to advance our understanding of the underlying cellular and molecular mechanisms to improve the treatment of BM failure in patients.
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Affiliation(s)
- Maria Fernanda Pascutti
- Landsteiner Laboratory, Department of Hematopoiesis, Sanquin, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Martje N. Erkelens
- Landsteiner Laboratory, Department of Hematopoiesis, Sanquin, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Martijn A. Nolte
- Landsteiner Laboratory, Department of Hematopoiesis, Sanquin, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
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48
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Kim N, Now H, Nguyen NTH, Yoo JY. Multilayered regulations of RIG-I in the anti-viral signaling pathway. J Microbiol 2016; 54:583-587. [PMID: 27572506 DOI: 10.1007/s12275-016-6322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 10/21/2022]
Abstract
RIG-I is a cytosolic receptor recognizing virus-specific RNA structures and initiates an antiviral signaling that induces the production of interferons and proinflammatory cytokines. Because inappropriate RIG-I signaling affects either viral clearance or immune toxicity, multiple regulations of RIG-I have been investigated since its discovery as the viral RNA detector. In this review, we describe the recent progress in research on the regulation of RIG-I activity or abundance. Specifically, we focus on the mechanism that modulates RIG-I-dependent antiviral response through post-translational modifications of or protein-protein interactions with RIG-I.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
| | - Hesung Now
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Nhung T H Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.
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49
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Bedsaul JR, Zaritsky LA, Zoon KC. Type I Interferon-Mediated Induction of Antiviral Genes and Proteins Fails to Protect Cells from the Cytopathic Effects of Sendai Virus Infection. J Interferon Cytokine Res 2016; 36:652-665. [PMID: 27508859 DOI: 10.1089/jir.2016.0051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sendai virus (SeV), a murine paramyxovirus, has been used to study the induction of type I interferon (IFN) subtypes in robust quantities. Few studies have measured whether the IFN that SeV induces actually fulfills its intended purpose of interfering with virus-mediated effects in the cells in which it is produced. We determined the effects of IFN on SeV-mediated cytopathic effects (CPE) and the ability of IFN to protect against virus infection. SeV-induced biologically active IFN resulted in Jak/STAT activation and the production of a number of interferon-stimulated genes (ISGs). However, these responses did not inhibit SeV replication or CPE. This observation was not due to SeV effects on canonical IFN signaling. Furthermore, pretreating cells with type I IFN and establishing an antiviral state before infection did not mediate SeV effects. Therefore, the induction of canonical IFN signaling pathways and ISGs does not always confer protection against the IFN-inducing virus. Because type I IFNs are approved to treat various infections, our findings suggest that typical markers of IFN activity may not be indicative of a protective antiviral response and should not be used alone to determine whether an antiviral state against a particular virus is achieved.
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Affiliation(s)
- Jacquelyn R Bedsaul
- Cytokine Biology Section, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, Maryland
| | - Luna A Zaritsky
- Cytokine Biology Section, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, Maryland
| | - Kathryn C Zoon
- Cytokine Biology Section, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Bethesda, Maryland
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50
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Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res 2016; 26:1397-1410. [PMID: 27470110 PMCID: PMC5052061 DOI: 10.1101/gr.207902.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3′-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 cDNA libraries, each from an individual pancreatic islet cell. ESAT identified nine distinct cell types, three distinct β-cell types, and a complex interplay between hormone secretion and vascularization. ESAT, then, offers a much-needed and generally applicable computational pipeline for either bulk or single-cell RNA end-sequencing.
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Affiliation(s)
- Alan Derr
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Chaoxing Yang
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rapolas Zilionis
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Institute of Biotechnology, Vilnius University, LT 02241 Vilnius, Lithuania
| | - Alexey Sergushichev
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia; Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - David M Blodgett
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sambra Redick
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Rita Bortell
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - David M Harlan
- Department of Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dale L Greiner
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allon Klein
- Department of System Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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