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Pandya M, Rasmussen M, Hansen A, Nielsen M, Buus S, Golde W, Barlow J. A modern approach for epitope prediction: identification of foot-and-mouth disease virus peptides binding bovine leukocyte antigen (BoLA) class I molecules. Immunogenetics 2016; 67:691-703. [PMID: 26496773 DOI: 10.1007/s00251-015-0877-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/07/2015] [Indexed: 01/20/2023]
Abstract
Major histocompatibility complex (MHC) class Imolecules regulate adaptive immune responses through the presentation of antigenic peptides to CD8+ T cells. Polymorphisms in the peptide binding region of class I molecules determine peptide binding affinity and stability during antigen presentation, and different antigen peptide motifs are associated with specific genetic sequences of class I molecules. Understanding bovine leukocyte antigen (BoLA), peptide-MHC class I binding specificities may facilitate development of vaccines or reagents for quantifying the adaptive immune response to intracellular pathogens, such as foot-and-mouth disease virus (FMDV). Six synthetic BoLA class I (BoLA-I) molecules were produced, and the peptide binding motif was generated for five of the six molecules using a combined approach of positional scanning combinatorial peptide libraries (PSCPLs) and neural network-based predictions (NetMHCpan). The updated NetMHCpan server was used to predict BoLA-I binding peptides within the P1 structural polyprotein sequence of FMDV (strain A24 Cruzeiro) for Bo-LA-1*01901, BoLA-2*00801, BoLA-2*01201, and BoLA-4*02401. Peptide binding affinity and stability were determined for these BoLA-I molecules using the luminescent oxygen channeling immunoassay (LOCI) and scintillation proximity assay (SPA). The functional diversity of known BoLA alleles was predicted using theMHCcluster tool, and functional predictions for peptide motifs were compared to observed data from this and prior studies. The results of these analyses showed that BoLA alleles cluster into three distinct groups with the potential to define BBoLA supertypes.^ This streamlined approach identifies potential T cell epitopes from pathogens, such as FMDV, and provides insight into T cell immunity following infection or vaccination.
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Hansen AM, Rasmussen M, Svitek N, Harndahl M, Golde WT, Barlow J, Nene V, Buus S, Nielsen M. Characterization of binding specificities of bovine leucocyte class I molecules: impacts for rational epitope discovery. Immunogenetics 2014; 66:705-18. [PMID: 25186069 PMCID: PMC4225172 DOI: 10.1007/s00251-014-0802-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
The binding of peptides to classical major histocompatibility complex (MHC) class I proteins is the single most selective step in antigen presentation. However, the peptide-binding specificity of cattle MHC (bovine leucocyte antigen, BoLA) class I (BoLA-I) molecules remains poorly characterized. Here, we demonstrate how a combination of high-throughput assays using positional scanning combinatorial peptide libraries, peptide dissociation, and peptide-binding affinity binding measurements can be combined with bioinformatics to effectively characterize the functionality of BoLA-I molecules. Using this strategy, we characterized eight BoLA-I molecules, and found the peptide specificity to resemble that of human MHC-I molecules with primary anchors most often at P2 and P9, and occasional auxiliary P1/P3/P5/P6 anchors. We analyzed nine reported CTL epitopes from Theileria parva, and in eight cases, stable and high affinity binding was confirmed. A set of peptides were tested for binding affinity to the eight BoLA proteins and used to refine the predictors of peptide-MHC binding NetMHC and NetMHCpan. The inclusion of BoLA-specific peptide-binding data led to a significant improvement in prediction accuracy for reported T. parva CTL epitopes. For reported CTL epitopes with weak or no predicted binding, these refined prediction methods suggested presence of nested minimal epitopes with high-predicted binding affinity. The enhanced affinity of the alternative peptides was in all cases confirmed experimentally. This study demonstrates how biochemical high-throughput assays combined with immunoinformatics can be used to characterize the peptide-binding motifs of BoLA-I molecules, boosting performance of MHC peptide-binding prediction methods, and empowering rational epitope discovery in cattle.
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Affiliation(s)
- Andreas M. Hansen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Rasmussen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas Svitek
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Mikkel Harndahl
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - William T. Golde
- Plum Island Animal Disease Center, Agricultural Research Service, USDA, Greenport, NY, USA
| | - John Barlow
- Department of Animal Sciences, University of Vermont, Burlington, VT, USA
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi 00100, Kenya
| | - Søren Buus
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby, Denmark,
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
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Macdonald IK, Harkiolaki M, Hunt L, Connelley T, Carroll AV, MacHugh ND, Graham SP, Jones EY, Morrison WI, Flower DR, Ellis SA. MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors. PLoS Pathog 2010; 6:e1001149. [PMID: 20976198 PMCID: PMC2954893 DOI: 10.1371/journal.ppat.1001149] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 09/10/2010] [Indexed: 01/07/2023] Open
Abstract
T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.
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Affiliation(s)
- Isabel K. Macdonald
- The Jenner Institute, University of Oxford, Compton, Berkshire, United Kingdom
| | - Maria Harkiolaki
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (MH, for structural data); (SAE)
| | - Lawrence Hunt
- Institute for Animal Health, Compton, Berkshire, United Kingdom
| | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - A. Victoria Carroll
- The Roslin Institute, Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Niall D. MacHugh
- The Roslin Institute, Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon P. Graham
- Veterinary Laboratories Agency, Addlestone, Surrey, United Kingdom
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - W. Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Darren R. Flower
- The Jenner Institute, University of Oxford, Compton, Berkshire, United Kingdom
| | - Shirley A. Ellis
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- * E-mail: (MH, for structural data); (SAE)
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Induction of a cross-reactive CD8(+) T cell response following foot-and-mouth disease virus vaccination. J Virol 2010; 84:12375-84. [PMID: 20861264 DOI: 10.1128/jvi.01545-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious infection in cloven-hoofed animals. Current inactivated FMDV vaccines generate short-term, serotype-specific protection, mainly through neutralizing antibody. An improved understanding of the mechanisms of protective immunity would aid design of more effective vaccines. We have previously reported the presence of virus-specific CD8(+) T cells in FMDV-vaccinated and -infected cattle. In the current study, we aimed to identify CD8(+) T cell epitopes in FMDV recognized by cattle vaccinated with inactivated FMDV serotype O. Analysis of gamma interferon (IFN-γ)-producing CD8(+) T cells responding to stimulation with FMDV-derived peptides revealed one putative CD8(+) T cell epitope present within the structural protein P1D, comprising residues 795 to 803 of FMDV serotype O UKG/2001. The restricting major histocompatibility complex (MHC) class I allele was N*02201, expressed by the A31 haplotype. This epitope induced IFN-γ release, proliferation, and target cell killing by αβ CD8(+) T cells, but not CD4(+) T cells. A protein alignment of representative samples from each of the 7 FMDV serotypes showed that the putative epitope is highly conserved. CD8(+) T cells from FMDV serotype O-vaccinated A31(+) cattle recognized antigen-presenting cells (APCs) loaded with peptides derived from all 7 FMDV serotypes, suggesting that CD8(+) T cells recognizing the defined epitope are cross-reactive to equivalent peptides derived from all of the other FMDV serotypes.
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Marchetti B, Ashrafi GH, Dornan ES, Araibi EH, Ellis SA, Campo MS. The E5 protein of BPV-4 interacts with the heavy chain of MHC class I and irreversibly retains the MHC complex in the Golgi apparatus. Oncogene 2006; 25:2254-63. [PMID: 16288210 DOI: 10.1038/sj.onc.1209245] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BPV-4 E5 inhibits transcription of the bovine MHC class I heavy chain (HC) gene, increases degradation of HC and downregulates surface expression of MHC class I by retaining the complex in the Golgi apparatus (GA). Here we report that transcription inhibition can be alleviated by interferon treatment and the degradation of HC can be reversed by treatment with inhibitors of proteasomes and lysosomes. However, the inhibition of transport of MHC class I to the cell surface is irreversible. We show that E5 is capable of physically interacting with HC. Together with the inhibition of the vacuolar ATPase (due to the interaction between E5 and 16k subunit c), the interaction between E5 and HC is likely to be responsible for retention of MHC class I in the GA. C-terminus deletion mutants of E5 are incapable of either downregulating surface MHC class I or interacting with HC, establishing that the C-terminus domain of E5 is important in the inhibition of MHC class I.
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Affiliation(s)
- B Marchetti
- Division of Pathological Sciences, Institute of Comparative Medicine, University of Glasgow, Glasgow, UK
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Gaddum RM, Cook RS, Furze JM, Ellis SA, Taylor G. Recognition of bovine respiratory syncytial virus proteins by bovine CD8+ T lymphocytes. Immunology 2003; 108:220-9. [PMID: 12562331 PMCID: PMC1782889 DOI: 10.1046/j.1365-2567.2003.01566.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CD8+ T lymphocytes play a major role in the clearance of bovine respiratory syncytial virus (BRSV), an important respiratory pathogen of young calves that shares many of the epidemiological and pathological features of human respiratory syncytial virus (HRSV) in infants. Recombinant vaccinia virus (rVV) and recombinant fowlpox virus (rFPV), expressing individual BRSV proteins, were used to demonstrate that the F, N and M2 proteins were the major antigens recognized by bovine CD8+ T cells in major histocompatibility complex (MHC)-defined cattle. BRSV protein recognition by CD8+ T cells was analysed using cytotoxic T lymphocyte (CTL) assays or by the production of interferon-gamma (IFN-gamma) following restimulation with BRSV proteins. Strong recognition of the G protein by CD8+ T cells was observed in cattle that had been vaccinated with rVV expressing this protein and subsequently challenged with BRSV. Although there is variation in the number of expressed MHC genes in cattle with different class I haplotypes, this did not appear to influence BRSV protein recognition by CD8+ T cells. Knowledge of the antigenic specificity of BRSV-specific CD8+ T cells will facilitate the qualitative and quantitative analysis of BRSV-specific CD8+ T-cell memory in cattle and help to ensure that potential vaccines induce a qualitatively appropriate CD8+ T-cell response.
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Affiliation(s)
- Ruth M Gaddum
- Institute for Animal Health, Compton, Newbury, Berkshire, UK
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Hegde NR, Srikumaran S. The use of bovine MHC class I allele-specific peptide motifs and proteolytic cleavage specificities for the prediction of potential cytotoxic T lymphocyte epitopes of bovine viral diarrhea virus. Virus Genes 1997; 14:111-21. [PMID: 9237350 DOI: 10.1023/a:1007913216861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cell mediated immunity (CMI) is crucial for the defense against viruses. Cytotoxic T lymphocytes (CTLs) play a major role in CMI. They recognize endogenous antigenic peptides presented by antigen presenting cells in association with the major histocompatibility complex (MHC) class I molecules. The elucidation of the sequence of CTL epitopes of viruses should help in designing better vaccines. In this study, we have identified candidate epitopes restricted by five bovine MHC class I molecules that are potentially available for presentation to CTLs. The candidate peptide epitopes were identified by using the computer programs available as a part of the Genetics Computer Group package and applying the information on allele-specific peptide motifs and intracellular enzymatic cleavage patterns to the bovine viral diarrhea virus polyprotein. Several candidate peptides were found for each of the bovine lymphocyte antigens (BoLA)-A11, -A20, -HD1, and -HD6 whereas no peptide was found for BoLA-HD7. Based on this finding, the probable contribution of genomic segments of BVDV to the CTL response and strategies for recombinant vaccines are discussed.
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Affiliation(s)
- N R Hegde
- Department of Veterinary and Biomedical Sciences, University of Nebraska-Lincoln 68583-0905, USA
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