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Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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2
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Chen L, Duvvuri B, Grigull J, Jamnik R, Wither JE, Wu GE. Experimental evidence that mutated-self peptides derived from mitochondrial DNA somatic mutations have the potential to trigger autoimmunity. Hum Immunol 2014; 75:873-9. [PMID: 24979674 DOI: 10.1016/j.humimm.2014.06.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 06/19/2014] [Accepted: 06/19/2014] [Indexed: 12/20/2022]
Abstract
Autoimmune disease is a critical health concern, whose etiology remains enigmatic. We hypothesized that immune responses to somatically mutated self proteins could have a role in the development of autoimmune disease. IFN-γ secretion by T cells stimulated with mitochondrial peptides encoded by published mitochondrial DNA was monitored to test the hypothesis. Human peripheral blood mononuclear cells (PBMCs) of healthy controls and autoimmune patients were assessed for their responses to the self peptides and mutated-self peptides differing from self by one amino acid. None of the self peptides but some of the mutated-self peptides elicited an immune response in healthy controls. In some autoimmune patients, PBMCs responded not only to some of the mutated-self peptides, but also to some of the self peptides, suggesting that there is a breach of self-tolerance in these patients. Although PBMCs from healthy controls failed to respond to self peptides when stimulated with self, the mutated-self peptide could elicit a response to the self peptide upon re-stimulation in vitro, suggesting that priming with mutated-self peptides elicits a cross-reactive response with self. The data raise the possibility that DNA somatic mutations are one of the events that trigger and/or sustain T cell responses in autoimmune diseases.
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Affiliation(s)
- Lina Chen
- Department of Kinesiology and Health Science, York University, Canada.
| | - Bhargavi Duvvuri
- Department of Kinesiology and Health Science, York University, Canada
| | - Jörg Grigull
- Department of Mathematics and Statistics, York University, Canada
| | - Roni Jamnik
- Department of Kinesiology and Health Science, York University, Canada
| | - Joan E Wither
- University Health Network and University of Toronto, Canada
| | - Gillian E Wu
- Department of Kinesiology and Health Science, York University, Canada
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3
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Quiñones-Parra S, Loh L, Brown LE, Kedzierska K, Valkenburg SA. Universal immunity to influenza must outwit immune evasion. Front Microbiol 2014; 5:285. [PMID: 24971078 PMCID: PMC4054793 DOI: 10.3389/fmicb.2014.00285] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/23/2014] [Indexed: 12/23/2022] Open
Abstract
Although an influenza vaccine has been available for 70 years, influenza virus still causes seasonal epidemics and worldwide pandemics. Currently available vaccines elicit strain-specific antibody (Ab) responses to the surface haemagglutinin (HA) and neuraminidase (NA) proteins, but these can be ineffective against serologically-distinct viral variants and novel subtypes. Thus, there is a great need for cross-protective or "universal" influenza vaccines to overcome the necessity for annual immunization against seasonal influenza and to provide immunity to reduce the severity of infection with pandemic or outbreak viruses. It is well established that natural influenza infection can provide cross-reactive immunity that can reduce the impact of infection with distinct influenza type A strains and subtypes, including H1N1, H3N2, H2N2, H5N1, and H7N9. The key to generating universal influenza immunity through vaccination is to target functionally-conserved regions of the virus, which include epitopes on the internal proteins for cross-reactive T cell immunity or on the HA stem for broadly reactive Ab responses. In the wake of the 2009 H1N1 pandemic, broadly neutralizing antibodies (bnAbs) have been characterized and isolated from convalescent and vaccinated individuals, inspiring development of new vaccination techniques to elicit such responses. Induction of influenza-specific T cell responses through vaccination has also been recently examined in clinical trials. Strong evidence is available from human and animal models of influenza to show that established influenza-specific T cell memory can reduce viral shedding and symptom severity. However, the published evidence also shows that CD8(+) T cells can efficiently select immune escape mutants early after influenza virus infection. Here, we discuss universal immunity to influenza viruses mediated by both cross-reactive T cells and Abs, the mechanisms of immune evasion in influenza, and propose how to counteract commonly occurring immune-escape variants.
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Affiliation(s)
- Sergio Quiñones-Parra
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville VIC, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville VIC, Australia
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville VIC, Australia
| | - Sophie A Valkenburg
- Centre for Influenza Research and School of Public Health, The University of Hong Kong Hong Kong, China
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4
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Lyngaa R, Pedersen NW, Schrama D, Thrue CA, Ibrani D, Met O, Thor Straten P, Nghiem P, Becker JC, Hadrup SR. T-cell responses to oncogenic merkel cell polyomavirus proteins distinguish patients with merkel cell carcinoma from healthy donors. Clin Cancer Res 2014; 20:1768-78. [PMID: 24526738 DOI: 10.1158/1078-0432.ccr-13-2697] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is a highly aggressive skin cancer with strong evidence of viral carcinogenesis. The association of MCC with the Merkel cell polyomavirus (MCPyV) may explain the explicit immunogenicity of MCC. Indeed, MCPyV-encoded proteins are likely targets for cytotoxic immune responses to MCC as they are both foreign to the host and necessary to maintain the oncogenic phenotype. However, to date only a single MCPyV-derived CD8 T-cell epitope has been described, thus impeding specific monitoring of T-cell responses to MCC. METHOD To overcome this limitation, we scanned the MCPyV oncoprotein large T and small T antigens and the virus capsid protein VP1 for potential T-cell epitopes, and tested for MHC class I affinity. We confirmed the relevance of these epitopes using a high-throughput platform for T-cell enrichment and combinatorial encoding of MHC class I multimers. RESULTS In peripheral blood from 38 patients with MCC and 30 healthy donors, we identified 53 MCPyV-directed CD8 T-cell responses against 35 different peptide sequences. Strikingly, T-cell responses against oncoproteins were exclusively present in patients with MCC, but not in healthy donors. We further demonstrate both the processing and presentation of the oncoprotein-derived epitopes, as well as the lytic activity of oncoprotein-specific T cells toward MHC-matched MCC cells. Demonstrating the presence of oncoprotein-specific T cells among tumor-infiltrating lymphocytes further substantiated the relevance of the identified epitopes. CONCLUSION These T-cell epitopes represent ideal targets for antigen-specific immune therapy of MCC, and enable tracking and characterization of MCPyV-specific immune responses.
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Affiliation(s)
- Rikke Lyngaa
- Authors' Affiliations: Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark; General Dermatology, Medical University of Graz, Graz, Austria; Departments of Medicine/Dermatology, Pathology, University of Washington; Fred Hutchinson Cancer Research Center, Seattle Cancer Center Care Alliance, Seattle, Washington; and Department of Oncology, University Hospital Herlev, Herlev, Denmark
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5
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van de Sandt CE, Kreijtz JHCM, de Mutsert G, Geelhoed-Mieras MM, Hillaire MLB, Vogelzang-van Trierum SE, Osterhaus ADME, Fouchier RAM, Rimmelzwaan GF. Human cytotoxic T lymphocytes directed to seasonal influenza A viruses cross-react with the newly emerging H7N9 virus. J Virol 2014; 88:1684-93. [PMID: 24257602 PMCID: PMC3911609 DOI: 10.1128/jvi.02843-13] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/12/2013] [Indexed: 01/05/2023] Open
Abstract
In February 2013, zoonotic transmission of a novel influenza A virus of the H7N9 subtype was reported in China. Although at present no sustained human-to-human transmission has been reported, a pandemic outbreak of this H7N9 virus is feared. Since neutralizing antibodies to the hemagglutinin (HA) globular head domain of the virus are virtually absent in the human population, there is interest in identifying other correlates of protection, such as cross-reactive CD8(+) T cells (cytotoxic T lymphocytes [CTLs]) elicited during seasonal influenza A virus infections. These virus-specific CD8(+) T cells are known to recognize conserved internal proteins of influenza A viruses predominantly, but it is unknown to what extent they cross-react with the newly emerging H7N9 virus. Here, we assessed the cross-reactivity of seasonal H3N2 and H1N1 and pandemic H1N1 influenza A virus-specific polyclonal CD8(+) T cells, obtained from HLA-typed study subjects, with the novel H7N9 virus. The cross-reactivity of CD8(+) T cells to H7N9 variants of known influenza A virus epitopes and H7N9 virus-infected cells was determined by their gamma interferon (IFN-γ) response and lytic activity. It was concluded that, apart from recognition of individual H7N9 variant epitopes, CD8(+) T cells to seasonal influenza viruses display considerable cross-reactivity with the novel H7N9 virus. The presence of these cross-reactive CD8(+) T cells may afford some protection against infection with the new virus.
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MESH Headings
- Adult
- Amino Acid Sequence
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Cells, Cultured
- China/epidemiology
- Cross Protection
- Cross Reactions
- Disease Outbreaks
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/chemistry
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/chemistry
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H7N9 Subtype/chemistry
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/immunology
- Influenza A Virus, H7N9 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Interferon-gamma/immunology
- Male
- Middle Aged
- Molecular Sequence Data
- Seasons
- Sequence Alignment
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/virology
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Affiliation(s)
| | | | | | | | | | | | | | - Ron A. M. Fouchier
- Viroscience Laboratory, Erasmus MC, Rotterdam, The Netherlands
- ViroClinics Biosciences BV, Rotterdam, The Netherlands
| | - Guus F. Rimmelzwaan
- Viroscience Laboratory, Erasmus MC, Rotterdam, The Netherlands
- ViroClinics Biosciences BV, Rotterdam, The Netherlands
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6
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Petrova G, Ferrante A, Gorski J. Cross-reactivity of T cells and its role in the immune system. Crit Rev Immunol 2012; 32:349-72. [PMID: 23237510 DOI: 10.1615/critrevimmunol.v32.i4.50] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T-cell receptors recognize peptides presented by the major histocompatibility complex (MHC) on the surface of antigen-presenting cells (APC). The ability of the T-cell receptor (TCR) to recognize more than one peptide-MHC structure defines cross-reactivity. Cross-reactivity is a documented phenomenon of the immune system whose importance is still under investigation. There are a number of rational arguments for cross-reactivity. These include the discrepancy between the theoretical high number of pathogen-derived peptides and the lower diversity of the T-cell repertoire, the need for recognition of escape variants, and the intrinsic low affinity of this receptor-ligand pair. However, quantifying the phenomenon has been difficult, and its immunological importance remains unknown. In this review, we examined the cases for and against an important role for cross reactivity. We argue that it may be an essential feature of the immune system from the point of view of biological robustness.
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Affiliation(s)
- Galina Petrova
- The Blood Research Institute, Blood Center of Wisconsin, Milwaukee, Wisconsin 53226, USA
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7
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Nuclear export signal and immunodominant CD8+ T cell epitope in influenza A virus matrix protein 1. J Virol 2012; 86:10258; author reply1259-60. [PMID: 22923812 DOI: 10.1128/jvi.00894-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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8
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Petrova GV, Gorski J. Cross-reactive responses to modified M1₅₈-₆₆ peptides by CD8⁺ T cells that use noncanonical BV genes can describe unknown repertoires. Eur J Immunol 2012; 42:3001-8. [PMID: 22865108 DOI: 10.1002/eji.201242596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/21/2012] [Accepted: 07/30/2012] [Indexed: 11/06/2022]
Abstract
Memory T-cell repertoires are populated by clonotypes selected by an individual's history of antigen exposures. Our previous analysis of middle-age CD8(+) T-cell memory repertoires to the influenza-derived epitope M1(58-66) , described a network of highly cross-reactive BV19 clonotypes responding to M1(58-66) and at least one peptide with a conservative amino acid substitution at either of two TCR contact positions. Here, we report that some substitutions abrogate BV19 responses and favor responses with different BV. Cross-reactive T cells using seven other BV families responded to 12 of 13 peptides tested. BV12 clonotypes define the most extensive cross-reactive network that encompasses seven peptides. We generated 3D networks based on the peptides recognized and BV family used and observed a cluster of five peptides that includes M1(58-66) and another cluster of five peptides that does not include M1(58-66) . The first cluster represents peptides structurally similar to M1(58-66) , and the second represents peptides with more considerable changes in epitope recognition surface. We hypothesize that the second cluster represents the cross-reactive network around another unknown epitope or epitopes. This data supports a model of stable CD8(+) T-cell memory networks that include a substantial contribution from cross-reactive T cells.
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Affiliation(s)
- Galina V Petrova
- The Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA
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9
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Valkenburg SA, Rutigliano JA, Ellebedy AH, Doherty PC, Thomas PG, Kedzierska K. Immunity to seasonal and pandemic influenza A viruses. Microbes Infect 2011; 13:489-501. [PMID: 21295153 PMCID: PMC3549300 DOI: 10.1016/j.micinf.2011.01.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/18/2011] [Indexed: 12/16/2022]
Abstract
The introduction of a new influenza strain into human circulation leads to rapid global spread. This review summarizes innate and adaptive immunity to influenza viruses, with an emphasis on T-cell responses that provide cross-protection between distinct subtypes and strains. We discuss antigenic variation within T-cell immunogenic peptides and our understanding of pre-existing immunity towards the pandemic A(H1N1) 2009 strain.
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Affiliation(s)
- Sophie A Valkenburg
- Department of Microbiology and Immunology, University of Melbourne, Royal Pde, Parkville 3010, Melbourne, Australia
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10
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Petrova GV, Naumova EN, Gorski J. The polyclonal CD8 T cell response to influenza M158-66 generates a fully connected network of cross-reactive clonotypes to structurally related peptides: a paradigm for memory repertoire coverage of novel epitopes or escape mutants. THE JOURNAL OF IMMUNOLOGY 2011; 186:6390-7. [PMID: 21518969 DOI: 10.4049/jimmunol.1004031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cross-reactivity of T cells is defined as recognition of two or more peptide-MHC complexes by the same T cell. Although examples of cross-reactivity have been reported, a detailed examination of cross-reactivity has not been performed. In this study, we took advantage of the high degree of polyclonality in the BV19 T cell repertoire responding to influenza M1(58-66) in HLA-A2 individuals to obtain a measure of simple cross-reactivity. We used substitutions that incrementally change the structure of the M1(58-66) peptide to measure how the HLA-A2-restricted response adapts to these changes. In three HLA-A2 adult subjects, we identified the BV19 clonotypes in the recall response to the influenza epitope M1(58-66) and 12 M1 peptides substituted at TCR contact position 63 or 65. The fraction of cross-reactive clonotypes in the M1(58-66) repertoire varied from 45-58% in the three donors. The extent of cross-reactivity, which is the additional number of peptides recognized by a single clonotype, is as high as six. We summarized the data using graph theory, with the cross-reactive clonotypes connecting the different HLA-A2 peptides recognized. The cross-reactive clonotypes form a well-connected network that could provide protection from virus-escape variants. We predict that any new pathogen with an epitope whose shape corresponds to that of the peptides that we studied would find a pre-existing repertoire ready to respond to it. We propose that in adult memory repertoires, previously encountered epitopes may have generated similar cross-reactive repertoires.
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Affiliation(s)
- Galina V Petrova
- Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA
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11
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Naumov YN, Naumova EN, Yassai MB, Gorski J. Selective T cell expansion during aging of CD8 memory repertoires to influenza revealed by modeling. THE JOURNAL OF IMMUNOLOGY 2011; 186:6617-24. [PMID: 21515795 DOI: 10.4049/jimmunol.1100091] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aging of T cell memory is often considered in terms of senescence, a process viewed as decay and loss of memory T cells. How senescence would affect memory is a function of the initial structure of the memory repertoire and whether the clonotypes that make up the repertoire decay at random. We examine this issue using the T cell memory generated to the conserved influenza A epitope M1(58-66), which induces a strong, focused, but polyclonal CD8 T cell response in HLA-A2 individuals. We analyzed the CD8 T cell memory repertoires in eight healthy middle-aged and eight healthy older blood donors representing an average age difference of ∼ 27 y. Although the repertoires show broadly similar clonotype distributions, the number of observable clonotypes decreases significantly. This decrease disproportionally affects low-frequency clonotypes. Rank frequency analysis shows the same two-component clonotype distribution described earlier for these repertoires. The first component includes lower frequency clonotypes for which distribution can be described by a power law. The slope of this first component is significantly steeper in the older cohort. Generating a representative repertoire for each healthy cohort allowed agent-based modeling of the aging process. Interestingly, simple senescence of middle-aged repertoires is insufficient to describe the older clonotype distribution. Rather, a selective clonotype expansion must be included to achieve the best fit. We propose that responses to periodic virus exposure may drive such expansion, ensuring that the remaining clonotypes are optimized for continued protection.
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Affiliation(s)
- Yuri N Naumov
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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12
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Cornberg M, Clute SC, Watkin LB, Saccoccio FM, Kim SK, Naumov YN, Brehm MA, Aslan N, Welsh RM, Selin LK. CD8 T cell cross-reactivity networks mediate heterologous immunity in human EBV and murine vaccinia virus infections. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:2825-38. [PMID: 20164414 PMCID: PMC3253758 DOI: 10.4049/jimmunol.0902168] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this study, we demonstrate complex networks of CD8 T cell cross-reactivities between influenza A virus and EBV in humans and between lymphocytic choriomeningitis virus and vaccinia virus in mice. We also show directly that cross-reactive T cells mediate protective heterologous immunity in mice. Subsets of T cell populations reactive with one epitope cross-reacted with either of several other epitopes encoded by the same or the heterologous virus. Human T cells specific to EBV-encoded BMLF1(280-288) could be cross-reactive with two influenza A virus or two other EBV epitopes. Mouse T cells specific to the vaccinia virus-encoded a11r(198-205) could be cross-reactive with three different lymphocytic choriomeningitis virus, one Pichinde virus, or one other vaccinia virus epitope. Patterns of cross-reactivity differed among individuals, reflecting the private specificities of the host's immune repertoire and divergence in the abilities of T cell populations to mediate protective immunity. Defining such cross-reactive networks between commonly encountered human pathogens may facilitate the design of vaccines.
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Affiliation(s)
- Markus Cornberg
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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13
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Naumova EN, Gorski J, Naumov YN. Two compensatory pathways maintain long-term stability and diversity in CD8 T cell memory repertoires. THE JOURNAL OF IMMUNOLOGY 2009; 183:2851-8. [PMID: 19635925 DOI: 10.4049/jimmunol.0900162] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The time-dependent changes of human memory T cell repertoires are still poorly understood. We define a T cell memory repertoire as the pool of clonotypic lineages participating in a recall response to the influenza M1(58-66) epitope. In HLA-A2 individuals, this response predominantly uses BV19 chains with Arg-Ser (RS) in the CDR3 loop. We previously showed that the repertoire is polyclonal with a large fraction of clonotype that are only observed once. In this study, we perform longitudinal analyses of memory repertoires in three middle-aged individuals at times that spanned from 7 to 10 years. In these individuals, who are well into thymic involution, a substantial number of clonotypes were stable, e.g., detected at two times. The shape of the repertoire was stable over time as reflected by a number of repertoire characteristics, including singletons, i.e., the fraction of clonotypes observed only once, and repertoire diversity. However, the RS-clonotype subset showed a significant decline in the fraction of singletons and in clonotypic diversity. Thus, repertoire structure is maintained over time by a recruitment of non-RS-clonotypes and a shift of existing RS-clonotypes into higher frequencies. The recruitment of new clonotypes into the low-frequency component of the repertoire implies a role for these clonotypes.
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Affiliation(s)
- Elena N Naumova
- Department of Public Health and Family Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
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14
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Recombinant vesicular stomatitis virus expressing influenza nucleoprotein induces CD8 T-cell responses that enhance antibody-mediated protection after lethal challenge with influenza virus. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2009; 16:488-98. [PMID: 19244472 DOI: 10.1128/cvi.00451-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Live attenuated vaccine vectors based on recombinant vesicular stomatitis viruses (rVSVs) expressing foreign antigens are highly effective vaccines in animal models. In this study, we report that an rVSV expressing influenza nucleoprotein (VSV NP) from the first position of the VSV genome induces robust anti-NP CD8 T cells in immunized mice. These CD8 T cells are phenotypically similar to those induced by natural influenza infection and are cytotoxic in vivo. Animals immunized with an rVSV expressing the influenza hemagglutinin (rVSV HA) were protected but still exhibited considerable morbidity after challenge. Animals receiving a cocktail vaccine of rVSV NP and rVSV HA had reduced pulmonary viral loads, less weight loss, and reduced clinical signs of illness after influenza virus challenge, relative to those vaccinated with rVSV HA alone. Influenza NP is a highly conserved antigen, and induction of protective anti-NP responses may be a productive strategy for generating heterologous protection against divergent influenza strains.
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15
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Naumov YN, Naumova EN, Yassai MB, Kota K, Welsh RM, Selin LK. Multiple glycines in TCR alpha-chains determine clonally diverse nature of human T cell memory to influenza A virus. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2008; 181:7407-19. [PMID: 18981164 PMCID: PMC2646260 DOI: 10.4049/jimmunol.181.10.7407] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detailed assessment of how the structural properties of T cell receptors affect clonal repertoires of Ag-specific cells is a prerequisite for a better understanding of human antiviral immunity. Herein we examine the alpha TCR repertoires of CD8 T cells reactive against the influenza A viral epitope M1(58-66), restricted by HLA-A2.1. Using molecular cloning, we systematically studied the impact of alpha-chain usage in the formation of T cell memory and revealed that M1(58-66)-specific, clonally diverse VB19 T cells express alpha-chains encoded by multiple AV genes with different CDR3 sizes. A unique feature of these alpha TCRs was the presence of CDR3 fitting to an AGA(G(n))GG-like amino acid motif. This pattern was consistent over time and among different individuals. Further molecular assessment of human CD4(+)CD8(-) and CD4(-)CD8(+) thymocytes led to the conclusion that the poly-Gly/Ala runs in CDR3alpha were a property of immune, but not naive, repertoires and could be attributed to influenza exposure. Repertoires of T cell memory are discussed in the context of clonal diversity, where poly-Gly/Ala runs in the CDR3 of alpha- and beta-chains might provide high levels of TCR flexibility during Ag recognition while gene-encoded CDR1 and CDR2 contribute to the fine specificity of the TCR-peptide MHC interaction.
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MESH Headings
- Adult
- Amino Acid Motifs/immunology
- CD8-Positive T-Lymphocytes/immunology
- Clone Cells
- Flow Cytometry
- Gene Rearrangement, alpha-Chain T-Cell Antigen Receptor
- Genes, T-Cell Receptor alpha
- Glycine/immunology
- HLA-A2 Antigen/immunology
- Humans
- Immunologic Memory
- Infant
- Influenza A virus/immunology
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Reverse Transcriptase Polymerase Chain Reaction
- Viral Matrix Proteins/immunology
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Affiliation(s)
- Yuri N Naumov
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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16
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Influenza A virus matrix protein 1-specific human CD8+ T-cell response induced in trivalent inactivated vaccine recipients. J Virol 2008; 82:9283-7. [PMID: 18614638 DOI: 10.1128/jvi.01047-08] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among 17 HLA-A2-positive healthy adults, CD8+ T-cell responses against an HLA-A2-restricted matrix protein 1 (M1) epitope increased after immunization with trivalent inactivated influenza vaccine (TIV) in two individuals. The presence of M1 in TIV was confirmed by Western blotting. T-cell cytotoxicity assays showed that TIV is processed and the epitope is presented by antigen-presenting cells to an M1 epitope-specific CD8+ T-cell line for specific lysis. These data show that TIV, which is formulated to contain surface glycoproteins to induce serotype-specific antibody responses, also contains M1, capable of inducing subtype cross-reactive CD8+ T-cell responses in some vaccinees.
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17
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Identification of an HLA-A*0201-restricted T-cell epitope on the MPT51 protein, a major secreted protein derived from Mycobacterium tuberculosis, by MPT51 overlapping peptide screening. Infect Immun 2008; 76:1565-71. [PMID: 18212086 DOI: 10.1128/iai.01381-07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD8+ T cells play a pivotal role in protection against Mycobacterium tuberculosis infection. We identified a novel HLA-A*0201-restricted CD8+ T-cell epitope on a dominant secreted antigen of M. tuberculosis, MPT51, in HLA-A*0201 transgenic HHD mice. HHD mice were immunized with plasmid DNA encoding MPT51 with gene gun bombardment, and gamma interferon (IFN-gamma) production by the immune splenocytes was analyzed. In response to overlapping synthetic peptides covering the mature MPT51 sequence, the splenocytes were stimulated to produce IFN-gamma by only one peptide, p51-70. Three-color flow cytometric analysis of intracellular IFN-gamma and cell surface CD4 and CD8 staining revealed that the MPT51 p51-70 peptide contains an immunodominant CD8+ T-cell epitope. Further analysis using computer algorithms permitted identification of a bona fide T-cell epitope, p53-62. A major histocompatibility complex class I stabilization assay using T2 cells confirmed that this epitope binds to HLA-A*0201. The T cells were capable of lysing MPT51 p53-62 peptide-pulsed T2 cells. In addition, MPT51 p53-62-specific memory CD8+ T cells were found in tuberculin skin test-positive HLA-A*0201+ healthy individuals. Use of this HLA-A*0201-restricted CD8+ T-cell epitope for analysis of the role of MPT51-specific T cells in M. tuberculosis infection and for design of vaccines against tuberculosis is feasible.
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18
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Létourneau S, Im EJ, Mashishi T, Brereton C, Bridgeman A, Yang H, Dorrell L, Dong T, Korber B, McMichael AJ, Hanke T. Design and pre-clinical evaluation of a universal HIV-1 vaccine. PLoS One 2007; 2:e984. [PMID: 17912361 PMCID: PMC1991584 DOI: 10.1371/journal.pone.0000984] [Citation(s) in RCA: 239] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 09/13/2007] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test. METHODOLOGY AND FINDINGS To address the HIV-1 variation, we designed a novel T cell immunogen, designated HIV(CONSV), by assembling the 14 most conserved regions of the HIV-1 proteome into one chimaeric protein. Each segment is a consensus sequence from one of the four major HIV-1 clades A, B, C and D, which alternate to ensure equal clade coverage. The gene coding for the HIV(CONSV) protein was inserted into the three most studied vaccine vectors, plasmid DNA, human adenovirus serotype 5 and modified vaccine virus Ankara (MVA), and induced HIV-1-specific T cell responses in mice. We also demonstrated that these conserved regions prime CD8(+) and CD4(+) T cell to highly conserved epitopes in humans and that these epitopes, although usually subdominant, generate memory T cells in patients during natural HIV-1 infection. SIGNIFICANCE Therefore, this vaccine approach provides an attractive and testable alternative for overcoming the HIV-1 variability, while focusing T cell responses on regions of the virus that are less likely to mutate and escape. Furthermore, this approach has merit in the simplicity of design and delivery, requiring only a single immunogen to provide extensive coverage of global HIV-1 population diversity.
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Affiliation(s)
- Sven Létourneau
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Eung-Jun Im
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tumelo Mashishi
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Choechoe Brereton
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Hongbing Yang
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Lucy Dorrell
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tao Dong
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, United States of America
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Andrew J. McMichael
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
| | - Tomáš Hanke
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe, Oxford, United Kingdom
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19
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Larke N, Im EJ, Wagner R, Williamson C, Williamson AL, McMichael AJ, Hanke T. Combined single-clade candidate HIV-1 vaccines induce T cell responses limited by multiple forms of in vivo immune interference. Eur J Immunol 2007; 37:566-77. [PMID: 17230443 DOI: 10.1002/eji.200636711] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We assessed in mice whether broad CD8+ T cell responses capable of efficient recognition of multiple HIV-1 clades could be induced using current single-clade vaccine constructs that were or will be used in clinical trials in Europe and Africa. We found that single-clade A, B and C vaccines applied alone induced only limited cross-clade reactivity and that the epitope hierarchy varied according to the immunizing clade. However, combining single-clade HIV-1 vaccines into multi-clade formulations resulted in multiple forms of in vivo immune interference such as original antigenic sin and antagonism, which dampened or even abrogated induction of responses to epitope variants and reduced the breadth of induced T cell responses. Simultaneous administration of individual clade-specific vaccines into anatomically separated sites on the body alleviated antagonism and increased the number of detectable epitope responses. Although cross-reactivity of murine CD8+ T cells does not directly translate to humans, the molecular interactions involved in triggering T cell responses are the same in mouse and man. Thus, these results have important ramifications for the design of both prophylactic and therapeutic vaccines against HIV-1 and other highly variable pathogens.
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Affiliation(s)
- Natasha Larke
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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20
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Donermeyer DL, Weber KS, Kranz DM, Allen PM. The study of high-affinity TCRs reveals duality in T cell recognition of antigen: specificity and degeneracy. THE JOURNAL OF IMMUNOLOGY 2007; 177:6911-9. [PMID: 17082606 DOI: 10.4049/jimmunol.177.10.6911] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
TCRs exhibit a high degree of Ag specificity, even though their affinity for the peptide/MHC ligand is in the micromolar range. To explore how Ag specificity is achieved, we studied murine T cells expressing high-affinity TCRs engineered by in vitro evolution for binding to hemoglobin peptide/class II complex (Hb/I-Ek). These TCRs were shown previously to maintain Ag specificity, despite having up to 800-fold higher affinity. We compared the response of the high-affinity TCRs and the low-affinity 3.L2 TCR toward a comprehensive set of peptides containing single substitutions at each TCR contact residue. This specificity analysis revealed that the increase in affinity resulted in a dramatic increase in the number of stimulatory peptides. The apparent discrepancy between observed degeneracy in the recognition of single amino acid-substituted Hb peptides and overall Ag specificity of the high-affinity TCRs was examined by generating chimeric peptides between the stimulatory Hb and nonstimulatory moth cytochrome c peptides. These experiments showed that MHC anchor residues significantly affected TCR recognition of peptide. The high-affinity TCRs allowed us to estimate the affinity, in the millimolar range, of immunologically relevant interactions of the TCR with peptide/MHC ligands that were previously unmeasurable because of their weak nature. Thus, through the study of high-affinity TCRs, we demonstrated that a TCR is more tolerant of single TCR contact residue substitutions than other peptide changes, revealing that recognition of Ag by T cells can exhibit both specificity and degeneracy.
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Affiliation(s)
- David L Donermeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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21
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DeLuca DS, Khattab B, Blasczyk R. A modular concept of HLA for comprehensive peptide binding prediction. Immunogenetics 2006; 59:25-35. [PMID: 17119951 DOI: 10.1007/s00251-006-0176-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Accepted: 10/25/2006] [Indexed: 11/26/2022]
Abstract
A variety of algorithms have been successful in predicting human leukocyte antigen (HLA)-peptide binding for HLA variants for which plentiful experimental binding data exist. Although predicting binding for only the most common HLA variants may provide sufficient population coverage for vaccine design, successful prediction for as many HLA variants as possible is necessary to understand the immune response in transplantation and immunotherapy. However, the high cost of obtaining peptide binding data limits the acquisition of binding data. Therefore, a prediction algorithm, which applies the binding information from well-studied HLA variants to HLA variants, for which no peptide data exist, is necessary. To this end, a modular concept of class I HLA-peptide binding prediction was developed. Accurate predictions were made for several alleles without using experimental peptide binding data specific to those alleles. We include a comparison of module-based prediction and supertype-based prediction. The modular concept increased the number of predictable alleles from 15 to 75 of HLA-A and 12 to 36 of HLA-B proteins. Under the modular concept, binding data of certain HLA alleles can make prediction possible for numerous additional alleles. We report here a ranking of HLA alleles, which have been identified to be the most informative. Modular peptide binding prediction is freely available to researchers on the web at http://www.peptidecheck.org .
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Affiliation(s)
- David S DeLuca
- Institute for Transfusion Medicine, Hanover Medical School, Carl-Neuberg-Str 1, 30625 Hanover, Germany.
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22
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Im EJ, Nkolola JP, di Gleria K, McMichael AJ, Hanke T. Induction of long-lasting multi-specific CD8+ T cells by a four-component DNA-MVA/HIVA-RENTA candidate HIV-1 vaccine in rhesus macaques. Eur J Immunol 2006; 36:2574-84. [PMID: 17013988 DOI: 10.1002/eji.200636482] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As a part of a long-term effort to develop vaccine against HIV-1 clade A inducing protective T cell responses in humans, we run mutually complementing studies in humans and non-human primates (NHP) with the aim to maximize vaccine immunogenicity. The candidate vaccine under development has four components, pTHr.HIVA and pTH.RENTA DNA, and modified vaccinia virus Ankara (MVA).HIVA and MVA.RENTA, delivered in a heterologous DNA prime-MVA boost regimen. While the HIVA (Gag/epitopes) components have been tested in NHP and over 300 human subjects, we plan to test in humans the RENTA (reverse transcriptase, gp41, Nef, Tat) vaccines designed to broaden HIVA-induced responses in year 2007. Here, we investigated the four-component vaccine long-term immunogenicity in Mamu-A*01-positive rhesus macaques and demonstrated that the vaccine-induced T cells were multi-specific, multi-functional, readily proliferated to recall peptides and were circulating in the peripheral blood of vaccine recipients over 1 year after vaccine administration. The consensus clade A-elicited T cells recognized 50% of tested epitope variants from other HIV-1 clades. Thus, the DNA-MVA/HIVA-RENTA vaccine induced memory T cells of desirable characteristics and similarities to those induced in humans by HIVA vaccines alone; however, single-clade vaccines may not elicit sufficiently cross-reactive responses.
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Affiliation(s)
- Eung-Jun Im
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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23
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Appay V, Speiser DE, Rufer N, Reynard S, Barbey C, Cerottini JC, Leyvraz S, Pinilla C, Romero P. Decreased specific CD8+ T cell cross-reactivity of antigen recognition following vaccination with Melan-A peptide. Eur J Immunol 2006; 36:1805-14. [PMID: 16761313 DOI: 10.1002/eji.200535805] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of T cell vaccines is the expansion of antigen-specific T cells able to confer immune protection against pathogens or tumors. Although increase in absolute cell numbers, effector functions and TCR repertoire of vaccine-induced T cells are often evaluated, their reactivity for the cognate antigen versus their cross-reactive potential is rarely considered. In fact, little information is available regarding the influence of vaccines on T cell fine specificity of antigen recognition despite the impact that this feature may have in protective immunity. To shed light on the cross-reactive potential of vaccine-induced cells, we analyzed the reactivity of CD8(+) T cells following vaccination of HLA-A2(+) melanoma patients with Melan-A peptide, incomplete Freund's adjuvant and CpG-oligodeoxynucleotide adjuvant, which was shown to induce strong expansion of Melan-A-reactive CD8(+) T cells in vivo. A collection of predicted Melan-A cross-reactive peptides, identified from a combinatorial peptide library, was used to probe functional antigen recognition of PBMC ex vivo and Melan-A-reactive CD8(+) T cell clones. While Melan-A-reactive CD8(+) T cells prior to vaccination are usually constituted of widely cross-reactive naive cells, we show that peptide vaccination resulted in expansion of memory T cells displaying a reactivity predominantly restricted to the antigen of interest. Importantly, these cells are tumor-reactive.
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Affiliation(s)
- Victor Appay
- Multidisciplinary Oncology Center, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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24
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Abstract
Influenza viruses are the etiological agents of influenza. Although vaccines and drugs are available for the prophylaxis and treatment of influenza virus infections, the generation of escape mutants has been reported. To develop vaccines and drugs that are less susceptible to the generation of escape mutants, it is important to understand the evolutionary mechanisms of the viruses. Here natural selection operating on all the proteins encoded by the H3N2 human influenza A virus genome was inferred by comparing the numbers of synonymous (d(S) [D(S)]) and nonsynonymous (d(N) [D(N)]) substitutions per site. Natural selection was also inferred for the groups of functional amino acid sites involved in B-cell epitopes (BCEs), T-cell epitopes (TCEs), drug resistance, and growth in eggs. The entire region of PB1-F2 was positively selected, and positive selection also appeared to operate on BCEs, TCEs, and growth in eggs. The frequency of escape mutant generation appeared to be positively correlated with the d(N)/d(S) (D(N)/D(S)) values for the targets of vaccines and drugs, suggesting that the amino acid sites under strong functional constraint are suitable targets. In particular, TCEs may represent candidate targets because the d(N)/d(S) (D(N)/D(S)) values were small and negative selection was inferred for many of them.
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Affiliation(s)
- Yoshiyuki Suzuki
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima-shi, Shizuoka-ken, Japan.
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25
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Zimmermann N, Rötzschke O, Falk K, Rognan D, Folkers G, Rammensee HG, Jung G. Moleküldynamiksimulation für ein allelspezifisches virales Nonapeptid aus dem Influenza-Matrix-protein in der Bindungstasche eines menschlichen MHC-Klasse-I-Proteins. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.19921040741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Buchli R, VanGundy RS, Hickman-Miller HD, Giberson CF, Bardet W, Hildebrand WH. Development and validation of a fluorescence polarization-based competitive peptide-binding assay for HLA-A*0201--a new tool for epitope discovery. Biochemistry 2005; 44:12491-507. [PMID: 16156661 DOI: 10.1021/bi050255v] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Various approaches are currently proposed to successfully develop therapies for the prevention and treatment of infectious diseases and cancer. One of the most promising approaches is the development of vaccines that elicit cytotoxic T lymphocyte (CTL) responses. Consequently, identification and exact definition of molecular parameters involved in peptide-MHC class-I interactions of putative CTL epitopes are of prime importance for the development of immunomodulating compounds. To better facilitate epitope discovery, we developed and validated a novel state-of-the-art biochemical HLA-A0201 assay, which is comprised of technologically advanced cutting edge reagents. The technique is based on competition and uses a FITC-labeled reference peptide and highly purified soluble HLA-A0201 molecules to quantitatively measure the binding capacity of nonlabeled peptide candidates. Detection by fluorescence polarization allows real-time measurement of binding ratios without separation steps. During standardization, the problem of assay parameter variation is discussed, showing the dramatic influence of HLA and reference peptide concentrations as well as the choice of the reference peptide itself on IC(50) determinations. For validation, a panel of 15 well-defined HLA-A0201 ligands from various sources covering a broad range of binding affinities was tested. Binding data were used to compare against pre-existing quantitative assay systems. The results obtained demonstrated significant correlation among assay procedures, suggesting that the application of fluorescence polarization in combination with recombinant sHLA molecules is highly advantageous for the accurate assessment of peptide binding. Furthermore, the assay also features high-throughput screening capacity, providing uniquely efficient means of identifying and evaluating immune target molecules.
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Affiliation(s)
- Rico Buchli
- Pure Protein L.L.C., Oklahoma City, Oklahoma 73104-3698, USA.
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27
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Berkhoff EGM, de Wit E, Geelhoed-Mieras MM, Boon ACM, Symons J, Fouchier RAM, Osterhaus ADME, Rimmelzwaan GF. Functional constraints of influenza A virus epitopes limit escape from cytotoxic T lymphocytes. J Virol 2005; 79:11239-46. [PMID: 16103176 PMCID: PMC1193597 DOI: 10.1128/jvi.79.17.11239-11246.2005] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Viruses can exploit a variety of strategies to evade immune surveillance by cytotoxic T lymphocytes (CTL), including the acquisition of mutations in CTL epitopes. Also for influenza A viruses a number of amino acid substitutions in the nucleoprotein (NP) have been associated with escape from CTL. However, other previously identified influenza A virus CTL epitopes are highly conserved, including the immunodominant HLA-A*0201-restricted epitope from the matrix protein, M1(58-66). We hypothesized that functional constraints were responsible for the conserved nature of influenza A virus CTL epitopes, limiting escape from CTL. To assess the impact of amino acid substitutions in conserved epitopes on viral fitness and recognition by specific CTL, we performed a mutational analysis of CTL epitopes. Both alanine replacements and more conservative substitutions were introduced at various positions of different influenza A virus CTL epitopes. Alanine replacements for each of the nine amino acids of the M1(58-66) epitope were tolerated to various extents, except for the anchor residue at the second position. Substitution of anchor residues in other influenza A virus CTL epitopes also affected viral fitness. Viable mutant viruses were used in CTL recognition experiments. The results are discussed in the light of the possibility of influenza viruses to escape from specific CTL. It was speculated that functional constraints limit variation in certain epitopes, especially at anchor residues, explaining the conserved nature of these epitopes.
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Affiliation(s)
- E G M Berkhoff
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
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28
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Kummer M, Lev A, Reiter Y, Biedermann BC. Vascular Endothelial Cells Have Impaired Capacity to Present Immunodominant, Antigenic Peptides: A Mechanism of Cell Type-Specific Immune Escape. THE JOURNAL OF IMMUNOLOGY 2005; 174:1947-53. [PMID: 15699122 DOI: 10.4049/jimmunol.174.4.1947] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vascular endothelial cells (EC) are an exposed target tissue in the course of CTL-mediated alloimmune diseases such as graft-vs-host disease (GVHD) or solid organ transplant rejection. The outcome of an interaction between CTL and target cells is determined by the amount of Ag presented and the costimulatory signals delivered by the target cells. We compared human EC with leukocytes and epithelial cells as targets for peptide-specific, MHC class I-restricted CTL clones. EC were poor targets for immunodominant CTL. Both endogenously processed antigenic proteins and exogenously added antigenic peptides are presented at 50- to 5000-fold lower levels on EC compared with any other target cell analyzed. This quantitative difference fully explained the poor CTL-mediated killing of EC. There was no evidence that lack of costimulation would contribute significantly to this cell type-specific difference in CTL activation. An HLA-A2-specific CTL clone that killed a broad selection of HLA A2-positive target cells equally well, killed EC less efficiently. Our data suggest that EC present a different Ag repertoire compared with other cell types. By this mechanism, these cells may escape an attack by effector CTL, which have been educated by professional APCs and are specific for immunodominant antigenic peptides.
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MESH Headings
- Antigen Presentation/immunology
- Antigens, Surface/biosynthesis
- Cell Death/immunology
- Cell Line, Transformed
- Cell Line, Tumor
- Cells, Cultured
- Clone Cells
- Cytotoxicity Tests, Immunologic
- Endothelium, Vascular/immunology
- Endothelium, Vascular/metabolism
- Endothelium, Vascular/pathology
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Female
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- Histone Demethylases
- Histone-Lysine N-Methyltransferase
- Humans
- Immunity, Cellular
- Immunodominant Epitopes/immunology
- Immunodominant Epitopes/metabolism
- Male
- Minor Histocompatibility Antigens
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Proteins/immunology
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Marco Kummer
- Department of Medicine, University Hospital Bruderholz, Bruderholz, Switzerland
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29
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Lee JK, Stewart-Jones G, Dong T, Harlos K, Di Gleria K, Dorrell L, Douek DC, van der Merwe PA, Jones EY, McMichael AJ. T cell cross-reactivity and conformational changes during TCR engagement. ACTA ACUST UNITED AC 2005; 200:1455-66. [PMID: 15583017 PMCID: PMC2211951 DOI: 10.1084/jem.20041251] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
All thymically selected T cells are inherently cross-reactive, yet many data indicate a fine specificity in antigen recognition, which enables virus escape from immune control by mutation in infections such as the human immunodeficiency virus (HIV). To address this paradox, we analyzed the fine specificity of T cells recognizing a human histocompatibility leukocyte antigen (HLA)-A2–restricted, strongly immunodominant, HIV gag epitope (SLFNTVATL). The majority of 171 variant peptides tested bound HLA-A2, but only one third were recognized. Surprisingly, one recognized variant (SLYNTVATL) showed marked differences in structure when bound to HLA-A2. T cell receptor (TCR) recognition of variants of these two peptides implied that they adopted the same conformation in the TCR–peptide–major histocompatibility complex (MHC) complex. However, the on-rate kinetics of TCR binding were identical, implying that conformational changes at the TCR–peptide–MHC binding interface occur after an initial permissive antigen contact. These findings have implications for the rational design of vaccines targeting viruses with unstable genomes.
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Affiliation(s)
- Jean K Lee
- Human Immunology Unit, Medical Research Council, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, England, UK
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30
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Lindstrom SE, Cox NJ, Klimov A. Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957-1972: evidence for genetic divergence and multiple reassortment events. Virology 2004; 328:101-19. [PMID: 15380362 DOI: 10.1016/j.virol.2004.06.009] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 03/10/2004] [Accepted: 06/01/2004] [Indexed: 10/26/2022]
Abstract
Phylogenic analysis of all gene segments of human H2N2 viruses isolated from 1957 to 1968 was undertaken to better understand the evolution of this virus subtype. Human H3N2 viruses isolated from 1968 to 1972 were also examined to investigate genetic events associated with their emergence in humans and to identify the putative H2N2 ancestral virus. All gene segments of human H2N2 viruses demonstrated divergent evolution into two distinct clades (I and II) among late H2N2 isolates. All gene segments of 1968 H3N2 viruses that were retained from human H2N2 viruses were most similar to clade I H2N2 genes. However, genes of both clades were found among H3N2 isolates of 1969-1971. Unique phylogenic topologies reflected multiple reassortment events among late H2N2 or H3N2 viruses that resulted in a variety of different genome constellations. These results suggest that H2N2 viruses continued to circulate after 1968 and that establishment of H3N2 viruses in humans was associated with multiple reassortment events that contributed to their genetic diversity.
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Affiliation(s)
- Stephen E Lindstrom
- Influenza Branch, MS-G16, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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31
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Rimmelzwaan GF, Boon ACM, Geelhoed-Mieras MM, Voeten JTM, Fouchier RAM, Osterhaus ADME. Human airway epithelial cells present antigen to influenza virus-specific CD8+ CTL inefficiently after incubation with viral protein together with ISCOMATRIX. Vaccine 2004; 22:2769-75. [PMID: 15246610 DOI: 10.1016/j.vaccine.2004.01.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Accepted: 01/08/2004] [Indexed: 11/24/2022]
Abstract
In the present paper, an in vitro model was established in which the interaction between influenza virus-specific CD8+ T cells and human airway epithelial cells can be studied. To this end, the human lung epithelial cell line A549 was transduced with the HLA-A*0201 gene. This MHC class I allele is involved in the presentation of the immunodominant M158-66 cytotoxic T lymphocyte (CTL) epitope of the influenza A virus matrix protein. The A549-HLA-A2 cells and a CD8+ T cell clone specific for the M158-66 epitope were used to evaluate ISCOMATRIX (IMX), which is considered a potential mucosal adjuvant for influenza vaccines, for its capacity to activate virus-specific CTL after incubation with epithelial cells. It was found that virus infected epithelial cells activated virus-specific CTL efficiently. However, incubation of epithelial cells with ISCOMATRIX and recombinant M1 protein activated CD8+ T cells inefficiently, unlike the incubation of C1R cells expressing a HLA-A2 trans gene or HLA-A2+ B-lymphoblastoid cells with these reagents. It was concluded that this lack of antigen presentation by epithelial cells indicate that these cells are not subject to killing by virus-specific CTL upon instillation with ISCOMATRIX-based vaccines, which may be a favorable property of mucosal vaccines.
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Affiliation(s)
- G F Rimmelzwaan
- Institute of Virology, National Influenza Center, Erasmus Medical Center, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands.
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32
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Zimmermann N, Rötzschke O, Falk K, Rognan D, Folkers G, Rammensee HG, Jung G. Molecular Modeling of the Class I Human Histocompatibility Molecule HLA-A2 Presenting an Allele-Specific Nonapeptide from Influenza Matrix Protein. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/anie.199208861] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Biddison WE, Turner RV, Gagnon SJ, Lev A, Cohen CJ, Reiter Y. Tax and M1 peptide/HLA-A2-specific Fabs and T cell receptors recognize nonidentical structural features on peptide/HLA-A2 complexes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 171:3064-74. [PMID: 12960332 DOI: 10.4049/jimmunol.171.6.3064] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Both TCRs and Ab molecules are capable of MHC-restricted recognition of peptide/MHC complexes. However, such MHC restriction is the predominant mode of recognition by T cells, but is extremely rare for B cells. The present study asks whether the dichotomy in Ag recognition modes of T and B cells could be due to fundamental differences in the methods by which TCRs and Abs recognize peptide/MHC complexes. We have compared MHC and peptide recognition by panels of CTL lines specific for the Tax and M1 peptides presented by HLA-A2 plus Tax and M1 peptide/HLA-A2-specific human Fabs that were selected from a naive phage display library. Collectively, the results indicate both striking similarities and important differences between Fab and TCR recognition of MHC and peptide components of the Tax and M1/HLA-A2 complexes. These findings suggest that these two classes of immunoreceptors have solved the problem of specific recognition of peptide/MHC complexes by nonidentical mechanisms. This conclusion is important in part because it indicates that Ab engineering approaches could produce second-generation Ab molecules that more closely mimic TCR fine specificity. Such efforts may produce more efficacious diagnostic and therapeutic agents.
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Affiliation(s)
- William E Biddison
- Molecular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
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34
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Trautmann A, Rückert B, Schmid-Grendelmeier P, Niederer E, Bröcker EB, Blaser K, Akdis CA. Human CD8 T cells of the peripheral blood contain a low CD8 expressing cytotoxic/effector subpopulation. Immunology 2003; 108:305-12. [PMID: 12603596 PMCID: PMC1782903 DOI: 10.1046/j.1365-2567.2003.01590.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Heterogeneity of lymphocyte populations demonstrates the diversity of cellular immune responses and provide a better understanding of the immune system. CD3+ CD8+ T cells exhibit a low CD8 expressing (CD8low) population in flow cytometric analysis of peripheral blood T cells. In healthy donors, this population consists of 0.2-7.0% of all CD8 T cells. The majority of the CD8low T cell population showed an elevated expression of CD25, CD45RA, and CD95L, and low levels of CD28, CD62L and CD45RO. Circulating CD8low T cells resemble cytotoxic effector cells because they express cytolytic mediators and are able to execute cytotoxicity. A restricted T cell receptor profile with increased Vbeta9, Vbeta14 and Vbeta23 expression was observed and the CD8low T cell population contain Epstein-Barr virus-specific T cells. Therefore, the CD8low population represent a subset of activated CD8 effector T cells, resulting most probably from a continuous and/or balanced immune response to intracellular pathogens.
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Affiliation(s)
- Axel Trautmann
- Swiss Institute of Allergy and Asthma Research (SIAF), Obere Strasse 22, CH-7270 Davos, Switzerland.
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35
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Larsson M, Wilkens DT, Fonteneau JF, Beadle TJ, Merritt MJ, Kost RG, Haslett PAJ, Cu-Uvin S, Bhardwaj N, Nixon DF, Shacklett BL. Amplification of low-frequency antiviral CD8 T cell responses using autologous dendritic cells. AIDS 2002; 16:171-80. [PMID: 11807300 DOI: 10.1097/00002030-200201250-00005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To utilize the potent antigen-presenting capacity of mature dendritic cells (MDC) in order to develop a rapid, sensitive method for quantifying antigen-specific CD8 T cells present at low frequency in peripheral blood. DESIGN Peripheral blood mononuclear cells (PBMC) were obtained from seven HIV-1-positive individuals with low to moderate CD8 T cell responses, including five on highly active antiretroviral therapy (HAART). IFN-gamma ELISPOT assays were performed using either monocytes or MDC to present antigens expressed by recombinant vaccinia viruses (r-VV). METHODS Peripheral blood-derived monocytes were cultured for 5-6 days in the presence of IL-4 and granulocyte macrophage colony-stimulating factor, then matured in monocyte-conditioned medium. MDC were infected with r-VV and co-cultured in an ELISPOT assay with autologous monocyte-depleted PBMC. RESULTS Relative to autologous monocytes, MDC amplified detection of antigen-specific CD8 T cells by 2-30-fold in response to antigens from HIV-1, Epstein-Barr virus and cytomegalovirus. Furthermore, antigenic specificities were revealed that had not been detected using standard ELISPOT of PBMC. CONCLUSION This assay will prove useful for the detection of memory T cells present at low frequency, and may be of interest for identifying subdominant cytotoxic T lymphocyte epitopes. This method may have broad applications for the detection of antiviral CD8 T cell responses in patient populations in whom such responses have been difficult to detect, including HIV-1-seropositive individuals with advanced disease or undergoing HAART.
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Affiliation(s)
- Marie Larsson
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, NY, USA
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36
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Maeda M, Otsuka T, Kimura N, Kozu T, Fukuyama T, Uchida N, Sugio Y, Itoh Y, Iino T, Inaba S, Niho Y. Induction of MTG8-specific cytotoxic T-cell lines: MTG8 is probably a tumour antigen that is recognized by cytotoxic T cells in AML1-MTG8-fused gene-positive acute myelogenous leukaemia. Br J Haematol 2000. [DOI: 10.1111/j.1365-2141.2000.02400.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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37
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Maeda M, Otsuka T, Kimura N, Kozu T, Fukuyama T, Uchida N, Sugio Y, Itoh Y, Iino T, Inaba S, Niho Y. Induction of MTG8-specific cytotoxic T-cell lines: MTG8 is probably a tumour antigen that is recognized by cytotoxic T cells in AML1-MTG8-fused gene-positive acute myelogenous leukaemia. Br J Haematol 2000; 111:570-9. [PMID: 11122105 DOI: 10.1046/j.1365-2141.2000.02400.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several reports have demonstrated the persistent detection of AML1-MTG8 fusion products, representing minimal residual disease (MRD), in patients with t(8;21) acute myelogenous leukaemia (AML) who are in long-term remission. It is probable that immune-mediated mechanisms that are able to suppress the expansion of MRD may result in the continuance of remission. It was previously shown that some t(8;21) AML patients had high anti-MTG8 antibody titres. MTG8 expression in normal adult tissues is limited to the brain or heart in which human leucocyte antigen (HLA) class I cell-surface antigens are either not or are only faintly detectable. We hypothesized that the overexpression of the MTG8 gene in t(8;21) AML cells could act as a possible tumour antigen, which might be able to induce the immune-mediated suppression of the expansion of MRD. We were able to induce HLA-A0201-restricted cytotoxic T-lymphocyte (CTL) lines against an MTG8 peptide (MTG8b amino acids 182-191) using monocyte-derived dendritic cells from a healthy donor. T-cell receptor (TCR)Valpha17, TCRVbeta14 and 15, and TCRJbeta2.1 and 2.3 are predominantly used in these CTL lines. Our data, which suggest that the MTG8 protein could be one of the tumour antigens recognized by CTLs, may be helpful in further investigations of TCR analysis in t(8;21) AML patients with HLA-A0201 who are in long-term remission.
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MESH Headings
- Antigens, Neoplasm/immunology
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit
- Cytotoxicity Tests, Immunologic
- DNA Primers
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/immunology
- Epitopes
- Histocompatibility Testing
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Lymphocyte Activation
- Neoplasm, Residual
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/immunology
- Polymerase Chain Reaction
- Polymorphism, Single-Stranded Conformational
- Proto-Oncogene Proteins
- RUNX1 Translocation Partner 1 Protein
- T-Lymphocytes, Cytotoxic/immunology
- Transcription Factors/genetics
- Transcription Factors/immunology
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- M Maeda
- The Cancer Centre, Kyushu University Hospital, The First Department of Internal Medicine, Fukuoka University, Fukuoka, Japan.
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38
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Gianfrani C, Oseroff C, Sidney J, Chesnut RW, Sette A. Human memory CTL response specific for influenza A virus is broad and multispecific. Hum Immunol 2000; 61:438-52. [PMID: 10773346 DOI: 10.1016/s0198-8859(00)00105-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Class I restricted cytotoxic T-lymphocyte (CTL) responses are thought to be focused against few immunodominant epitopes. In humans, an often quoted example of such narrow focus is the influenza A (FLU) matrix 58-66 specific memory CTL activity, detectable in HLA-A2 individuals as a result of natural infection. Herein, we analyzed the repertoire of memory, FLU-specific CTLs in A2 and A11 positive individuals. Eighteen A2.1 binding peptides, derived from the FLU-Puerto Rico/8/34 (PR8) isolate, elicited CTL activity in A2. 1/Kb transgenic mice upon direct immunization. These peptides were also tested for their capacity to recall memory CTL responses from peripheral blood mononuclear cells (PBMC) of human A2.1 donors. Besides the known dominant M1.58 peptide, 5 new epitopes (PA.46, PA. 225, PB1.413, NA.75 and M1.59) were identified. Similarly, eleven, A11-binding, FLU-PR8 peptides, which were immunogenic in HLA-A11/Kb transgenic mice, were assayed for induction of recall CTL responses using peripheral blood lymphocytes from a cohort of A11-positive donors. Eight different peptides (NP.188, NP.342, HA.63(,) HA.149, HA.450, M1.13, M1.178, and M2.70) induced memory CTL activity. Several of these peptides were found to be highly conserved amongst different FLU isolates, and also capable of binding multiple A2 and A11 supertype molecules. Finally, 37 HLA-B7 binding peptides were also identified. In conclusion, a previously unappreciated breadth of FLU-specific, memory CTL responses in humans was revealed. The relevance of these findings to the design of multiepitope vaccines is discussed.
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Affiliation(s)
- C Gianfrani
- Department of Immunology, Epimmune Inc., San Diego, CA 92121, USA
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39
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Berke Z, Andersen MH, Pedersen M, Fugger L, Zeuthen J, Haurum JS. Peptides spanning the junctional region of both the abl/bcr and the bcr/abl fusion proteins bind common HLA class I molecules. Leukemia 2000; 14:419-26. [PMID: 10720136 DOI: 10.1038/sj.leu.2401703] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The Philadelphia (Ph) chromosome, resulting from the t(9;22) translocation, is characteristic of chronic myeloid leukemia (CML). As a result of this translocation, two novel chimeric genes are generated and the bcr/abl and abl/bcr fusion proteins expressed. The bcr/abl fusion mRNA is present in all CML patients, whereas the reciprocal abl/bcr fusion mRNA is detectable in about 80% of the Ph+ CML patients. These fusion proteins may undergo enzymatic degradation in the cytosol and give rise to MHC class I restricted peptide epitopes originating from the junctional regions of the translocation products, which thus may serve as novel tumor specific antigens. Previously, other groups have tested peptides corresponding to the junctional region of the bcr/abl protein for their binding capacity to HLA class I molecules and have identified a few candidate epitopes. Peptides originating from the abl/bcr fusion protein have on the other hand so far been neglected, for no apparent reason. We have now extended these studies to include also the reciprocal abl/bcr translocation product by testing a large panel of synthetic peptides corresponding to the junctional regions of both the abl/bcr and the bcr/abl fusion proteins for their ability to stabilize HLA class I molecules. We find that the abl/bcr translocation product may be an even more important source of CML specific peptide antigens and together the junctional sequences of both these proteins contain peptide sequences which bind efficiently to a number of HLA molecules (HLA-A1, -A2, -A3, -A11, -B7, -B27, -B35) and thus may serve as candidate CML specific tumor antigens.
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MESH Headings
- Amino Acid Sequence
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Epitopes/chemistry
- Epitopes/immunology
- Fusion Proteins, bcr-abl/chemistry
- Fusion Proteins, bcr-abl/immunology
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- HLA-B Antigens/immunology
- HLA-B Antigens/metabolism
- Humans
- Immunotherapy
- Interferon-gamma/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Molecular Sequence Data
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/immunology
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding
- RNA, Messenger/genetics
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Z Berke
- Institute of Cancer Biology, the Danish Cancer Society, Copenhagen
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40
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Huang XL, Fan Z, Kalinyak C, Mellors JW, Rinaldo CR. CD8(+) T-cell gamma interferon production specific for human immunodeficiency virus type 1 (HIV-1) in HIV-1-infected subjects. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2000; 7:279-87. [PMID: 10702505 PMCID: PMC95861 DOI: 10.1128/cdli.7.2.279-287.2000] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/1999] [Accepted: 01/10/2000] [Indexed: 11/20/2022]
Abstract
The CD8(+)-T-cell response to human immunodeficiency virus type 1 (HIV-1) is considered to be important in host control of infection and prevention of AIDS. We have developed a single-cell enzyme immunoassay (enzyme-linked immunospot assay) specific for gamma interferon (IFN-gamma) production stimulated by either autologous B-lymphoblastoid cell lines (B-LCL) infected with vaccinia virus vectors expressing HIV-1 proteins or synthetic peptides representing known HIV-1 CD8(+) cytotoxic T-lymphocyte (CTL) epitopes. Single-cell IFN-gamma production stimulated by HIV-1 Gag-, Pol-, and Env-expressing B-LCL was a reliable measure of HIV-1-specific T-cell immunity in peripheral blood CD8(+) T cells from HIV-1 infected individuals. This method was more sensitive than stimulation of IFN-gamma by direct infection of the cultures with HIV-1-vaccinia virus vectors. Comparable results were found for IFN-gamma production in CD8(+) T cells from HIV-1-negative, cytomegalovirus (CMV)-seropositive, healthy donors stimulated with B-LCL expressing the CMV pp65 lower matrix protein. HIV-1 peptides were immunodominant for both CD8(+) single-cell IFN-gamma production and CTL precursor frequencies. The number of cells producing IFN-gamma decreased in individuals with late-stage HIV-1 infection and was temporally enhanced during combination antiretroviral therapy with two reverse transcriptase nucleoside inhibitors and a protease inhibitor.
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Affiliation(s)
- X L Huang
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
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41
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Zarling AL, Johnson JG, Hoffman RW, Lee DR. Induction of Primary Human CD8+ T Lymphocyte Responses In Vitro Using Dendritic Cells. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.9.5197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The ability of two different human professional APCs, specifically macrophages (Mφ) and dendritic cells (DC), to stimulate primary responses in human CD8+ T lymphocytes was examined using both allogeneic and Ag-pulsed autologous APCs. CTL responses in CD8+ T lymphocytes isolated from HIV-uninfected donors were evaluated against six different HIV epitopes that are restricted by four different HLA alleles using autologous human PBMC-derived Mφ and DCs for primary stimulation. In a side-by-side experiment, immature DCs, but not Mφ, were able to prime a CTL response against the B14-restricted p24gag 298–306 epitope; mature DCs were also able to prime a response against this epitope. In addition, DCs were capable of priming CD8+ CTL responses against the B8-restricted p24gag 259–267 epitope. In contrast, Mφ were unable to prime strong CTL responses against other epitopes. Since the Ag-specific cytotoxic responses required subsequent rounds of restimulation before they could be detected, the ability of the allogeneic Mφ and DCs to directly prime CD8+ T lymphocyte responses without subsequent restimulation was examined. Similar to the aforementioned peptide-specific results, DCs were more efficient than Mφ in priming both allogeneic proliferative and cytotoxic responses in human CD8+ T lymphocytes. Collectively, these results promote an enhanced status for DCs in the primary stimulation of human CD8+ T lymphocytes.
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Affiliation(s)
- Angela L. Zarling
- *Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212; and
| | - Julia G. Johnson
- *Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212; and
| | - Robert W. Hoffman
- †Division of Immunology and Rheumatology, Department of Internal Medicine, University of Missouri School of Medicine, and the Medical Research Service, Veterans Affairs Medical Center, Columbia, MO 65212
| | - David R. Lee
- *Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212; and
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42
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Abstract
The binding of a major histocompatibility complex (MHC) molecule to a peptide originating in an antigen is essential to recognizing antigens in immune systems, and it has proved to be important to use computers to predict the peptides that will bind to an MHC molecule. The purpose of this paper is twofold: First, we propose to apply supervised learning of hidden Markov models (HMMs) to this problem, which can surpass existing methods for the problem of predicting MHC-binding peptides. Second, we generate peptides that have high probabilities to bind to a certain MHC molecule, based on our proposed method using peptides binding to MHC molecules as a set of training data. From our experiments, in a type of cross-validation test, the discrimination accuracy of our supervised learning method is usually approximately 2-15% better than those of other methods, including backpropagation neural networks, which have been regarded as the most effective approach to this problem. Furthermore, using an HMM trained for HLA-A2, we present new peptide sequences that are provided with high binding probabilities by the HMM and that are thus expected to bind to HLA-A2 proteins. Peptide sequences not shown in this paper but with rather high binding probabilities can be obtained from the author.
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Affiliation(s)
- H Mamitsuka
- C&C Media Research Laboratories, NEC Corporation, Kawasaki, Kanagawa, Japan.
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43
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Faulkner L, Borysiewicz LK, Man S. The use of human leucocyte antigen class I transgenic mice to investigate human immune function. J Immunol Methods 1998; 221:1-16. [PMID: 9894893 DOI: 10.1016/s0022-1759(98)00162-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
HLA class I transgenic mice are a powerful research tool which have been used as models for human immune responses. This review describes the generation of the different HLA class I transgenic mice, the techniques used to improve expression of the transgene and use of the transgene product in immune responses. It also illustrates how HLA class I transgenic mice have provided insights into the nature of the allogeneic and xenogeneic response, the generation of CTL responses, the development of autoimmune diseases, and their use for the generation of anti-HLA class I antibodies. Despite these advances, the use of available HLA class I transgenic mice as models for human disease and immune responses has been limited. The development of new transgenic strains incorporating multiple human transgenes may allow the potential of HLA class I transgenic mice to be realised.
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Affiliation(s)
- L Faulkner
- Department of Medicine, University of Wales College of Medicine, Heath Park, Cardiff, UK.
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44
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Wood P, Elliott T. Glycan-regulated antigen processing of a protein in the endoplasmic reticulum can uncover cryptic cytotoxic T cell epitopes. J Exp Med 1998; 188:773-8. [PMID: 9705959 PMCID: PMC2213365 DOI: 10.1084/jem.188.4.773] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/1998] [Revised: 05/04/1998] [Indexed: 11/25/2022] Open
Abstract
We and others have shown that influenza A nucleoprotein (NP) targeted to the secretory pathway cannot be processed to yield several cytotoxic T lymphocyte (CTL) epitopes in cell lines that lack the transporter associated with antigen processing (TAP). However, a large COOH-terminal fragment of NP is processed and presented in these cells. Full-length NP is cotranslationally glycosylated in the lumen of the endoplasmic reticulum at two sites distal to the major H2-Kk and H2-Db restricted CTL epitopes, and we show here that pharmacological or genetic inhibition of N-linked glycosylation, leads to the processing and presentation of both these epitopes in a TAP-independent way.
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Affiliation(s)
- P Wood
- Institute for Molecular Medicine and Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
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45
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Collins EJ, Frelinger JA. Altered peptide ligand design: altering immune responses to class I MHC/peptide complexes. Immunol Rev 1998; 163:151-60. [PMID: 9700508 DOI: 10.1111/j.1600-065x.1998.tb01194.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Class I proteins are responsible for binding proteins from endogenously synthesized proteins and displaying them on the cell surface. Our understanding of this process has reached the point where we can manipulate the biochemical properties of peptide/class I binding and determine the effects of this alteration on subsequent immune responses. In this article, we will review the biochemistry of peptide/class I binding, and the effects of structure on this interaction between class I proteins and their peptide ligands. We will review the data which suggest that the major relevant biochemical parameter of class I peptide binding is the off-rate. We will show that the design of altered ligands with improved binding, thermostability and immunogenicity is possible.
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Affiliation(s)
- E J Collins
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, USA.
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46
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Albert ML, Sauter B, Bhardwaj N. Dendritic cells acquire antigen from apoptotic cells and induce class I-restricted CTLs. Nature 1998; 392:86-9. [PMID: 9510252 DOI: 10.1038/32183] [Citation(s) in RCA: 1707] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CD8+ cytotoxic T lymphocytes (CTLs) mediate resistance to infectious agents and tumours. Classically, CTLs recognize antigens that are localized in the cytoplasm of target cells, processed and presented as peptide complexes with class I molecules of the major histocompatibility complex (MHC). However, there is evidence for an exogenous pathway whereby antigens that are not expected to gain access to the cytoplasm are presented on MHC class I molecules. The most dramatic example is the in vivo phenomenon of cross-priming: antigens from donor cells are acquired by bone-marrow-derived host antigen-presenting cells (APCs) and presented on MHC class I molecules. Two unanswered questions concern the identity of this bone-marrow-derived cell and how such antigens are acquired. Here we show that human dendritic cells, but not macrophages, efficiently present antigen derived from apoptotic cells, stimulating class I-restricted CD8+ CTLs. Our findings suggest a mechanism by which potent APCs acquire antigens from tumours, transplants, infected cells, or even self-tissue, for stimulation or tolerization of CTLs.
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Affiliation(s)
- M L Albert
- Laboratory of Cellular Physiology and Immunology, The Rockefeller University, New York, New York 10021, USA
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Altuvia Y, Sette A, Sidney J, Southwood S, Margalit H. A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets. Hum Immunol 1997; 58:1-11. [PMID: 9438204 DOI: 10.1016/s0198-8859(97)00210-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Binding of peptides to MHC class I molecules is a prerequisite for their recognition by cytotoxic T cells. Consequently, identification of peptides that will bind to a given MHC molecule must constitute a central part of any algorithm for prediction of T-cell antigenic peptides based on the amino acid sequence of the protein. Binding motifs, defined by anchor positions only, have proven to be insufficient to ensure binding, suggesting that other positions along the peptide sequence also affect peptide-MHC interaction. The second phase of prediction schemes therefore take into account the effect of all positions along the peptide sequence, and are based on position-dependent-coefficients that are used in the calculation of a peptide score. These coefficients can be extracted from a large ensemble of binding sequences that were tested experimentally, or derived from structural considerations, as in the algorithm developed by us recently. This algorithm uses the coordinates of solved complexes to evaluate the interactions of peptide amino acids with MHC contact residues, and results in a peptide score that reflects its binding energy. Here we present our analysis for peptide binding to four MHC alleles (HLA-A2, HLA-A68, HLA-B27 and H-2Kb), and compare the predictions of the algorithm to experimental binding data. The algorithm performs successfully in predicting peptide binding to MHC molecules with hydrophobic binding pockets but not when MHC molecules with hydrophilic, charged pockets are considered. For MHC molecules with hydrophobic pockets it is demonstrated how the algorithm succeeds in distinguishing binding from non-binding peptides, and in high ranking of immunogenic peptides within all overlapping same-length peptides spanning their respective protein sequences. The latter property of the algorithm makes it a useful tool in the rational design of peptide vaccines aimed at T-cell immunity.
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Affiliation(s)
- Y Altuvia
- Department of Molecular Genetics and Biotechnology, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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Burrows SR, Silins SL, Khanna R, Burrows JM, Rischmueller M, McCluskey J, Moss DJ. Cross-reactive memory T cells for Epstein-Barr virus augment the alloresponse to common human leukocyte antigens: degenerate recognition of major histocompatibility complex-bound peptide by T cells and its role in alloreactivity. Eur J Immunol 1997; 27:1726-36. [PMID: 9247584 DOI: 10.1002/eji.1830270720] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the present report, cytotoxic T lymphocyte (CTL) clones are described that display dual specificity for one of two common human leukocyte antigens (HLA B14 or B35) as alloantigens, and an immunodominant epitope (FLRGRAYGL) from Epstein-Barr virus (EBV) that binds to HLA B8. These T cell clonotypes were isolated from several unrelated HLA B8+, EBV-exposed individuals, and each distinct cross-reactivity pattern was associated with a common, public T cell receptor (TCR). In some individuals, CTL cross-reactive with these alloantigens completely dominated the memory response to this EBV epitope. Moreover, these memory T cells to EBV could be reactivated as a significant component of the repertoire of CTL responding to allogeneic stimulator cells expressing either HLA B14 or B35. These data illustrate how a history of infection with an immunogenic virus such as EBV can augment responsiveness to particular alloantigens; such influences may underlie the observed clinical association between herpesvirus infection and both allograft rejection and graft-versus-host disease. We have also explored the molecular basis for T cell cross-reactivity with alloantigens using the HLA B35 allo-reactive CTL clonotype. To elucidate the structural features of peptides that may be cross-recognized by these T cells, mono-substituted analogs of the viral epitope were screened for recognition, revealing broad specificity for major histocompatibility complex (MHC)-bound peptide. Based on the particular amino acid changes tolerated by the CTL at each peptide position, the human protein sequence database was searched for possible sequences that were recognized in association with HLA B35. Four peptides were identified (MPEATVYGL, IPIAPVYGM, KPSPPYFGL, and KPIVVLHGY) that were powerful activating ligands for the CTL when presented on HLA B35 but not B8. Thus, equivalent epitopes, capable of fully activating a single TCR, were formed by peptides with minimal obvious sequence homology bound to either HLA B8 or B35. These data indicate that degenerate peptide recognition by TCR may play an important role in the vigorous response of self-MHC-restricted T cells to alloantigens.
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Affiliation(s)
- S R Burrows
- Queensland Institute of Medical Research, Bancroft Centre, Brisbane, Australia.
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Abstract
Cytotoxic T lymphocytes (CTL) play a crucial role in the attempt to control infection with human immunodeficiency virus (HIV). Variation in epitopes recognized by CTL is common and frequently offers potential escape routes for mutant virus. Proof of escape, however, requires demonstration of increased frequency of virus particles or provirus that carry the escape sequence. There are now several recorded examples of virus variants that escape from CTL and are then selected. Most dramatic are those in which the CTL response has been dominated by CTL recognizing a single epitope that has suddenly changed, resulting in escape to fixation. This has been seen both early and late in the infection, leaving no doubt that escape occurs. Such escape is likely to be favored when the antiviral CTL response is oligoclonal and focused on a small number of immunodominant epitopes. The heterogeneous CTL response seen in many HIV-infected patients may result from successive waves of virus escape followed by new CTL responses specific for subdominant epitopes. Mutant virus can escape by several different routes, including failure of the mutated peptide to bind to the presenting HLA molecule and altered interactions with T cell receptors (TCR), including antagonism.
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Affiliation(s)
- A J McMichael
- Nuffield Department of Medicine, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom. andrew.mcmichael%
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