1
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Neto TAP, Sidney J, Grifoni A, Sette A. Correlative CD4 and CD8 T-cell immunodominance in humans and mice: Implications for preclinical testing. Cell Mol Immunol 2023; 20:1328-1338. [PMID: 37726420 PMCID: PMC10616275 DOI: 10.1038/s41423-023-01083-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
Antigen-specific T-cell recognition is restricted by Major Histocompatibility Complex (MHC) molecules, and differences between CD4 and CD8 immunogenicity in humans and animal species used in preclinical vaccine testing are yet to be fully understood. In this study, we addressed this matter by analyzing experimentally identified epitopes based on published data curated in the Immune Epitopes DataBase (IEDB) database. We first analyzed SARS-CoV-2 spike (S) and nucleoprotein (N), which are two common targets of the immune response and well studied in both human and mouse systems. We observed a weak but statistically significant correlation between human and H-2b mouse T-cell responses (CD8 S specific (r = 0.206, p = 1.37 × 10-13); CD4 S specific (r = 0.118, p = 2.63 × 10-5) and N specific (r = 0.179, p = 2.55 × 10-4)). Due to intrinsic differences in MHC molecules across species, we also investigated the association between the immunodominance of common Human Leukocyte Antigen (HLA) alleles for which HLA transgenic mice are available, namely, A*02:01, B*07:02, DRB1*01:01, and DRB1*04:01, and found higher significant correlations for both CD8 and CD4 (maximum r = 0.702, p = 1.36 × 10-31 and r = 0.594, p = 3.04-122, respectively). Our results further indicated that some regions are commonly immunogenic between humans and mice (either H-2b or HLA transgenic) but that others are human specific. Finally, we noted a significant correlation between CD8 and CD4 S- (r = 0.258, p = 7.33 × 1021) and N-specific (r = 0.369, p = 2.43 × 1014) responses, suggesting that discrete protein subregions can be simultaneously recognized by T cells. These findings were confirmed in other viral systems, providing general guidance for the use of murine models to test T-cell immunogenicity of viral antigens destined for human use.
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Affiliation(s)
- Tertuliano Alves Pereira Neto
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
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2
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Yakubitskiy SN, Sergeev AA, Titova KA, Shulgina IS, Starostina EV, Borgoyakova MB, Karpenko LI, Shchelkunov SN. Effect of the ati Gene Deletion on the Pathogenicity and Immunogenicity of the Vaccinia Virus. Acta Naturae 2023; 15:82-90. [PMID: 37908769 PMCID: PMC10615193 DOI: 10.32607/actanaturae.17872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 11/02/2023] Open
Abstract
Among the nonvirion proteins of the vaccinia virus (VACV), a 94-kDa long protein is most abundantly present; the protein is a truncated form of the 150-kDa A-type inclusion (ATI) protein of the cowpox virus encoded by the ati gene. This VACV protein does not form intracellular ATIs, being as it is a major immunogen upon infection/immunization of humans or animals with the VACV. Antibodies specific to this protein are not virus-neutralizing. The present study focused on the effect of the production of this nonstructural major immunogenic VACV protein on the manifestation of pathogenicity and immunogenicity of the virus in the BALB/c mouse model of infection. In order to introduce a targeted deletion into the VACV LIVP genome, the recombinant integration/deletion plasmid pΔati was constructed and further used to generate the recombinant virus LIVPΔati. The pathogenicity of the VACV LIVP and LIVPΔati strains was studied in 3-week-old mice. The mice were intranasally infected with the viruses at a dose of 107 pfu; 50% of the animals infected with the parent LIVP strain died, while infection with the LIVPΔati strain led to the death of only 20% of the mice. Intradermal vaccination of mice aged 6- weeks with the LIVPΔati virus statistically significantly increased the production of VACV-specific IgG, compared to that after intradermal vaccination with VACV LIVP. Meanwhile, no differences were noted in the cell-mediated immune response to the vaccination of mice with VACV LIVP or LIVPΔati, which was assessed by ELISpot according to the number of splenocytes producing IFN-γ in response to stimulation with virus-specific peptides. Intranasal infection of mice with lethal doses of the cowpox virus or the ectromelia virus on day 60 post-immunization with the studied VACV variants demonstrated that the mutant LIVPΔati elicits a stronger protective response compared to the parent LIVP.
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Affiliation(s)
- S. N. Yakubitskiy
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - A. A. Sergeev
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - K. A. Titova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - I. S. Shulgina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - E. V. Starostina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - M. B. Borgoyakova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - L. I. Karpenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
| | - S. N. Shchelkunov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk region, 630559 Russian Federation
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3
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Langenmayer MC, Luelf-Averhoff AT, Marr L, Jany S, Freudenstein A, Adam-Neumair S, Tscherne A, Fux R, Rojas JJ, Blutke A, Sutter G, Volz A. Newly Designed Poxviral Promoters to Improve Immunogenicity and Efficacy of MVA-NP Candidate Vaccines against Lethal Influenza Virus Infection in Mice. Pathogens 2023; 12:867. [PMID: 37513714 PMCID: PMC10383309 DOI: 10.3390/pathogens12070867] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Influenza, a respiratory disease mainly caused by influenza A and B, viruses of the Orthomyxoviridae, is still a burden on our society's health and economic system. Influenza A viruses (IAV) circulate in mammalian and avian populations, causing seasonal outbreaks with high numbers of cases. Due to the high variability in seasonal IAV triggered by antigenic drift, annual vaccination is necessary, highlighting the need for a more broadly protective vaccine against IAV. The safety tested Modified Vaccinia virus Ankara (MVA) is licensed as a third-generation vaccine against smallpox and serves as a potent vector system for the development of new candidate vaccines against different pathogens. Here, we generated and characterized recombinant MVA candidate vaccines that deliver the highly conserved internal nucleoprotein (NP) of IAV under the transcriptional control of five newly designed chimeric poxviral promoters to further increase the immunogenic properties of the recombinant viruses (MVA-NP). Infections of avian cell cultures with the recombinant MVA-NPs demonstrated efficient synthesis of the IAV-NP which was expressed under the control of the five new promoters. Prime-boost or single shot immunizations in C57BL/6 mice readily induced circulating serum antibodies' binding to recombinant IAV-NP and the robust activation of IAV-NP-specific CD8+ T cell responses. Moreover, the MVA-NP candidate vaccines protected C57BL/6 mice against lethal respiratory infection with mouse-adapted IAV (A/Puerto Rico/8/1934/H1N1). Thus, further studies are warranted to evaluate the immunogenicity and efficacy of these recombinant MVA-NP vaccines in other IAV challenge models in more detail.
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Affiliation(s)
- Martin C Langenmayer
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 80539 Munich, Germany
| | | | - Lisa Marr
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, Paracelsus Medical University, Klinikum Nürnberg, 90419 Nuremberg, Germany
| | - Sylvia Jany
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
| | - Astrid Freudenstein
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
| | - Silvia Adam-Neumair
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
| | - Alina Tscherne
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 80539 Munich, Germany
| | - Robert Fux
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
| | - Juan J Rojas
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- Immunology Unit, Department of Pathology and Experimental Therapies, Faculty of Medicine and Health Sciences, University of Barcelona-Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain
| | - Andreas Blutke
- Research Unit Analytical Pathology, Helmholtz Zentrum Munich, 85764 Neuherberg, Germany
- Institute for Veterinary Pathology, LMU Munich, 80539 Munich, Germany
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, 80539 Munich, Germany
| | - Asisa Volz
- Institute for Infectious Diseases and Zoonoses, LMU Munich, 80539 Munich, Germany
- Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
- German Center of Infection Research (DZIF), Partner Site Hannover-Braunschweig, 30559 Hannover, Germany
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4
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Grifoni A, Zhang Y, Tarke A, Sidney J, Rubiro P, Reina-Campos M, Filaci G, Dan JM, Scheuermann RH, Sette A. Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans. Cell Host Microbe 2022; 30:1662-1670.e4. [PMID: 36463861 PMCID: PMC9718645 DOI: 10.1016/j.chom.2022.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/17/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The monkeypox virus (MPXV) outbreak confirmed in May 2022 in non-endemic countries is raising concern about the pandemic potential of novel orthopoxviruses. Little is known regarding MPXV immunity in the context of MPXV infection or vaccination with vaccinia-based vaccines (VACV). As with vaccinia, T cells are likely to provide an important contribution to overall immunity to MPXV. Here, we leveraged the epitope information available in the Immune Epitope Database (IEDB) on VACV to predict potential MPXV targets recognized by CD4+ and CD8+ T cell responses. We found a high degree of conservation between VACV epitopes and MPXV and defined T cell immunodominant targets. These analyses enabled the design of peptide pools able to experimentally detect VACV-specific T cell responses and MPXV cross-reactive T cells in a cohort of vaccinated individuals. Our findings will facilitate the monitoring of cellular immunity following MPXV infection and vaccination.
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Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Center of Excellence for Biomedical Research, Department of Experimental Medicine, University of Genoa, Genoa 16132, Italy
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Maria Reina-Campos
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, Genoa 16132, Italy,Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Richard H. Scheuermann
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA,Global Virus Network, Baltimore, MD 21201, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA,Corresponding author
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5
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Shchelkunov SN, Yakubitskiy SN, Sergeev AA, Starostina EV, Titova KA, Pyankov SA, Shchelkunova GA, Borgoyakova MB, Zadorozhny AM, Orlova LA, Kisakov DN, Karpenko LI. Enhancing the Immunogenicity of Vaccinia Virus. Viruses 2022; 14:v14071453. [PMID: 35891430 PMCID: PMC9317313 DOI: 10.3390/v14071453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
The conventional live smallpox vaccine based on the vaccinia virus (VACV) cannot be widely used today because it is highly reactogenic. Therefore, there is a demand for designing VACV variants possessing enhanced immunogenicity, making it possible to reduce the vaccine dose and, therefore, significantly eliminate the pathogenic effect of the VACV on the body. In this study, we analyzed the development of the humoral and T cell-mediated immune responses elicited by immunizing mice with low-dose VACV variants carrying the mutant A34R gene (which increases production of extracellular virions) or the deleted A35R gene (whose protein product inhibits antigen presentation by the major histocompatibility complex class II). The VACV LIVP strain, which is used as a smallpox vaccine in Russia, and its recombinant variants LIVP-A34R*, LIVP-dA35R, and LIVP-A34R*-dA35R, were compared upon intradermal immunization of BALB/c mice at a dose of 104 pfu/animal. The strongest T cell-mediated immunity was detected in mice infected with the LIVP-A34R*-dA35R virus. The parental LIVP strain induced a significantly lower antibody level compared to the strains carrying the modified A34R and A35R genes. Simultaneous modification of the A34R gene and deletion of the A35R gene in VACV LIVP synergistically enhanced the immunogenic properties of the LIVP-A34R*-dA35R virus.
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6
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Zhang H, He C, Jiang F, Cao S, Zhao B, Ding H, Dong T, Han X, Shang H. A longitudinal analysis of immune escapes from HLA-B*13-restricted T-cell responses at early stage of CRF01_AE subtype HIV-1 infection and implications for vaccine design. BMC Immunol 2022; 23:15. [PMID: 35366796 PMCID: PMC8976269 DOI: 10.1186/s12865-022-00491-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying immunogens which can elicit effective T cell responses against human immunodeficiency virus type 1 (HIV-1) is important for developing a T-cell based vaccine. It has been reported that human leukocyte antigen (HLA)-B*13-restricted T-cell responses contributed to HIV control in subtype B' and C infected individuals. However, the kinetics of B*13-restricted T-cell responses, viral evolution within epitopes, and the impact on disease progression in CRF01_AE subtype HIV-1-infected men who have sex with men (MSM) are not known. RESULTS Interferon-γ ELISPOT assays and deep sequencing of viral RNAs were done in 14 early HLA-B*13-positive CRF01_AE subtype HIV-1-infected MSM. We found that responses to RQEILDLWV (Nef106-114, RV9), GQMREPRGSDI (Gag226-236, GI11), GQDQWTYQI (Pol487-498, GI9), and VQNAQGQMV (Gag135-143, VV9) were dominant. A higher relative magnitude of Gag-specific T-cell responses, contributed to viral control, whereas Nef-specific T-cell responses were associated with rapid disease progression. GI11 (Gag) was conserved and strong GI11 (Gag)-specific T-cell responses showed cross-reactivity with a dominant variant, M228I, found in 3/12 patients; GI11 (Gag)-specific T-cell responses were positively associated with CD4 T-cell counts (R = 0.716, P = 0.046). Interestingly, the GI9 (Pol) epitope was also conserved, but GI9 (Pol)-specific T-cell responses did not influence disease progression (P > 0.05), while a D490G variant identified in one patient did not affect CD4 T-cell counts. All the other epitopes studied [VV9 (Gag), RQYDQILIEI (Pol113-122, RI10), HQSLSPRTL (Gag144-152, HL9), and RQANFLGRL (Gag429-437, RL9)] developed escape mutations within 1 year of infection, which may have contributed to overall disease progression. Intriguingly, we found early RV9 (Nef)-specific T-cell responses were associated with rapid disease progression, likely due to escape mutations. CONCLUSIONS Our study strongly suggested the inclusion of GI11 (Gag) and exclusion of RV9 (Nef) for T-cell-based vaccine design for B*13-positive CRF01_AE subtype HIV-1-infected MSM and high-risk individuals.
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Affiliation(s)
- Hui Zhang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Chuan He
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412636.40000 0004 1757 9485Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001 China
| | - Fanming Jiang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412636.40000 0004 1757 9485Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001 China
| | - Shuang Cao
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China ,grid.412449.e0000 0000 9678 1884Department of Laboratory Medicine, China Medical University Shengjing Hospital Nanhu Branch, Shenyang, 110001 China
| | - Bin Zhao
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Haibo Ding
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Tao Dong
- grid.4991.50000 0004 1936 8948Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, Oxford University, Oxford, UK ,grid.4991.50000 0004 1936 8948Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, UK
| | - Xiaoxu Han
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
| | - Hong Shang
- grid.412636.40000 0004 1757 9485NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001 Liaoning Province China ,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, 110001 China ,Key Laboratory of AIDS Immunology of Liaoning Province, Shenyang, 110001 China ,grid.13402.340000 0004 1759 700XCollaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Street, Hangzhou, 310003 China
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7
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Ceglia V, Kelley EJ, Boyle AS, Zurawski S, Mead HL, Harms CE, Blanck JP, Flamar AL, Kirschman JH, Ogongo P, Ernst JD, Levy Y, Zurawski G, Altin JA. A Framework to Identify Antigen-Expanded T Cell Receptor Clusters Within Complex Repertoires. Front Immunol 2021; 12:735584. [PMID: 34917073 PMCID: PMC8670329 DOI: 10.3389/fimmu.2021.735584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire provides a global view that is limited only in terms of theoretical sensitivity due to the depth of available sampling; however, the assignment of antigen specificities within TCR repertoires has become a bottleneck. This study combines antigen-driven expansion, deep TCR sequencing, and a novel analysis framework to show that homologous ‘Clusters of Expanded TCRs (CETs)’ can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse uncultured repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.
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Affiliation(s)
- Valentina Ceglia
- Baylor Institute for Immunology Research, Dallas, TX, United States.,Université Paris-Est Créteil, Sciences de la Vie et de la Santé, Créteil, France.,Vaccine Research Institute, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Erin J Kelley
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Annalee S Boyle
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Sandra Zurawski
- Baylor Institute for Immunology Research, Dallas, TX, United States.,Vaccine Research Institute, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Heather L Mead
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | - Caroline E Harms
- Translational Genomics Research Institute, Flagstaff, AZ, United States
| | | | - Anne-Laure Flamar
- Baylor Institute for Immunology Research, Dallas, TX, United States.,Université Paris-Est Créteil, Sciences de la Vie et de la Santé, Créteil, France.,Vaccine Research Institute, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | | | - Paul Ogongo
- Department of Medicine, Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Joel D Ernst
- Department of Medicine, Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Yves Levy
- Université Paris-Est Créteil, Sciences de la Vie et de la Santé, Créteil, France.,Vaccine Research Institute, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - Gerard Zurawski
- Baylor Institute for Immunology Research, Dallas, TX, United States.,Vaccine Research Institute, INSERM, Unité U955, Institut Mondor de Recherche Biomédicale, Créteil, France
| | - John A Altin
- Translational Genomics Research Institute, Flagstaff, AZ, United States
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8
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Adaptive Immune Response to Vaccinia Virus LIVP Infection of BALB/c Mice and Protection against Lethal Reinfection with Cowpox Virus. Viruses 2021; 13:v13081631. [PMID: 34452494 PMCID: PMC8402668 DOI: 10.3390/v13081631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
Mass vaccination has played a critical role in the global eradication of smallpox. Various vaccinia virus (VACV) strains, whose origin has not been clearly documented in most cases, have been used as live vaccines in different countries. These VACV strains differed in pathogenicity towards various laboratory animals and in reactogenicity exhibited upon vaccination of humans. In this work, we studied the development of humoral and cellular immune responses in BALB/c mice inoculated intranasally (i.n.) or intradermally (i.d.) with the VACV LIVP strain at a dose of 105 PFU/mouse, which was used in Russia as the first generation smallpox vaccine. Active synthesis of VACV-specific IgM in the mice occurred on day 7 after inoculation, reached a maximum on day 14, and decreased by day 29. Synthesis of virus-specific IgG was detected only from day 14, and the level increased significantly by day 29 after infection of the mice. Immunization (i.n.) resulted in significantly higher production of VACV-specific antibodies compared to that upon i.d. inoculation of LIVP. There were no significant differences in the levels of the T cell response in mice after i.n. or i.d. VACV administration at any time point. The maximum level of VACV-specific T-cells was detected on day 14. By day 29 of the experiment, the level of VACV-specific T-lymphocytes in the spleen of mice significantly decreased for both immunization procedures. On day 30 after immunization with LIVP, mice were infected with the cowpox virus at a dose of 46 LD50. The i.n. immunized mice were resistant to this infection, while 33% of i.d. immunized mice died. Our findings indicate that the level of the humoral immune response to vaccination may play a decisive role in protection of animals from orthopoxvirus reinfection.
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9
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Grifoni A, Sidney J, Vita R, Peters B, Crotty S, Weiskopf D, Sette A. SARS-CoV-2 human T cell epitopes: Adaptive immune response against COVID-19. Cell Host Microbe 2021; 29:1076-1092. [PMID: 34237248 PMCID: PMC8139264 DOI: 10.1016/j.chom.2021.05.010] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/23/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Over the past year, numerous studies in the peer reviewed and preprint literature have reported on the virological, epidemiological and clinical characteristics of the coronavirus, SARS-CoV-2. To date, 25 studies have investigated and identified SARS-CoV-2-derived T cell epitopes in humans. Here, we review these recent studies, how they were performed, and their findings. We review how epitopes identified throughout the SARS-CoV2 proteome reveal significant correlation between number of epitopes defined and size of the antigen provenance. We also report additional analysis of SARS-CoV-2 human CD4 and CD8 T cell epitope data compiled from these studies, identifying 1,400 different reported SARS-CoV-2 epitopes and revealing discrete immunodominant regions of the virus and epitopes that are more prevalently recognized. This remarkable breadth of epitope repertoire has implications for vaccine design, cross-reactivity, and immune escape by SARS-CoV-2 variants.
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Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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10
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Sidney J, Peters B, Sette A. Epitope prediction and identification- adaptive T cell responses in humans. Semin Immunol 2020; 50:101418. [PMID: 33131981 DOI: 10.1016/j.smim.2020.101418] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022]
Abstract
Epitopes, in the context of T cell recognition, are short peptides typically derived by antigen processing, and presented on the cell surface bound to MHC molecules (HLA molecules in humans) for TCR scrutiny. The identification of epitopes is a context-dependent process, with consideration given to, for example, the source pathogen and protein, the host organism, and state of the immune reaction (e.g., following natural infection, vaccination, etc.). In the following review, we consider the various approaches used to define T cell epitopes, including both bioinformatic and experimental approaches, and discuss the concepts of immunodominance and immunoprevalence. We also discuss HLA polymorphism and epitope restriction, and the resulting impact on the identification of, and potential population coverage afforded by, epitopes or epitope-based vaccines. Finally, some examples of the practical application of T cell epitope identification are provided, showing how epitopes have been valuable for deriving novel immunological insights in the context of the immune response to various pathogens and allergens.
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Affiliation(s)
- John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA.
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11
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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] [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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12
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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] [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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13
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Weak vaccinia virus-induced NK cell regulation of CD4 T cells is associated with reduced NK cell differentiation and cytolytic activity. Virology 2018; 519:131-144. [PMID: 29715623 DOI: 10.1016/j.virol.2018.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 03/31/2018] [Accepted: 04/16/2018] [Indexed: 11/20/2022]
Abstract
Natural killer (NK) cells control antiviral adaptive immune responses in mice during some virus infections, but the universality of this phenomenon remains unknown. Lymphocytic choriomeningitis virus (LCMV) infection of mice triggered potent cytotoxic activity of NK cells (NKLCMV) against activated CD4 T cells, tumor cells, and allogeneic lymphocytes. In contrast, NK cells activated by vaccinia virus (VACV) infection (NKVACV) exhibited weaker cytolytic activity against each of these target cells. Relative to NKLCMV cells, NKVACV cells exhibited a more immature (CD11b-CD27+) phenotype, and lower expression levels of the activation marker CD69, cytotoxic effector molecules (perforin, granzyme B), and the transcription factor IRF4. NKVACV cells expressed higher levels of the inhibitory molecule NKG2A than NKLCMV cells. Consistent with this apparent lethargy, NKVACV cells only weakly constrained VACV-specific CD4 T-cell responses. This suggests that NK cell regulation of adaptive immunity, while universal, may be limited with viruses that poorly activate NK cells.
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14
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Malm M, Tamminen K, Heinimäki S, Vesikari T, Blazevic V. Functionality and avidity of norovirus-specific antibodies and T cells induced by GII.4 virus-like particles alone or co-administered with different genotypes. Vaccine 2018; 36:484-490. [PMID: 29246474 DOI: 10.1016/j.vaccine.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/10/2017] [Accepted: 12/04/2017] [Indexed: 12/21/2022]
Abstract
Norovirus (NoV) is the main cause of acute gastroenteritis worldwide across all age groups. Current NoV vaccine candidates are based on non-infectious highly immunogenic virus-like particles (VLPs) produced in cell cultures in vitro. As NoVs infecting human population are highly divergent, it is proposed that the vaccine should contain at least two different NoV genotypes, potentially affecting the immunogenicity of each other. We investigated the immunogenicity of NoV GII.4 VLPs administered by intramuscular (IM) or intradermal (ID) injections to BALB/c mice either alone or co-delivered with genogroup I (GI) and other genogroup GII VLPs. Serum NoV-specific IgG binding antibody titers and antibody functionality in terms of avidity and blocking potential were assessed. Furthermore, the specificity and functional avidity of CD4+ and CD8+ T cell responses were analyzed using synthetic peptides previously identified to contain NoV VP1 P2 domain-specific H-2d epitopes. The results showed that IM and ID immunization induced comparable GII.4-specific antibodies and T cell responses. Similar magnitude and functionality of antibodies and interferon-gamma producing T cells were developed using monovalent GII.4 VLPs or different genotype combinations. For the first time, degranulation assay using multicolor flow cytometry showed that NoV GII.4-specific CD8+ T cells had cytotoxic T lymphocyte phenotype. To conclude, our results demonstrate that there is no immunological interference even if up to five different NoV VLP genotypes were co-administered at the same time. Furthermore, no inhibition of NoV-specific antibody functionality or the magnitude, specificity and affinity of T cell responses was observed in any of the immunized animals, observations relevant for the development of a multivalent NoV VLP vaccine.
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Affiliation(s)
- Maria Malm
- Vaccine Research Center, University of Tampere, Biokatu 10, 33520 Tampere, Finland; University of Tampere, Faculty of Medicine and Life Sciences, Tampere, Finland
| | - Kirsi Tamminen
- Vaccine Research Center, University of Tampere, Biokatu 10, 33520 Tampere, Finland; University of Tampere, Faculty of Medicine and Life Sciences, Tampere, Finland
| | - Suvi Heinimäki
- Vaccine Research Center, University of Tampere, Biokatu 10, 33520 Tampere, Finland; University of Tampere, Faculty of Medicine and Life Sciences, Tampere, Finland
| | - Timo Vesikari
- Vaccine Research Center, University of Tampere, Biokatu 10, 33520 Tampere, Finland; University of Tampere, Faculty of Medicine and Life Sciences, Tampere, Finland
| | - Vesna Blazevic
- Vaccine Research Center, University of Tampere, Biokatu 10, 33520 Tampere, Finland; University of Tampere, Faculty of Medicine and Life Sciences, Tampere, Finland.
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15
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Gilchuk P, Knight FC, Wilson JT, Joyce S. Eliciting Epitope-Specific CD8+ T Cell Response by Immunization with Microbial Protein Antigens Formulated with α-Galactosylceramide: Theory, Practice, and Protocols. Methods Mol Biol 2017; 1494:321-352. [PMID: 27718206 DOI: 10.1007/978-1-4939-6445-1_25] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CD8+ cytotoxic T lymphocytes confer protection against infectious diseases caused by viruses, bacteria, and parasites. Hence, significant efforts have been invested into devising ways to generate CD8+ T cell-targeted vaccines. Generation of microbe-free protein subunit vaccines requires a thorough knowledge of protective target antigens. Such antigens are proteolytically processed peptides presented by MHC class I molecules. To induce a robust antigen-specific CD8+ T cell response through vaccination, it is essential to formulate the antigen with an effective adjuvant. Here, we describe a versatile method for generating high-frequency antigen-specific CD8+ T cells through immunization of mice using the invariant natural killer T cell agonist α-galactosylceramide as the adjuvant.
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Affiliation(s)
- Pavlo Gilchuk
- Veterans Administration Tennessee Valley Healthcare System, US Department of Veterans Affairs, Nashville, TN, 37332, USA.,Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University, A4223 Medical Centre North, 1161 21st Avenue South, Nashville, TN, 37332, USA
| | - Frances C Knight
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37332, USA
| | - John T Wilson
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37332, USA.,Department of Chemical & Biomolecular Engineering, School of Engineering, Vanderbilt University, Nashville, TN, 37332, USA
| | - Sebastian Joyce
- Veterans Administration Tennessee Valley Healthcare System, US Department of Veterans Affairs, Nashville, TN, 37332, USA. .,Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University, A4223 Medical Centre North, 1161 21st Avenue South, Nashville, TN, 37332, USA.
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16
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Oseroff C, Christensen LH, Westernberg L, Pham J, Lane J, Paul S, Greenbaum J, Stranzl T, Lund G, Hoof I, Holm J, Würtzen PA, Meno KH, Frazier A, Schulten V, Andersen PS, Peters B, Sette A. Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. Clin Exp Allergy 2016; 47:577-592. [PMID: 27684489 DOI: 10.1111/cea.12829] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND House dust mite (HDM) allergens are a common cause of allergy and allergic asthma. A comprehensive analysis of proteins targeted by T cells, which are implicated in the development and regulation of allergic disease independent of their antibody reactivity, is still lacking. OBJECTIVE To comprehensively analyse the HDM-derived protein targets of T cell responses in HDM-allergic individuals, and investigate their correlation with IgE/IgG responses and protein function. METHODS Proteomic analysis (liquid chromatography-tandem mass spectrometry) of HDM extracts identified 90 distinct protein clusters, corresponding to 29 known allergens and 61 novel proteins. Peripheral blood mononuclear cells (PBMC) from 20 HDM-allergic individuals were stimulated with HDM extracts and assayed with a set of ~2500 peptides derived from these 90 protein clusters and predicted to bind the most common HLA class II types. 2D immunoblots were made in parallel to elucidate IgE and IgG reactivity, and putative function analyses were performed in silico according to Gene Ontology annotations. RESULTS Analysis of T cell reactivity revealed a large number of T cell epitopes. Overall response magnitude and frequency was comparable for known and novel proteins, with 15 antigens (nine of which were novel) dominating the total T cell response. Most of the known allergens that were dominant at the T cell level were also IgE reactive, as expected, while few novel dominant T cell antigens were IgE reactive. Among known allergens, hydrolase activity and detectable IgE/IgG reactivity are strongly correlated, while no protein function correlates with immunogenicity of novel proteins. A total of 106 epitopes accounted for half of the total T cell response, underlining the heterogeneity of T cell responses to HDM allergens. CONCLUSIONS AND CLINICAL RELEVANCE Herein, we define the T cell targets for both known allergens and novel proteins, which may inform future diagnostics and immunotherapeutics for allergy to HDM.
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Luise Westernberg
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Pham
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jerome Lane
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Gitte Lund
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Ilka Hoof
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Jens Holm
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | | | - Kåre H Meno
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - April Frazier
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | | | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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17
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Spencer CT, Bezbradica JS, Ramos MG, Arico CD, Conant SB, Gilchuk P, Gray JJ, Zheng M, Niu X, Hildebrand W, Link AJ, Joyce S. Viral infection causes a shift in the self peptide repertoire presented by human MHC class I molecules. Proteomics Clin Appl 2016; 9:1035-52. [PMID: 26768311 DOI: 10.1002/prca.201500106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/26/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022]
Abstract
PURPOSE MHC class I presentation of peptides allows T cells to survey the cytoplasmic protein milieu of host cells. During infection, presentation of self peptides is, in part, replaced by presentation of microbial peptides. However, little is known about the self peptides presented during infection, despite the fact that microbial infections alter host cell gene expression patterns and protein metabolism. EXPERIMENTAL DESIGN The self peptide repertoire presented by HLA-A*01;01, HLA-A*02;01, HLA-B*07;02, HLA-B*35;01, and HLA-B*45;01 (where HLA is human leukocyte antigen) was determined by tandem MS before and after vaccinia virus infection. RESULTS We observed a profound alteration in the self peptide repertoire with hundreds of self peptides uniquely presented after infection for which we have coined the term "self peptidome shift." The fraction of novel self peptides presented following infection varied for different HLA class I molecules. A large part (approximately 40%) of the self peptidome shift arose from peptides derived from type I interferon-inducible genes, consistent with cellular responses to viral infection. Interestingly, approximately 12% of self peptides presented after infection showed allelic variation when searched against approximately 300 human genomes. CONCLUSION AND CLINICAL RELEVANCE Self peptidome shift in a clinical transplant setting could result in alloreactivity by presenting new self peptides in the context of infection-induced inflammation.
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Affiliation(s)
- Charles T Spencer
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Jelena S Bezbradica
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Mireya G Ramos
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Chenoa D Arico
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Stephanie B Conant
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA
| | - Pavlo Gilchuk
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA.,Veterans Administration Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Jennifer J Gray
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA
| | - Mu Zheng
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xinnan Niu
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Science Centre, Oklahoma City, OK, USA
| | - Andrew J Link
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sebastian Joyce
- Department of Pathology, Microbiology and Immunology, Nashville, TN, USA.,Veterans Administration Tennessee Valley Healthcare System, Nashville, TN, USA
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18
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Jiang F, Han X, Zhang H, Zhao B, An M, Xu J, Chu Z, Dong T, Shang H. Multi-layered Gag-specific immunodominant responses contribute to improved viral control in the CRF01_AE subtype of HIV-1-infected MSM subjects. BMC Immunol 2016; 17:28. [PMID: 27577610 PMCID: PMC5006414 DOI: 10.1186/s12865-016-0166-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The purpose of this study was to characterize specific cytotoxic T-cell (CTL) responses in men who have sex with men (MSM) subjects infected with the human immunodeficiency virus type 1 (HIV-1) CRF01_AE subtype during the first year of infection and impacts on viral control and evolution. RESULTS Fifteen HIV-1 primary infected cases were recruited from Liaoning MSM prospective cohort. CTL responses to Gag, Pol and Nef proteins at 3 month and 1 year post infection were detected with Gamma interferon enzyme-linked immunospot (ELISPOT) assay using optimized consensus overlapping peptides, as well as the viral quasispecies sequences from the synchronous plasma. Gag and Nef proteins were the main targets of CTL responses during the first year of HIV-1 infection, and this was evident from the data after adjusting for the length of amino acids by dividing the amino acids number of the corresponding protein and multiplying by 100. Additionally, relative magnitudes of Gag at both 3 months and 1 year post infection were significantly negatively correlated with the viral set point (p = 0.002, r = -0.726; p = 0.025, r = -0.574). While the relative magnitude of Nef at 1 year post infection were significantly positively correlated with viral set point (p = 0.004, r = 0.697). Subjects with multi-layered Gag immunodominant responses during the first year of infection had significantly lower viral set points than subjects without such responses (p = 0.002). CONCLUSION Multi-layered Gag immunodominant responses during the first year of infection were correlated with viral control, which provides a theoretical basis for vaccine design targeting MSM subjects with the CRF01_AE subtype.
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Affiliation(s)
- Fanming Jiang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hui Zhang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Bin Zhao
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Minghui An
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Junjie Xu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Zhenxing Chu
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tao Dong
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford, OX3 9DS United Kingdom
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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Influence of adenovirus and MVA vaccines on the breadth and hierarchy of T cell responses. Vaccine 2016; 34:4470-4474. [PMID: 27484012 PMCID: PMC5009894 DOI: 10.1016/j.vaccine.2016.07.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 12/31/2022]
Abstract
Viral-vectored vaccines are in clinical development for several infectious diseases where T-cell responses can mediate protection, and responses to sub-dominant epitopes is needed. Little is known about the influence of MVA or adenoviral vectors on the hierarchy of the dominant and sub-dominant T-cell epitopes. We investigated this aspect in mice using a malaria immunogen. Our results demonstrate that the T-cell hierarchy is influenced by the timing of analysis, rather than by the vector after a single immunization, with hierarchy changing over time. Repeated homologous immunization reduced the breadth of responses, while heterologous prime-boost induced the strongest response to the dominant epitope, albeit with only modest response to the sub-dominant epitopes.
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Hinz D, Oseroff C, Pham J, Sidney J, Peters B, Sette A. Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens. Clin Exp Allergy 2016; 45:1601-12. [PMID: 25652035 DOI: 10.1111/cea.12507] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Allergens from house dust mites (HDM) are a common cause of asthma. Der p and Der f from Dermatophagoides sp. are strong immunogens in humans. Allergen extracts are used to study T helper (Th2) cell responses to HDM, which are implicated in the development and regulation of allergic disease. OBJECTIVE To define an epitope mixture that recapitulates, and might substitute for, HDM extract in terms of detecting and characterizing Th2 cell responses. METHODS Peripheral blood mononuclear cells (PBMC) from 52 HDM allergic and 10 non-allergic individuals were stimulated with HDM extracts and assayed with a set of 178 peptides spanning mite allergens group Der p 1, 2, 23 and Der f group 1 and 2 allergens. A pool of the most dominant T cell epitopes identified in the present study and from published literature was assembled and tested for ex vivo T cell responses. Correlation with HDM-specific IgE titres was examined. RESULTS Patterns of T cell reactivity to Der p and Der f - derived peptides revealed a large number of epitopes. Clear patterns of immunodominance were apparent, with HDM allergen group 1 and 2 dominant over group 23. Furthermore, within a given antigen, 6-11 epitopes accounted for the vast majority of responses. Based on these results and published data, a comprehensive dust mite pool (DMP) of epitopes was designed and found to allow detection of ex vivo T cell responses. DMP ex vivo reactivity correlated with HDM-specific IgE titres and was similar to that detected with commonly used HDM extracts. Ex vivo DMP stimulation was associated with a predominant Th2 response in allergic donors, and minor reactivity of T cells producing IFNγ, IL17 and IL10. CONCLUSIONS & CLINICAL RELEVANCE A detailed map of Der p and Der f antigens defined a pool of epitopes that can be used to detect ex vivo HDM responses.
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Affiliation(s)
- D Hinz
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - C Oseroff
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - B Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
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Chevaleyre C, Benhamouda N, Favry E, Fabre E, Mhoumadi A, Nozach H, Marcon E, Cosler G, Vinatier E, Oudard S, Hans S, Le Pimpec-Barthes F, Bats AS, Castelli FA, Tartour E, Maillère B. The Tumor Antigen Cyclin B1 Hosts Multiple CD4 T Cell Epitopes Differently Recognized by Pre-Existing Naive and Memory Cells in Both Healthy and Cancer Donors. THE JOURNAL OF IMMUNOLOGY 2015; 195:1891-901. [DOI: 10.4049/jimmunol.1402548] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 06/03/2015] [Indexed: 11/19/2022]
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Gilchuk P, Hill TM, Wilson JT, Joyce S. Discovering protective CD8 T cell epitopes--no single immunologic property predicts it! Curr Opin Immunol 2015; 34:43-51. [PMID: 25660347 PMCID: PMC5023008 DOI: 10.1016/j.coi.2015.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 01/19/2015] [Accepted: 01/19/2015] [Indexed: 01/25/2023]
Abstract
Once a burgeoning field of study, over the past decade or so, T cell epitope discovery has lost some luster. The contributory factors perchance are the general notion that any newly discovered epitope will reveal very little about an immune response and that knowledge of epitopes are less critical for vaccine design. Despite these notions, the breadth and depth of T cell epitopes derived from clinically important microbial agents of human diseases largely remain ill defined. We review here a flurry of recent reports that have rebirthed the field. These reports reveal that epitope discovery is an essential step toward rational vaccine design and critical for monitoring vaccination efficacy. The new findings also indicate that neither immunogenicity nor immunodominance predict protective immunity. Hence, an immunogenic epitope is but a peptide unless proven protective against disease.
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Affiliation(s)
- Pavlo Gilchuk
- Veterans Administration Tennessee Valley Healthcare System, Vanderbilt University, Nashville, TN 37332, USA; Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University, Nashville, TN 37332, USA
| | - Timothy M Hill
- Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University, Nashville, TN 37332, USA
| | - John T Wilson
- Department of Chemical & Biomolecular Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37332, USA
| | - Sebastian Joyce
- Veterans Administration Tennessee Valley Healthcare System, Vanderbilt University, Nashville, TN 37332, USA; Department of Pathology, Microbiology and Immunology, School of Medicine, Vanderbilt University, Nashville, TN 37332, USA.
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Investigation of IRES Insertion into the Genome of Recombinant MVA as a Translation Enhancer in the Context of Transcript Decapping. PLoS One 2015; 10:e0127978. [PMID: 26011541 PMCID: PMC4444188 DOI: 10.1371/journal.pone.0127978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 04/21/2015] [Indexed: 11/29/2022] Open
Abstract
Recombinant modified vaccinia virus Ankara (MVA) has been used to deliver vaccine candidate antigens against infectious diseases and cancer. MVA is a potent viral vector for inducing high magnitudes of antigen-specific CD8+ T cells; however the cellular immune responses to a recombinant antigen in MVA could be further enhanced by increasing transgene expression. Previous reports showed the importance of utilizing an early poxviral promoter for increasing transgene expression and therefore enhancing cellular immune responses. However, the vaccinia D10 decapping enzyme is reported to target and decap vaccinia virus early transcripts – a mechanism that could limit the usefulness of early promoters in MVA viral vectors if this enzyme shows the same activity in this closely related virus. Therefore, we attempted to increase transgene expression in recombinant MVA by inserting the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) upstream of a transgene sequence that is controlled by the B8R early promoter, and assessed D10 enzyme decapping activity in MVA. The aim of the IRES element was to initiate translation of the transgene transcript (after the removal of the cap structure by the D10 decapping protein) in a cap-independent manner. Here, we report that overexpression of the D10 decapping protein, in trans, in MVA reduced growth and transgene expression; however, the IRES element was not able to compensate for the negative effect of the D10 decapping protein. Recombinant MVA with EMCV IRES induced levels of both gene expression and transcription that were similar to the control recombinant MVA, encoding the same transgene but without the IRES element. Both viruses were tested in BALB/c mice and induced similar magnitudes of epitope-specific CD8+ T cells. This work indicates that the MVA version of the D10 decapping enzyme, overexpressed using a plasmid, is functional, but its negative effect on transgene expression by recombinant MVA cannot be overcome by the use of the EMCV IRES inserted upstream of the transgene initiation codon.
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Crauste F, Terry E, Mercier IL, Mafille J, Djebali S, Andrieu T, Mercier B, Kaneko G, Arpin C, Marvel J, Gandrillon O. Predicting pathogen-specific CD8 T cell immune responses from a modeling approach. J Theor Biol 2015; 374:66-82. [PMID: 25846273 DOI: 10.1016/j.jtbi.2015.03.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 03/04/2015] [Accepted: 03/09/2015] [Indexed: 12/21/2022]
Abstract
The primary CD8 T cell immune response constitutes a major mechanism to fight an infection by intra-cellular pathogens. We aim at assessing whether pathogen-specific dynamical parameters of the CD8 T cell response can be identified, based on measurements of CD8 T cell counts, using a modeling approach. We generated experimental data consisting in CD8 T cell counts kinetics during the response to three different live intra-cellular pathogens: two viruses (influenza, vaccinia) injected intranasally, and one bacteria (Listeria monocytogenes) injected intravenously. All pathogens harbor the same antigen (NP68), but differ in their interaction with the host. In parallel, we developed a mathematical model describing the evolution of CD8 T cell counts and pathogen amount during an immune response. This model is characterized by 9 parameters and includes relevant feedback controls. The model outputs were compared with the three data series and an exhaustive estimation of the parameter values was performed. By focusing on the ability of the model to fit experimental data and to produce a CD8 T cell population mainly composed of memory cells at the end of the response, critical parameters were identified. We show that a small number of parameters (2-4) define the main features of the CD8 T cell immune response and are characteristic of a given pathogen. Among these parameters, two are related to the effector CD8 T cell mediated control of cell and pathogen death. The parameter associated with memory cell death is shown to play no relevant role during the main phases of the CD8 T cell response, yet it becomes essential when looking at the predictions of the model several months after the infection.
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Affiliation(s)
- F Crauste
- Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France; Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France.
| | - E Terry
- Université de Lyon, Université Lyon 1, CNRS UMR 5208, Institut Camille Jordan 43 blvd du 11 novembre 1918, F-69622 Villeurbanne-Cedex, France; Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France; Université de Lyon, Université Lyon 1, CNRS UMR 5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, F-69622 Villeurbanne-Cedex, France.
| | - I Le Mercier
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - J Mafille
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - S Djebali
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - T Andrieu
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - B Mercier
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - G Kaneko
- Université de Lyon, Université Lyon 1, CNRS UMR 5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, F-69622 Villeurbanne-Cedex, France; Université de Lyon, INSA-Lyon, INRIA, Laboratoire d׳InfoRmatique en Image et Systèmes d׳information (LIRIS), CNRS UMR5205, F-69621 Lyon, France.
| | - C Arpin
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France.
| | - J Marvel
- CIRI, INSERM U1111, CNRS UMR 5308; Université Lyon 1, UMS3444/US8; ENS de Lyon, Université de Lyon, 21 Avenue Tony Garnier, F-69007 Lyon, France
| | - O Gandrillon
- Inria Team Dracula, Inria Center Grenoble Rhône-Alpes, France; Université de Lyon, Université Lyon 1, CNRS UMR 5534, Centre de Génétique et de Physiologie Moléculaire et Cellulaire, F-69622 Villeurbanne-Cedex, France.
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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] [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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26
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Wambre E, DeLong JH, James EA, Torres-Chinn N, Pfützner W, Möbs C, Durham SR, Till SJ, Robinson D, Kwok WW. Specific immunotherapy modifies allergen-specific CD4(+) T-cell responses in an epitope-dependent manner. J Allergy Clin Immunol 2013; 133:872-9.e7. [PMID: 24373351 DOI: 10.1016/j.jaci.2013.10.054] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND Understanding the mechanisms by which the immune system induces and controls allergic inflammation at the T-cell epitope level is critical for the design of new allergy vaccine strategies. OBJECTIVE We sought to characterize allergen-specific T-cell responses linked with allergy or peripheral tolerance and to determine how CD4(+) T-cell responses to individual allergen-derived epitopes change over allergen-specific immunotherapy. METHODS Timothy grass pollen (TGP) allergy was used as a model for studying grass pollen allergies. The breadth, magnitude, epitope hierarchy, and phenotype of the DR04:01-restricted TGP-specific T-cell responses in 10 subjects with grass pollen allergy, 5 nonatopic subjects, and 6 allergy vaccine-treated subjects was determined by using an ex vivo peptide-MHC class II tetramer approach. RESULTS CD4(+) T cells in allergic subjects are directed to a broad range of TGP epitopes characterized by defined immunodominance hierarchy patterns and with distinct functional profiles that depend on the epitope recognized. Epitopes that are restricted specifically to either TH2 or TH1/TR1 responses were identified. Allergen-specific immunotherapy was associated with preferential deletion of allergen-specific TH2 cells and without a significant change in the frequency of TH1/TR1 cells. CONCLUSIONS Preferential allergen-specific TH2 cell deletion after repeated high-dose antigen stimulation can be another independent mechanism to restore tolerance to allergen during immunotherapy.
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Affiliation(s)
- Erik Wambre
- Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | | | - Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | | | - Wolfgang Pfützner
- Department of Dermatology and Allergology, University Medical Center, Marburg, Germany
| | - Christian Möbs
- Department of Dermatology and Allergology, University Medical Center, Marburg, Germany
| | - Stephen R Durham
- Department of Allergy and Clinical Immunology, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Stephen J Till
- Allergy, Asthma and Lung Biology, King's College London, London, United Kingdom
| | | | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, Wash; Department of Medicine, University of Washington, Seattle, Wash.
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Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. THE JOURNAL OF IMMUNOLOGY 2013; 191:5831-9. [PMID: 24190657 DOI: 10.4049/jimmunol.1302101] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prediction of HLA binding affinity is widely used to identify candidate T cell epitopes, and an affinity of 500 nM is routinely used as a threshold for peptide selection. However, the fraction (percentage) of peptides predicted to bind with affinities of 500 nM varies by allele. For example, of a large collection of ~30,000 dengue virus-derived peptides only 0.3% were predicted to bind HLA A*0101, whereas nearly 5% were predicted for A*0201. This striking difference could not be ascribed to variation in accuracy of the algorithms used, as predicted values closely correlated with affinity measured in vitro with purified HLA molecules. These data raised the question whether different alleles would also vary in terms of epitope repertoire size, defined as the number of associated epitopes or, alternatively, whether alleles vary drastically in terms of the affinity threshold associated with immunogenicity. To address this issue, strains of HLA transgenic mice with wide (A*0201), intermediate (B*0702), or narrow (A*0101) repertoires were immunized with peptides of varying binding affinity and relative percentile ranking. The results show that absolute binding capacity is a better predictor of immunogenicity, and analysis of epitopes from the Immune Epitope Database revealed that predictive efficacy is increased using allele-specific affinity thresholds. Finally, we investigated the genetic and structural basis of the phenomenon. Although no stringent correlate was defined, on average HLA B alleles are associated with significantly narrower repertoires than are HLA A alleles.
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Affiliation(s)
- Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
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Wennier ST, Brinkmann K, Steinhäußer C, Mayländer N, Mnich C, Wielert U, Dirmeier U, Hausmann J, Chaplin P, Steigerwald R. A novel naturally occurring tandem promoter in modified vaccinia virus ankara drives very early gene expression and potent immune responses. PLoS One 2013; 8:e73511. [PMID: 23951355 PMCID: PMC3741161 DOI: 10.1371/journal.pone.0073511] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 01/06/2023] Open
Abstract
Modified vaccinia virus Ankara (MVA) has been shown to be suitable for the generation of experimental vaccines against cancer and infectious diseases, eliciting strong humoral and cellular immune responses. In viral vectored vaccines, strong recombinant antigen expression and timing of expression influence the quantity and quality of the immune response. Screening of synthetic and native poxvirus promoters for strong protein expression in vitro and potent immune responses in vivo led to the identification of the MVA13.5L promoter, a unique and novel naturally occurring tandem promoter in MVA composed of two 44 nucleotide long repeated motifs, each containing an early promoter element. The MVA13.5L gene is highly conserved across orthopoxviruses, yet its function is unknown. The unique structure of its promoter is not found for any other gene in the MVA genome and is also conserved in other orthopoxviruses. Comparison of the MVA13.5L promoter activity with synthetic poxviral promoters revealed that the MVA13.5L promoter produced higher levels of protein early during infection in HeLa cells and particularly in MDBK cells, a cell line in which MVA replication stops at an early stage before the expression of late genes. Finally, a recombinant antigen expressed under the control of this novel promoter induced high antibody titers and increased CD8 T cell responses in homologous prime-boost immunization compared to commonly used promoters. In particular, the recombinant antigen specific CD8 T cell responses dominated over the immunodominant B8R vector-specific responses after three vaccinations and even more during the memory phase. These results have identified the native MVA13.5L promoter as a new potent promoter for use in MVA vectored preventive and therapeutic vaccines.
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Affiliation(s)
- Sonia T. Wennier
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Kay Brinkmann
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | | | - Nicole Mayländer
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Claudia Mnich
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Ursula Wielert
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Ulrike Dirmeier
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Jürgen Hausmann
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Paul Chaplin
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
| | - Robin Steigerwald
- Infectious Disease Division, Bavarian Nordic GmbH, Martinsried, Germany
- * E-mail:
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Paran N, Lustig S, Zvi A, Erez N, Israely T, Melamed S, Politi B, Ben-Nathan D, Schneider P, Lachmi B, Israeli O, Stein D, Levin R, Olshevsky U. Active vaccination with vaccinia virus A33 protects mice against lethal vaccinia and ectromelia viruses but not against cowpoxvirus; elucidation of the specific adaptive immune response. Virol J 2013; 10:229. [PMID: 23842430 PMCID: PMC3722049 DOI: 10.1186/1743-422x-10-229] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 07/05/2013] [Indexed: 11/12/2022] Open
Abstract
Vaccinia virus protein A33 (A33VACV) plays an important role in protection against orthopoxviruses, and hence is included in experimental multi-subunit smallpox vaccines. In this study we show that single-dose vaccination with recombinant Sindbis virus expressing A33VACV, is sufficient to protect mice against lethal challenge with vaccinia virus WR (VACV-WR) and ectromelia virus (ECTV) but not against cowpox virus (CPXV), a closely related orthopoxvirus. Moreover, a subunit vaccine based on the cowpox virus A33 ortholog (A33CPXV) failed to protect against cowpox and only partially protected mice against VACV-WR challenge. We mapped regions of sequence variation between A33VACV and A33CPXVand analyzed the role of such variations in protection. We identified a single protective region located between residues 104–120 that harbors a putative H-2Kd T cell epitope as well as a B cell epitope - a target for the neutralizing antibody MAb-1G10 that blocks spreading of extracellular virions. Both epitopes in A33CPXV are mutated and predicted to be non-functional. Whereas vaccination with A33VACV did not induce in-vivo CTL activity to the predicted epitope, inhibition of virus spread in-vitro, and protection from lethal VACV challenge pointed to the B cell epitope highlighting the critical role of residue L118 and of adjacent compensatory residues in protection. This epitope’s critical role in protection, as well as its modifications within the orthopoxvirus genus should be taken in context with the failure of A33 to protect against CPXV as demonstrated here. These findings should be considered when developing new subunit vaccines and monoclonal antibody based therapeutics against orthopoxviruses, especially variola virus, the etiologic agent of smallpox.
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Affiliation(s)
- Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, P.O. box 19, Ness-Ziona 74100, Israel.
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Lin LCW, Flesch IEA, Tscharke DC. Immunodomination during peripheral vaccinia virus infection. PLoS Pathog 2013; 9:e1003329. [PMID: 23633956 PMCID: PMC3635974 DOI: 10.1371/journal.ppat.1003329] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/14/2013] [Indexed: 11/20/2022] Open
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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Walline CC, Sehra S, Fisher AJ, Guindon LM, Kratzke IM, Montgomery JB, Lipking KP, Glosson NL, Benson HL, Sandusky GE, Wilkes DS, Brutkiewicz RR, Kaplan MH, Blum JS. Allergic airway disease in mice alters T and B cell responses during an acute respiratory poxvirus infection. PLoS One 2013; 8:e62222. [PMID: 23620814 PMCID: PMC3631162 DOI: 10.1371/journal.pone.0062222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 03/19/2013] [Indexed: 11/18/2022] Open
Abstract
Pulmonary viral infections can exacerbate or trigger the development of allergic airway diseases via multiple mechanisms depending upon the infectious agent. Respiratory vaccinia virus transmission is well established, yet the effects of allergic airway disease on the host response to intra-pulmonary vaccinia virus infection remain poorly defined. As shown here BALB/c mice with preexisting airway disease infected with vaccinia virus developed more severe pulmonary inflammation, higher lung virus titers and greater weight loss compared with mice inoculated with virus alone. This enhanced viremia was observed despite increased pulmonary recruitment of CD8+ T effectors, greater IFNγ production in the lung, and high serum levels of anti-viral antibodies. Notably, flow cytometric analyses of lung CD8+ T cells revealed a shift in the hierarchy of immunodominant viral epitopes in virus inoculated mice with allergic airway disease compared to mice treated with virus only. Pulmonary IL-10 production by T cells and antigen presenting cells was detected following virus inoculation of animals and increased dramatically in allergic mice exposed to virus. IL-10 modulation of host responses to this respiratory virus infection was greatly influenced by the localized pulmonary microenvironment. Thus, blocking IL-10 signaling in virus-infected mice with allergic airway disease enhanced pulmonary CD4+ T cell production of IFNγ and increased serum anti-viral IgG1 levels. In contrast, pulmonary IFNγ and virus-specific IgG1 levels were reduced in vaccinia virus-treated mice with IL-10 receptor blockade. These observations demonstrate that pre-existing allergic lung disease alters the quality and magnitude of immune responses to respiratory poxviruses through an IL-10-dependent mechanism.
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Affiliation(s)
- Crystal C. Walline
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sarita Sehra
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Amanda J. Fisher
- Center for Immunobiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Lynette M. Guindon
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ian M. Kratzke
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jessica B. Montgomery
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Kelsey P. Lipking
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Nicole L. Glosson
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Heather L. Benson
- Center for Immunobiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - George E. Sandusky
- Department of Pathology & Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - David S. Wilkes
- Center for Immunobiology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Randy R. Brutkiewicz
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Mark H. Kaplan
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Janice S. Blum
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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Sidney J, Southwood S, Moore C, Oseroff C, Pinilla C, Grey HM, Sette A. Measurement of MHC/peptide interactions by gel filtration or monoclonal antibody capture. CURRENT PROTOCOLS IN IMMUNOLOGY 2013; Chapter 18:Unit 18.3.. [PMID: 23392640 PMCID: PMC3626435 DOI: 10.1002/0471142735.im1803s100] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This unit describes a technique for the direct and quantitative measurement of the capacity of peptide ligands to bind Class I and Class II MHC molecules. The binding of a peptide of interest to MHC is assessed based on its ability to inhibit the binding of a radiolabeled probe peptide to purified MHC molecules. This unit includes protocols for the purification of Class I and Class II MHC molecules by affinity chromatography, and for the radiolabeling of peptides using the chloramine T method. An alternate protocol describes alterations in the basic protocol that are necessary when performing direct binding assays, which are required for (1) selecting appropriate high-affinity, assay-specific, radiolabeled ligands, and (2) determining the amount of MHC necessary to yield assays with the highest sensitivity. After a predetermined incubation period, dependent upon the allele under examination, the bound and unbound radiolabeled species are separated, and their relative amounts are determined. Three methods for separation are described, two utilizing size-exclusion gel-filtration chromatography and a third using monoclonal antibody capture of MHC. Data analysis for each method is also explained.
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Affiliation(s)
- John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
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Platt RJ, Khodai T, Townend TJ, Bright HH, Cockle P, Perez-Tosar L, Webster R, Champion B, Hickling TP, Mirza F. CD8+ T Lymphocyte Epitopes From The Herpes Simplex Virus Type 2 ICP27, VP22 and VP13/14 Proteins To Facilitate Vaccine Design And Characterization. Cells 2013; 2:19-42. [PMID: 24709642 PMCID: PMC3972665 DOI: 10.3390/cells2010019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 11/22/2012] [Accepted: 12/27/2012] [Indexed: 11/16/2022] Open
Abstract
CD8+ T cells have the potential to control HSV-2 infection. However, limited information has been available on CD8+ T cell epitopes or the functionality of antigen specific T cells during infection or following immunization with experimental vaccines. Peptide panels from HSV-2 proteins ICP27, VP22 and VP13/14 were selected from in silico predictions of binding to human HLA-A*0201 and mouse H-2Kd, Ld and Dd molecules. Nine previously uncharacterized CD8+ T cell epitopes were identified from HSV-2 infected BALB/c mice. HSV-2 specific peptide sequences stabilized HLA-A*02 surface expression with intermediate or high affinity binding. Peptide specific CD8+ human T cell lines from peripheral blood lymphocytes were generated from a HLA-A*02+ donor. High frequencies of peptide specific CD8+ T cell responses were elicited in mice by DNA vaccination with ICP27, VP22 and VP13/14, as demonstrated by CD107a mobilization. Vaccine driven T cell responses displayed a more focused immune response than those induced by viral infection. Furthermore, vaccination with ICP27 reduced viral shedding and reduced the clinical impact of disease. In conclusion, this study describes novel HSV-2 epitopes eliciting strong CD8+ T cell responses that may facilitate epitope based vaccine design and aid immunomonitoring of antigen specific T cell frequencies in preclinical and clinical settings.
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Affiliation(s)
- Rebecca J Platt
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Tansi Khodai
- New Opportunities Unit, Pfizer Global Research and Development, Sandwich, Kent, CT13 -9NJ, UK.
| | - Tim J Townend
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Helen H Bright
- New Opportunities Unit, Pfizer Global Research and Development, Sandwich, Kent, CT13 -9NJ, UK.
| | - Paul Cockle
- Vaccine Research Unit, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Luis Perez-Tosar
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Rob Webster
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Brian Champion
- Vaccine Research Unit, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Timothy P Hickling
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
| | - Fareed Mirza
- Biotherapeutics and Translational Research, Pharmacokinetics, Dynamics & Metabolism, Pfizer Global Research and Development, Sandwich, Kent, CT13-9NJ, UK.
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CD4 T-cell memory responses to viral infections of humans show pronounced immunodominance independent of duration or viral persistence. J Virol 2012; 87:2617-27. [PMID: 23255792 DOI: 10.1128/jvi.03047-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Little is known concerning immunodominance within the CD4 T-cell response to viral infections and its persistence into long-term memory. We tested CD4 T-cell reactivity against each viral protein in persons immunized with vaccinia virus (VV), either recently or more than 40 years ago, as a model self-limited viral infection. Similar tests were done with persons with herpes simplex virus 1 (HSV-1) infection as a model chronic infection. We used an indirect method capable of counting the CD4 T cells in blood reactive with each individual viral protein. Each person had a clear CD4 T-cell dominance hierarchy. The top four open reading frames accounted for about 40% of CD4 virus-specific T cells. Early and long-term memory CD4 T-cell responses to vaccinia virus were mathematically indistinguishable for antigen breadth and immunodominance. Despite the chronic intermittent presence of HSV-1 antigen, the CD4 T-cell dominance and diversity patterns for HSV-1 were identical to those observed for vaccinia virus. The immunodominant CD4 T-cell antigens included both long proteins abundantly present in virions and shorter, nonstructural proteins. Limited epitope level and direct ex vivo data were also consistent with pronounced CD4 T-cell immunodominance. We conclude that human memory CD4 T-cell responses show a pattern of pronounced immunodominance for both chronic and self-limited viral infections and that this pattern can persist over several decades in the absence of antigen.
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36
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Liu MKP, Hawkins N, Ritchie AJ, Ganusov VV, Whale V, Brackenridge S, Li H, Pavlicek JW, Cai F, Rose-Abrahams M, Treurnicht F, Hraber P, Riou C, Gray C, Ferrari G, Tanner R, Ping LH, Anderson JA, Swanstrom R, Cohen M, Karim SSA, Haynes B, Borrow P, Perelson AS, Shaw GM, Hahn BH, Williamson C, Korber BT, Gao F, Self S, McMichael A, Goonetilleke N. Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest 2012; 123:380-93. [PMID: 23221345 DOI: 10.1172/jci65330] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/05/2012] [Indexed: 12/26/2022] Open
Abstract
HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell-mediated in vivo control of HIV-1. Primary HIV-1-specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response was associated with more rapid escape, the most significant T cell measure was its relative immunodominance measured in acute infection. This identified subject-level or "vertical" immunodominance as the primary determinant of in vivo CD8+ T cell pressure in HIV-1 infection. Conversely, escape was slowed significantly by lower population variability, or entropy, of the epitope targeted. Immunodominance and epitope entropy combined to explain half of all the variability in time to escape. These data explain how CD8+ T cells can exert significant and sustained HIV-1 pressure even when escape is very slow and that within an individual, the impacts of other T cell factors on HIV-1 escape should be considered in the context of immunodominance.
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Affiliation(s)
- Michael K P Liu
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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Probst A, Besse A, Favry E, Imbert G, Tanchou V, Castelli FA, Maillere B. Human CD4 T cell epitopes selective for Vaccinia versus Variola virus. Mol Immunol 2012; 53:453-9. [PMID: 23147561 PMCID: PMC9528225 DOI: 10.1016/j.molimm.2012.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/09/2012] [Accepted: 10/15/2012] [Indexed: 12/25/2022]
Abstract
Due to the high degree of sequence identity between Orthopoxvirus species, the specific B and T cell responses raised against these viruses are largely cross-reactive and poorly selective. We therefore searched for CD4 T cell epitopes present in the conserved parts of the Vaccinia genome (VACV) but absent from Variola viruses (VARV), with a view to identifying immunogenic sequences selective for VACV. We identified three long peptide fragments from the B7R, B10R and E7R proteins by in silico comparisons of the poxvirus genomes, and evaluated the recognition of these fragments by VACV-specific T cell lines derived from healthy donors. For the 12 CD4 T cell epitopes identified, we assessed their binding to common HLA-DR allotypes and their capacity to induce peptide-specific CD4 T-cell lines. Four peptides from B7R and B10R displayed a broad binding specificity for HLA-DR molecules and induced multiple T cell lines from healthy donors. Besides their absence from VARV, the two B10R peptide sequences were mutated in the Cowpox virus and completely absent from the Monkeypox genome. This work contributes to the development of differential diagnosis of poxvirus infections.
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Affiliation(s)
- Alicia Probst
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Labex LERMIT, Labex VRI, Gif Sur Yvette F-91191, France
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Maybeno M, Redeker A, Welten SPM, Peters B, Loughhead SM, Schoenberger SP, Sette A, Arens R. Polyfunctional CD4+ T cell responses to immunodominant epitopes correlate with disease activity of virulent Salmonella. PLoS One 2012; 7:e43481. [PMID: 22912884 PMCID: PMC3422266 DOI: 10.1371/journal.pone.0043481] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 07/20/2012] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serovars are intracellular bacteria capable of causing typhoid fever and gastroenteritis of significant morbidity and mortality worldwide. Current prophylactic and therapeutic treatment is hampered by the emergence of multidrug-resistant (MDR) strains of Salmonella, and vaccines provide only temporal and partial protection in vaccinees. To develop more effective Salmonella vaccines, it is important to understand the development of protective adaptive immunity to virulent Salmonella. Here we report the identification of novel CD4(+) T cell peptide epitopes, which are conserved among Salmonella serovars. Immunization of Salmonella-infected mice with these peptide epitopes reduces the burden of Salmonella disease. Furthermore, we show that distinct polyfunctional (interferon-γ(+), tumor necrosis factor(+), and interleukin-2(+)) Salmonella-specific CD4(+) T cell responses develop with respect to magnitude and kinetics. Moreover, we found that CD4(+) T cell responses against immunodominant epitopes are predictive for active Salmonella disease. Collectively, these data could contribute to improved diagnosis of Salmonella-related diseases and rational design of Salmonella vaccines.
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Affiliation(s)
- Matt Maybeno
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Anke Redeker
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Suzanne P. M. Welten
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Scott M. Loughhead
- Laboratory of Cellular Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Stephen P. Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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Oseroff C, Sidney J, Vita R, Tripple V, McKinney DM, Southwood S, Brodie TM, Sallusto F, Grey H, Alam R, Broide D, Greenbaum JA, Kolla R, Peters B, Sette A. T cell responses to known allergen proteins are differently polarized and account for a variable fraction of total response to allergen extracts. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:1800-11. [PMID: 22786768 PMCID: PMC3411923 DOI: 10.4049/jimmunol.1200850] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A panel of 133 allergens derived from 28 different sources, including fungi, trees, grasses, weeds, and indoor allergens, was surveyed utilizing prediction of HLA class II-binding peptides and ELISPOT assays with PBMC from allergic donors, resulting in the identification of 257 T cell epitopes. More than 90% of the epitopes were novel, and for 14 allergen sources were the first ever identified to our knowledge. The epitopes identified in the different allergen sources summed up to a variable fraction of the total extract response. In cases of allergens in which the identified T cell epitopes accounted for a minor fraction of the extract response, fewer known protein sequences were available, suggesting that for low epitope coverage allergen sources, additional allergen proteins remain to be identified. IL-5 and IFN-γ responses were measured as prototype Th2 and Th1 responses, respectively. Whereas in some cases (e.g., orchard grass, Alternaria, cypress, and Russian thistle) IL-5 production greatly exceeded IFN-γ, in others (e.g., Aspergillus, Penicillum, and alder) the production of IFN-γ exceeded IL-5. Thus, different allergen sources are associated with variable polarization of the responding T cells. The present study represents the most comprehensive survey to date of human allergen-derived T cell epitopes. These epitopes might be used to characterize T cell phenotype/T cell plasticity as a function of seasonality, or as a result of specific immunotherapy treatment or varying disease severity (asthma or rhinitis).
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Randi Vita
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Victoria Tripple
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - Scott Southwood
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Tess M. Brodie
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | | | - Howard Grey
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - David Broide
- University of California, San Diego, La Jolla, CA, 92037
| | | | - Ravi Kolla
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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Oseroff C, Sidney J, Tripple V, Grey H, Wood R, Broide DH, Greenbaum J, Kolla R, Peters B, Pomés A, Sette A. Analysis of T cell responses to the major allergens from German cockroach: epitope specificity and relationship to IgE production. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:679-88. [PMID: 22706084 PMCID: PMC3392449 DOI: 10.4049/jimmunol.1200694] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Bla g allergens are major targets of IgE responses associated with cockroach allergies. However, little is known about corresponding T cell responses, despite their potential involvement in immunopathology and the clinical efficacy of specific immunotherapy. Bioinformatic predictions of the capacity of Bla g 1, 2, 4, 5, 6, and 7 peptides to bind HLA-DR, -DP, and -DQ molecules, and PBMC responses from 30 allergic donors, identified 25 T cell epitopes. Five immunodominant epitopes accounted for more than half of the response. Bla g 5, the most dominant allergen, accounted for 65% of the response, and Bla g 6 accounted for 20%. Bla g 5 induced both IL-5 and IFN-γ responses, whereas Bla g 6 induced mostly IL-5, and, conversely, Bla g 2 induced only IFN-γ. Thus, responses to allergens within a source are independently regulated, suggesting a critical role for the allergen itself, and not extraneous stimulation from other allergens or copresented immunomodulators. In comparing Ab with T cell responses for several donor/allergen combinations, we detected IgE titers in the absence of detectable T cell responses, suggesting that unlinked T cell-B cell help might support development of IgE responses. Finally, specific immunotherapy resulted in IL-5 down modulation, which was not associated with development of IFN-γ or IL-10 responses to any of the Bla g-derived peptides. In summary, the characteristics of T cell responses to Bla g allergens appear uncorrelated with IgE responses. Monitoring these responses may therefore yield important information relevant to understanding cockroach allergies and their treatment.
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Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Victoria Tripple
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Howard Grey
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Robert Wood
- The Johns Hopkins University, Baltimore, MD, 21201
| | | | - Jason Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Ravi Kolla
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, 22903
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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Orubu T, Alharbi NK, Lambe T, Gilbert SC, Cottingham MG. Expression and cellular immunogenicity of a transgenic antigen driven by endogenous poxviral early promoters at their authentic loci in MVA. PLoS One 2012; 7:e40167. [PMID: 22761956 PMCID: PMC3384612 DOI: 10.1371/journal.pone.0040167] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 06/02/2012] [Indexed: 01/12/2023] Open
Abstract
CD8(+) T cell responses to vaccinia virus are directed almost exclusively against early gene products. The attenuated strain modified vaccinia virus Ankara (MVA) is under evaluation in clinical trials of new vaccines designed to elicit cellular immune responses against pathogens including Plasmodium spp., M. tuberculosis and HIV-1. All of these recombinant MVAs (rMVA) utilize the well-established method of linking the gene of interest to a cloned poxviral promoter prior to insertion into the viral genome at a suitable locus by homologous recombination in infected cells. Using BAC recombineering, we show that potent early promoters that drive expression of non-functional or non-essential MVA open reading frames (ORFs) can be harnessed for immunogenic expression of recombinant antigen. Precise replacement of the MVA orthologs of C11R, F11L, A44L and B8R with a model antigen positioned to use the same translation initiation codon allowed early transgene expression similar to or slightly greater than that achieved by the commonly-used p7.5 or short synthetic promoters. The frequency of antigen-specific CD8(+) T cells induced in mice by single shot or adenovirus-prime, rMVA-boost vaccination were similarly equal or marginally enhanced using endogenous promoters at their authentic genomic loci compared to the traditional constructs. The enhancement in immunogenicity observed using the C11R or F11L promoters compared with p7.5 was similar to that obtained with the mH5 promoter compared with p7.5. Furthermore, the growth rates of the viruses were unimpaired and the insertions were genetically stable. Insertion of a transgenic ORF in place of a viral ORF by BAC recombineering can thus provide not only a potent promoter, but also, concomitantly, a suitable insertion site, potentially facilitating development of MVA vaccines expressing multiple recombinant antigens.
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Affiliation(s)
- Toritse Orubu
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | - Teresa Lambe
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Sarah C. Gilbert
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
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42
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Abstract
Mouse models of immunology are frequently used to study host responses to poxviruses or poxvirus-based recombinant vaccines. In this context, the magnitude of CD8(+) T cell responses is often of interest. Methods to evaluate CD8(+) T cell responses extend from those that rely on indirect measurement of effector function only, such as cytotoxicity assays, to those that only measure antiviral CD8(+) T cell numbers and not function, like peptide MHC tetramers. In this chapter, five methods are provided that cover this range: DimerX staining (a variant of peptide-MHC tetramers), intracellular cytokine staining for interferon-γ, CD62L/Granzyme B staining, and in vitro and ex vivo cytotoxicity assays. We also include tables of vaccinia virus peptide epitopes for use in most of these assays.
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43
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St Leger AJ, Hendricks RL. CD8+ T cells patrol HSV-1-infected trigeminal ganglia and prevent viral reactivation. J Neurovirol 2011; 17:528-34. [PMID: 22161682 DOI: 10.1007/s13365-011-0062-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/11/2011] [Accepted: 11/13/2011] [Indexed: 01/11/2023]
Abstract
A hallmark of herpes viruses is their capacity to cause recurrent disease. Recurrences of herpes simplex virus (HSV)-1 disease do not result from reinfection from external sources, but rather from reactivation of virus that is maintained in a latent state in sensory neurons and periodically reactivates from latency to cause recurrent disease. Recent findings implicate HSV-specific CD8(+) T cells in immune surveillance of HSV-1 latently infected sensory neurons in trigeminal ganglia (TG) and inhibition of HSV-1 reactivation from latency. This review summarizes recent findings regarding the characteristics of the TG-resident CD8(+) T cell population and certain unique obstacles that might complicate the development of therapeutic vaccines.
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Affiliation(s)
- Anthony J St Leger
- Graduate Program in Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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García-Arriaza J, Nájera JL, Gómez CE, Tewabe N, Sorzano COS, Calandra T, Roger T, Esteban M. A candidate HIV/AIDS vaccine (MVA-B) lacking vaccinia virus gene C6L enhances memory HIV-1-specific T-cell responses. PLoS One 2011; 6:e24244. [PMID: 21909386 PMCID: PMC3164197 DOI: 10.1371/journal.pone.0024244] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022] Open
Abstract
The vaccinia virus (VACV) C6 protein has sequence similarities with the poxvirus family Pox_A46, involved in regulation of host immune responses, but its role is unknown. Here, we have characterized the C6 protein and its effects in virus replication, innate immune sensing and immunogenicity in vivo. C6 is a 18.2 kDa protein, which is expressed early during virus infection and localizes to the cytoplasm of infected cells. Deletion of the C6L gene from the poxvirus vector MVA-B expressing HIV-1 Env, Gag, Pol and Nef antigens from clade B (MVA-B ΔC6L) had no effect on virus growth kinetics; therefore C6 protein is not essential for virus replication. The innate immune signals elicited by MVA-B ΔC6L in human macrophages and monocyte-derived dendritic cells (moDCs) are characterized by the up-regulation of the expression of IFN-β and IFN-α/β-inducible genes. In a DNA prime/MVA boost immunization protocol in mice, flow cytometry analysis revealed that MVA-B ΔC6L enhanced the magnitude and polyfunctionality of the HIV-1-specific CD4+ and CD8+ T-cell memory immune responses, with most of the HIV-1 responses mediated by the CD8+ T-cell compartment with an effector phenotype. Significantly, while MVA-B induced preferentially Env- and Gag-specific CD8+ T-cell responses, MVA-B ΔC6L induced more Gag-Pol-Nef-specific CD8+ T-cell responses. Furthermore, MVA-B ΔC6L enhanced the levels of antibodies against Env in comparison with MVA-B. These findings revealed that C6 can be considered as an immunomodulator and that deleting C6L gene in MVA-B confers an immunological benefit by enhancing IFN-β-dependent responses and increasing the magnitude and quality of the T-cell memory immune responses to HIV-1 antigens. Our observations are relevant for the improvement of MVA vectors as HIV-1 vaccines.
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Affiliation(s)
- Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José Luis Nájera
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carmen E. Gómez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Nolawit Tewabe
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos Oscar S. Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Thierry Calandra
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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45
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Insights into human CD8(+) T-cell memory using the yellow fever and smallpox vaccines. Immunol Cell Biol 2011; 89:340-5. [PMID: 21301482 DOI: 10.1038/icb.2010.155] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Live virus vaccines provide a unique opportunity to study human CD8(+) T-cell memory in the context of a controlled, primary acute viral infection. Yellow fever virus-17D and Dryvax are two such live-virus vaccines that are highly efficacious, used worldwide and provide long-term immunity against yellow fever and smallpox respectively. In this review, we describe the properties of virus-specific memory CD8(+) T cells generated in smallpox and yellow fever vaccinees. We address fundamental questions regarding magnitude, functional quality and longevity of the CD8(+) T-cell response, which are otherwise challenging to address in humans. These findings provide insights into the attributes of the human immune system as well as provide a benchmark for the optimal quality of a CD8(+) T-cell response that can be used to evaluate novel candidate vaccines.
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46
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Rutkowski MR, Stevens CA, Green WR. Impaired memory CD8 T cell responses against an immunodominant retroviral cryptic epitope. Virology 2011; 412:256-68. [PMID: 21295815 DOI: 10.1016/j.virol.2010.11.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/04/2010] [Accepted: 11/15/2010] [Indexed: 11/16/2022]
Abstract
The immunodominant cryptic epitope SYNTGRFPPL, encoded within open reading frame 2 of the LP-BM5 retroviral gag gene, is critical for protection against retroviral-induced pathogenesis. The goal of this study was to dissect the memory response against this unique immunodominant cryptic epitope. Unlike the protective acute effector population of SYNTGRFPPL-specific CD8 T cells, long-lived SYNTGRFPPL-specific CD8 T cells lacked the ability to protect susceptible mice infected with LP-BM5 retrovirus. Compared to memory CD8 T cells against a conventional epitope with similar MHC-I specificity, primed and restimulated using similar conditions, long-lived SYNTGRFPPL-specific CD8 T cells were impaired in their ability to recall against antigen, with reduced cytolytic capabilities and cytokine production. Since similar priming and restimulation regimes were utilized to generate each effector CD8 T cell population, this study has potentially broad implications with regard to the selection criteria of potent, highly conserved cryptic epitopes for use in epitope-based vaccines.
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Affiliation(s)
- Melanie R Rutkowski
- Department of Microbiology and Immunology and Norris Cotton Cancer Center, Dartmouth Medical School, One Medical Center Drive, Borwell Bldg, Lebanon, NH 03756, USA
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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] [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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48
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Abstract
The Plasmodium parasite, the causative agent of malaria, is an excellent model for immunomic-based approaches to vaccine development. The Plasmodium parasite has a complex life cycle with multiple stages and stage-specific expression of ∼5300 putative proteins. No malaria vaccine has yet been licensed. Many believe that an effective vaccine will need to target several antigens and multiple stages, and will require the generation of both antibody and cellular immune responses. Vaccine efforts to date have been stage-specific and based on only a very limited number of proteins representing <0.5% of the genome. The recent availability of comprehensive genomic, proteomic and transcriptomic datasets from human and selected non-human primate and rodent malarias provide a foundation to exploit for vaccine development. This information can be mined to identify promising vaccine candidate antigens, by proteome-wide screening of antibody and T cell reactivity using specimens from individuals exposed to malaria and technology platforms such as protein arrays, high throughput protein production and epitope prediction algorithms. Such antigens could be incorporated into a rational vaccine development process that targets specific stages of the Plasmodium parasite life cycle with immune responses implicated in parasite elimination and control. Immunomic approaches which enable the selection of the best possible targets by prioritising antigens according to clinically relevant criteria may overcome the problem of poorly immunogenic, poorly protective vaccines that has plagued malaria vaccine developers for the past 25 years. Herein, current progress and perspectives regarding Plasmodium immunomics are reviewed.
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Affiliation(s)
- Denise L Doolan
- Division of Immunology, Queensland Institute of Medical Research, The Bancroft Centre, 300 Herston Road, P.O. Royal Brisbane Hospital, Brisbane, QLD 4029, Australia.
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49
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Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. J Biomed Biotechnol 2010; 2010:832341. [PMID: 20625421 PMCID: PMC2896900 DOI: 10.1155/2010/832341] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/02/2009] [Accepted: 03/24/2010] [Indexed: 12/03/2022] Open
Abstract
Using the currently available proteome databases and based on the concept that a rare sequence is a potential epitope, epitopic sequences derived from Mycobacterium tuberculosis were examined for similarity score to the proteins of the host in which the epitopes were defined. We found that: (i) most of the bacterial linear determinants had peptide fragment(s) that were rarely found in the host proteins and (ii) the relationship between low similarity and epitope definition appears potentially applicable to T-cell determinants. The data confirmed the hypothesis that low-sequence similarity shapes or determines the epitope definition at the molecular level and provides a potential tool for designing new approaches to prevent, diagnose, and treat tuberculosis and other infectious diseases.
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50
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Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A. Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol 2010; 5:221-39. [PMID: 20143946 DOI: 10.2217/fmb.09.110] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vaccinia virus (VACV) was used as the vaccine strain to eradicate smallpox. VACV is still administered to healthcare workers or researchers who are at risk of contracting the virus, and to military personnel. Thus, VACV represents a weapon against outbreaks, both natural (e.g., monkeypox) or man-made (bioterror). This virus is also used as a vector for experimental vaccine development (cancer/infectious disease). As a prototypic poxvirus, VACV is a model system for studying host-pathogen interactions. Until recently, little was known about the targets of host immune responses, which was likely owing to VACVs large genome (>200 open reading frames). However, the last few years have witnessed an explosion of data, and VACV has quickly become a useful model to study adaptive immune responses. This review summarizes and highlights key findings based on identification of VACV antigens targeted by the immune system (CD4, CD8 and antibodies) and the complex interplay between responses.
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Affiliation(s)
- Magdalini Moutaftsi
- Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
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