1
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Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Hernandez GM, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. Cell Rep 2024; 43:113596. [PMID: 38117652 PMCID: PMC10860710 DOI: 10.1016/j.celrep.2023.113596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/08/2023] [Accepted: 12/01/2023] [Indexed: 12/22/2023] Open
Abstract
Targeted synthetic vaccines have the potential to transform our response to viral outbreaks, yet the design of these vaccines requires a comprehensive knowledge of viral immunogens. Here, we report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides that are naturally processed and loaded onto human leukocyte antigen-II (HLA-II) complexes in infected cells. We identify over 500 unique viral peptides from canonical proteins as well as from overlapping internal open reading frames. Most HLA-II peptides colocalize with known CD4+ T cell epitopes in coronavirus disease 2019 patients, including 2 reported immunodominant regions in the SARS-CoV-2 membrane protein. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and nonstructural and noncanonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize vaccine effectiveness.
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Affiliation(s)
- Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.
| | - Da-Yuan Chen
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Hannah B Taylor
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Matteo Gentili
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Leah R Pearlman
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Matthew R Bauer
- Harvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard University Medical School, Boston, MA, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | | | - Mohsan Saeed
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
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2
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. PLoS Pathog 2023; 19:e1011032. [PMID: 37498934 PMCID: PMC10409285 DOI: 10.1371/journal.ppat.1011032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/08/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023] Open
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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3
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Weingarten-Gabbay S, Chen DY, Sarkizova S, Taylor HB, Gentili M, Pearlman LR, Bauer MR, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. The HLA-II immunopeptidome of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542482. [PMID: 37398281 PMCID: PMC10312465 DOI: 10.1101/2023.05.26.542482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Targeted synthetic vaccines have the potential to transform our response to viral outbreaks; yet the design of these vaccines requires a comprehensive knowledge of viral immunogens, including T-cell epitopes. Having previously mapped the SARS-CoV-2 HLA-I landscape, here we report viral peptides that are naturally processed and loaded onto HLA-II complexes in infected cells. We identified over 500 unique viral peptides from canonical proteins, as well as from overlapping internal open reading frames (ORFs), revealing, for the first time, the contribution of internal ORFs to the HLA-II peptide repertoire. Most HLA-II peptides co-localized with the known CD4+ T cell epitopes in COVID-19 patients. We also observed that two reported immunodominant regions in the SARS-CoV-2 membrane protein are formed at the level of HLA-II presentation. Overall, our analyses show that HLA-I and HLA-II pathways target distinct viral proteins, with the structural proteins accounting for most of the HLA-II peptidome and non-structural and non-canonical proteins accounting for the majority of the HLA-I peptidome. These findings highlight the need for a vaccine design that incorporates multiple viral elements harboring CD4+ and CD8+ T cell epitopes to maximize the vaccine effectiveness.
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4
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Becerra-Artiles A, Nanaware PP, Muneeruddin K, Weaver GC, Shaffer SA, Calvo-Calle JM, Stern LJ. Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.01.518643. [PMID: 36482973 PMCID: PMC9727760 DOI: 10.1101/2022.12.01.518643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines. Author Summary There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.
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Affiliation(s)
- Aniuska Becerra-Artiles
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Padma P. Nanaware
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Khaja Muneeruddin
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
| | - Grant C. Weaver
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Scott A. Shaffer
- Mass Spectrometry Facility, UMass Chan Medical School, Shrewsbury MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - J. Mauricio Calvo-Calle
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
| | - Lawrence J. Stern
- Department of Pathology, Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester MA
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA 01655, USA
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5
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Quach HQ, Ovsyannikova IG, Poland GA, Kennedy RB. Evaluating immunogenicity of pathogen-derived T-cell epitopes to design a peptide-based smallpox vaccine. Sci Rep 2022; 12:15401. [PMID: 36100624 PMCID: PMC9470075 DOI: 10.1038/s41598-022-19679-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/01/2022] [Indexed: 11/09/2022] Open
Abstract
Despite the eradication in 1980, developing safe and effective smallpox vaccines remains an active area of research due to the recent outbreaks and the public health concern that smallpox viruses could be used as bioterrorism weapons. Identifying immunogenic peptides (epitopes) would create a foundation for the development of a robust peptide-based vaccine. We previously identified a library of naturally-processed, human leukocyte antigen class I-presented vaccinia-derived peptides from infected B cells. In the current study, we evaluated the immunogenicity of these T-cell peptides in both transgenic mouse models and human peripheral blood mononuclear cells. A vaccine based on four selected peptides provided 100% protection against a lethal viral challenge. In addition, responses from memory T cells remained unchanged up to five months. Our results validate a practical approach for identifying and verifying immunogenic peptides for vaccine development and highlight the potential of peptide-based vaccines for various infectious diseases.
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Affiliation(s)
- Huy Quang Quach
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, 55905, USA
| | - Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN, 55905, USA.
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6
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Crooke SN, Ovsyannikova IG, Kennedy RB, Poland GA. Identification of naturally processed Zika virus peptides by mass spectrometry and validation of memory T cell recall responses in Zika convalescent subjects. PLoS One 2021; 16:e0252198. [PMID: 34077451 PMCID: PMC8171893 DOI: 10.1371/journal.pone.0252198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Once an obscure pathogen, Zika virus (ZIKV) has emerged as a significant global public health concern. Several studies have linked ZIKV infection in pregnant women with the development of microcephaly and other neurological abnormalities, emphasizing the need for a safe and effective vaccine to combat the spread of this disease. Preclinical studies and vaccine development efforts have largely focused on the role of humoral immunity in disease protection. Consequently, relatively little is known in regard to cellular immunity against ZIKV, although an effective vaccine will likely need to engage both the humoral and cellular arms of the immune system. To that end, we utilized two-dimensional liquid chromatography coupled with tandem mass spectrometry to identify 90 ZIKV peptides that were naturally processed and presented on HLA class I and II molecules (HLA-A*02:01/HLA-DRB1*04:01) of an immortalized B cell line infected with ZIKV (strain PRVABC59). Sequence identity clustering was used to filter the number of candidate peptides prior to evaluating memory T cell recall responses in ZIKV convalescent subjects. Peptides that individually elicited broad (4 of 7 subjects) and narrow (1 of 7 subjects) T cell responses were further analyzed using a suite of predictive algorithms and in silico modeling to evaluate HLA binding and peptide structural properties. A subset of nine broadly reactive peptides was predicted to provide robust global population coverage (97.47% class I; 70.74% class II) and to possess stable structural properties amenable for vaccine formulation, highlighting the potential clinical benefit for including ZIKV T cell epitopes in experimental vaccine formulations.
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Affiliation(s)
- Stephen N. Crooke
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Inna G. Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard B. Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Gregory A. Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota, United States of America
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7
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Knierman MD, Lannan MB, Spindler LJ, McMillian CL, Konrad RJ, Siegel RW. The Human Leukocyte Antigen Class II Immunopeptidome of the SARS-CoV-2 Spike Glycoprotein. Cell Rep 2020; 33:108454. [PMID: 33220791 PMCID: PMC7664343 DOI: 10.1016/j.celrep.2020.108454] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/16/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022] Open
Abstract
Precise elucidation of the antigen sequences for T cell immunosurveillance greatly enhances our ability to understand and modulate humoral responses to viral infection or active immunization. Mass spectrometry is used to identify 526 unique sequences from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein extracellular domain in a complex with human leukocyte antigen class II molecules on antigen-presenting cells from a panel of healthy donors selected to represent a majority of allele usage from this highly polymorphic molecule. The identified sequences span the entire spike protein, and several sequences are isolated from a majority of the sampled donors, indicating promiscuous binding. Importantly, many peptides derived from the receptor binding domain used for cell entry are identified. This work represents a precise and comprehensive immunopeptidomic investigation with the SARS-CoV-2 spike glycoprotein and allows detailed analysis of features that may aid vaccine development to end the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Michael D Knierman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Megan B Lannan
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Laura J Spindler
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Carl L McMillian
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Robert J Konrad
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Robert W Siegel
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA.
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8
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Koşaloğlu-Yalçın Z, Sidney J, Chronister W, Peters B, Sette A. Comparison of HLA ligand elution data and binding predictions reveals varying prediction performance for the multiple motifs recognized by HLA-DQ2.5. Immunology 2020; 162:235-247. [PMID: 33064841 PMCID: PMC7808151 DOI: 10.1111/imm.13279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Binding prediction tools are commonly used to identify peptides presented on MHC class II molecules. Recently, a wealth of data in the form of naturally eluted ligands has become available and discrepancies between ligand elution data and binding predictions have been reported. Quantitative metrics for such comparisons are currently lacking. In this study, we assessed how efficiently MHC class II binding predictions can identify naturally eluted peptides, and investigated instances with discrepancies between the two methods in detail. We found that, in general, MHC class II eluted ligands are predicted to bind to their reported restriction element with high affinity. But, for several studies reporting an increased number of ligands that were not predicted to bind, we found that the reported MHC restriction was ambiguous. Additional analyses determined that most of the ligands predicted to not bind, are predicted to bind other co‐expressed MHC class II molecules. For selected alleles, we addressed discrepancies between elution data and binding predictions by experimental measurements and found that predicted and measured affinities correlate well. For DQA1*05:01/DQB1*02:01 (DQ2.5) however, binding predictions did miss several peptides that were determined experimentally to be binders. For these peptides and several known DQ2.5 binders, we determined key residues for conferring DQ2.5 binding capacity, which revealed that DQ2.5 utilizes two different binding motifs, of which only one is predicted effectively. These findings have important implications for the interpretation of ligand elution data and for the improvement of MHC class II binding predictions.
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Affiliation(s)
| | - John Sidney
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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9
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Poland GA, Ovsyannikova IG, Crooke SN, Kennedy RB. SARS-CoV-2 Vaccine Development: Current Status. Mayo Clin Proc 2020; 95:2172-2188. [PMID: 33012348 PMCID: PMC7392072 DOI: 10.1016/j.mayocp.2020.07.021] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023]
Abstract
In the midst of the severe acute respiratory syndrome coronavirus 2 pandemic and its attendant morbidity and mortality, safe and efficacious vaccines are needed that induce protective and long-lived immune responses. More than 120 vaccine candidates worldwide are in various preclinical and phase 1 to 3 clinical trials that include inactivated, live-attenuated, viral-vectored replicating and nonreplicating, protein- and peptide-based, and nucleic acid approaches. Vaccines will be necessary both for individual protection and for the safe development of population-level herd immunity. Public-private partnership collaborative efforts, such as the Accelerating COVID-19 Therapeutic Interventions and Vaccines mechanism, are key to rapidly identifying safe and effective vaccine candidates as quickly and efficiently as possible. In this article, we review the major vaccine approaches being taken and issues that must be resolved in the quest for vaccines to prevent coronavirus disease 2019. For this study, we scanned the PubMed database from 1963 to 2020 for all publications using the following search terms in various combinations: SARS, MERS, COVID-19, SARS-CoV-2, vaccine, clinical trial, coronavirus, pandemic, and vaccine development. We also did a Web search for these same terms. In addition, we examined the World Health Organization, Centers for Disease Control and Prevention, and other public health authority websites. We excluded abstracts and all articles that were not written in English.
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Key Words
- ace2, angiotensin-converting enzyme 2
- ade, antibody-dependent enhancement
- covid-19, coronavirus disease 2019
- il, interleukin
- mers, middle east respiratory syndrome
- mva, modified vaccinia virus ankara
- nih, national institutes of health
- rbd, receptor-binding domain
- s, spike
- sars, severe acute respiratory syndrome
- sars-cov, sars coronavirus
- tlr, toll-like receptor
- vlp, virus-like particle
- who, world health organization
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10
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Becerra-Artiles A, Cruz J, Leszyk JD, Sidney J, Sette A, Shaffer SA, Stern LJ. Naturally processed HLA-DR3-restricted HHV-6B peptides are recognized broadly with polyfunctional and cytotoxic CD4 T-cell responses. Eur J Immunol 2019; 49:1167-1185. [PMID: 31020640 DOI: 10.1002/eji.201948126] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/13/2019] [Accepted: 04/23/2019] [Indexed: 01/06/2023]
Abstract
Human herpes virus 6B (HHV-6B) is a widespread virus that infects most people early in infancy and establishes a chronic life-long infection with periodic reactivation. CD4 T cells have been implicated in control of HHV-6B, but antigenic targets and functional characteristics of the CD4 T-cell response are poorly understood. We identified 25 naturally processed MHC-II peptides, derived from six different HHV-6B proteins, and showed that they were recognized by CD4 T-cell responses in HLA-matched donors. The peptides were identified by mass spectrometry after elution from HLA-DR molecules isolated from HHV-6B-infected T cells. The peptides showed strong binding to matched HLA alleles and elicited recall T-cell responses in vitro. T-cell lines expanded in vitro were used for functional characterization of the response. Responding cells were mainly CD3+ CD4+ , produced IFN-γ, TNF-α, and low levels of IL-2, alone or in combination, highlighting the presence of polyfunctional T cells in the overall response. Many of the responding cells mobilized CD107a, stored granzyme B, and mediated specific killing of peptide-pulsed target cells. These results highlight a potential role for polyfunctional cytotoxic CD4 T cells in the long-term control of HHV-6B infection.
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Affiliation(s)
| | - John Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA
| | - John D Leszyk
- Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, San Diego, CA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, San Diego, CA.,Department of Medicine, University of California, San Diego, CA
| | - Scott A Shaffer
- Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA
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11
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Haralambieva IH, Kennedy RB, Ovsyannikova IG, Schaid DJ, Poland GA. Current perspectives in assessing humoral immunity after measles vaccination. Expert Rev Vaccines 2019; 18:75-87. [PMID: 30585753 PMCID: PMC6413513 DOI: 10.1080/14760584.2019.1559063] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Repeated measles outbreaks in countries with relatively high vaccine coverage are mainly due to failure to vaccinate and importation; however, cases in immunized individuals exist raising questions about suboptimal measles vaccine-induced humoral immunity and/or waning immunity in a low measles-exposure environment. AREAS COVERED The plaque reduction neutralization measurement of functional measles-specific antibodies correlates with protection is the gold standard in measles serology, but it does not assess cellular-immune or other parameters that may be associated with durable and/or protective immunity after vaccination. Additional correlates of protection and long-term immunity and new determinants/signatures of vaccine responsiveness such as specific CD46 and IFI44L genetic variants associated with neutralizing antibody titers after measles vaccination are under investigation. Current and future systems biology studies, coupled with new technology/assays and analytical approaches, will lead to an increasingly sophisticated understanding of measles vaccine-induced humoral immunity and will identify 'signatures' of protective and durable immune responses. EXPERT OPINION This will translate into the development of highly predictive assays of measles vaccine efficacy, effectiveness, and durability for prospective identification of potential low/non-responders and susceptible individuals who require additional vaccine doses. Such new advances may drive insights into the development of new/improved vaccine formulations and delivery systems.
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Affiliation(s)
| | - Richard B Kennedy
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
| | | | - Daniel J Schaid
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
- b Department of Health Sciences Research , Mayo Clinic , Rochester , MN , USA
| | - Gregory A Poland
- a Mayo Clinic Vaccine Research Group , Mayo Clinic , Rochester , MN , USA
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Haralambieva IH, Kennedy RB, Ovsyannikova IG, Whitaker JA, Poland GA. Variability in Humoral Immunity to Measles Vaccine: New Developments. Trends Mol Med 2015; 21:789-801. [PMID: 26602762 DOI: 10.1016/j.molmed.2015.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/19/2022]
Abstract
Despite the existence of an effective measles vaccine, resurgence in measles cases in the USA and across Europe has occurred, including in individuals vaccinated with two doses of the vaccine. Host genetic factors result in inter-individual variation in measles vaccine-induced antibodies, and play a role in vaccine failure. Studies have identified HLA (human leukocyte antigen) and non-HLA genetic influences that individually or jointly contribute to the observed variability in the humoral response to vaccination among healthy individuals. In this exciting era, new high-dimensional approaches and techniques including vaccinomics, systems biology, GWAS, epitope prediction and sophisticated bioinformatics/statistical algorithms provide powerful tools to investigate immune response mechanisms to the measles vaccine. These might predict, on an individual basis, outcomes of acquired immunity post measles vaccination.
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Affiliation(s)
- Iana H Haralambieva
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard B Kennedy
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Inna G Ovsyannikova
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jennifer A Whitaker
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA; Mayo Clinic Division of General Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Phelan DM, Poland GA. HLA-DR specific monoclonal antibodies block lymphoproliferative response to measles vaccine in vitro: a pilot study. Vaccine 2012; 30:6628-31. [PMID: 22944627 DOI: 10.1016/j.vaccine.2012.08.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 08/16/2012] [Accepted: 08/17/2012] [Indexed: 11/24/2022]
Abstract
Humoral and cell-mediated immune responses are important in protection against measles. Non-response to vaccination has been associated with specific HLA-DR and HLA-DQ alleles; however, little is known about the relative importance of these alleles in the cellular immune response induced by measles virus vaccine. To investigate the role of HLA-DR/DQ class II restriction, a small pilot study was conducted. Lymphoproliferation assays using class II DR and DQ-specific monoclonal antibodies (MoAb) were performed at one week and two weeks post immunization with MMRII vaccine. The mean stimulation index (SI) was 4.4 and 5.3 at one and two weeks with reductions in SI of 47.6% and 70.2%, respectively, following the addition of DR-specific MoAb (p<0.001). These results clearly show that a significant proportion of the cell-mediated immune response to measles virus vaccine, as measured by SI, is HLA-DR restricted.
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Affiliation(s)
- David M Phelan
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, MN 55905, USA
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Ovsyannikova IG, Poland GA. Vaccinomics: current findings, challenges and novel approaches for vaccine development. AAPS J 2011; 13:438-44. [PMID: 21671143 PMCID: PMC3160164 DOI: 10.1208/s12248-011-9281-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 05/05/2011] [Indexed: 02/06/2023] Open
Abstract
Recent years have witnessed a growing interest in a field of vaccinology that we have named vaccinomics. The overall idea behind vaccinomics is to identify genetic and other mechanisms and pathways that determine immune responses, and thereby provide new candidate vaccine approaches. Considerable data show that host genetic polymorphisms act as important determinants of innate and adaptive immunity to vaccines. This review highlights examples of the role of immunogenetics and immunogenomics in understanding immune responses to vaccination, which are highly variable across the population. The influence of HLA genes, non-HLA, and innate genes in inter-individual variations in immune responses to viral vaccines are examined using population-based gene/SNP association studies. The ability to understand relationships between immune response gene variants and vaccine-specific immunity may assist in designing new vaccines. At the same time, application of state-of-the-art next-generation sequencing technology (and bioinformatics) is desired to provide new genetic information and its relationship to the immune response.
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Affiliation(s)
- Inna G. Ovsyannikova
- />Vaccine Research Group, Mayo Clinic, Rochester, Minnesota USA
- />Program in Translational Immunovirology and Biodefense, Rochester, Minnesota USA
- />Department of Medicine, Mayo Clinic, Rochester, Minnesota USA
| | - Gregory A. Poland
- />Vaccine Research Group, Mayo Clinic, Rochester, Minnesota USA
- />Program in Translational Immunovirology and Biodefense, Rochester, Minnesota USA
- />Department of Medicine, Mayo Clinic, Rochester, Minnesota USA
- />Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota USA
- />Mayo Clinic, 611C Guggenheim Building, 200 First Street, SW, Rochester, Minnesota 55905 USA
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Poland GA, Ovsyannikova IG, Kennedy RB, Haralambieva IH, Jacobson RM. Vaccinomics and a new paradigm for the development of preventive vaccines against viral infections. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:625-36. [PMID: 21732819 PMCID: PMC3166201 DOI: 10.1089/omi.2011.0032] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this article we define vaccinomics as the integration of immunogenetics and immunogenomics with systems biology and immune profiling. Vaccinomics is based on the use of cutting edge, high-dimensional (so called "omics") assays and novel bioinformatics approaches to the development of next-generation vaccines and the expansion of our capabilities in individualized medicine. Vaccinomics will allow us to move beyond the empiric "isolate, inactivate, and inject" approach characterizing past vaccine development efforts, and toward a more detailed molecular and systemic understanding of the carefully choreographed series of biological processes involved in developing viral vaccine-induced "immunity." This enhanced understanding will then be applied to overcome the obstacles to the creation of effective vaccines to protect against pathogens, particularly hypervariable viruses, with the greatest current impact on public health. Here we provide an overview of how vaccinomics will inform vaccine science, the development of new vaccines and/or clinically relevant biomarkers or surrogates of protection, vaccine response heterogeneity, and our understanding of immunosenescence.
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Affiliation(s)
- Gregory A Poland
- Mayo Clinic Vaccine Research Group, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Strug I, Calvo-Calle JM, Green KM, Cruz J, Ennis FA, Evans JE, Stern LJ. Vaccinia peptides eluted from HLA-DR1 isolated from virus-infected cells are recognized by CD4+ T cells from a vaccinated donor. J Proteome Res 2008; 7:2703-11. [PMID: 18507432 DOI: 10.1021/pr700780x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Class II MHC proteins bind peptides and present them to CD4 (+) T cells as part of the immune system's surveillance of bodily tissues for foreign and pathogenic material. Antigen processing and presentation pathways have been characterized in detail in normal cells, but there is little known about the actual viral peptides that are presented to CD4 (+) T cells that signal infection. In this study, two-dimensional LC-MS/MS was used to identify vaccinia virus-derived peptides among the hundreds to thousands of peptide antigens bound to the human class II MHC protein HLA-DR1 on the surface of vaccinia virus-infected cells. The peptides, derived from the I6L, D6R, and A10L viral proteins, were 15 residues in length, bound efficiently to HLA-DR1 as synthetic peptides, and were recognized by vaccinia-specific CD4 (+) T cells obtained from an immunized donor.
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Affiliation(s)
- Iwona Strug
- Department of Pathology, Proteomic and Mass Spectrometry Core Facility, Center for Infectious Disease and Vaccine Research, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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Yoo KH. Clinical Year in Review of Asthma for Pulmonary Physicians : The Epidemiologic Hypothesis for the Relationship between Asthma and Infectious Disease. Tuberc Respir Dis (Seoul) 2008. [DOI: 10.4046/trd.2008.65.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Kwang-Ha Yoo
- Department of Internal Medicine, Konkuk University College of Medicine, Seoul, Korea
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Ovsyannikova IG, Johnson KL, Bergen HR, Poland GA. Mass spectrometry and peptide-based vaccine development. Clin Pharmacol Ther 2007; 82:644-52. [PMID: 17971823 DOI: 10.1038/sj.clpt.6100389] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The development of new vaccines against pathogens is an important part of infectious disease control. In the last decade, a variety of proteins giving rise to naturally processed pathogen-derived antigenic peptides, representing B-cell and T-cell epitopes, have been characterized. Numerous candidate vaccines consisting of synthetic peptides are being designed and evaluated, with encouraging results. In this context, the application of mass spectrometry based on the isolation and identification of pathogen-derived peptides from the human leukocyte antigen (HLA) molecules is a major focus of peptide-based vaccine development. Dramatic improvements have been made in mass spectrometer performance for peptide sequencing in terms of increased sensitivity, the ability to rapidly obtain data-directed tandem mass spectra, and the accuracy of mass measurement. This review focuses on the efforts to identify T-cell epitopes for viral and microbial pathogens for directed vaccine development.
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Affiliation(s)
- I G Ovsyannikova
- Mayo Vaccine Research Group, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
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Homann D, Lewicki H, Brooks D, Eberlein J, Mallet-Designé V, Teyton L, Oldstone MBA. Mapping and restriction of a dominant viral CD4+ T cell core epitope by both MHC class I and MHC class II. Virology 2007; 363:113-23. [PMID: 17320138 PMCID: PMC1976554 DOI: 10.1016/j.virol.2006.12.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/12/2006] [Accepted: 12/08/2006] [Indexed: 11/25/2022]
Abstract
Virus-specific CD4(+) T cells contribute to effective virus control through a multiplicity of mechanisms including direct effector functions as well as "help" for B cell and CD8(+) T cell responses. Here, we have used the lymphocytic choriomeningitis virus (LCMV) system to assess the minimal constraints of a dominant antiviral CD4(+) T cell response. We report that the core epitope derived from the LCMV glycoprotein (GP) is 11 amino acids in length and provides optimal recognition by epitope-specific CD4(+) T cells. Surprisingly, this epitope is also recognized by LCMV-specific CD8(+) T cells and thus constitutes a unique viral determinant with dual MHC class I- and II-restriction.
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Affiliation(s)
- Dirk Homann
- Barbara Davis Center, University of Colorado at Denver and Health Sciences Center, 12801 East 17th Avenue, Aurora CO, USA
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20
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Juhn YJ, Kita H, Lee LA, Swanson RJ, Smith R, Bagniewski SM, Weaver AL, Pankratz VS, Jacobson RM, Poland GA. Childhood asthma and measles vaccine response. Ann Allergy Asthma Immunol 2006; 97:469-76. [PMID: 17069101 DOI: 10.1016/s1081-1206(10)60937-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
BACKGROUND Asthmatic patients have a TH2-predominant milieu that is associated with humoral immunity. However, little is known about whether humoral immune responses to viral antigens differ between asthmatic and nonasthmatic children. OBJECTIVE To determine whether humoral immune response differs in asthmatic patients vs nonasthmatic patients. METHODS Measles virus specific IgG antibody levels were determined for the Rochester Family Measles Study cohort (n = 876), a convenience sample of healthy children 5 to 12 years of age in Rochester, MN. We conducted comprehensive medical record reviews of 838 children who were eligible for this study. We determined the child's asthma status at the time of determination of antibody levels by applying predetermined criteria for asthma. Comparisons were made using the 2-sample t test or chi2 test. RESULTS Of the 838 children, 156 (18.6%) had asthma at the time of the determination of antibody levels and were not taking systemic steroids within 14 days of specimen collection. Among those with a nonequivocal antibody reading, the seropositive response rates were similar in asthmatic patients and nonasthmatic patients (89.7% vs 90.3%, respectively; P = .83). However, the equivocal response rates were slightly higher among asthmatic patients than nonasthmatic patients (6.4% vs 4.7%, respectively). CONCLUSION Asthmatic children seem to have similar humoral immune responses to measles vaccine as those without asthma. Although the findings reassure health care practitioners, whether this finding is generalizable to other vaccines and whether asthmatic patients with low antibody levels have normal cell-mediated immunity need to be elucidated in future studies.
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Affiliation(s)
- Young J Juhn
- Division of Pediatric and Adolescent Medicine, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.
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Ovsyannikova IG, Vierkant RA, Poland GA. Importance of HLA-DQ and HLA-DP polymorphisms in cytokine responses to naturally processed HLA-DR-derived measles virus peptides. Vaccine 2006; 24:5381-9. [PMID: 16714073 PMCID: PMC1853367 DOI: 10.1016/j.vaccine.2006.04.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 04/25/2006] [Indexed: 11/18/2022]
Abstract
We studied the association between class II human leukocyte antigen (HLA)-DRB1*0301 presented measles virus (MV) peptide-specific cytokine responses and DQB1 and DPB1 alleles among 313 individuals who received two doses of measles-mumps-rubella-II vaccine. The overall median IFN-gamma secretion levels (first and third quartiles) for the 19-amino acid MV phosphoprotein (MV-P)- and 14-amino acid MV nucleoprotein (MV-N)-derived peptides were 27.7 pg/ml (1.8, 109.4) and 1.9 pg/ml (-6.2, 13.0), respectively; median IL-4 secretion levels were -0.6 pg/ml (-7.1, 6.2) and 2.4 pg/ml (-3.2, 9.3), respectively. Primary statistical analyses were adjusted for previously identified DRB1 associations. A marginally significant increase in the frequency of the DQB1*0604 (p=0.02) allele was found among subjects who demonstrated detectable IL-4 levels to the MV-P peptide. Further, DPB1*0201 (p=0.02) and DPB1*1301 (p=0.09) alleles provided suggestive evidence of an association with MV-P-induced IL-4 secretion. Examination of IFN-gamma responses to MV-P and MV-N indicated that none of the individual alleles of the DQB1 and DPB1 loci were associated with peptide-induced T cell response. An increase in the frequency of DPB1*0501 (p=0.01) was found among subjects who failed to produce MV-N peptide-specific IL-4 responses. These data further confirm that HLA-DRB1 alleles are the major restriction molecules for MV-P and MV-N measles virus antigen presentation to T cells. We speculate that MV-P and MV-N peptides derived from DRB1*0301 could potentially be recognized in association with different HLA molecules, including DQB1 and DPB1; however, statistical adjustments for the effect of HLA-DR locus could potentially alter these genetic relationships. This concept provides important information supporting the use of promiscuous peptides in a peptide-based vaccine approach.
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Affiliation(s)
- Inna G. Ovsyannikova
- Mayo Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, USA
| | | | - Gregory A. Poland
- Mayo Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, USA
- Program in Translational Immunovirology and Biodefense, Mayo Clinic and Foundation, Rochester, MN, USA
- * Corresponding author at: Mayo Vaccine Research Group, Guggenheim 611C, 200 First Street SW, Rochester, MN 55905, USA. Tel.: +1 507 284 4968; fax: +1 507 266 4716. E-mail address: (G.A. Poland)
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22
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Johnson KL, Ovsyannikova IG, Poland GA, Muddiman DC. Identification of class II HLA-DRB1*03-bound measles virus peptides by 2D-liquid chromatography tandem mass spectrometry. J Proteome Res 2006; 4:2243-9. [PMID: 16335972 DOI: 10.1021/pr0501416] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two-dimensional liquid chromatography (2D-LC), combined with gas phase fractionation tandem mass spectrometry, was used to identify 13 naturally processed peptides originating from measles virus that were presented by HLA-DRB1*03 class II molecules. The peptides are from three of the six measles structural proteins: phosphoprotein, nucleocapsid, and hemagglutinin. These peptides provide an important first step toward understanding the mechanism of immune response to measles virus and development of a new generation of peptide-based vaccines.
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Affiliation(s)
- Kenneth L Johnson
- Mayo Proteomics Research Center, Mayo Vaccine Research Group, Program in Translational Immunovirology and Biodefense, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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23
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Johnson KL, Ovsyannikova IG, Madden BJ, Poland GA, Muddiman DC. Accurate mass precursor ion data and tandem mass spectrometry identify a class I human leukocyte antigen A*0201-presented peptide originating from vaccinia virus. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1812-7. [PMID: 16185891 DOI: 10.1016/j.jasms.2005.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 07/23/2005] [Accepted: 07/26/2005] [Indexed: 05/04/2023]
Abstract
We have used accurate mass precursor ion data generated on a hybrid linear-ion trap-Fourier transform ion cyclotron resonance mass spectrometer to augment tandem mass spectrometry (MS/MS) data generated on two different instrument types. Results from these experiments have allowed us for the first time to identify a naturally processed peptide presented by a class I human leukocyte antigen allele (HLA-A*0201) that was isolated from B cells infected by live vaccinia, the viral agent of the smallpox vaccine. The accurate mass data, in conjunction with MS/MS data, was able to identify the sequence IVIEAIHTV (aa 187-195) from the protein thymidylate kinase of vaccinia, distinguishing it from a similar sequence IVLEAIAEH: a "self-peptide" from the human protein phospholipase Cbeta3. Accurate mass data for the doubly charged species from the naturally processed and presented peptide was 497.8006, which was within 0.8 ppm of the calculated m/z of 497.8002, while being -37.3 ppm from the calculated m/z (497.7820) of the second-ranked peptide sequence IVLEAIAEH. Accurate mass data ranged from less than 0.1 to 1.2 ppm for other peptides identified in this sample. A BLAST search shows this sequence, IVIEAIHTV, is conserved in the same protein of a number of other orthopoxviruses, including the variola (smallpox) virus. Additionally, accurate mass data were able to uncover a false positive search result that was not distinguished by scoring of the match to the MS/MS data.
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Affiliation(s)
- Kenneth L Johnson
- The W. M. Keck FT-ICR Mass Spectrometry Laboratory, and Mayo Proteomics Research Center, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
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Ovsyannikova IG, Jacobson RM, Poland GA. Variation in vaccine response in normal populations. Pharmacogenomics 2004; 5:417-27. [PMID: 15165177 DOI: 10.1517/14622416.5.4.417] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Genetic polymorphisms of the human leukocyte antigen (HLA) system significantly influence the variation in immune responses to viral vaccines. Considerable data on the genetic determinants of immune responses to the measles vaccine support the importance of HLA genes in determining the variation in vaccine response. HLA class I and class II, TAP, and HLA-DM allele associations with measles-specific antibody levels following measles vaccination have revealed, in part, the immunologic basis for mechanisms of measles immunity variation. Associations between HLA genotype and immune responses have also been reported for other vaccines and infectious diseases, such as hepatitis B and C, human papillomaviruses, and influenza. Vaccine pharmacogenomics may provide important insights for the design and development of new peptide-based vaccines against measles and other pathogens.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Vaccine Research Group, 611C Guggenheim Building, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA
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Dhiman N, Ovsyannikova IG, Howe RC, Ryan JE, Jacobson RM, Poland GA. Interleukin-4 induced by measles virus and measles-derived peptides as measured by IL-4 receptor-blocking ELISA. J Immunol Methods 2004; 287:217-25. [PMID: 15099769 DOI: 10.1016/j.jim.2004.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 02/06/2004] [Accepted: 02/08/2004] [Indexed: 11/28/2022]
Abstract
Interleukin-4 (IL-4) is a signature cytokine for T-helper 2 (Th2) type immune responses in humans. However, data on antigen-specific secretion of IL-4 is limited due to difficulties detecting IL-4. We evaluated an IL-4 receptor-blocking assay for the detection of secreted IL-4 in peripheral blood mononuclear cells (PBMC) stimulated in vitro with measles virus (MV) and MV-derived nucleoprotein (N) and phosphoprotein (P) peptides. We recruited 20 healthy subjects, previously immunized with two doses of measles-mumps-rubella-II (MMR-II) vaccine. We evaluated the cellular and humoral immune status of these study subjects by an in vitro lymphoproliferation assay and an enzyme-linked immunosorbent assay (ELISA), respectively. We analyzed the MV-induced and N and P peptide-induced IL-4 levels in PBMC culture supernatants. Using the IL-4 receptor blocking assay, 50% of the subjects were positive for secreted IL-4 in response to MV stimulation, and 5% and 23.1% of study subjects were positive for secreted IL-4 in response to MV-derived N and P peptides, respectively. In contrast, we did not find any positive secreted IL-4 response to MV using conventional ELISA without IL-4 receptor-blocking antibody in our optimization study. Further, we found very low frequencies of IL-4 secreting cells using an alternate ELISpot technique, accounting for only a 5% positive response to MV and no response to P peptide. We propose that the IL-4 receptor-blocking assay is an easy-to-adapt technique for screening antigen-specific immune responses in large-scale population-based studies.
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Affiliation(s)
- Neelam Dhiman
- Mayo Vaccine Research Group, Mayo Clinic and Foundation, Rochester, MN 55905, USA
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26
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Ovsyannikova IG, Poland GA, Easler NJ, Vierkant RA. Influence of HLA-DRB1 alleles on lymphoproliferative responses to a naturally processed and presented measles virus phosphoprotein in measles immunized individuals. Hum Immunol 2004; 65:209-17. [PMID: 15041159 PMCID: PMC1853292 DOI: 10.1016/j.humimm.2003.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2003] [Revised: 12/03/2003] [Accepted: 12/05/2003] [Indexed: 12/01/2022]
Abstract
Identification of stimulatory T-cell epitopes recognized by CD4+ T lymphocytes is important for vaccine development. Our previous studies using mass spectrometry identified a naturally processed HLA class II restricted DRB1*0301 T cell epitope in the measles virus phosphoprotein, MV-P1 (residues 179-197). Here we provide lymphocyte proliferation data from peripheral blood mononuclear cells (PBMC) obtained from 131 HLA-DRB1*0301-positive and HLA-DRB1*0301-negative (HLA discordant) individuals previously immunized against measles and report that a single amino acid substitution in the MV-P1 T cell epitope can reduce T cell proliferation and CD4+ T-cell recognition. Measles virus and measles peptide-specific lymphoproliferative responses and HLA-DRB1 allele associations reveal that the DRB1*0701 allele provided suggestive evidence of association with both measles virus (p = 0.03) and MV-P1 peptide (p = 0.06) lymphoproliferation. A marginally significant increase in the frequency of the *0301 allele (p = 0.10) was found among subjects who demonstrated low cellular responses to the measles virus. We found no associations between proliferation levels to the MV-P1 and MV-P2 peptides with *0301 alleles. We speculate that the glutamic acid at position 192 of the measles phosphoprotein is a critical immunogenicity factor and may influence the antigenicity of the naturally processed HLA class II MV-P1 epitope.
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Ovsyannikova IG, Johnson KL, Muddiman DC, Vierkant RA, Poland GA. Identification and characterization of novel, naturally processed measles virus class II HLA-DRB1 peptides. J Virol 2004; 78:42-51. [PMID: 14671086 PMCID: PMC303425 DOI: 10.1128/jvi.78.1.42-51.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we identified a naturally processed and presented measles virus (MV) 19-amino-acid peptide, ASDVETAEGGEIHELLRLQ (MV-P), derived from the phosphoprotein and eluted from the human leukocyte antigen (HLA) class II molecule by using mass spectrometry. We report here the identification of a 14-amino-acid peptide, SAGKVSSTLASELG, derived from the MV nucleoprotein (MV-N) bound to HLA-DRB1*0301. Peripheral blood mononuclear cells (PBMC) from 281 previously vaccinated measles-mumps-rubella II (MMR-II) subjects (HLA discordant) were studied for peptide recognition by T cells. Significant gamma interferon (IFN-gamma) responses to MV-P and MV-N peptides were observed in 55.9 and 15.3% of subjects, respectively. MV-P- and MV-N-specific interleukin-4 (IL-4) responses were detected in 19.2 and 23.1%, respectively, of PBMC samples. Peptide-specific cytokine responses and HLA-DRB1 allele associations revealed that, for the MV-P peptide, the allele with the strongest association with both IFN-gamma (P = 0.02) and IL-4 (P = 0.03) secretion was DRB1*0301. For MV-N, the allele with the strongest association with IFN-gamma secretion was DRB1*1501 (P = 0.04), and the alleles with the strongest associations with IL-4 secretion were DRB1*1103 and DRB1*1303 (P = 0.01). These results indicate that HLA class II MV proteins can be processed, presented, and identified, and the ability to generate cell-mediated immune responses can be demonstrated. This information is promising for new vaccine design strategies with peptide-based vaccines.
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Affiliation(s)
- Inna G Ovsyannikova
- Mayo Vaccine Research Group, Mayo Clinic and College of Medicine, Rochester, Minnesota 55905, USA
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