1
|
Connelley T, Nicastri A, Sheldrake T, Vrettou C, Fisch A, Reynisson B, Buus S, Hill A, Morrison I, Nielsen M, Ternette N. Immunopeptidomic Analysis of BoLA-I and BoLA-DR Presented Peptides from Theileria parva Infected Cells. Vaccines (Basel) 2022; 10:vaccines10111907. [PMID: 36423003 PMCID: PMC9699068 DOI: 10.3390/vaccines10111907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
The apicomplexan parasite Theileria parva is the causative agent of East Coast fever, usually a fatal disease for cattle, which is prevalent in large areas of eastern, central, and southern Africa. Protective immunity against T. parva is mediated by CD8+ T cells, with CD4+ T-cells thought to be important in facilitating the full maturation and development of the CD8+ T-cell response. T. parva has a large proteome, with >4000 protein-coding genes, making T-cell antigen identification using conventional screening approaches laborious and expensive. To date, only a limited number of T-cell antigens have been described. Novel approaches for identifying candidate antigens for T. parva are required to replace and/or complement those currently employed. In this study, we report on the use of immunopeptidomics to study the repertoire of T. parva peptides presented by both BoLA-I and BoLA-DR molecules on infected cells. The study reports on peptides identified from the analysis of 13 BoLA-I and 6 BoLA-DR datasets covering a range of different BoLA genotypes. This represents the most comprehensive immunopeptidomic dataset available for any eukaryotic pathogen to date. Examination of the immunopeptidome data suggested the presence of a large number of coprecipitated and non-MHC-binding peptides. As part of the work, a pipeline to curate the datasets to remove these peptides was developed and used to generate a final list of 74 BoLA-I and 15 BoLA-DR-presented peptides. Together, the data demonstrated the utility of immunopeptidomics as a method to identify novel T-cell antigens for T. parva and the importance of careful curation and the application of high-quality immunoinformatics to parse the data generated.
Collapse
Affiliation(s)
- Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
- Correspondence:
| | - Annalisa Nicastri
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Tara Sheldrake
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Christina Vrettou
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of São Paulo, Av Bandeirantes, Ribeirão Preto 3900, Brazil
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
| | - Soren Buus
- Laboratory of Experimental Immunology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Adrian Hill
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| | - Ivan Morrison
- The Roslin Institute, The Royal (Dick) School of Veterinary Science, The University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Copenhagen, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín CP1650, Argentina
| | - Nicola Ternette
- The Jenner Institute, Nuffield Department of Medicine, The University of Oxford, Oxford OX3 7BN, UK
| |
Collapse
|
2
|
Svitek N, Saya R, Zhang H, Nene V, Steinaa L. Systematic Determination of TCR–Antigen and Peptide–MHC Binding Kinetics among Field Variants of a Theileria parva Polymorphic CTL Epitope. THE JOURNAL OF IMMUNOLOGY 2022; 208:549-561. [PMID: 35031580 PMCID: PMC8802549 DOI: 10.4049/jimmunol.2100400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/23/2021] [Indexed: 11/24/2022]
Abstract
Positions 1–3 in the Tp9 CTL epitope are required for binding to BoLA-1*023:01. Positions 5–8 in the Tp9 epitope are required for TCR recognition in diverse CTLs. Tp9-specific CTLs from Muguga-immunized animals can cross-react with variants 4 and 7.
CTLs are known to contribute to immunity toward Theileria parva, the causative agent of East Coast fever. The Tp967–75 CTL epitope from the Muguga strain of T. parva is polymorphic in other parasite strains. Identifying the amino acids important for MHC class I binding, as well as TCR recognition of epitopes, can allow the strategic selection of Ags to induce cellular immunity toward T. parva. In this study, we characterized the amino acids important for MHC class I binding and TCR recognition in the Tp967–75 epitope using alanine scanning and a series of variant peptide sequences to probe these interactions. In a peptide–MHC class I binding assay, we found that the amino acids at positions 1, 2, and 3 were critical for binding to its restricting MHC class I molecule BoLA-1*023:01. With IFN-γ ELISPOT and peptide–MHC class I Tet staining assays on two parasite-specific bovine CTL lines, we showed that amino acids at positions 5–8 in the epitope were required for TCR recognition. Only two of eight naturally occurring polymorphic Tp9 epitopes were recognized by both CTLs. Finally, using a TCR avidity assay, we found that a higher TCR avidity was associated with a stronger functional response toward one of two variants recognized by the CTL. These data add to the growing knowledge on the cross-reactivity of epitope-specific CTLs and specificities that may be required in the selection of Ags in the design of a wide-spectrum vaccine for East Coast fever.
Collapse
Affiliation(s)
- Nicholas Svitek
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Rosemary Saya
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Houshuang Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Minhang District, Shanghai, China
| | - Vishvanath Nene
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| | - Lucilla Steinaa
- International Livestock Research Institute, Animal and Human Health Program, Nairobi, Kenya; and
| |
Collapse
|
3
|
Svitek N, Taracha ELN, Saya R, Awino E, Nene V, Steinaa L. Analysis of the Cellular Immune Responses to Vaccines. Methods Mol Biol 2022; 2465:283-301. [PMID: 35118627 DOI: 10.1007/978-1-0716-2168-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Flow cytometry, enzyme-linked immunospot (ELISpot), and cellular cytotoxicity assays are powerful tools for studying the cellular immune response toward intracellular pathogens and vaccines in livestock species. Lymphocytes from immunized animals can be purified using Ficoll-Paque density gradient centrifugation and evaluated for their antigen specificity or reactivity toward a vaccine. Here, we describe staining of bovine lymphocytes with peptide (p)-MHC class I tetramers and antibodies specific toward cellular activation markers for evaluation by multiparametric flow cytometry, as well as interferon (IFN)-γ ELISpot and cytotoxicity using chromium (51Cr) release assays. A small component on the use of immunoinformatics for fine-tuning the identification of a minimal CTL epitope is included, and a newly developed and simple assay to measure TCR avidity.
Collapse
Affiliation(s)
- Nicholas Svitek
- Animal and Human Health, International Livestock Research Institute, Nairobi, Kenya
| | | | - Rosemary Saya
- Animal and Human Health, International Livestock Research Institute, Nairobi, Kenya
| | - Elias Awino
- Animal and Human Health, International Livestock Research Institute, Nairobi, Kenya
| | - Vish Nene
- Animal and Human Health, International Livestock Research Institute, Nairobi, Kenya
| | - Lucilla Steinaa
- Animal and Human Health, International Livestock Research Institute, Nairobi, Kenya.
| |
Collapse
|
4
|
Sahin U, Muik A, Vogler I, Derhovanessian E, Kranz LM, Vormehr M, Quandt J, Bidmon N, Ulges A, Baum A, Pascal KE, Maurus D, Brachtendorf S, Lörks V, Sikorski J, Koch P, Hilker R, Becker D, Eller AK, Grützner J, Tonigold M, Boesler C, Rosenbaum C, Heesen L, Kühnle MC, Poran A, Dong JZ, Luxemburger U, Kemmer-Brück A, Langer D, Bexon M, Bolte S, Palanche T, Schultz A, Baumann S, Mahiny AJ, Boros G, Reinholz J, Szabó GT, Karikó K, Shi PY, Fontes-Garfias C, Perez JL, Cutler M, Cooper D, Kyratsous CA, Dormitzer PR, Jansen KU, Türeci Ö. BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans. Nature 2021; 595:572-577. [PMID: 34044428 DOI: 10.1101/2020.12.09.20245175] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/19/2021] [Indexed: 05/21/2023]
Abstract
BNT162b2, a nucleoside-modified mRNA formulated in lipid nanoparticles that encodes the SARS-CoV-2 spike glycoprotein (S) stabilized in its prefusion conformation, has demonstrated 95% efficacy in preventing COVID-191. Here we extend a previous phase-I/II trial report2 by presenting data on the immune response induced by BNT162b2 prime-boost vaccination from an additional phase-I/II trial in healthy adults (18-55 years old). BNT162b2 elicited strong antibody responses: at one week after the boost, SARS-CoV-2 serum geometric mean 50% neutralizing titres were up to 3.3-fold above those observed in samples from individuals who had recovered from COVID-19. Sera elicited by BNT162b2 neutralized 22 pseudoviruses bearing the S of different SARS-CoV-2 variants. Most participants had a strong response of IFNγ+ or IL-2+ CD8+ and CD4+ T helper type 1 cells, which was detectable throughout the full observation period of nine weeks following the boost. Using peptide-MHC multimer technology, we identified several BNT162b2-induced epitopes that were presented by frequent MHC alleles and conserved in mutant strains. One week after the boost, epitope-specific CD8+ T cells of the early-differentiated effector-memory phenotype comprised 0.02-2.92% of total circulating CD8+ T cells and were detectable (0.01-0.28%) eight weeks later. In summary, BNT162b2 elicits an adaptive humoral and poly-specific cellular immune response against epitopes that are conserved in a broad range of variants, at well-tolerated doses.
Collapse
Affiliation(s)
- Ugur Sahin
- BioNTech, Mainz, Germany.
- TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
| | | | | | | | | | | | | | | | | | - Alina Baum
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Martin Bexon
- Bexon Clinical Consulting LLC, Upper Montclair, NJ, USA
| | | | | | - Armin Schultz
- CRS Clinical Research Services Mannheim GmbH, Mannheim, Germany
| | | | | | | | | | | | | | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Sahin U, Muik A, Vogler I, Derhovanessian E, Kranz LM, Vormehr M, Quandt J, Bidmon N, Ulges A, Baum A, Pascal KE, Maurus D, Brachtendorf S, Lörks V, Sikorski J, Koch P, Hilker R, Becker D, Eller AK, Grützner J, Tonigold M, Boesler C, Rosenbaum C, Heesen L, Kühnle MC, Poran A, Dong JZ, Luxemburger U, Kemmer-Brück A, Langer D, Bexon M, Bolte S, Palanche T, Schultz A, Baumann S, Mahiny AJ, Boros G, Reinholz J, Szabó GT, Karikó K, Shi PY, Fontes-Garfias C, Perez JL, Cutler M, Cooper D, Kyratsous CA, Dormitzer PR, Jansen KU, Türeci Ö. BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans. Nature 2021; 595:572-577. [PMID: 34044428 DOI: 10.1038/s41586-021-03653-6] [Citation(s) in RCA: 483] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/19/2021] [Indexed: 01/02/2023]
Abstract
BNT162b2, a nucleoside-modified mRNA formulated in lipid nanoparticles that encodes the SARS-CoV-2 spike glycoprotein (S) stabilized in its prefusion conformation, has demonstrated 95% efficacy in preventing COVID-191. Here we extend a previous phase-I/II trial report2 by presenting data on the immune response induced by BNT162b2 prime-boost vaccination from an additional phase-I/II trial in healthy adults (18-55 years old). BNT162b2 elicited strong antibody responses: at one week after the boost, SARS-CoV-2 serum geometric mean 50% neutralizing titres were up to 3.3-fold above those observed in samples from individuals who had recovered from COVID-19. Sera elicited by BNT162b2 neutralized 22 pseudoviruses bearing the S of different SARS-CoV-2 variants. Most participants had a strong response of IFNγ+ or IL-2+ CD8+ and CD4+ T helper type 1 cells, which was detectable throughout the full observation period of nine weeks following the boost. Using peptide-MHC multimer technology, we identified several BNT162b2-induced epitopes that were presented by frequent MHC alleles and conserved in mutant strains. One week after the boost, epitope-specific CD8+ T cells of the early-differentiated effector-memory phenotype comprised 0.02-2.92% of total circulating CD8+ T cells and were detectable (0.01-0.28%) eight weeks later. In summary, BNT162b2 elicits an adaptive humoral and poly-specific cellular immune response against epitopes that are conserved in a broad range of variants, at well-tolerated doses.
Collapse
Affiliation(s)
- Ugur Sahin
- BioNTech, Mainz, Germany.
- TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
| | | | | | | | | | | | | | | | | | - Alina Baum
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Martin Bexon
- Bexon Clinical Consulting LLC, Upper Montclair, NJ, USA
| | | | | | - Armin Schultz
- CRS Clinical Research Services Mannheim GmbH, Mannheim, Germany
| | | | | | | | | | | | | | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Immunoinformatics is a discipline that applies methods of computer science to study and model the immune system. A fundamental question addressed by immunoinformatics is how to understand the rules of antigen presentation by MHC molecules to T cells, a process that is central to adaptive immune responses to infections and cancer. In the modern era of personalized medicine, the ability to model and predict which antigens can be presented by MHC is key to manipulating the immune system and designing strategies for therapeutic intervention. Since the MHC is both polygenic and extremely polymorphic, each individual possesses a personalized set of MHC molecules with different peptide-binding specificities, and collectively they present a unique individualized peptide imprint of the ongoing protein metabolism. Mapping all MHC allotypes is an enormous undertaking that cannot be achieved without a strong bioinformatics component. Computational tools for the prediction of peptide-MHC binding have thus become essential in most pipelines for T cell epitope discovery and an inescapable component of vaccine and cancer research. Here, we describe the development of several such tools, from pioneering efforts to the current state-of-the-art methods, that have allowed for accurate predictions of peptide binding of all MHC molecules, even including those that have not yet been characterized experimentally.
Collapse
Affiliation(s)
- Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP 1650 San Martin, Buenos Aires, Argentina
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP 1650 San Martin, Buenos Aires, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Søren Buus
- Department of Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| |
Collapse
|
7
|
Warimwe GM, Purushotham J, Perry BD, Hill AV, Gilbert SC, Dungu B, Charleston B. Tackling human and animal health threats through innovative vaccinology in Africa. AAS Open Res 2018; 1:18. [PMID: 32259020 PMCID: PMC7118973 DOI: 10.12688/aasopenres.12877.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 07/27/2023] Open
Abstract
Africa bears the brunt of many of the world's most devastating human and animal infectious diseases, a good number of which have no licensed or effective vaccines available. The continent's potential to generate novel interventions against these global health threats is however largely untapped. Strengthening Africa's vaccine research and development (R&D) sector could accelerate discovery, development and deployment of effective countermeasures against locally prevalent infectious diseases, many of which are neglected and have the capacity to spread to new geographical settings. Here, we review Africa's human and veterinary vaccine R&D sectors and identify key areas that should be prioritized for investment, and synergies that could be exploited from Africa's veterinary vaccine industry, which is surprisingly strong and has close parallels with human vaccine R&D.
Collapse
Affiliation(s)
- George M. Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- The Pirbright Institute, Woking, GU24 0NF, UK
| | | | - Brian D. Perry
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | | | | | | | | |
Collapse
|
8
|
Warimwe GM, Purushotham J, Perry BD, Hill AVS, Gilbert SC, Dungu B, Charleston B. Tackling human and animal health threats through innovative vaccinology in Africa. AAS Open Res 2018; 1:18. [PMID: 32259020 PMCID: PMC7118973 DOI: 10.12688/aasopenres.12877.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2018] [Indexed: 11/20/2022] Open
Abstract
Africa bears the brunt of many of the world's most devastating human and animal infectious diseases, a good number of which have no licensed or effective vaccines available. The continent's potential to generate novel interventions against these global health threats is however largely untapped. Strengthening Africa's vaccine research and development (R&D) sector could accelerate discovery, development and deployment of effective countermeasures against locally prevalent infectious diseases, many of which are neglected and have the capacity to spread to new geographical settings. Here, we review Africa's human and veterinary vaccine R&D sectors and identify key areas that should be prioritized for investment, and synergies that could be exploited from Africa's veterinary vaccine industry, which is surprisingly strong and has close parallels with human vaccine R&D.
Collapse
Affiliation(s)
- George M Warimwe
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,The Pirbright Institute, Woking, GU24 0NF, UK
| | | | - Brian D Perry
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | - Adrian V S Hill
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sarah C Gilbert
- The Jenner Institute, University of Oxford, Oxford, OX3 7DQ, UK
| | | | | |
Collapse
|
9
|
Svitek N, Saya R, Awino E, Munyao S, Muriuki R, Njoroge T, Pellé R, Ndiwa N, Poole J, Gilbert S, Nene V, Steinaa L. An Ad/MVA vectored Theileria parva antigen induces schizont-specific CD8 + central memory T cells and confers partial protection against a lethal challenge. NPJ Vaccines 2018; 3:35. [PMID: 30245859 PMCID: PMC6134044 DOI: 10.1038/s41541-018-0073-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/22/2018] [Accepted: 07/02/2018] [Indexed: 01/03/2023] Open
Abstract
The parasite Theileria parva is the causative agent of East Coast fever (ECF), one of the most serious cattle diseases in sub-Saharan Africa, and directly impacts smallholder farmers’ livelihoods. There is an efficient live-parasite vaccine, but issues with transmission of vaccine strains, need of a cold chain, and antibiotics limit its utilization. This has fostered research towards subunit vaccination. Cytotoxic T lymphocytes (CTL) are crucial in combating the infection by lysing T. parva-infected cells. Tp1 is an immunodominant CTL antigen, which induces Tp1-specific responses in 70–80% of cattle of the A18 or A18v haplotype during vaccination with the live vaccine. In this study, human adenovirus serotype 5 (HAd5) and modified vaccinia Ankara (MVA) were assessed for their ability to induce Tp1-specific immunity. Both viral vectors expressing the Tp1 antigen were inoculated in cattle by a heterologous prime-boost vaccination regimen. All 15 animals responded to Tp1 as determined by ELISpot. Of these, 14 reacted to the known Tp1 epitope, assayed by ELISpot and tetramer analyses, with CTL peaking 1-week post-MVA boost. Eleven animals developed CTL with specific cytotoxic activity towards peripheral blood mononuclear cells (PBMC) pulsed with the Tp1 epitope. Moreover, 36% of the animals with a Tp1 epitope-specific response survived a lethal challenge with T. parva 5 weeks post-MVA boost. Reduction of the parasitemia correlated with increased percentages of central memory lymphocytes in the Tp1 epitope-specific CD8+ populations. These results indicate that Tp1 is a promising antigen to include in a subunit vaccine and central memory cells are crucial for clearing the parasite. A vaccine expressing parasitic proteins offers more convenient East Coast fever prophylaxis. Current vaccination for the cattle disease, caused by the parasite Theileria parva and a detriment to sub-Saharan African farmers, involves inconvenient injection with live parasites before antibiotic treatment (ITM). A collaboration led by Nicholas Svitek, of the Kenyan International Livestock Research Institute, designed a candidate to provoke cellular immune responses against the parasitic antigen Tp1—an ITM vaccine candidate. In tests on cattle, 93% created Tp1-targeting T cells, and 33% survived a lethal dose of T. parva. The East Coast fever reduction seen in animals in this research outperformed a recent study and was able to generate the same immune memory cells that ITM inspires to provide long-lasting protection. Future research might integrate more antigens with this Tp1 vaccine to provide more comprehensive protection.
Collapse
Affiliation(s)
- Nicholas Svitek
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Rosemary Saya
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Elias Awino
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Stephen Munyao
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Robert Muriuki
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Thomas Njoroge
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Roger Pellé
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Nicholas Ndiwa
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Jane Poole
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Sarah Gilbert
- 2The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive Oxford, OX3 7DQ UK
| | - Vishvanath Nene
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| | - Lucilla Steinaa
- 1International Livestock Research Institute (ILRI), P.O. Box 30709, 00100 Nairobi, Kenya
| |
Collapse
|
10
|
Theileria parva antigens recognized by CD8+ T cells show varying degrees of diversity in buffalo-derived infected cell lines. Parasitology 2018; 145:1430-1439. [PMID: 29729680 PMCID: PMC6126638 DOI: 10.1017/s0031182018000264] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The extent of sequence diversity among the genes encoding 10 antigens (Tp1–10) known to be recognized by CD8+ T lymphocytes from cattle immune to Theileria parva was analysed. The sequences were derived from parasites in 23 buffalo-derived cell lines, three cattle-derived isolates and one cloned cell line obtained from a buffalo-derived stabilate. The results revealed substantial variation among the antigens through sequence diversity. The greatest nucleotide and amino acid diversity were observed in Tp1, Tp2 and Tp9. Tp5 and Tp7 showed the least amount of allelic diversity, and Tp5, Tp6 and Tp7 had the lowest levels of protein diversity. Tp6 was the most conserved protein; only a single non-synonymous substitution was found in all obtained sequences. The ratio of non-synonymous: synonymous substitutions varied from 0.84 (Tp1) to 0.04 (Tp6). Apart from Tp2 and Tp9, we observed no variation in the other defined CD8+ T cell epitopes (Tp4, 5, 7 and 8), indicating that epitope variation is not a universal feature of T. parva antigens. In addition to providing markers that can be used to examine the diversity in T. parva populations, the results highlight the potential for using conserved antigens to develop vaccines that provide broad protection against T. parva.
Collapse
|
11
|
Steinaa L, Svitek N, Awino E, Saya R, Toye P. Cytotoxic T lymphocytes from cattle sharing the same MHC class I haplotype and immunized with live Theileria parva sporozoites differ in antigenic specificity. BMC Res Notes 2018; 11:44. [PMID: 29343295 PMCID: PMC5773172 DOI: 10.1186/s13104-018-3145-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/09/2018] [Indexed: 12/04/2022] Open
Abstract
Objectives The objective of this study was to assess whether cytotoxic T cells (CTL) generated by the live vaccine, known as “ITM Muguga cocktail”, which is used for the cattle disease East Cost fever (ECF) in Sub-Saharan Africa, showed a broad reactivity against many different strains of the causative parasite Theileria parva. We also assessed whether immune responses were similar in cattle expressing the same MHC class I haplotypes. Results The antigenic specificity of CTL from MHC class I-matched cattle vaccinated with the Muguga cocktail were different. Three cattle of MHC class I haplotype A18, one A18/A19 and two haploidentical (A18v/A12) animals, showed differential recognition of autologous cells infected with a panel of T. parva isolates. This could have implications in the field where certain strains could break through the vaccine. Furthermore, neither of the haploidentical cattle recognized the CTL epitope (Tp1214–224), presented by the A18 haplotype, in contrast to the third animal, showing differences in immunodominance in animals of the same haplotype A18. This suggests that the CTL specificities following immunization with the Muguga cocktail can vary even between haploidentical individuals and that some parasite strains may break through immunity generated by the Muguga cocktail. Electronic supplementary material The online version of this article (10.1186/s13104-018-3145-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lucilla Steinaa
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya.
| | - Nicholas Svitek
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Elias Awino
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Rosemary Saya
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Philip Toye
- International Livestock Research Institute, P.O. Box 30709, Nairobi, 00100, Kenya
| |
Collapse
|
12
|
Nielsen M, Connelley T, Ternette N. Improved Prediction of Bovine Leucocyte Antigens (BoLA) Presented Ligands by Use of Mass-Spectrometry-Determined Ligand and in Vitro Binding Data. J Proteome Res 2017; 17:559-567. [PMID: 29115832 PMCID: PMC5759033 DOI: 10.1021/acs.jproteome.7b00675] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Peptide
binding to MHC class I molecules is the single most selective
step in antigen presentation and the strongest single correlate to
peptide cellular immunogenicity. The cost of experimentally characterizing
the rules of peptide presentation for a given MHC-I molecule is extensive,
and predictors of peptide–MHC interactions constitute an attractive
alternative. Recently, an increasing amount of MHC presented peptides
identified by mass spectrometry (MS ligands) has been published. Handling
and interpretation of MS ligand data is, in general, challenging due
to the polyspecificity nature of the data. We here outline a general
pipeline for dealing with this challenge and accurately annotate ligands
to the relevant MHC-I molecule they were eluted from by use of GibbsClustering
and binding motif information inferred from in silico models. We illustrate
the approach here in the context of MHC-I molecules (BoLA) of cattle.
Next, we demonstrate how such annotated BoLA MS ligand data can readily
be integrated with in vitro binding affinity data in a prediction
model with very high and unprecedented performance for identification
of BoLA-I restricted T-cell epitopes. The prediction model is freely
available at http://www.cbs.dtu.dk/services/NetMHCpan/NetBoLApan. The approach has here been applied to the BoLA-I system, but the
pipeline is readily applicable to MHC systems in other species.
Collapse
Affiliation(s)
- Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark , DK-2800 Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín , CP1650 San Martín, Argentina
| | - Tim Connelley
- The Roslin Institute , Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Nicola Ternette
- The Jenner Institute , Target Discovery Institute Mass Spectrometry Laboratory, Oxford OX37FZ, United Kingdom
| |
Collapse
|
13
|
Hart J, MacHugh ND, Sheldrake T, Nielsen M, Morrison WI. Identification of immediate early gene products of bovine herpes virus 1 (BHV-1) as dominant antigens recognized by CD8 T cells in immune cattle. J Gen Virol 2017; 98:1843-1854. [PMID: 28671533 DOI: 10.1099/jgv.0.000823] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In common with other herpes viruses, bovine herpes virus 1 (BHV-1) induces strong virus-specific CD8 T-cell responses. However, there is a paucity of information on the antigenic specificity of the responding T-cells. The development of a system to generate virus-specific CD8 T-cell lines from BHV-1-immune cattle, employing Theileria-transformed cell lines for antigen presentation, has enabled us to address this issue. Use of this system allowed the study to screen for CD8 T-cell antigens that are efficiently presented on the surface of virus-infected cells. Screening of a panel of 16 candidate viral gene products with CD8 T-cell lines from 3 BHV-1-immune cattle of defined MHC genotypes identified 4 antigens, including 3 immediate early (IE) gene products (ICP4, ICP22 and Circ) and a tegument protein (UL49). Identification of the MHC restriction specificities revealed that the antigens were presented by two or three class I MHC alleles in each animal. Six CD8 T-cell epitopes were identified in the three IE proteins by screening of synthetic peptides. Use of an algorithm (NetMHCpan) that predicts the peptide-binding characteristics of restricting MHC alleles confirmed and, in some cases refined, the identity of the epitopes. Analyses of the epitope specificity of the CD8 T-cell lines showed that a large component of the response is directed against these IE epitopes. The results indicate that these IE gene products are dominant targets of the CD8 T-cell response in BHV-I-immune cattle and hence are prime-candidate antigens for the generation of a subunit vaccine.
Collapse
Affiliation(s)
- Jane Hart
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Niall D MacHugh
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Tara Sheldrake
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Morten Nielsen
- Department of Bio and Health Informatics, Centre for Biological Science Sequence Analysis, The Technical University, Lyngby, Denmark
| | - W Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Biotechnological Research Institute, National University of San Martin, San Martin, Buenos Aires, Argentina
| |
Collapse
|
14
|
Altman JD, Davis MM. MHC‐Peptide Tetramers to Visualize Antigen‐Specific T Cells. ACTA ACUST UNITED AC 2016; 115:17.3.1-17.3.44. [DOI: 10.1002/cpim.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Mark M. Davis
- Stanford University School of Medicine and The Howard Hughes Medical Institute Palo Alto California
| |
Collapse
|
15
|
Connelley TK, Li X, MacHugh N, Colau D, Graham SP, van der Bruggen P, Taracha EL, Gill A, Morrison WI. CD8 T-cell responses against the immunodominant Theileria parva peptide Tp249-59 are composed of two distinct populations specific for overlapping 11-mer and 10-mer epitopes. Immunology 2016; 149:172-85. [PMID: 27317384 PMCID: PMC5011678 DOI: 10.1111/imm.12637] [Citation(s) in RCA: 9] [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: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 01/30/2023] Open
Abstract
Immunity against Theileria parva is associated with CD8 T-cell responses that exhibit immunodominance, focusing the response against limited numbers of epitopes. As candidates for inclusion in vaccines, characterization of responses against immunodominant epitopes is a key component in novel vaccine development. We have previously demonstrated that the Tp249-59 and Tp1214-224 epitopes dominate CD8 T-cell responses in BoLA-A10 and BoLA-18 MHC I homozygous animals, respectively. In this study, peptide-MHC I tetramers for these epitopes, and a subdominant BoLA-A10-restricted epitope (Tp298-106 ), were generated to facilitate accurate and rapid enumeration of epitope-specific CD8 T cells. During validation of these tetramers a substantial proportion of Tp249-59 -reactive T cells failed to bind the tetramer, suggesting that this population was heterogeneous with respect to the recognized epitope. We demonstrate that Tp250-59 represents a distinct epitope and that tetramers produced with Tp50-59 and Tp49-59 show no cross-reactivity. The Tp249-59 and Tp250-59 epitopes use different serine residues as the N-terminal anchor for binding to the presenting MHC I molecule. Molecular dynamic modelling predicts that the two peptide-MHC I complexes adopt structurally different conformations and Tcell receptor β sequence analysis showed that Tp249-59 and Tp250-59 are recognized by non-overlapping T-cell receptor repertoires. Together these data demonstrate that although differing by only a single residue, Tp249-59 and Tp250-59 epitopes form distinct ligands for T-cell receptor recognition. Tetramer analysis of T. parva-specific CD8 T-cell lines confirmed the immunodominance of Tp1214-224 in BoLA-A18 animals and showed in BoLA-A10 animals that the Tp249-59 epitope response was generally more dominant than the Tp250-59 response and confirmed that the Tp298-106 response was subdominant.
Collapse
Affiliation(s)
- Timothy K. Connelley
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - Xiaoying Li
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
- Present address: School of Life Sciences and TechnologyXinxiang Medical UniversityLaboratory Building Room 232XinxiangHenanCN 453003China
| | - Niall MacHugh
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - Didier Colau
- Ludwig Institute for Cancer Research and de Duve InstituteUniversite catholique de LouvainBrusselsBelgium
| | - Simon P. Graham
- The International Livestock Research InstituteNairobiKenya
- Present address: The Pirbright InstituteAsh RoadPirbrightGU24 0NFUK
| | - Pierre van der Bruggen
- Ludwig Institute for Cancer Research and de Duve InstituteUniversite catholique de LouvainBrusselsBelgium
| | - Evans L. Taracha
- The International Livestock Research InstituteNairobiKenya
- Present address: Institute of Primate ResearchPO Box 24481‐00502KarenKenya
| | - Andy Gill
- Division of NeurobiologyThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - William Ivan Morrison
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
| |
Collapse
|
16
|
Transcriptomic Analysis of Persistent Infection with Foot-and-Mouth Disease Virus in Cattle Suggests Impairment of Apoptosis and Cell-Mediated Immunity in the Nasopharynx. PLoS One 2016; 11:e0162750. [PMID: 27643611 PMCID: PMC5028045 DOI: 10.1371/journal.pone.0162750] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022] Open
Abstract
In order to investigate the mechanisms of persistent foot-and-mouth disease virus (FMDV) infection in cattle, transcriptome alterations associated with the FMDV carrier state were characterized using a bovine whole-transcriptome microarray. Eighteen cattle (8 vaccinated with a recombinant FMDV A vaccine, 10 non-vaccinated) were challenged with FMDV A24 Cruzeiro, and the gene expression profiles of nasopharyngeal tissues collected between 21 and 35 days after challenge were compared between 11 persistently infected carriers and 7 non-carriers. Carriers and non-carriers were further compared to 2 naïve animals that had been neither vaccinated nor challenged. At a controlled false-discovery rate of 10% and a minimum difference in expression of 50%, 648 genes were differentially expressed between FMDV carriers and non-carriers, and most (467) had higher expression in carriers. Among these, genes associated with cellular proliferation and the immune response-such as chemokines, cytokines and genes regulating T and B cells-were significantly overrepresented. Differential gene expression was significantly correlated between non-vaccinated and vaccinated animals (biological correlation +0.97), indicating a similar transcriptome profile across these groups. Genes related to prostaglandin E2 production and the induction of regulatory T cells were overexpressed in carriers. In contrast, tissues from non-carrier animals expressed higher levels of complement regulators and pro-apoptotic genes that could promote virus clearance. Based on these findings, we propose a working hypothesis for FMDV persistence in nasopharyngeal tissues of cattle, in which the virus may be maintained by an impairment of apoptosis and the local suppression of cell-mediated antiviral immunity by inducible regulatory T cells.
Collapse
|
17
|
Identification of Theileria lestoquardi Antigens Recognized by CD8+ T Cells. PLoS One 2016; 11:e0162571. [PMID: 27611868 PMCID: PMC5017765 DOI: 10.1371/journal.pone.0162571] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/24/2016] [Indexed: 11/19/2022] Open
Abstract
As part of an international effort to develop vaccines for Theileria lestoquardi, we undertook a limited screen to test T. lestoquardi orthologues of antigens recognised by CD8+ T lymphocyte responses against T. annulata and T. parva in cattle. Five MHC defined sheep were immunized by live T. lestoquardi infection and their CD8+ T lymphocyte responses determined. Thirteen T. lestoquardi orthologues of T. parva and T. annulata genes, previously shown to be targets of CD8+ T lymphocyte responses of immune cattle, were expressed in autologous fibroblasts and screened for T cell recognition using an IFNγ assay. Genes encoding T. lestoquardi antigens Tl8 (putative cysteine proteinase, 349 aa) or Tl9 (hypothetical secreted protein, 293 aa) were recognise by T cells from one animal that displayed a unique MHC class I genotype. Antigenic 9-mer peptide epitopes of Tl8 and Tl9 were identified through peptide scans using CD8+ T cells from the responding animal. These experiments identify the first T. lestoquardi antigens recognised by CD8+ T cell responses linked to specific MHC class I alleles.
Collapse
|
18
|
The biology of Theileria parva and control of East Coast fever – Current status and future trends. Ticks Tick Borne Dis 2016; 7:549-64. [DOI: 10.1016/j.ttbdis.2016.02.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 01/02/2023]
|
19
|
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.
Collapse
|
20
|
Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters. Immunogenetics 2016; 68:339-52. [DOI: 10.1007/s00251-016-0902-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022]
|
21
|
Svitek N, Taracha ELN, Saya R, Awino E, Nene V, Steinaa L. Analysis of the Cellular Immune Responses to Vaccines. Methods Mol Biol 2016; 1349:247-262. [PMID: 26458841 DOI: 10.1007/978-1-4939-3008-1_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Flow cytometry, enzyme-linked immunospot (ELISpot) and cellular cytotoxicity assays are powerful tools for studying the cellular immune response towards intracellular pathogens and vaccines in livestock species. Lymphocytes from immunized animals can be purified using Ficoll-Paque density gradient centrifugation and evaluated for their antigen specificity or reactivity towards a vaccine. Here, we describe staining of bovine lymphocytes with peptide (p)-MHC class I tetramers and antibodies specific towards cellular activation markers for evaluation by multiparametric flow cytometry, as well as interferon (IFN)-γ ELISpot and cytotoxicity using chromium ((51)Cr) release assays. A small component on the use of immunoinformatics for fine-tuning the identification of a minimal CTL epitope is included.
Collapse
Affiliation(s)
- Nicholas Svitek
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya
| | - Evans L N Taracha
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya
| | - Rosemary Saya
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya
| | - Elias Awino
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya
| | - Vishvanath Nene
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya
| | - Lucilla Steinaa
- Vaccine Biosciences, International Livestock Research Institute, Att: Lucilla Steinaa, Vaccine Biosciences, 30709, 00100, Nairobi, Kenya.
| |
Collapse
|
22
|
Svitek N, Awino E, Nene V, Steinaa L. BoLA-6*01301 and BoLA-6*01302, two allelic variants of the A18 haplotype, present the same epitope from the Tp1 antigen of Theileria parva. Vet Immunol Immunopathol 2015; 167:80-5. [PMID: 26139380 DOI: 10.1016/j.vetimm.2015.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 05/28/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
Abstract
We have recently shown that the BoLA-A18 variant haplotype (BoLA-6*01302) is more prevalent than the BoLA-A18 haplotype (BoLA-6*01301) in a sample of Holstein/Friesian cattle in Kenya. These MHC class I allelic variants differ by a single amino acid polymorphism (Glu97 to Leu97) in the peptide-binding groove. We have previously mapped an 11-mer peptide epitope from the Theileria parva antigen Tp1 (Tp1214-224) that is presented by BoLA-6*01301. Crystal structure data indicates that Glu97 in the MHC molecule plays a role in epitope binding through electro-static interaction with a lysine residue in position 5 of the epitope, which also functions as an additional anchor residue. In contrast to expectations, we demonstrate that the amino acid substitution in BoLA-6*01302 does not divert the CTL response away from Tp1214-224. The two MHC molecules exhibit similar affinity for the Tp1 epitope and can present the epitope to parasite-specific CTLs derived from either BoLA allelic variants. These data confirm that this BoLA polymorphism does not alter Tp1 epitope specificity and that both allelic variants can be used for Tp1 vaccine studies.
Collapse
Affiliation(s)
- N Svitek
- Vaccine Biosciences, International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.
| | - E Awino
- Vaccine Biosciences, International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.
| | - V Nene
- Vaccine Biosciences, International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.
| | - L Steinaa
- Vaccine Biosciences, International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, Kenya.
| |
Collapse
|
23
|
Svitek N, Nzau B, Steinaa L, Nene V. A method to discriminate between closely related bovine major histocompatibility complex class I alleles by combining established PCR-SSP assays with RFLPs. ACTA ACUST UNITED AC 2015; 85:278-82. [PMID: 25789713 DOI: 10.1111/tan.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 11/22/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022]
Abstract
We have developed a polymerase chain reaction-sequence-specific primers-restriction fragment length polymorphism (PCR-SSP-RFLP) method to rapidly differentiate between the A18 and A18 variant (v) BoLA haplotypes and between A14 and A15/A15v BoLA haplotypes in Holstein/Friesian cattle. We used published SSP to PCR amplify BoLA alleles expressed in animals of known haplotype and exposed the amplicons to the restriction enzyme PvuII that was predicted to cut at a unique site in the middle of BoLA-6*01302 (A18v) and BoLA-1*00901 (A15) but not in BoLA-6*01301 (A18) or BoLA-1*02301 (A14) alleles. Whereas the method does not discriminate between the A15 and A15v haplotypes, as the BoLA-1*00902 allele associated with A15v also contains a PvuII site, we are interested in cattle of A18 and A14 haplotype for vaccine related studies. Our results also indicated that the BoLA-6*01302 (A18v) allele is much more abundant than BoLA-6*01301 (A18) in the cattle that we sampled.
Collapse
Affiliation(s)
- N Svitek
- International Livestock Research Institute (ILRI), Vaccine Biosciences, Nairobi 00100, Kenya
| | | | | | | |
Collapse
|
24
|
Functional restoration of exhausted CD4(+) and CD8(+) T cells in chronic viral infection by vinegar-processed flos of Daphne genkwa. Comp Immunol Microbiol Infect Dis 2015; 39:25-37. [PMID: 25744061 DOI: 10.1016/j.cimid.2015.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/26/2015] [Accepted: 02/04/2015] [Indexed: 02/08/2023]
Abstract
T-cell exhaustion has become an important issue in chronic infection because exhausted antigen-specific T cells show impaired abilities to eradicate persistently infected pathogens and produce effector cytokines, such as IFN-γ and TNF-α. Thus, strategies to either restore endogenous exhausted T cell responses or provide functional T cells are needed for therapeutics of chronic infection. Despite promising developments using antibodies and cell immunotherapy, there have been no reported attempts to restore exhausted T cells using treatment with materials derived from natural resources. Here, using a mouse model of chronic infection with lymphocytic choriomeningitis virus (LCMV), we found that vinegar-processed flowers (flos) of Daphne genkwa (vp-genkwa), which was composed mainly of four index components, restored exhausted CD4(+) and CD8(+) T cells significantly, as corroborated by evidence that vp-genkwa treatment enhanced functional LCMV-specific CD4(+) and CD8(+) T cells, both quantitatively and qualitatively. Furthermore, pretreatment with vp-genkwa prevented the generation of exhausted LCMV-specific CD8(+) T cells. Such restorations of exhausted LCMV-specific CD4(+) and CD8(+) T cells by vp-genkwa were closely associated with reduced viral burden in sera and tissues. More interestingly, vp-genkwa treatment induced down-regulation of negative molecules, such as PD-1 and Tim-3, in exhausted CD4(+) and CD8(+) T cells with more apparent down-regulation of Tim-3, suggesting that Tim-3 molecule may be a major target in restoring exhausted T cell responses. Collectively, these results provide valuable new insights into the use of vp-genkwa to develop a therapeutic strategy for chronic human diseases, such as hepatitis B and C virus, human immunodeficiency virus, and cancers.
Collapse
|
25
|
Guzman E, Taylor G. Immunology of bovine respiratory syncytial virus in calves. Mol Immunol 2014; 66:48-56. [PMID: 25553595 DOI: 10.1016/j.molimm.2014.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/28/2014] [Accepted: 12/07/2014] [Indexed: 12/31/2022]
Abstract
Bovine respiratory syncytial virus (BRSV) is an important cause of respiratory disease in young calves. The virus is genetically and antigenically closely related to human (H)RSV, which is a major cause of respiratory disease in young infants. As a natural pathogen of calves, BRSV infection recapitulates the pathogenesis of respiratory disease in man more faithfully than semi-permissive, animal models of HRSV infection. With the increasing availability of immunological reagents, the calf can be used to dissect the pathogenesis of and mechanisms of immunity to RSV infection, to analyse the ways in which the virus proteins interact with components of the innate response, and to evaluate RSV vaccine strategies. Passively transferred, neutralising bovine monoclonal antibodies, which recognise the same epitopes in the HRSV and BRSV fusion (F) protein, can protect calves against BRSV infection, and depletion of different T cells subsets in calves has highlighted the importance of CD8(+) T cells in viral clearance. Calves can be used to model maternal-antibody mediated suppression of RSV vaccine efficacy, and to increase understanding of the mechanisms responsible for RSV vaccine-enhanced respiratory disease.
Collapse
Affiliation(s)
- Efrain Guzman
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Geraldine Taylor
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
| |
Collapse
|
26
|
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: 18] [Impact Index Per Article: 1.8] [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.
Collapse
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
| |
Collapse
|