1
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Lee AR, Wilson KR, Clarke M, Engel S, Tscharke DC, Gebhardt T, Bedoui S, Bachem A. GPR41 and GPR43 regulate CD8 + T cell priming during herpes simplex virus type 1 infection. Front Immunol 2024; 15:1332588. [PMID: 38524121 PMCID: PMC10957577 DOI: 10.3389/fimmu.2024.1332588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/13/2024] [Indexed: 03/26/2024] Open
Abstract
Naïve CD8+ T cells need to undergo a complex and coordinated differentiation program to gain the capacity to control virus infections. This not only involves the acquisition of effector functions, but also regulates the development of a subset of effector CD8+ T cells into long-lived and protective memory cells. Microbiota-derived metabolites have recently gained interest for their influence on T cells, but much remains unclear about their role in CD8+ T cell differentiation. In this study, we investigated the role of the G protein-coupled receptors (GPR)41 and GPR43 that can bind microbiota-derived short chain fatty acids (SCFAs) in CD8+ T cell priming following epicutaneous herpes simplex virus type 1 (HSV-1) infection. We found that HSV-specific CD8+ T cells in GPR41/43-deficient mice were impaired in the antigen-elicited production of interferon-gamma (IFN-γ), tumour necrosis factor-alpha (TNF-α), granzyme B and perforin, and failed to differentiate effectively into memory precursors. The defect in controlling HSV-1 at the site of infection could be restored when GPR41 and GPR43 were expressed exclusively by HSV-specific CD8+ T cells. Our findings therefore highlight roles for GPR41 and GPR43 in CD8+ T cell differentiation, emphasising the importance of metabolite sensing in fine-tuning anti-viral CD8+ T cell priming.
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Affiliation(s)
- Ariane Renita Lee
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Kayla Roberta Wilson
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Michele Clarke
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Sven Engel
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Thomas Gebhardt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Annabell Bachem
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
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2
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Samer C, McWilliam HE, McSharry BP, Velusamy T, Burchfield JG, Stanton RJ, Tscharke DC, Rossjohn J, Villadangos JA, Abendroth A, Slobedman B. Multi-targeted loss of the antigen presentation molecule MR1 during HSV-1 and HSV-2 infection. iScience 2024; 27:108801. [PMID: 38303725 PMCID: PMC10831258 DOI: 10.1016/j.isci.2024.108801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
The major histocompatibility complex (MHC), Class-I-related (MR1) molecule presents microbiome-synthesized metabolites to Mucosal-associated invariant T (MAIT) cells, present at sites of herpes simplex virus (HSV) infection. During HSV type 1 (HSV-1) infection there is a profound and rapid loss of MR1, in part due to expression of unique short 3 protein. Here we show that virion host shutoff RNase protein downregulates MR1 protein, through loss of MR1 transcripts. Furthermore, a third viral protein, infected cell protein 22, also downregulates MR1, but not classical MHC-I molecules. This occurs early in the MR1 trafficking pathway through proteasomal degradation. Finally, HSV-2 infection results in the loss of MR1 transcripts, and intracellular and surface MR1 protein, comparable to that seen during HSV-1 infection. Thus HSV coordinates a multifaceted attack on the MR1 antigen presentation pathway, potentially protecting infected cells from MAIT cell T cell receptor-mediated detection at sites of primary infection and reactivation.
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Affiliation(s)
- Carolyn Samer
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Hamish E.G. McWilliam
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Brian P. McSharry
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Thilaga Velusamy
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - James G. Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Richard J. Stanton
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, Wales
| | - David C. Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Jamie Rossjohn
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, Wales
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jose A. Villadangos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Allison Abendroth
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Barry Slobedman
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
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3
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Randall KL, Flesch IEA, Mei Y, Miosge LA, Aye R, Yu Z, Domaschenz H, Hollett NA, Russell TA, Stefanovic T, Wong YC, Seneviratne S, Ballard F, Hernandez Gallardo R, Croft SN, Goodnow CC, Bertram EM, Enders A, Tscharke DC. DOCK2-deficiency causes defects in anti-viral T cell responses and impaired control of herpes simplex virus infection. J Infect Dis 2024:jiae077. [PMID: 38366567 DOI: 10.1093/infdis/jiae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The expanding number of rare immunodeficiency syndromes offers an opportunity to understand key genes that support immune defence against infectious diseases. However, analysis of these in patients is complicated by their treatments and co-morbid infections requiring the use of mouse models for detailed investigations. Here we develop a mouse model of DOCK2 immunodeficiency and demonstrate that these mice have delayed clearance of herpes simplex virus type 1 (HSV-1) infections. We also uncovered a critical, cell intrinsic role of DOCK2 in the priming of anti-viral CD8+ T cells and in particular their initial expansion, despite apparently normal early activation of these cells. When this defect was overcome by priming in vitro, DOCK2-deficient CD8+ T cells were surprisingly protective against HSV-1-disease, albeit not as effectively as wild type cells. These results shed light on a cellular deficiency that is likely to impact anti-viral immunity in DOCK2-deficient patients.
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Affiliation(s)
- Katrina L Randall
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
- School of Medicine and Psychology, Australian National University, Canberra ACT 2600
| | - Inge E A Flesch
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Yan Mei
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Lisa A Miosge
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Racheal Aye
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Zhijia Yu
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Heather Domaschenz
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Natasha A Hollett
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Tiffany A Russell
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Tijana Stefanovic
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Yik Chun Wong
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Sandali Seneviratne
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Fiona Ballard
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Raquel Hernandez Gallardo
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Sarah N Croft
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Christopher C Goodnow
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
- Garvan Institute of Medical Research, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Edward M Bertram
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Anselm Enders
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
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4
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Velusamy T, Singh N, Croft S, Smith S, Tscharke DC. The expression and function of HSV ICP47 and its promoter in mice. J Virol 2023; 97:e0110723. [PMID: 37902400 PMCID: PMC10688380 DOI: 10.1128/jvi.01107-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Immune evasion and latency are key mechanisms that underlie the success of herpesviruses. In each case, interactions between viral and host proteins are required and due to co-evolution, not all mechanisms are preserved across host species, even if infection is possible. This is highlighted by the herpes simplex virus (HSV) protein immediate early-infected cell protein (ICP)47, which inhibits the detection of infected cells by killer T cells and acts with high efficiency in humans, but poorly, if at all in mouse cells. Here, we show that ICP47 retains modest but detectable function in mouse cells, but in an in vivo model we found no role during acute infection or latency. We also explored the activity of the ICP47 promoter, finding that it could be active during latency, but this was dependent on genome location. These results are important to interpret HSV pathogenesis work done in mice.
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Affiliation(s)
- Thilaga Velusamy
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Navneet Singh
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Sarah Croft
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - Stewart Smith
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University , Canberra, ACT, Australia
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5
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Witney MJ, Purcell AW, Tscharke DC. Need to know which MHCs protect against COVID? There's an App for that! Immunol Cell Biol 2023; 101:789-792. [PMID: 37638731 DOI: 10.1111/imcb.12680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
In this article, we discuss the recent observation by Augusto et al. made using a novel mobile phone application-based COVID-19 Citizen Science Study that an HLA genetic variant, HLA-B*15:01, is associated with asymptomatic SARS-CoV-2 infection. To explain this association, Augusto et al. describe a cross-reactive memory CD8+ T-cell response in HLA-B*15:01+ SARS-CoV-2 unexposed individuals that retains high avidity for two structurally conserved epitopes found in SARS-CoV-2 and seasonal coronavirus strains. These observations provide an insight into potential molecular determinants that facilitate rapid, early clearance of virus.
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Affiliation(s)
- Matthew J Witney
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Anthony W Purcell
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Acton, ACT, Australia
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6
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Witney MJ, Tscharke DC. BMX-A and BMX-S: Accessible cell-free methods to estimate peptide-MHC-I affinity and stability. Mol Immunol 2023; 161:1-10. [PMID: 37478775 DOI: 10.1016/j.molimm.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
The affinity and stability of peptide binding to Major Histocompatibility Complex Class I (MHC-I) molecules are fundamental parameters that underpin the specificity and magnitude of CD8+ T cell responses. These parameters can be estimated in some cases by computational tools, but experimental validation remains valuable, especially for stability. Methods to measure peptide binding can be broadly categorised into either cell-based assays using TAP-deficient cell lines such as RMA/S, or cell-free strategies, such as peptide competition-binding assays and surface plasmon resonance. Cell-based assays are subject to confounding biological activity, including peptide trimming by peptidases and dilution of peptide-loaded MHC-I on the surface of cells through cell division. Current cell-free methods require in-house production and purification of MHC-I. In this study, we present the development of new cell-free assays to estimate the relative affinity and dissociation kinetics of peptide binding to MHC-I. These assays, which we have called BMX-A (relative affinity) and BMX-S (kinetic stability), are reliable, scalable and accessible, in that they use off-the-shelf commercial reagents and standard flow cytometry techniques.
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Affiliation(s)
- Matthew J Witney
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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7
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Randall KL, Flesch IEA, Mei Y, Miosge LA, Aye R, Yu Z, Domaschenz H, Hollett NA, Russell TA, Stefanovic T, Wong YC, Goodnow CC, Bertram EM, Enders A, Tscharke DC. DOCK2-deficiency causes defects in anti-viral T cell responses and poor control of herpes simplex virus infection. bioRxiv 2023:2023.08.02.551154. [PMID: 37577614 PMCID: PMC10418165 DOI: 10.1101/2023.08.02.551154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The expanding number of rare immunodeficiency syndromes offers an opportunity to understand key genes that support immune defence against infectious diseases. However, patients with these diseases are by definition rare. In addition, any analysis is complicated by treatments and co-morbid infections requiring the use of mouse models for detailed investigations. Here we develop a mouse model of DOCK2 immunodeficiency and demonstrate that these mice have delayed clearance of herpes simplex virus type 1 (HSV-1) infections. Further, we found that they have a critical, cell intrinsic role of DOCK2 in the clonal expansion of anti-viral CD8+ T cells despite normal early activation of these cells. Finally, while the major deficiency is in clonal expansion, the ability of primed and expanded DOCK2-deficient CD8+ T cells to protect against HSV-1-infection is also compromised. These results provide a contributing cause for the frequent and devastating viral infections seen in DOCK2-deficient patients and improve our understanding of anti-viral CD8+ T cell immunity.
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Affiliation(s)
- Katrina L Randall
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
- School of Medicine and Psychology, Australian National University, Canberra ACT 2600
| | - Inge E A Flesch
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Yan Mei
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Lisa A Miosge
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Racheal Aye
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Zhijia Yu
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Heather Domaschenz
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Natasha A Hollett
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Tiffany A Russell
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Tijana Stefanovic
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Yik Chun Wong
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Christopher C Goodnow
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
- Garvan Institute of Medical Research, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Edward M Bertram
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - Anselm Enders
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601
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8
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Hao Y, Miraghazadeh B, Chand R, Davies AR, Cardinez C, Kwong K, Downes MB, Sweet RA, Cañete PF, D'Orsogna LJ, Fulcher DA, Choo S, Yip D, Peters G, Yip S, Witney MJ, Nekrasov M, Feng ZP, Tscharke DC, Vinuesa CG, Cook MC. CTLA4 protects against maladaptive cytotoxicity during the differentiation of effector and follicular CD4 + T cells. Cell Mol Immunol 2023:10.1038/s41423-023-01027-8. [PMID: 37161048 PMCID: PMC10166697 DOI: 10.1038/s41423-023-01027-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
As chronic antigenic stimulation from infection and autoimmunity is a feature of primary antibody deficiency (PAD), analysis of affected patients could yield insights into T-cell differentiation and explain how environmental exposures modify clinical phenotypes conferred by single-gene defects. CD57 marks dysfunctional T cells that have differentiated after antigenic stimulation. Indeed, while circulating CD57+ CD4+ T cells are normally rare, we found that they are increased in patients with PAD and markedly increased with CTLA4 haploinsufficiency or blockade. We performed single-cell RNA-seq analysis of matched CD57+ CD4+ T cells from blood and tonsil samples. Circulating CD57+ CD4+ T cells (CD4cyt) exhibited a cytotoxic transcriptome similar to that of CD8+ effector cells, could kill B cells, and inhibited B-cell responses. CTLA4 restrained the formation of CD4cyt. While CD57 also marked an abundant subset of follicular helper T cells, which is consistent with their antigen-driven differentiation, this subset had a pre-exhaustion transcriptomic signature marked by TCF7, TOX, and ID3 expression and constitutive expression of CTLA4 and did not become cytotoxic even after CTLA4 inhibition. Thus, CD57+ CD4+ T-cell cytotoxicity and exhaustion phenotypes are compartmentalised between blood and germinal centers. CTLA4 is a key modifier of CD4+ T-cell cytotoxicity, and the pathological CD4cyt phenotype is accentuated by infection.
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Affiliation(s)
- Yuwei Hao
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rochna Chand
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Ainsley R Davies
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Chelisa Cardinez
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kristy Kwong
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Morgan B Downes
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Rebecca A Sweet
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Pablo F Cañete
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Lloyd J D'Orsogna
- Department of Immunology, Fiona Stanley Hospital, Perth, WA, Australia
| | - David A Fulcher
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sharon Choo
- Department of Immunology, The Royal Children's Hospital, Melbourne, VIC, Australia
| | - Desmond Yip
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Geoffrey Peters
- Department of Medical Oncology, The Canberra Hospital, Canberra, ACT, Australia
- ANU Medical School, The Australian National University, Canberra, ACT, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Unit, The University of Sydney, Sydney, NSW, Australia
| | - Matthew J Witney
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Maxim Nekrasov
- The ACRF Biomolecular Resource Facility, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Zhi-Ping Feng
- ANU Bioinformatics Consultancy, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- Translational Research Unit, The Canberra Hospital, Canberra, ACT, Australia.
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
- ANU Medical School, The Australian National University, Canberra, ACT, Australia.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom.
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9
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Ashok D, Taheri M, Garg P, Webb D, Parajuli P, Wang Y, Funnell B, Taylor B, Tscharke DC, Tsuzuki T, Verma NK, Tricoli A, Nisbet DR. Shielding Surfaces from Viruses and Bacteria with a Multiscale Coating. Adv Sci (Weinh) 2022; 9:e2201415. [PMID: 35657076 PMCID: PMC9376840 DOI: 10.1002/advs.202201415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The spread of viral and bacterial pathogens mediated by contact with surfaces is a leading cause of infection worldwide. COVID-19 and the continuous rise of deaths associated with antibiotic-resistant bacteria highlight the need to impede surface-mediated transmission. A sprayable coating with an intrinsic ability to resist the uptake of bacteria and viruses from surfaces and droplets, such as those generated by sneezing or coughing, is reported. The coating also provides an effective microbicidal functionality against bacteria, providing a dual barrier against pathogen uptake and transmission. This antimicrobial functionality is fully preserved following scratching and other induced damage to its surface or 9 days of submersion in a highly concentrated suspension of bacteria. The coatings also register an 11-fold decrease in viral contamination compared to the noncoated surfaces.
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Affiliation(s)
- Deepu Ashok
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
- Nanotechnology Research LaboratoryResearch School of ChemistryThe Australian National UniversityCanberra2601Australia
| | - Mahdiar Taheri
- Laboratory of Advanced Nanomaterials for SustainabilityResearch School of ElectricalEnergy and Materials EngineeringThe Australian National UniversityCanberra2601Australia
| | - Puneet Garg
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
- Nanotechnology Research LaboratoryResearch School of ChemistryThe Australian National UniversityCanberra2601Australia
| | - Daryl Webb
- Centre for Advanced MicroscopyAustralian National UniversityCanberra2601Australia
| | - Pawan Parajuli
- Division of Biomedical Science and BiochemistryResearch School of BiologyThe Australian National UniversityCanberra2601Australia
| | - Yi Wang
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
| | - Bronte Funnell
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
| | - Bradley Taylor
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
| | - David C. Tscharke
- John Curtin School of Medical ResearchAustralian National University131 Garran RoadActonACT2601Australia
| | - Takuya Tsuzuki
- Laboratory of Advanced Nanomaterials for SustainabilityResearch School of ElectricalEnergy and Materials EngineeringThe Australian National UniversityCanberra2601Australia
| | - Naresh K. Verma
- Division of Biomedical Science and BiochemistryResearch School of BiologyThe Australian National UniversityCanberra2601Australia
| | - Antonio Tricoli
- Nanotechnology Research LaboratoryResearch School of ChemistryThe Australian National UniversityCanberra2601Australia
- Nanotechnology Research LaboratoryFaculty of EngineeringThe University of SydneySydney2006Australia
| | - David R. Nisbet
- Laboratory of Advanced BiomaterialsResearch School of Chemistry and the John Curtin School of Medical ResearchThe Australian National UniversityCanberra2601Australia
- The Graeme Clark InstituteFaculty of Engineering and Information Technology and Faculty of MedicineDentistry and Health ServicesThe University of MelbourneMelbourne3010Australia
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10
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Gowripalan A, Smith SA, Tscharke DC. Selection of Vaccinia Virus Recombinants Using CRISPR/Cas9. Bio Protoc 2021; 11:e4270. [PMID: 35087929 DOI: 10.21769/bioprotoc.4270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/07/2021] [Accepted: 10/26/2021] [Indexed: 11/02/2022] Open
Abstract
The engineering of poxvirus genomes is fundamental to primary and applied virology research. Indeed, recombinant poxviruses form the basis for many novel vaccines and virotherapies but producing and purifying these viruses can be arduous. In recent years, CRISPR/Cas9 has become the favoured approach for genome manipulation due to its speed and high success rate. However, recent data suggests poxvirus genomes are not repaired well following Cas9 cleavage. As a result, CRISPR/Cas9 is inefficient as an editing tool, but very effective as a programmable selection agent. Here, we describe protocols for the generation and enrichment of recombinant vaccinia viruses using targeted Cas9 as a selection tool. This novel use of Cas9 is a simple addition to current homologous recombination-based methods that are widespread in the field, facilitating implementation in laboratories already working with poxviruses. This is also the first method that allows for isolation of new vaccinia viruses in less than a fortnight, without the need to incorporate a marker gene or manipulation of large poxvirus genomes in vitro and reactivation with helper viruses. Whilst this protocol describes applications for laboratory strains of vaccinia virus, it should be readily adaptable to other poxviruses. Graphic abstract: Pipeline for Cas9 selection of recombinant poxviruses.
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Affiliation(s)
- Anjali Gowripalan
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Stewart A Smith
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
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11
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Purohit SK, Samer C, McWilliam HEG, Traves R, Steain M, McSharry BP, Kinchington PR, Tscharke DC, Villadangos JA, Rossjohn J, Abendroth A, Slobedman B. Varicella Zoster Virus Impairs Expression of the Nonclassical Major Histocompatibility Complex Class I-Related Gene Protein (MR1). J Infect Dis 2021; 227:391-401. [PMID: 34648018 PMCID: PMC9891426 DOI: 10.1093/infdis/jiab526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/13/2021] [Indexed: 02/04/2023] Open
Abstract
The antigen presentation molecule MR1 (major histocompatibility complex, class I-related) presents ligands derived from the riboflavin (vitamin B) synthesis pathway, which is not present in mammalian species or viruses, to mucosal-associated invariant T (MAIT) cells. In this study, we demonstrate that varicella zoster virus (VZV) profoundly suppresses MR1 expression. We show that VZV targets the intracellular reservoir of immature MR1 for degradation, while preexisting, ligand-bound cell surface MR1 is protected from such targeting, thereby highlighting an intricate temporal relationship between infection and ligand availability. We also identify VZV open reading frame (ORF) 66 as functioning to suppress MR1 expression when this viral protein is expressed during transient transfection, but this is not apparent during infection with a VZV mutant virus lacking ORF66 expression. This indicates that VZV is likely to encode multiple viral genes that target MR1. Overall, we identify an immunomodulatory function of VZV whereby infection suppresses the MR1 biosynthesis pathway.
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Affiliation(s)
| | | | - Hamish E G McWilliam
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Renee Traves
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Megan Steain
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Brian P McSharry
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Paul R Kinchington
- Department of Ophthalmology and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David C Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia,Institute of Infection and Immunity, Cardiff University School of Medicine, Wales, United Kingdom
| | | | - Barry Slobedman
- Correspondence: Barry Slobedman, BSc (Hons), PhD, Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, Charles Perkins Centre, University of Sydney, Camperdown NSW 2006, Australia ()
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12
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Abstract
Viperin is a gene with a broad spectrum of antiviral functions and various mechanisms of action. The role of viperin in herpes simplex virus type 1 (HSV-1) infection is unclear, with conflicting data in the literature that is derived from a single human cell type. We have addressed this gap by investigating viperin during HSV-1 infection in several cell types, spanning species and including immortalized, non-immortalized and primary cells. We demonstrate that viperin upregulation by HSV-1 infection is cell-type-specific, with mouse cells typically showing greater increases compared with those of human origin. Further, overexpression and knockout of mouse, but not human viperin significantly impedes and increases HSV-1 replication, respectively. In primary mouse fibroblasts, viperin upregulation by infection requires viral gene transcription and occurs in a predominantly IFN-independent manner. Further we identify the N-terminal domain of viperin as being required for the anti-HSV-1 activity. Interestingly, this is the region of viperin that differs most between mouse and human, which may explain the apparent species-specific activity against HSV-1. Finally, we show that HSV-1 virion host shutoff (vhs) protein is a key viral factor that antagonises viperin in mouse cells. We conclude that viperin can be upregulated by HSV-1 in mouse and human cells, and that mouse viperin has anti-HSV-1 activity.
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Affiliation(s)
- Yeu-Yang Tseng
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anjali Gowripalan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sarah N. Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Stewart A. Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Karla J. Helbig
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Si Ming Man
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- *Correspondence: David C. Tscharke,
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13
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Lin LCW, Croft SN, Croft NP, Wong YC, Smith SA, Tang SS, Purcell AW, Tscharke DC. Direct Priming of CD8 + T Cells Persists in the Face of Cowpox Virus Inhibitors of Antigen Presentation. J Virol 2021; 95:JVI.00186-21. [PMID: 33692206 PMCID: PMC8139650 DOI: 10.1128/jvi.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/27/2021] [Indexed: 11/30/2022] Open
Abstract
Vaccinia virus (VACV) was the vaccine used to eradicate smallpox and is being repurposed as a vaccine vector. CD8+ T cells are key anti-viral mediators, but require priming to become effector or memory cells. Priming requires an interaction with dendritic cells that are either infected (direct priming), or that have acquired virus proteins but remain uninfected (cross priming). To investigate CD8+ T cell priming pathways for VACV, we engineered the virus to express CPXV12 and CPXV203, two inhibitors of antigen presentation encoded by cowpox virus. These intracellular proteins would be expected to block direct but not cross priming. The inhibitors had diverse impacts on the size of anti-VACV CD8+ T cell responses across epitopes and by different infection routes in mice, superficially suggesting variable use of direct and cross priming. However, when we then tested a form of antigen that requires direct priming, we found surprisingly that CD8+ T cell responses were not diminished by co-expression with CPXV12 and CPXV203. We then directly quantified the impact of CPXV12 and CPXV203 on viral antigen presentation using mass spectrometry, which revealed strong, but incomplete inhibition of antigen presentation by the CPXV proteins. Therefore, direct priming of CD8+ T cells by poxviruses is robust enough to withstand highly potent viral inhibitors of antigen presentation. This is a reminder of the limits of viral immune evasion and shows that viral inhibitors of antigen presentation cannot be assumed to dissect cleanly direct and cross priming of anti-viral CD8+ T cells.ImportanceCD8+ T cells are key to anti-viral immunity, so it is important to understand how they are activated. Many viruses have proteins that protect infected cells from T cell attack by interfering with the process that allows virus infection to be recognised by CD8+ T cells. It is thought that these proteins would also stop infected cells from activating T cells in the first place. However, we show here that this is not the case for two very powerful inhibitory proteins from cowpox virus. This demonstrates the flexibility and robustness of immune processes that turn on the immune responses required to fight infection.
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Affiliation(s)
- Leon C. W. Lin
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Sarah N. Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Nathan P. Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Stewart A. Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Swee-Seong Tang
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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14
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Crosse KM, Monson EA, Dumbrepatil AB, Smith M, Tseng YY, Van der Hoek KH, Revill PA, Saker S, Tscharke DC, G Marsh EN, Beard MR, Helbig KJ. Viperin binds STING and enhances the type-I interferon response following dsDNA detection. Immunol Cell Biol 2020; 99:373-391. [PMID: 33131099 DOI: 10.1111/imcb.12420] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 01/01/2023]
Abstract
Viperin is an interferon-inducible protein that is pivotal for eliciting an effective immune response against an array of diverse viral pathogens. Here we describe a mechanism of viperin's broad antiviral activity by demonstrating the protein's ability to synergistically enhance the innate immune dsDNA signaling pathway to limit viral infection. Viperin co-localized with the key signaling molecules of the innate immune dsDNA sensing pathway, STING and TBK1; binding directly to STING and inducing enhanced K63-linked polyubiquitination of TBK1. Subsequent analysis identified viperin's necessity to bind the cytosolic iron-sulfur assembly component 2A, to prolong its enhancement of the type-I interferon response to aberrant dsDNA. Here we show that viperin facilitates the formation of a signaling enhanceosome, to coordinate efficient signal transduction following activation of the dsDNA signaling pathway, which results in an enhanced antiviral state. We also provide evidence for viperin's radical SAM enzymatic activity to self-limit its immunomodulatory functions. These data further define viperin's role as a positive regulator of innate immune signaling, offering a mechanism of viperin's broad antiviral capacity.
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Affiliation(s)
- Keaton M Crosse
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Ebony A Monson
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Arti B Dumbrepatil
- Department of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Monique Smith
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Yeu-Yang Tseng
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kylie H Van der Hoek
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Peter A Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Subir Saker
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - E Neil G Marsh
- Department of Chemistry and Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Beard
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Karla J Helbig
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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15
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Croft S, Wong YC, Smith SA, Flesch IEA, Tscharke DC. Surprisingly Effective Priming of CD8 + T Cells by Heat-Inactivated Vaccinia Virus Virions. J Virol 2020; 94:e01486-20. [PMID: 32759313 PMCID: PMC7527048 DOI: 10.1128/jvi.01486-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 12/29/2022] Open
Abstract
Robust priming of CD8+ T cells by viruses is considered to require infection and de novo expression of viral antigens. A corollary of this is that inactivated viruses are thought of as being inevitably poor vaccines for eliciting these responses. In contrast to this dogma, we found that some antigens present in vaccinia virus (VACV) virions prime strong CD8+ T cell responses when the virus was rendered noninfectious by heat. More surprisingly, in some cases these responses were similar in magnitude to those primed by infectious virus administered at an equivalent dose. Next, we tested whether this was a special property of particular antigens and their epitopes and found that foreign epitopes tagged onto three different VACV virion proteins were able to elicit CD8+ T cell responses irrespective of whether the virus was viable or heat killed. Further, the polyfunctionality and cytotoxic ability of the CD8+ T cells primed by these VACVs was equivalent irrespective of whether they were administered to mice as inactivated or live viruses. Finally, we used these VACVs in prime-boost combinations of inactivated and live virus and found that priming with dead virus before a live booster was the most immunogenic regime. We conclude that VACV virions can be efficient vectors for targeting antigens to dendritic cells for effective priming of CD8+ T cells, even when rendered noninfectious and speculate that this might also be the case for other viruses.IMPORTANCE The design of viral vectored vaccines is often considered to require a trade-off between efficacy and safety. This is especially the case for vaccines that aim to induce killer (CD8+) T cells, where there is a well-established dogma that links infection in vaccinated individuals with effective induction of immunity. However, we found that some proteins of vaccinia virus generate strong CD8+ T cell responses even when the virus preparation was inactivated by heat prior to administration as a vaccine. We took advantage of this finding by engineering a new vaccine vector virus that could be used as an inactivated vaccine. These results suggest that vaccinia virus may be a more versatile vaccine vector than previously appreciated and that in some instances safety can be prioritized by the complete elimination of viral replication without a proportional loss of immunogenicity.
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Affiliation(s)
- Sarah Croft
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Yik Chun Wong
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Stewart A Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Inge E A Flesch
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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16
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Assmus LM, Guan J, Wu T, Farenc C, Sng XYX, Zareie P, Nguyen A, Nguyen AT, Tscharke DC, Thomas PG, Rossjohn J, Gras S, Croft NP, Purcell AW, La Gruta NL. Overlapping Peptides Elicit Distinct CD8 + T Cell Responses following Influenza A Virus Infection. J Immunol 2020; 205:1731-1742. [PMID: 32868409 DOI: 10.4049/jimmunol.2000689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
The presentation of pathogen-derived peptides on MHC class I molecules is essential for the initiation of adaptive CD8+ T cell immunity, which in turn is critical for effective control of many significant human infections. The identification of immunogenic pathogen-derived epitopes and a detailed understanding of how they are recognized by TCRs is essential for the design of effective T cell-based vaccines. In this study, we have characterized the T cell recognition and immune responses in mice to two naturally presented influenza A virus-derived peptides previously identified from virally infected cells via mass spectrometry. These neuraminidase-derived peptides, NA181-190 (SGPDNGAVAV) and NA181-191 (SGPDNGAVAVL), are completely overlapping with the exception of a 1 aa extension at the C terminus of the longer peptide. This minor peptidic difference results in the induction of two completely independent and non-cross-reactive T cell populations that show distinct functional characteristics after influenza A virus infection of B6 mice. We show that the unique TCR reactivity to the overlapping peptides is present in the naive repertoire prior to immune expansion in B6 mice. Moreover, we provide a structural explanation underlying the distinct CD8+ T cell reactivities, which reinforces the concept that peptide length is a key determinant of Ag specificity in CD8+ T cell responses.
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Affiliation(s)
- Lisa M Assmus
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia.,Institute of Experimental Immunology, University Hospital Bonn, 53105 Bonn, Germany
| | - Jing Guan
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ting Wu
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Carine Farenc
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xavier Y X Sng
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Pirooz Zareie
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Angela Nguyen
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
| | - Nicole L La Gruta
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia;
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17
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Paul S, Croft NP, Purcell AW, Tscharke DC, Sette A, Nielsen M, Peters B. Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system. PLoS Comput Biol 2020; 16:e1007757. [PMID: 32453790 PMCID: PMC7274474 DOI: 10.1371/journal.pcbi.1007757] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/05/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022] Open
Abstract
T cell epitope candidates are commonly identified using computational prediction tools in order to enable applications such as vaccine design, cancer neoantigen identification, development of diagnostics and removal of unwanted immune responses against protein therapeutics. Most T cell epitope prediction tools are based on machine learning algorithms trained on MHC binding or naturally processed MHC ligand elution data. The ability of currently available tools to predict T cell epitopes has not been comprehensively evaluated. In this study, we used a recently published dataset that systematically defined T cell epitopes recognized in vaccinia virus (VACV) infected C57BL/6 mice (expressing H-2Db and H-2Kb), considering both peptides predicted to bind MHC or experimentally eluted from infected cells, making this the most comprehensive dataset of T cell epitopes mapped in a complex pathogen. We evaluated the performance of all currently publicly available computational T cell epitope prediction tools to identify these major epitopes from all peptides encoded in the VACV proteome. We found that all methods were able to improve epitope identification above random, with the best performance achieved by neural network-based predictions trained on both MHC binding and MHC ligand elution data (NetMHCPan-4.0 and MHCFlurry). Impressively, these methods were able to capture more than half of the major epitopes in the top N = 277 predictions within the N = 767,788 predictions made for distinct peptides of relevant lengths that can theoretically be encoded in the VACV proteome. These performance metrics provide guidance for immunologists as to which prediction methods to use, and what success rates are possible for epitope predictions when considering a highly controlled system of administered immunizations to inbred mice. In addition, this benchmark was implemented in an open and easy to reproduce format, providing developers with a framework for future comparisons against new tools. Computational prediction tools are used to screen peptides to identify potential T cell epitope candidates. These tools, developed using machine learning methods, save time and resources in many immunological studies including vaccine discovery and cancer neoantigen identification. In addition to the already existing methods several epitope prediction tools are being developed these days but they lack a comprehensive and uniform evaluation to see which method performs best. In this study we did a comprehensive evaluation of publicly accessible MHC I restricted T cell epitope prediction tools using a recently published dataset of Vaccinia virus epitopes identified in the context of H-2Db and H-2Kb. We found that methods based on artificial neural network architecture and trained on both MHC binding and ligand elution data showed very high performance (NetMHCPan-4.0 and MHCFlurry). This benchmark analysis will help immunologists to choose the right prediction method for their desired work and will also serve as a framework for tool developers to evaluate new prediction methods.
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Affiliation(s)
- Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Nathan P. Croft
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Anthony W. Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, DK Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP San Martín, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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18
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Fox D, Mathur A, Xue Y, Liu Y, Tan WH, Feng S, Pandey A, Ngo C, Hayward JA, Atmosukarto II, Price JD, Johnson MD, Jessberger N, Robertson AAB, Burgio G, Tscharke DC, Fox EM, Leyton DL, Kaakoush NO, Märtlbauer E, Leppla SH, Man SM. Bacillus cereus non-haemolytic enterotoxin activates the NLRP3 inflammasome. Nat Commun 2020; 11:760. [PMID: 32029733 PMCID: PMC7005308 DOI: 10.1038/s41467-020-14534-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Inflammasomes are important for host defence against pathogens and homeostasis with commensal microbes. Here, we show non-haemolytic enterotoxin (NHE) from the neglected human foodborne pathogen Bacillus cereus is an activator of the NLRP3 inflammasome and pyroptosis. NHE is a non-redundant toxin to haemolysin BL (HBL) despite having a similar mechanism of action. Via a putative transmembrane region, subunit C of NHE initiates binding to the plasma membrane, leading to the recruitment of subunit B and subunit A, thus forming a tripartite lytic pore that is permissive to efflux of potassium. NHE mediates killing of cells from multiple lineages and hosts, highlighting a versatile functional repertoire in different host species. These data indicate that NHE and HBL operate synergistically to induce inflammation and show that multiple virulence factors from the same pathogen with conserved function and mechanism of action can be exploited for sensing by a single inflammasome.
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Affiliation(s)
- Daniel Fox
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Anukriti Mathur
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Yansong Xue
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Yunqi Liu
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Wei Hong Tan
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Shouya Feng
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Abhimanu Pandey
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Chinh Ngo
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Jenni A Hayward
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Ines I Atmosukarto
- Lipotek Pty Ltd. The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Jason D Price
- Lipotek Pty Ltd. The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Matthew D Johnson
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Nadja Jessberger
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
| | - Avril A B Robertson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David C Tscharke
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Edward M Fox
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Denisse L Leyton
- Research School of Biology, The Australian National University, Canberra, Australia.,Medical School, The Australian National University, Canberra, Australia
| | - Nadeem O Kaakoush
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
| | - Stephen H Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Si Ming Man
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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19
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Abstract
The CRISPR/Cas9 gene editing system is a robust and versatile technology that has revolutionized our capacity for genome engineering and is applicable in a wide range of organisms, including large dsDNA viruses. Here we provide an efficient methodology that can be used both for marker-based and for marker-free CRISPR/Cas9-mediated editing of the HSV-1 genome. In our method, Cas9, guide RNAs and a homology-directed repair template are provided to cells by cotransection of plasmids, followed by introduction of the HSV genome by infection. This method offers a great deal of flexibility, facilitating editing of the HSV genome that spans the range from individual nucleotide changes to large deletions and insertions.
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Affiliation(s)
- Thilaga Velusamy
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Anjali Gowripalan
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.
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20
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Zanker DJ, Oveissi S, Tscharke DC, Duan M, Wan S, Zhang X, Xiao K, Mifsud NA, Gibbs J, Izzard L, Dlugolenski D, Faou P, Laurie KL, Vigneron N, Barr IG, Stambas J, Van den Eynde BJ, Bennink JR, Yewdell JW, Chen W. Influenza A Virus Infection Induces Viral and Cellular Defective Ribosomal Products Encoded by Alternative Reading Frames. J Immunol 2019; 202:3370-3380. [PMID: 31092636 DOI: 10.4049/jimmunol.1900070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
Abstract
The importance of antiviral CD8+ T cell recognition of alternative reading frame (ARF)-derived peptides is uncertain. In this study, we describe an epitope (NS1-ARF21-8) present in a predicted 14-residue peptide encoded by the +1 register of NS1 mRNA in the influenza A virus (IAV). NS1-ARF21-8 elicits a robust, highly functional CD8+ T cell response in IAV-infected BALB/c mice. NS1-ARF21-8 is presented from unspliced NS mRNA, likely from downstream initiation on a Met residue that comprises the P1 position of NS1-ARF21-8 Derived from a 14-residue peptide with no apparent biological function and negligible impacts on IAV infection, infectivity, and pathogenicity, NS1-ARF21-8 provides a clear demonstration of how immunosurveillance exploits natural errors in protein translation to provide antiviral immunity. We further show that IAV infection enhances a model cellular ARF translation, which potentially has important implications for virus-induced autoimmunity.
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Affiliation(s)
- Damien J Zanker
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sara Oveissi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - David C Tscharke
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Siyuan Wan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Xiaomu Zhang
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Kun Xiao
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia.,Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - James Gibbs
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lenny Izzard
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Daniel Dlugolenski
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Karen L Laurie
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia; and
| | | | - Ian G Barr
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia; and
| | - John Stambas
- School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
| | | | - Jack R Bennink
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
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21
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Croft NP, Smith SA, Pickering J, Sidney J, Peters B, Faridi P, Witney MJ, Sebastian P, Flesch IEA, Heading SL, Sette A, La Gruta NL, Purcell AW, Tscharke DC. Most viral peptides displayed by class I MHC on infected cells are immunogenic. Proc Natl Acad Sci U S A 2019; 116:3112-3117. [PMID: 30718433 PMCID: PMC6386720 DOI: 10.1073/pnas.1815239116] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
CD8+ T cells are essential effectors in antiviral immunity, recognizing short virus-derived peptides presented by MHC class I (pMHCI) on the surface of infected cells. However, the fraction of viral pMHCI on infected cells that are immunogenic has not been shown for any virus. To approach this fundamental question, we used peptide sequencing by high-resolution mass spectrometry to identify more than 170 vaccinia virus pMHCI presented on infected mouse cells. Next, we screened each peptide for immunogenicity in multiple virus-infected mice, revealing a wide range of immunogenicities. A surprisingly high fraction (>80%) of pMHCI were immunogenic in at least one infected mouse, and nearly 40% were immunogenic across more than half of the mice screened. The high number of peptides found to be immunogenic and the distribution of responses across mice give us insight into the specificity of antiviral CD8+ T cell responses.
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Affiliation(s)
- Nathan P Croft
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Stewart A Smith
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Jana Pickering
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Pouya Faridi
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Witney
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Prince Sebastian
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Inge E A Flesch
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Sally L Heading
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Nicole L La Gruta
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia;
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22
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Gebhardt T, Palendira U, Tscharke DC, Bedoui S. Tissue-resident memory T cells in tissue homeostasis, persistent infection, and cancer surveillance. Immunol Rev 2018; 283:54-76. [DOI: 10.1111/imr.12650] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas Gebhardt
- Department of Microbiology and Immunology; The University of Melbourne at the Peter Doherty Institute for Infection and Immunity; Melbourne Vic. Australia
| | - Umaimainthan Palendira
- Centenary Institute; The University of Sydney; Sydney NSW Australia
- Sydney Medical School; The University of Sydney; Sydney NSW Australia
| | - David C. Tscharke
- The John Curtin School of Medical Research; The Australian National University; Canberra ACT Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology; The University of Melbourne at the Peter Doherty Institute for Infection and Immunity; Melbourne Vic. Australia
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23
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Russell TA, Velusamy T, Tseng YY, Tscharke DC. Increasing antigen presentation on HSV-1-infected cells increases lesion size but does not alter neural infection or latency. J Gen Virol 2018; 99:682-692. [PMID: 29620508 PMCID: PMC5994700 DOI: 10.1099/jgv.0.001059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
CD8+ T cells have a role in the control of acute herpes simplex virus (HSV) infection and may also be important in the maintenance of latency. In this study we have explored the consequences of boosting the efficacy of CD8+ T cells against HSV by increasing the amount of an MHC I-presented epitope on the surface of infected cells. To do this we used HSVs engineered to express an extra copy of the immunodominant CD8+ T cell epitope in C57Bl/6 mice, namely gB498 (SSIEFARL). Despite greater presentation of gB498 on infected cells, CD8+ T cell responses to these viruses in mice were similar to those elicited by a control virus. Further, the expression of extra gB498 did not significantly alter the extent or stability of latency in our mouse model, and virus loads in skin and sensory ganglia of infected mice were not affected. Surprisingly, mice infected with these viruses developed significantly larger skin lesions than those infected with control viruses and notably, this phenotype was dependent on MHC haplotype. Therefore increasing the visibility of HSV-infected cells to CD8+ T cell attack did not impact neural infection or latency, but rather enhanced pathology in the skin.
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Affiliation(s)
- Tiffany A Russell
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Present address: Department of Microbial Sciences, University of Surrey, Guildford, UK
| | - Thilaga Velusamy
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Yeu-Yang Tseng
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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24
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Westwood JA, Ellis S, Danne J, Johnson C, Oorschot V, Ramm G, Tscharke DC, Davenport AJ, Whisstock JC, Darcy PK, Kershaw MH, Slaney CY. An ultrastructural investigation of tumors undergoing regression mediated by immunotherapy. Oncotarget 2017; 8:115215-115229. [PMID: 29383154 PMCID: PMC5777766 DOI: 10.18632/oncotarget.23215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022] Open
Abstract
While immunotherapy employing chimeric antigen receptor (CAR) T cells can be effective against a variety of tumor types, little is known about what happens within the tumor at an ultrastructural level during tumor regression. Here, we used transmission electron microscopy to investigate morphologic and cellular features of tumors responding to immunotherapy composed of adoptive transfer of dual-specific CAR T cells and a vaccine, supported by preconditioning irradiation and interleukin-2. Tumors responded rapidly, and large areas of cell death were apparent by 4 days after treatment. The pleomorphic and metabolically active nature of tumor cells and phagocytic activity of macrophages were apparent in electron microscopic images of tumors prior to treatment. Following treatment, morphologic features of various types of tumor cell death were observed, including apoptosis, paraptosis and necrosis. Large numbers of lipid droplets were evident in tumor cells undergoing apoptosis. Macrophages were the predominant leukocyte type infiltrating tumors before treatment. Macrophages decreased in frequency and number after treatment, whereas an increasing accumulation of neutrophils and T lymphocytes was observed following treatment. Phagocytic activity of macrophages and neutrophils was apparent, while T cells could be observed in close association with tumor cells with potential immunological synapses present. These observations highlight the cellular composition and ultrastructural appearance of tumors undergoing regression mediated by immunotherapy.
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Affiliation(s)
- Jennifer A Westwood
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia
| | - Sarah Ellis
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Jill Danne
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Chad Johnson
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Viola Oorschot
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, Australia
| | - Georg Ramm
- Monash Ramaciotti Centre for Cryo Electron Microscopy, Monash University, Clayton, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | | - James C Whisstock
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Australia
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Michael H Kershaw
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Clare Y Slaney
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
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25
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Melo-Silva CR, Tscharke DC, Lobigs M, Koskinen A, Müllbacher A, Regner M. Ectromelia virus N1L is essential for virulence but not dissemination in a classical model of mousepox. Virus Res 2017; 228:61-65. [PMID: 27865865 DOI: 10.1016/j.virusres.2016.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/08/2016] [Accepted: 11/10/2016] [Indexed: 10/20/2022]
Abstract
Mousepox is caused by the orthopoxvirus ectromelia virus (ECTV), and is thought to be transmitted via skin abrasions. We studied the ECTV virulence factor N1 following subcutaneous infection of mousepox-susceptible BALB/c mice. In this model, ECTV lacking N1L gene was attenuated more than 1000-fold compared with wild-type virus and replication was profoundly reduced as early as four days after infection. However, in contrast to data from an intranasal model, N1 protein was not required for virus dissemination. Further, neither T cell nor cytokine responses were enhanced in the absence of N1. Together with the early timing of reduced virus titres, this suggests that in a cutaneous model, N1 exerts its function at the level of infected cells or in the inhibition of the very earliest effectors of innate immunity.
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Affiliation(s)
- Carolina R Melo-Silva
- Department of Emerging Pathogens and Vaccines, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia.
| | - David C Tscharke
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia
| | - Mario Lobigs
- Department of Emerging Pathogens and Vaccines, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia
| | - Aulikki Koskinen
- Department of Emerging Pathogens and Vaccines, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia
| | - Arno Müllbacher
- Department of Emerging Pathogens and Vaccines, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia; Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia
| | - Matthias Regner
- Department of Emerging Pathogens and Vaccines, The John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia
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26
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Slaney CY, von Scheidt B, Davenport AJ, Beavis PA, Westwood JA, Mardiana S, Tscharke DC, Ellis S, Prince HM, Trapani JA, Johnstone RW, Smyth MJ, Teng MW, Ali A, Yu Z, Rosenberg SA, Restifo NP, Neeson P, Darcy PK, Kershaw MH. Dual-specific Chimeric Antigen Receptor T Cells and an Indirect Vaccine Eradicate a Variety of Large Solid Tumors in an Immunocompetent, Self-antigen Setting. Clin Cancer Res 2016; 23:2478-2490. [PMID: 27965307 DOI: 10.1158/1078-0432.ccr-16-1860] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022]
Abstract
Purpose: While adoptive transfer of T cells bearing a chimeric antigen receptor (CAR) can eliminate substantial burdens of some leukemias, the ultimate challenge remains the eradication of large solid tumors for most cancers. We aimed to develop an immunotherapy approach effective against large tumors in an immunocompetent, self-antigen preclinical mouse model.Experimental Design: In this study, we generated dual-specific T cells expressing both a CAR specific for Her2 and a TCR specific for the melanocyte protein (gp100). We used a regimen of adoptive cell transfer incorporating vaccination (ACTIV), with recombinant vaccinia virus expressing gp100, to treat a range of tumors including orthotopic breast tumors and large liver tumors.Results: ACTIV therapy induced durable complete remission of a variety of Her2+ tumors, some in excess of 150 mm2, in immunocompetent mice expressing Her2 in normal tissues, including the breast and brain. Vaccinia virus induced extensive proliferation of T cells, leading to massive infiltration of T cells into tumors. Durable tumor responses required the chemokine receptor CXCR3 and exogenous IL2, but were independent of IFNγ. Mice were resistant to tumor rechallenge, indicating immune memory involving epitope spreading. Evidence of limited neurologic toxicity was observed, associated with infiltration of cerebellum by T cells, but was only transient.Conclusions: This study supports a view that it is possible to design a highly effective combination immunotherapy for solid cancers, with acceptable transient toxicity, even when the target antigen is also expressed in vital tissues. Clin Cancer Res; 23(10); 2478-90. ©2016 AACR.
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Affiliation(s)
- Clare Y Slaney
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Bianca von Scheidt
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexander J Davenport
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Jennifer A Westwood
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Sherly Mardiana
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - David C Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Sarah Ellis
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - H Miles Prince
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Joseph A Trapani
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ricky W Johnstone
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michele W Teng
- Cancer Immunoregulation and Immunotherapy Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Aesha Ali
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Zhiya Yu
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Steven A Rosenberg
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Nicholas P Restifo
- Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, Maryland
| | - Paul Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Phillip K Darcy
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Immunology, Monash University, Clayton, Australia
| | - Michael H Kershaw
- Cancer Immunology Program, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Immunology, Monash University, Clayton, Australia
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27
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Abstract
Herpes simplex virus (HSV) has provided the prototype for viral latency with previously well-defined acute or lytic and latent phases. More recently, the deep quiescence of HSV latency has been questioned with evidence that lytic genes can be transcribed in this state. However, to date the only evidence that these transcripts might be translated has come from immunological studies that show activated T cells persist in the nervous system during latency. Here we use a highly sensitive Cre-marking model to show that lytic and latent phases are less clearly defined in two significant ways. First, around half of the HSV spread leading to latently infected sites occurred beyond the initial acute infection and second, we show direct evidence that lytic promoters can drive protein expression during latency. Herpes simplex virus, which causes cold sores and genital herpes, has active and inactive (or latent) phases of infection that have been considered to be distinct. In this study we found that the active phase of infection, including spread in the nervous system, continues longer than has been previously appreciated. We also show evidence that virus genes previously only associated with active infection are turned on during latency. These genes are of particular interest because other work has found that they are targets of the immune response to HSV. The extent and nature of residual viral activity during latency is important to understand because it may suggest therapeutic targets to reduce recurrent HSV disease.
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Affiliation(s)
- Tiffany A. Russell
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David C. Tscharke
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
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28
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Abstract
Vaccinia virus (VACV) genes are characterized as either essential or non-essential for growth in culture. It seems intuitively obvious that if a gene can be deleted without imparting a growth defect in vitro it does not have a function related to basic replication or spread. However, this interpretation relies on the untested assumption that there is no redundancy across the genes that have roles in growth in cell culture. First, we provide a comprehensive summary of the literature that describes the essential genes of VACV. Next, we looked for interactions between large blocks of non-essential genes located at the ends of the genome by investigating sets of VACVs with large deletions at the genomic termini. Viruses with deletions at either end of the genome behaved as expected, exhibiting only mild or host-range defects. In contrast, combining deletions at both ends of the genome for the VACV Western Reserve (WR) strain caused a devastating growth defect on all cell lines tested. Unexpectedly, we found that the well-studied VACV growth factor homologue encoded by C11R has a role in growth in vitro that is exposed when 42 genes are absent from the left end of the VACV WR genome. These results demonstrate that some non-essential genes contribute to basic viral growth, but redundancy means these functions are not revealed by single-gene-deletion mutants.
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Affiliation(s)
- Bianca M Dobson
- Division of Biomedical Science and Biochemistry, Research School of Biology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia.,Division of Biomedical Science and Biochemistry, Research School of Biology, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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29
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Gram AM, Oosenbrug T, Lindenbergh MFS, Büll C, Comvalius A, Dickson KJI, Wiegant J, Vrolijk H, Lebbink RJ, Wolterbeek R, Adema GJ, Griffioen M, Heemskerk MHM, Tscharke DC, Hutt-Fletcher LM, Wiertz EJHJ, Hoeben RC, Ressing ME. The Epstein-Barr Virus Glycoprotein gp150 Forms an Immune-Evasive Glycan Shield at the Surface of Infected Cells. PLoS Pathog 2016; 12:e1005550. [PMID: 27077376 PMCID: PMC4831753 DOI: 10.1371/journal.ppat.1005550] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 03/14/2016] [Indexed: 12/15/2022] Open
Abstract
Cell-mediated immunity plays a key role in host control of viral infection. This is exemplified by life-threatening reactivations of e.g. herpesviruses in individuals with impaired T-cell and/or iNKT cell responses. To allow lifelong persistence and virus production in the face of primed immunity, herpesviruses exploit immune evasion strategies. These include a reduction in viral antigen expression during latency and a number of escape mechanisms that target antigen presentation pathways. Given the plethora of foreign antigens expressed in virus-producing cells, herpesviruses are conceivably most vulnerable to elimination by cell-mediated immunity during the replicative phase of infection. Here, we show that a prototypic herpesvirus, Epstein-Barr virus (EBV), encodes a novel, broadly acting immunoevasin, gp150, that is expressed during the late phase of viral replication. In particular, EBV gp150 inhibits antigen presentation by HLA class I, HLA class II, and the non-classical, lipid-presenting CD1d molecules. The mechanism of gp150-mediated T-cell escape does not depend on degradation of the antigen-presenting molecules nor does it require gp150’s cytoplasmic tail. Through its abundant glycosylation, gp150 creates a shield that impedes surface presentation of antigen. This is an unprecedented immune evasion mechanism for herpesviruses. In view of its likely broader target range, gp150 could additionally have an impact beyond escape of T cell activation. Importantly, B cells infected with a gp150-null mutant EBV displayed rescued levels of surface antigen presentation by HLA class I, HLA class II, and CD1d, supporting an important role for iNKT cells next to classical T cells in fighting EBV infection. At the same time, our results indicate that EBV gp150 prolongs the timespan for producing viral offspring at the most vulnerable stage of the viral life cycle. The human herpesvirus Epstein-Barr virus (EBV) is an important human pathogen involved in infectious mononucleosis and several malignant tumors, including lymphomas in the immunosuppressed. Upon primary infection, a balance between virus and host is established, to which EBV’s capacity to dodge T cell-mediated attack contributes. Here we identify the late protein EBV gp150 as a novel immunoevasin, frustrating antigen presentation by HLA class I, class II, and CD1d molecules. EBV gp150’s many sialoglycans create a shield impeding surface detection of presented antigen. Interestingly, exploiting glycan shielding as a mechanism to mask surface exposed proteins on infected cells could permit EBV to additionally modulate other aspects of host antiviral defense. B cells producing wild-type EBV escaped immune recognition more efficiently than those infected with a gp150-null virus, pointing towards a role for gp150 in natural infection. Our results reveal a novel, broadly active strategy by which a herpesvirus glycoprotein, EBV gp150, blocks antigen presentation to T cells through glycan shielding, a new paradigm in herpesvirus immune evasion.
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Affiliation(s)
- Anna M. Gram
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Timo Oosenbrug
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Christian Büll
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Anouskha Comvalius
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kathryn J. I. Dickson
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Joop Wiegant
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Vrolijk
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ron Wolterbeek
- Department of Medical Statistics & Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gosse J. Adema
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - David C. Tscharke
- John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Lindsey M. Hutt-Fletcher
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, United States of America
| | | | - Rob C. Hoeben
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Maaike E. Ressing
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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30
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Purcell AW, Croft NP, Tscharke DC. Immunology by numbers: quantitation of antigen presentation completes the quantitative milieu of systems immunology! Curr Opin Immunol 2016; 40:88-95. [PMID: 27060633 DOI: 10.1016/j.coi.2016.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/15/2016] [Accepted: 03/20/2016] [Indexed: 10/22/2022]
Abstract
We review approaches to quantitate antigen presentation using a variety of biological and biochemical readouts and highlight the emerging role of mass spectrometry (MS) in defining and quantifying MHC-bound peptides presented at the cell surface. The combination of high mass accuracy in the determination of the molecular weight of the intact peptide of interest and its signature pattern of fragmentation during tandem MS provide an unambiguous and definitive identification. This is in contrast to the potential receptor cross-reactivity towards closely related peptides and variable dose responsiveness seen in biological readouts. In addition, we gaze into the not too distant future where big data approaches in MS can be accommodated to quantify whole immunopeptidomes both in vitro and in vivo.
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Affiliation(s)
- Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
| | - Nathan P Croft
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - David C Tscharke
- The John Curtin School of Medical Research, ANU College of Medicine, Biology & Environment, Australian National University, Acton, ACT 2601, Australia.
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31
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32
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Flesch IEA, Hollett NA, Wong YC, Quinan BR, Howard D, da Fonseca FG, Tscharke DC. Extent of Systemic Spread Determines CD8+ T Cell Immunodominance for Laboratory Strains, Smallpox Vaccines, and Zoonotic Isolates of Vaccinia Virus. J Immunol 2015. [PMID: 26195812 DOI: 10.4049/jimmunol.1402508] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
CD8(+) T cells that recognize virus-derived peptides presented on MHC class I are vital antiviral effectors. Such peptides presented by any given virus vary greatly in immunogenicity, allowing them to be ranked in an immunodominance hierarchy. However, the full range of parameters that determine immunodominance and the underlying mechanisms remain unknown. In this study, we show across a range of vaccinia virus strains, including the current clonal smallpox vaccine, that the ability of a strain to spread systemically correlated with reduced immunodominance. Reduction in immunodominance was observed both in the lymphoid system and at the primary site of infection. Mechanistically, reduced immunodominance was associated with more robust priming and especially priming in the spleen. Finally, we show this is not just a property of vaccine and laboratory strains of virus, because an association between virulence and immunodominance was also observed in isolates from an outbreak of zoonotic vaccinia virus that occurred in Brazil.
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Affiliation(s)
- Inge E A Flesch
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Natasha A Hollett
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Yik Chun Wong
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Bárbara Resende Quinan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia; Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; and
| | - Debbie Howard
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Flávio G da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil; and
| | - David C Tscharke
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia; John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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33
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Croft NP, Purcell AW, Tscharke DC. Quantifying epitope presentation using mass spectrometry. Mol Immunol 2015; 68:77-80. [PMID: 26118903 DOI: 10.1016/j.molimm.2015.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/01/2023]
Abstract
Understanding the absolute quantities of MHC-bound epitopes (pMHC) presented on the surface of cells has long been a critical missing element in our knowledge of antigen presentation to T cells. Until recently, attaining such information has been restricted to the use of pMHC complex-specific monoclonal antibodies or T cell assays probing fractionated peptides eluted from cells. Although successful in a variety of cases, such approaches are limited in their scope and feasibility due to the nature of the reagents they are reliant upon. Here we report on the advancement of targeted mass spectrometry techniques to provide simultaneous and direct measurements of the relative and absolute levels of pMHC molecules and its potential for impact upon the field of antigen processing and presentation.
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Affiliation(s)
- Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3141, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3141, Australia
| | - David C Tscharke
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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34
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Flesch IEA, Randall KL, Hollett NA, Di Law H, Miosge LA, Sontani Y, Goodnow CC, Tscharke DC. Delayed control of herpes simplex virus infection and impaired CD4(+) T-cell migration to the skin in mouse models of DOCK8 deficiency. Immunol Cell Biol 2015; 93:517-21. [PMID: 25776845 PMCID: PMC4496291 DOI: 10.1038/icb.2015.32] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/01/2015] [Accepted: 02/14/2015] [Indexed: 12/19/2022]
Abstract
DOCK8 deficiency in humans and mice leads to multiple defects in immune cell numbers and function. Patients with this immunodeficiency have a high morbidity and mortality, and are distinguished by chronic cutaneous viral infections, including those caused by herpes simplex virus (HSV). The underlying mechanism of the specific susceptibility to these chronic cutaneous viral infections is currently unknown, largely because the effect of DOCK8 deficiency has not been studied in suitable models. A better understanding of these mechanisms is required to underpin the development of more specific therapies. Here we show that DOCK8-deficient mice have poor control of primary cutaneous herpes simplex lesions and this is associated with increased virus loads. Furthermore, DOCK8-deficient mice showed a lack of CD4(+) T-cell infiltration into HSV-infected skin.
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Affiliation(s)
- Inge E A Flesch
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Katrina L Randall
- 1] John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia [2] ANU Medical School, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Natasha A Hollett
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hsei Di Law
- 1] John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia [2] ANU Medical School, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Lisa A Miosge
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yovina Sontani
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christopher C Goodnow
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David C Tscharke
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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35
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Croft NP, de Verteuil DA, Smith SA, Wong YC, Schittenhelm RB, Tscharke DC, Purcell AW. Simultaneous Quantification of Viral Antigen Expression Kinetics Using Data-Independent (DIA) Mass Spectrometry. Mol Cell Proteomics 2015; 14:1361-72. [PMID: 25755296 DOI: 10.1074/mcp.m114.047373] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Indexed: 11/06/2022] Open
Abstract
The generation of antigen-specific reagents is a significant bottleneck in the study of complex pathogens that express many hundreds to thousands of different proteins or to emerging or new strains of viruses that display potential pandemic qualities and therefore require rapid investigation. In these instances the development of antibodies for example can be prohibitively expensive to cover the full pathogen proteome, or the lead time may be unacceptably long in urgent cases where new highly pathogenic viral strains may emerge. Because genomic information on such pathogens can be rapidly acquired this opens up avenues using mass spectrometric approaches to study pathogen antigen expression, host responses and for screening the utility of therapeutics. In particular, data-independent acquisition (DIA) modalities on high-resolution mass spectrometers generate spectral information on all components of a complex sample providing depth of coverage hitherto only seen in genomic deep sequencing. The spectral information generated by DIA can be iteratively interrogated for potentially any protein of interest providing both evidence of protein expression and quantitation. Here we apply a solely DIA mass spectrometry based methodology to profile the viral antigen expression in cells infected with vaccinia virus up to 9 h post infection without the need for antigen specific antibodies or other reagents. We demonstrate deep coverage of the vaccinia virus proteome using a SWATH-MS acquisition approach, extracting quantitative kinetics of 100 virus proteins within a single experiment. The results highlight the complexity of vaccinia protein expression, complementing what is known at the transcriptomic level, and provide a valuable resource and technique for future studies of viral infection and replication kinetics. Furthermore, they highlight the utility of DIA and mass spectrometry in the dissection of host-pathogen interactions.
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Affiliation(s)
- Nathan P Croft
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - Danielle A de Verteuil
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - Stewart A Smith
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Yik Chun Wong
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Ralf B Schittenhelm
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia
| | - David C Tscharke
- §Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
| | - Anthony W Purcell
- From the ‡Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3141, Australia;
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36
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Russell TA, Stefanovic T, Tscharke DC. Engineering herpes simplex viruses by infection-transfection methods including recombination site targeting by CRISPR/Cas9 nucleases. J Virol Methods 2014; 213:18-25. [PMID: 25479355 DOI: 10.1016/j.jviromet.2014.11.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/20/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022]
Abstract
Herpes simplex viruses (HSVs) are frequent human pathogens and the ability to engineer these viruses underpins much research into their biology and pathogenesis. Often the ultimate aim is to produce a virus that has the desired phenotypic change and no additional alterations in characteristics. This requires methods that minimally disrupt the genome and, for insertions of foreign DNA, sites must be found that can be engineered without disrupting HSV gene function or expression. This study advances both of these requirements. Firstly, the use of homologous recombination between the virus genome and plasmids in mammalian cells is a reliable way to engineer HSV such that minimal genome changes are made. This has most frequently been achieved by cotransfection of plasmid and isolated viral genomic DNA, but an alternative is to supply the virus genome by infection in a transfection-infection method. Such approaches can also incorporate CRISPR/Cas9 genome engineering methods. Current descriptions of infection-transfection methods, either with or without the addition of CRISPR/Cas9 targeting, are limited in detail and the extent of optimization. In this study it was found that transfection efficiency and the length of homologous sequences improve the efficiency of recombination in these methods, but the targeting of the locus to be engineered by CRISPR/Cas9 nucleases has an overriding positive impact. Secondly, the intergenic space between UL26 and UL27 was reexamined as a site for the addition of foreign DNA and a position identified that allows insertions without compromising HSV growth in vitro or in vivo.
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Affiliation(s)
- Tiffany A Russell
- Research School of Biology, The Australian National University, Bldg #134 Linnaeus Way, Canberra, ACT 0200, Australia.
| | - Tijana Stefanovic
- Research School of Biology, The Australian National University, Bldg #134 Linnaeus Way, Canberra, ACT 0200, Australia
| | - David C Tscharke
- Research School of Biology, The Australian National University, Bldg #134 Linnaeus Way, Canberra, ACT 0200, Australia.
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37
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Trujillo JA, Croft NP, Dudek NL, Channappanavar R, Theodossis A, Webb AI, Dunstone MA, Illing PT, Butler NS, Fett C, Tscharke DC, Rossjohn J, Perlman S, Purcell AW. The cellular redox environment alters antigen presentation. J Biol Chem 2014; 289:27979-91. [PMID: 25135637 DOI: 10.1074/jbc.m114.573402] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cysteine-containing peptides represent an important class of T cell epitopes, yet their prevalence remains underestimated. We have established and interrogated a database of around 70,000 naturally processed MHC-bound peptides and demonstrate that cysteine-containing peptides are presented on the surface of cells in an MHC allomorph-dependent manner and comprise on average 5-10% of the immunopeptidome. A significant proportion of these peptides are oxidatively modified, most commonly through covalent linkage with the antioxidant glutathione. Unlike some of the previously reported cysteine-based modifications, this represents a true physiological alteration of cysteine residues. Furthermore, our results suggest that alterations in the cellular redox state induced by viral infection are communicated to the immune system through the presentation of S-glutathionylated viral peptides, resulting in altered T cell recognition. Our data provide a structural basis for how the glutathione modification alters recognition by virus-specific T cells. Collectively, these results suggest that oxidative stress represents a mechanism for modulating the virus-specific T cell response.
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Affiliation(s)
- Jonathan A Trujillo
- From the Department of Microbiology and the Interdisciplinary Program in Immunology, University of Iowa, Iowa City, Iowa 52242
| | - Nathan P Croft
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
| | - Nadine L Dudek
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
| | | | | | - Andrew I Webb
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Patricia T Illing
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Noah S Butler
- From the Department of Microbiology and the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia, and
| | | | - David C Tscharke
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, the Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Stanley Perlman
- From the Department of Microbiology and the Interdisciplinary Program in Immunology, University of Iowa, Iowa City, Iowa 52242,
| | - Anthony W Purcell
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
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38
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Macleod BL, Bedoui S, Hor JL, Mueller SN, Russell TA, Hollett NA, Heath WR, Tscharke DC, Brooks AG, Gebhardt T. Distinct APC subtypes drive spatially segregated CD4+ and CD8+ T-cell effector activity during skin infection with HSV-1. PLoS Pathog 2014; 10:e1004303. [PMID: 25121482 PMCID: PMC4133397 DOI: 10.1371/journal.ppat.1004303] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/25/2014] [Indexed: 12/13/2022] Open
Abstract
Efficient infection control requires potent T-cell responses at sites of pathogen replication. However, the regulation of T-cell effector function in situ remains poorly understood. Here, we show key differences in the regulation of effector activity between CD4+ and CD8+ T-cells during skin infection with HSV-1. IFN-γ-producing CD4+ T cells disseminated widely throughout the skin and draining lymph nodes (LN), clearly exceeding the epithelial distribution of infectious virus. By contrast, IFN-γ-producing CD8+ T cells were only found within the infected epidermal layer of the skin and associated hair follicles. Mechanistically, while various subsets of lymphoid- and skin-derived dendritic cells (DC) elicited IFN-γ production by CD4+ T cells, CD8+ T cells responded exclusively to infected epidermal cells directly presenting viral antigen. Notably, uninfected cross-presenting DCs from both skin and LNs failed to trigger IFN-γ production by CD8+ T-cells. Thus, we describe a previously unappreciated complexity in the regulation of CD4+ and CD8+ T-cell effector activity that is subset-specific, microanatomically distinct and involves largely non-overlapping types of antigen-presenting cells (APC). HSV-1 is a widely distributed pathogen causing a life-long latent infection associated with periodic bouts of reactivation and severe clinical complications. Adaptive immune responses encompassing CD4+ and CD8+ T-cell activities are key to both the clearance of infectious virus and the control of latent infection. However, precisely how such T-cell responses are regulated, particularly within acutely infected peripheral tissues, remains poorly understood. Using a mouse model of HSV-1 skin infection, we describe a complex regulation of T-cell responses at the site of acute infection. These responses were subset-specific and anatomically distinct, with CD4+ and CD8+ T-cell activities being directed to distinct anatomical compartments within the skin. While IFN-γ-producing CD4+ T cells were broadly distributed, including skin regions a considerable distance away from infected cells, CD8+ T-cell activity was strictly confined to directly infected epithelial compartments. This unexpected spatial segregation was a direct consequence of the involvement of largely non-overlapping types of antigen-presenting cells in driving CD4+ and CD8+ T-cell effector activity. Our results provide novel insights into the cellular regulation of T-cell immunity within peripheral tissues and have the potential to guide the development of T-cell subset-specific approaches for therapeutic and prophylactic intervention in antimicrobial immunity and autoimmunity.
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Affiliation(s)
- Bethany L. Macleod
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sammy Bedoui
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jyh Liang Hor
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Scott N. Mueller
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tiffany A. Russell
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Natasha A. Hollett
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - William R. Heath
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David C. Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Thomas Gebhardt
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- * E-mail:
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Ma JZ, Russell TA, Spelman T, Carbone FR, Tscharke DC. Lytic gene expression is frequent in HSV-1 latent infection and correlates with the engagement of a cell-intrinsic transcriptional response. PLoS Pathog 2014; 10:e1004237. [PMID: 25058429 PMCID: PMC4110040 DOI: 10.1371/journal.ppat.1004237] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/23/2014] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex viruses (HSV) are significant human pathogens that provide one of the best-described examples of viral latency and reactivation. HSV latency occurs in sensory neurons, being characterized by the absence of virus replication and only fragmentary evidence of protein production. In mouse models, HSV latency is especially stable but the detection of some lytic gene transcription and the ongoing presence of activated immune cells in latent ganglia have been used to suggest that this state is not entirely quiescent. Alternatively, these findings can be interpreted as signs of a low, but constant level of abortive reactivation punctuating otherwise silent latency. Using single cell analysis of transcription in mouse dorsal root ganglia, we reveal that HSV-1 latency is highly dynamic in the majority of neurons. Specifically, transcription from areas of the HSV genome associated with at least one viral lytic gene occurs in nearly two thirds of latently-infected neurons and more than half of these have RNA from more than one lytic gene locus. Further, bioinformatics analyses of host transcription showed that progressive appearance of these lytic transcripts correlated with alterations in expression of cellular genes. These data show for the first time that transcription consistent with lytic gene expression is a frequent event, taking place in the majority of HSV latently-infected neurons. Furthermore, this transcription is of biological significance in that it influences host gene expression. We suggest that the maintenance of HSV latency involves an active host response to frequent viral activity. Primary herpes simplex virus (HSV) infections are characterized by acute disease that resolves rapidly, but the virus persists in a latent form in sensory neurons that can be a source of renewed disease. Analyzing gene expression in single mouse neurons harboring latent HSV, we show directly that HSV latency is dynamic and heterogeneous. HSV lytic gene transcripts were frequently detected in latently infected neurons and often in combinations. Expression of selected cellular anti-viral and survival genes showed that transcriptional profiles differed between latently infected and uninfected neurons from the same ganglia. The pattern of host gene expression also differed between latently infected neurons that were and were not experiencing HSV lytic gene expression. Our study suggests that HSV latency is characterized by very frequent switching on of lytic genes and a rapid response by the host, presumably to halt progression to reactivation.
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Affiliation(s)
- Joel Z. Ma
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (JZM); (FRC); (DCT)
| | - Tiffany A. Russell
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tim Spelman
- Victorian Infectious Diseases Service, Melbourne Health, Melbourne, Victoria, Australia
- Centre of Population Health, Burnet Institute, Melbourne, Victoria, Australia
| | - Francis R. Carbone
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail: (JZM); (FRC); (DCT)
| | - David C. Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (JZM); (FRC); (DCT)
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Quinan BR, Flesch IEA, Pinho TMG, Coelho FM, Tscharke DC, da Fonseca FG. An intact signal peptide on dengue virus E protein enhances immunogenicity for CD8(+) T cells and antibody when expressed from modified vaccinia Ankara. Vaccine 2014; 32:2972-9. [PMID: 24726244 DOI: 10.1016/j.vaccine.2014.03.093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/20/2014] [Accepted: 03/26/2014] [Indexed: 10/25/2022]
Abstract
Dengue is a global public health concern and this is aggravated by a lack of vaccines or antiviral therapies. Despite the well-known role of CD8(+) T cells in the immunopathogenesis of Dengue virus (DENV), only recent studies have highlighted the importance of this arm of the immune response in protection against the disease. Thus, the majority of DENV vaccine candidates are designed to achieve protective titers of neutralizing antibodies, with less regard for cellular responses. Here, we used a mouse model to investigate CD8(+) T cell and humoral responses to a set of potential DENV vaccines based on recombinant modified vaccinia virus Ankara (rMVA). To enable this study, we identified two CD8(+) T cell epitopes in the DENV-3 E protein in C57BL/6 mice. Using these we found that all the rMVA vaccines elicited DENV-specific CD8(+) T cells that were cytotoxic in vivo and polyfunctional in vitro. Moreover, vaccines expressing the E protein with an intact signal peptide sequence elicited more DENV-specific CD8(+) T cells than those expressing E proteins in the cytoplasm. Significantly, it was these same ER-targeted E protein vaccines that elicited antibody responses. Our results support the further development of rMVA vaccines expressing DENV E proteins and add to the tools available for dengue vaccine development.
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Affiliation(s)
- Bárbara R Quinan
- Laboratory of Basic and Applied Virology, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, CEP: 31270-901, Belo Horizonte, MG, Brazil; Division of Biomedical Science and Biochemistry, Research School of Biology, Bldg. 134 Linnaeus Way, The Australian National University, Canberra, ACT 0200, Australia
| | - Inge E A Flesch
- Division of Biomedical Science and Biochemistry, Research School of Biology, Bldg. 134 Linnaeus Way, The Australian National University, Canberra, ACT 0200, Australia
| | - Tânia M G Pinho
- Laboratory of Basic and Applied Virology, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, CEP: 31270-901, Belo Horizonte, MG, Brazil
| | - Fabiana M Coelho
- Laboratory of Basic and Applied Virology, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, CEP: 31270-901, Belo Horizonte, MG, Brazil
| | - David C Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, Bldg. 134 Linnaeus Way, The Australian National University, Canberra, ACT 0200, Australia.
| | - Flávio G da Fonseca
- Laboratory of Basic and Applied Virology, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, CEP: 31270-901, Belo Horizonte, MG, Brazil; Centro de Pesquisas René Rachou, FIOCRUZ, Belo Horizonte, MG, Brazil.
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41
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Russell TA, Tscharke DC. Strikingly poor CD8+ T-cell immunogenicity of vaccinia virus strain MVA in BALB/c mice. Immunol Cell Biol 2014; 92:466-9. [PMID: 24566805 PMCID: PMC4037371 DOI: 10.1038/icb.2014.10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 02/02/2014] [Accepted: 02/02/2014] [Indexed: 01/24/2023]
Abstract
Vaccinia virus (VACV) strain MVA is a highly attenuated vector for
vaccines that is being explored in clinical trials. We compared the
CD8+ T cell immunogenicity of MVA with that of a virulent
laboratory strain of VACV (strain WR) in BALB/c mice by examining
epitope-specific responses as well as estimating the total number of activated
CD8+ T cells, irrespective of specificity. We found that
MVA elicited total CD8+ T cell responses that were reduced by
at least 20-fold compared with strain WR in BALB/c mice. In C57Bl/6 mice we also
found a substantial difference in immunogenicity between these VACV strains, but
it was more modest at around 5-fold. Of note, the size of responses to the
virulent WR virus were similar in both strains of mice suggesting that BALB/c
mice can mount robust CD8+ T cell responses to VACV. While
the data for total responses clearly showed that MVA overall is poorly
immunogenic in BALB/c mice, we found one epitope for which strong responses were
made irrespective of virus strain. Therefore in the context of a vaccine, some
recombinant epitopes may have similar immunogenicity when expressed from MVA and
other strains of VACV, but we would expect these to be exceptions. These data
show clearly the substantial difference in immunogenicity between MVA and
virulent VACV strains and suggest that the impact of host genetics on responses
to attenuated vaccine vectors like MVA requires more consideration.
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Affiliation(s)
- Tiffany A Russell
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David C Tscharke
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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Dobson BM, Tscharke DC. Truncation of gene F5L partially masks rescue of vaccinia virus strain MVA growth on mammalian cells by restricting plaque size. J Gen Virol 2013; 95:466-471. [PMID: 24145605 DOI: 10.1099/vir.0.058495-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Modified vaccinia virus Ankara (MVA) is a candidate vaccine vector that is severely attenuated due to mutations acquired during several hundred rounds of serial passage in vitro. A previous study used marker rescue to produce a set of MVA recombinants with improved replication on mammalian cells. Here, we extended the characterization of these rescued MVA strains and identified vaccinia virus (VACV) gene F5L as a determinant of plaque morphology but not replication in vitro. F5 joins a growing group of VACV proteins that influence plaque formation more strongly than virus replication and which are disrupted in MVA. These defective genes in MVA confound the interpretation of marker rescue experiments designed to map mutations responsible for the attenuation of this important VACV strain.
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Affiliation(s)
- Bianca M Dobson
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Canberra, ACT, Australia
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Wijesundara DK, Jackson RJ, Tscharke DC, Ranasinghe C. IL-4 and IL-13 mediated down-regulation of CD8 expression levels can dampen anti-viral CD8+ T cell avidity following HIV-1 recombinant pox viral vaccination. Vaccine 2013; 31:4548-55. [DOI: 10.1016/j.vaccine.2013.07.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/25/2013] [Indexed: 01/23/2023]
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Abstract
Immunodominance is a fundamental property of CD8(+) T cell responses to viruses and vaccines. It had been observed that route of administration alters immunodominance after vaccinia virus (VACV) infection, but only a few epitopes were examined and no mechanism was provided. We re-visited this issue, examining a panel of 15 VACV epitopes and four routes, namely intradermal (i.d.), subcutaneous (s.c.), intraperitoneal (i.p.) and intravenous (i.v.) injection. We found that immunodominance is sharpened following peripheral routes of infection (i.d. and s.c.) compared with those that allow systemic virus dissemination (i.p. and i.v.). This increased immunodominance was demonstrated with native epitopes of VACV and with herpes simplex virus glycoprotein B when expressed from VACV. Responses to some subdominant epitopes were altered by as much as fourfold. Tracking of virus, examination of priming sites, and experiments restricting virus spread showed that priming of CD8(+) T cells in the spleen was necessary, but not sufficient to broaden responses. Further, we directly demonstrated that immunodomination occurs more readily when priming is mainly in lymph nodes. Finally, we were able to reduce immunodominance after i.d., but not i.p. infection, using a VACV expressing the costimulators CD80 (B7-1) and CD86 (B7-2), which is notable because VACV-based vaccines incorporating these molecules are in clinical trials. Taken together, our data indicate that resources for CD8(+) T cell priming are limiting in local draining lymph nodes, leading to greater immunodomination. Further, we provide evidence that costimulation can be a limiting factor that contributes to immunodomination. These results shed light on a possible mechanism of immunodomination and highlight the need to consider multiple epitopes across the spectrum of immunogenicities in studies aimed at understanding CD8(+) T cell immunity to viruses.
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Affiliation(s)
- Leon C. W. Lin
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Inge E. A. Flesch
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David C. Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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45
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Wijesundara DK, Tscharke DC, Jackson RJ, Ranasinghe C. Reduced interleukin-4 receptor α expression on CD8+ T cells correlates with higher quality anti-viral immunity. PLoS One 2013; 8:e55788. [PMID: 23383283 PMCID: PMC3561338 DOI: 10.1371/journal.pone.0055788] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 12/31/2012] [Indexed: 11/18/2022] Open
Abstract
With the hope of understanding how interleukin (IL)-4 and IL-13 modulated quality of anti-viral CD8+ T cells, we evaluated the expression of receptors for these cytokines following a range of viral infections (e.g. pox viruses and influenza virus). Results clearly indicated that unlike other IL-4/IL-13 receptor subunits, IL-4 receptor α (IL-4Rα) was significantly down-regulated on anti-viral CD8+ T cells in a cognate antigen dependent manner. The infection of gene knockout mice and wild-type (WT) mice with vaccinia virus (VV) or VV expressing IL-4 confirmed that IL-4, IL-13 and signal transducer and activator of transcription 6 (STAT6) were required to increase IL-4Rα expression on CD8+ T cells, but not interferon (IFN)-γ. STAT6 dependent elevation of IL-4Rα expression on CD8+ T cells was a feature of poor quality anti-viral CD8+ T cell immunity as measured by the production of IFN-γ and tumor necrosis factor α (TNF-α) in response to VV antigen stimulation in vitro. We propose that down-regulation of IL-4Rα, but not the other IL-4/IL-13 receptor subunits, is a mechanism by which CD8+ T cells reduce responsiveness to IL-4 and IL-13. This can improve the quality of anti-viral CD8+ T cell immunity. Our findings have important implications in understanding anti-viral CD8+ T cell immunity and designing effective vaccines against chronic viral infections.
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Affiliation(s)
- Danushka K Wijesundara
- The Molecular Mucosal Vaccine Immunology Group, The Department of Immunology, The John Curtin School of Medical Research, The Australian National University, Acton, Canberra, Australia.
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46
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Croft NP, Smith SA, Wong YC, Tan CT, Dudek NL, Flesch IEA, Lin LCW, Tscharke DC, Purcell AW. Kinetics of antigen expression and epitope presentation during virus infection. PLoS Pathog 2013; 9:e1003129. [PMID: 23382674 PMCID: PMC3561264 DOI: 10.1371/journal.ppat.1003129] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 11/26/2012] [Indexed: 01/20/2023] Open
Abstract
Current knowledge about the dynamics of antigen presentation to T cells during viral infection is very poor despite being of fundamental importance to our understanding of anti-viral immunity. Here we use an advanced mass spectrometry method to simultaneously quantify the presentation of eight vaccinia virus peptide-MHC complexes (epitopes) on infected cells and the amounts of their source antigens at multiple times after infection. The results show a startling 1000-fold range in abundance as well as strikingly different kinetics across the epitopes monitored. The tight correlation between onset of protein expression and epitope display for most antigens provides the strongest support to date that antigen presentation is largely linked to translation and not later degradation of antigens. Finally, we show a complete disconnect between the epitope abundance and immunodominance hierarchy of these eight epitopes. This study highlights the complexity of viral antigen presentation by the host and demonstrates the weakness of simple models that assume total protein levels are directly linked to epitope presentation and immunogenicity. A major mechanism for the detection of virus infection is the recognition by T cells of short peptide fragments (epitopes) derived from the degradation of intracellular proteins presented at the cell surface in a complex with class I MHC. Whilst the mechanics of antigen degradation and the loading of peptides onto MHC are now well understood, the kinetics of epitope presentation have only been studied for individual model antigens. We addressed this issue by studying vaccinia virus, best known as the smallpox vaccine, using advanced mass spectrometry. Precise and simultaneous quantification of multiple peptide-MHC complexes showed that the surface of infected cells provides a surprisingly dynamic landscape from the point of view of anti-viral T cells. Further, concurrent measurement of virus protein levels demonstrated that in most cases, peak presentation of epitopes occurs at the same time or precedes the time of maximum protein build up. Finally, we found a complete disconnect between the abundance of epitopes on infected cells and the size of the responding T cell populations. These data provide new insights into how virus infected cells are seen by T cells, which is crucial to our understanding of anti-viral immunity and development of vaccines.
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Affiliation(s)
- Nathan P. Croft
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Stewart A. Smith
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yik Chun Wong
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Chor Teck Tan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Nadine L. Dudek
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Inge E. A. Flesch
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Leon C. W. Lin
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - David C. Tscharke
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: (DCT); (AWP)
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- * E-mail: (DCT); (AWP)
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Kerr PJ, Ghedin E, DePasse JV, Fitch A, Cattadori IM, Hudson PJ, Tscharke DC, Read AF, Holmes EC. Evolutionary history and attenuation of myxoma virus on two continents. PLoS Pathog 2012; 8:e1002950. [PMID: 23055928 PMCID: PMC3464225 DOI: 10.1371/journal.ppat.1002950] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/22/2012] [Indexed: 01/05/2023] Open
Abstract
The attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence. However, the evolutionary genetics of this profound change in host-pathogen relationship is unknown. We describe the genome-scale evolution of MYXV covering a range of virulence grades sampled over 49 years from the parallel Australian and European epidemics, including the high-virulence progenitor strains released in the early 1950s. MYXV evolved rapidly over the sampling period, exhibiting one of the highest nucleotide substitution rates ever reported for a double-stranded DNA virus, and indicative of a relatively high mutation rate and/or a continually changing selective environment. Our comparative sequence data reveal that changes in virulence involved multiple genes, likely losses of gene function due to insertion-deletion events, and no mutations common to specific virulence grades. Hence, despite the similarity in selection pressures there are multiple genetic routes to attain either highly virulent or attenuated phenotypes in MYXV, resulting in convergence for phenotype but not genotype. The text-book example of the evolution of virulence is the attenuation of myxoma virus (MYXV) following its introduction as a biological control into the European rabbit populations of Australia and Europe in the 1950s. However, the key work on this topic, most notably by Frank Fenner and his colleagues, occurred before the availability of genome sequence data. The evolutionary genetic basis to the major changes in virulence in both the Australian and European epidemics is therefore largely unknown. We provide, for the first time, key details on the genome-wide changes that underpin this landmark example of pathogen emergence and virulence evolution. By sequencing and comparing MYXV genomes, including the original strains released in the 1950s, we show that (i) MYXV evolved rapidly in both Australia and Europe, producing one of the highest rates of evolutionary change ever recorded for a DNA virus, (ii) that changes in virulence were caused by mutations in multiple genes, often involving losses of gene function due to insertions and deletions, and that (iii) strains of the same virulence were defined by different mutations, such that both attenuated and virulent MYXV strains are produced by a variety genetic pathways, and generating convergent evolution for phenotype but not genotype.
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Affiliation(s)
- Peter J. Kerr
- CSIRO Ecosystem Sciences, Canberra, Australian Capital Territory, Australia
| | - Elodie Ghedin
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jay V. DePasse
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Adam Fitch
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - David C. Tscharke
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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48
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Abstract
Enumeration of anti-viral CD8(+) T cells to make comparisons between mice, viruses and vaccines is a frequently used approach, but controversy persists as to the most appropriate methods. Use of peptide-MHC tetramers (or variants) and intracellular staining for cytokines, in particular IFNγ, after a short ex vivo stimulation are now common, as are a variety of cytotoxicity assays, but few direct comparisons have been made. It has been argued that use of tetramers leads to the counting of non-functional T cells and that measurement of single cytokines will fail to identify cells with alternative functions. Further, the linear range of these methods has not been tested and this is required to give confidence that relative quantifications can be compared across samples. Here we show for two acute virus infections and CD8(+) T cells activated in vitro that DimerX (a tetramer variant) and intracellular staining for IFNγ, alone or in combination with CD107 to detect degranulation, gave comparable results at the peak of the response. Importantly, these methods were highly linear over nearly two orders of magnitude. In contrast, in vitro and in vivo assays for cytotoxicity were not linear, suffering from high background killing, plateaus in maximal killing and substantial underestimation of differences in magnitude of responses.
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Affiliation(s)
- Inge E. A. Flesch
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Natasha A. Hollett
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Yik Chun Wong
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - David C. Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
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49
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Wong YC, Lin LCW, Melo-Silva CR, Smith SA, Tscharke DC. Engineering recombinant poxviruses using a compact GFP-blasticidin resistance fusion gene for selection. J Virol Methods 2010; 171:295-8. [PMID: 21073901 DOI: 10.1016/j.jviromet.2010.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 10/27/2010] [Accepted: 11/01/2010] [Indexed: 11/29/2022]
Abstract
Recombinant poxviruses are important tools for research and some are candidate vaccines. To make these viruses a simple, small vector that can be used to engineer multiple strains of vaccinia virus and other model poxviruses, including ectromelia virus is of value. Here a set of plasmids and methods for making these viruses that uses an enhanced green fluorescent protein-blasticidin resistance (GFP-bsd) fusion gene as a transient selectable marker are described. This gene is smaller than any of the bi-functional selection markers used previously. The versatility of the method across different poxviruses is demonstrated by engineering changes into multiple loci of the WR and Modified Vaccinia Ankara (MVA) strains of vaccinia virus and also ectromelia virus. Finally, a set of vaccinia virus sequences for directing homologous recombination that are very highly conserved was designed and tested. These sequences allow a single plasmid to be used to insert a transgene into multiple strains of the virus.
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Affiliation(s)
- Yik Chun Wong
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
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50
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Yuen TJ, Flesch IEA, Hollett NA, Dobson BM, Russell TA, Fahrer AM, Tscharke DC. Analysis of A47, an immunoprevalent protein of vaccinia virus, leads to a reevaluation of the total antiviral CD8+ T cell response. J Virol 2010; 84:10220-9. [PMID: 20668091 PMCID: PMC2937773 DOI: 10.1128/jvi.01281-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022] Open
Abstract
Vaccinia virus (VACV) is the prototypic orthopoxvirus and was the live vaccine used to eradicate smallpox. In addition, VACV is a possible vector for recombinant vaccines. Despite these reasons for study, the roles of many VACV genes are unknown, and some fundamental aspects, such as the total size of immune responses, remain poorly characterized. VACV gene A47L is of interest because it is highly transcribed, has no sequence similarity to any nonpoxvirus gene, and contains a larger-than-expected number of CD8(+) T cell epitopes. Here it is shown that A47L is not required for growth in vitro and does not contribute to virulence in mice. However, we confirmed that this one protein primes CD8(+) T cells to three different epitopes in C57BL/6 mice. In the process, one of these epitopes was redefined and shown to be the most dominant in A47 and one of the more highly ranked in VACV as a whole. The relatively high immunogenicity of this epitope led to a reevaluation of the total CD8(+) T cell response to VACV. By the use of two methods, the true size of the response was found to be around double previous estimates and at its peak is on the order of 60% of all CD8(+) T cells. We speculate that more CD8(+) T cell epitopes remain to be mapped for VACV and that underestimation of responses is unlikely to be unique to VACV, so there would be merit in revisiting this issue for other viruses.
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Affiliation(s)
- Tracy J. Yuen
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Inge E. A. Flesch
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Natasha A. Hollett
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Bianca M. Dobson
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Tiffany A. Russell
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - Aude M. Fahrer
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
| | - David C. Tscharke
- Division of Biomedical Science and Biochemistry, Research School of Biology, College of Medicine, Biology and the Environment, The Australian National University, Canberra, ACT, Australia
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