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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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2
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Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T. High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. Genes (Basel) 2023; 14:1422. [PMID: 37510326 PMCID: PMC10379315 DOI: 10.3390/genes14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
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Affiliation(s)
- Deepali Vasoya
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Thomas Tzelos
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lindert Benedictus
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anna Eleonora Karagianni
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Scott Pirie
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Celia Marr
- Rossdales Equine Hospital, Cotton End Road, Exning, Newmarket CD8 7NN, UK
| | - Charlotta Oddsdóttir
- The Institute for Experimental Pathology at Keldur, University of Iceland Keldnavegur 3, 112 Reykjavík, Iceland
| | - Constanze Fintl
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
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Silwamba I, Vasoya D, Simuunza M, Tzelos T, Nalubamba KS, Simulundu E, Vrettou C, Mainda G, Watson M, Muma JB, Connelley T. High throughput analysis of MHC class I and class II diversity of Zambian indigenous cattle populations. HLA 2023; 101:458-483. [PMID: 36680506 PMCID: PMC10952738 DOI: 10.1111/tan.14976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
The classical MHC class I and class II molecules play key roles in determining the antigenic-specificity of CD8+ and CD4+ T-cell responses-as such characterisation of the repertoire of MHCI and MHCII allelic diversity is fundamental to our ability to understand, and potentially, exploit how genetic diversity influences the outcome of immune responses. Cattle remain one of the most economically livestock species, with particular importance to many small-holder farmers in low-and-middle income countries (LMICs). However, our knowledge of MHC (BoLA) diversity in the indigenous breeds that form the mainstay of cattle populations in many LMICs remains very limited. In this study we develop a MiSeq-based platform to enable the rapid analysis of BoLA-DQA and BoLA-DQB, and combine this with similar platforms to analyse BoLA-I and BoLA-DRB repertoires, to study a large cohort of cattle (~800 animals) representing the 3 major indigenous breeds (Angoni, Barotse, Tonga) in Zambia. The data presented confirms the capacity of this high-throughput and high-resolution approach to provide a full characterisation of the MHCI-MHCII genotypes of cattle for which little previous MHC sequence data has been obtained. The cattle in Zambia were found to express a diverse range of MHCI, MHCII and extended MHCI-MHCII haplotypes. The combined MHCI-MHCII genotyping now possible opens new opportunities to rapidly expand our knowledge of MHC diversity in cattle that could find applications in a related translational disciplines such as vaccine development.
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Affiliation(s)
- Isaac Silwamba
- Department of Laboratory and DiagnosticsLivestock Services Cooperative SocietyLusakaZambia
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Deepali Vasoya
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Thomas Tzelos
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
| | - King S. Nalubamba
- Department of Clinical Studies, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
- Macha Research TrustChomaZambia
| | - Christina Vrettou
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
| | - Geoffrey Mainda
- Department of Veterinary Services, Ministry of Fisheries and LivestockCentral Veterinary Research InstituteLusakaZambia
| | - Mick Watson
- The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary MedicineUniversity of ZambiaLusakaZambia
| | - Timothy Connelley
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
- The Roslin InstituteUniversity of Edinburgh, Easter Bush CampusRoslinUK
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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5
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Talenti A, Powell J, Wragg D, Chepkwony M, Fisch A, Ferreira BR, Mercadante MEZ, Santos IM, Ezeasor CK, Obishakin ET, Muhanguzi D, Amanyire W, Silwamba I, Muma JB, Mainda G, Kelly RF, Toye P, Connelley T, Prendergast J. Optical mapping compendium of structural variants across global cattle breeds. Sci Data 2022; 9:618. [PMID: 36229544 PMCID: PMC9561109 DOI: 10.1038/s41597-022-01684-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/04/2022] [Indexed: 11/30/2022] Open
Abstract
Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution. Measurement(s) | Optical Mapping | Technology Type(s) | Optical Mapping | Factor Type(s) | Structural variants | Sample Characteristic - Organism | Bos taurus | Sample Characteristic - Location | United Kingdom • Kenya • Zambia • Uganda • Brazil • Nigeria |
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Affiliation(s)
- A Talenti
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.
| | - J Powell
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - D Wragg
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.,Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - M Chepkwony
- The International Livestock Research Institute, PO Box 30709, Nairobi, Kenya.,Centre for Tropical Livestock Genetics and Health, ILRI Kenya, Nairobi, 30709-00100, Kenya
| | - A Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - B R Ferreira
- Ribeirão Preto College of Nursing, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - M E Z Mercadante
- Institute of Animal Science, Agriculture Department of São Paulo Government, Sertãozinho, SP, 14.174-000, Brazil
| | - I M Santos
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - C K Ezeasor
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - E T Obishakin
- Biotechnology Division, National Veterinary Research Institute, Vom, Plateau State, Nigeria.,Biomedical Research Centre, Ghent University Global Campus, Songdo, Incheon, South Korea
| | - D Muhanguzi
- School of Biosecurity, Biotechnology and Laboratory Sciences (SBLS), College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O Box 7062, Kampala, Uganda
| | - W Amanyire
- School of Biosecurity, Biotechnology and Laboratory Sciences (SBLS), College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O Box 7062, Kampala, Uganda
| | - I Silwamba
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O BOX 32379, Lusaka, Zambia.,Department of Laboratory and Diagnostics, Livestock Services Cooperative Society, P.O. BOX 32025, Lusaka, Zambia
| | - J B Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O BOX 32379, Lusaka, Zambia
| | - G Mainda
- Department of Veterinary Services, Ministry of Fisheries and Livestock, Central Veterinary Research Institute, P.O. Box 33980, Lusaka, Zambia
| | - R F Kelly
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.,Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - P Toye
- The International Livestock Research Institute, PO Box 30709, Nairobi, Kenya
| | - T Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom. .,Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK.
| | - J Prendergast
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom. .,Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK.
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6
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Gillespie A, Loonie K, Zhang F, Prendergast J, Connelley T, Baldwin CL. Next generation sequencing of transcribed genes in ruminant γδ T cell populations. Mol Immunol 2022; 149:129-142. [PMID: 35810664 DOI: 10.1016/j.molimm.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
Abstract
Bovine γδ T cells are distinguished by expression of WC1, hybrid pattern recognition receptors and co-receptors to the T cell receptor (TCR), or their absence. WC1 molecules bind pathogens and the ability of γδ T cells to respond to pathogens largely correlates with their expression of particular WC1 genes. Following activation, the TCR and WC1 molecules co-localize and knocking down WC1 abrogates the ability of WC1-expressing γδ T cells to respond to antigen. It is known that these two major populations, WC1+ and WC1-, differ in their TCR gene expression and previous studies showed other differences using semi-quantitative RT-PCR and serial analysis of gene expression. Differences in genes expressed would influence the functional outcome when WC1+ vs. WC1- γδ T cells respond to pathogens. To identify unique aspects of their transcriptome, here we performed RNA-Seq of flow cytometrically sorted bovine WC1+ and WC1- γδ T cells and compared them to all mononuclear cells in blood. The greatest differences in gene expression were found between γδ T cells and other mononuclear cells and included those involved in lymphocyte activation and effector processes. Only minor differences occurred between ex vivo WC1+ vs. WC1- γδ T cells with those gene products being involved in cell adhesion and chemotaxis. After culturing cells from primed animals with Leptospira antigens major difference in the transcriptome was evident, with over 600 genes significantly differentially expressed including those focused on cytokine signaling. Unexpectedly, antigen-responding and non-responding populations of WC1+ γδ T cells had few differences in their transcriptomes outside of cytotoxic factors although they had more WC1-1, WC1-2 and WC1-13 transcripts. Through differential gene expression we were able to define properties of ex vivo and stimulated WC1+ cells which will be useful in understanding their functional biology.
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Affiliation(s)
- Alexandria Gillespie
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kathleen Loonie
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Fengqiu Zhang
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | | | | | - Cynthia L Baldwin
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA; Program in Molecular & Cellular Biology, University of Massachusetts, Amherst, MA, USA.
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Wragg D, Cook EAJ, Latré de Laté P, Sitt T, Hemmink JD, Chepkwony MC, Njeru R, Poole EJ, Powell J, Paxton EA, Callaby R, Talenti A, Miyunga AA, Ndambuki G, Mwaura S, Auty H, Matika O, Hassan M, Marshall K, Connelley T, Morrison LJ, Bronsvoort BMD, Morrison WI, Toye PG, Prendergast JGD. A locus conferring tolerance to Theileria infection in African cattle. PLoS Genet 2022; 18:e1010099. [PMID: 35446841 PMCID: PMC9022807 DOI: 10.1371/journal.pgen.1010099] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
East Coast fever, a tick-borne cattle disease caused by the Theileria parva parasite, is among the biggest natural killers of cattle in East Africa, leading to over 1 million deaths annually. Here we report on the genetic analysis of a cohort of Bos indicus (Boran) cattle demonstrating heritable tolerance to infection with T. parva (h2 = 0.65, s.e. 0.57). Through a linkage analysis we identify a 6 Mb genomic region on bovine chromosome 15 that is significantly associated with survival outcome following T. parva exposure. Testing this locus in an independent cohort of animals replicates this association with survival following T. parva infection. A stop gained variant in a paralogue of the FAF1 gene in this region was found to be highly associated with survival across both related and unrelated animals, with only one of the 20 homozygote carriers (T/T) of this change succumbing to the disease in contrast to 44 out of 97 animals homozygote for the reference allele (C/C). Consequently, we present a genetic locus linked to tolerance of one of Africa’s most important cattle diseases, raising the promise of marker-assisted selection for cattle that are less susceptible to infection by T. parva. More than a million cattle die of East Coast fever in Africa each year, the impact of which disproportionately falls onto low-income, smallholder farmers. The lack of a widely accessible vaccine, heavy reliance on chemicals to control the tick vector and inadequate drug treatments means that new approaches for controlling the disease are urgently required. Through a genetic study of an extended pedigree of Boran cattle that are more than three times less likely to succumb to the disease than matched controls, we identify a region on chromosome 15 of the cattle genome associated with a high level of tolerance to the disease. We show that a nonsense variant in a predicted paralogue of FAS-associated factor 1 (FAF1) in this region is also associated with survival in an independent cohort, and is linked to rates of cell expansion during infection. This genetic variant can therefore support marker-assisted selection, allowing farmers to breed tolerant cattle and offers a route to introduce this beneficial DNA to non-native breeds, enabling reduced disease incidence and increased productivity, which would be of benefit to millions of rural smallholder farmers across Africa.
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Affiliation(s)
- David Wragg
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Elizabeth A. J. Cook
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | - Perle Latré de Laté
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | | | - Johanneke D. Hemmink
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | | | - Regina Njeru
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | | | - Jessica Powell
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Edith A. Paxton
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rebecca Callaby
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- The Epidemiology, Economics and Risk Assessment (EEA) Group, Easter Bush Campus, Edinburgh, United Kingdom
| | - Andrea Talenti
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Antoinette A. Miyunga
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | - Gideon Ndambuki
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | | | - Harriet Auty
- Institute of Biodiversity Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Oswald Matika
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Musa Hassan
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Marshall
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
| | - Timothy Connelley
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Liam J. Morrison
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - B. Mark deC. Bronsvoort
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - W. Ivan Morrison
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Philip G. Toye
- Centre for Tropical Livestock Genetics and Health (CTLGH), ILRI Kenya, Nairobi, Kenya
- ILRI Kenya, Nairobi, Kenya
- * E-mail: (PGT); (JGDP)
| | - James G. D. Prendergast
- Centre for Tropical Livestock Genetics and Health (CTLGH), Easter Bush Campus, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (PGT); (JGDP)
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8
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Martini V, Edmans M, Gubbins S, Jayaraman S, Paudyal B, Morgan S, McNee A, Morin T, Rijal P, Gerner W, Sewell AK, Inoue R, Bailey M, Connelley T, Charleston B, Townsend A, Beverley P, Tchilian E. Spatial, temporal and molecular dynamics of swine influenza virus-specific CD8 tissue resident memory T cells. Mucosal Immunol 2022; 15:428-442. [PMID: 35145208 PMCID: PMC9038527 DOI: 10.1038/s41385-021-00478-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023]
Abstract
For the first time we have defined naïve, central memory, effector memory and differentiated effector porcine CD8 T cells and analyzed their distribution in lymphoid and respiratory tissues after influenza infection or immunization, using peptide-MHC tetramers of three influenza nucleoprotein (NP) epitopes. The hierarchy of response to the three epitopes changes during the response in different tissues. Most NP-specific CD8 T cells in broncho-alveolar lavage (BAL) and lung are tissue resident memory cells (TRM) that express CD69 and downregulate CD45RA and CCR7. NP-specific cells isolated from BAL express genes characteristic of TRM, but gene expression differs at 7, 21 and 63 days post infection. In all tissues the frequency of NP-specific CD8 cells declines over 63 days almost to background levels but is best maintained in BAL. The kinetic of influenza specific memory CD8 T cell in this natural host species differs from that in small animal models.
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Affiliation(s)
- Veronica Martini
- The Pirbright Institute, Pirbright, UK.
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Institute for Research in Biomedicine, Bellinzona, Switzerland.
| | | | | | | | | | | | | | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Pramila Rijal
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Ryo Inoue
- Laboratory of Animal Science, Setsunan University, Osaka, Japan
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Langford, UK
| | | | | | - Alain Townsend
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter Beverley
- National Heart and Lung Institute, St Mary's Campus, Imperial College, London, UK
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9
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Morrison WI, Sheldrake T, Connelley T. Antibodies that react with bovine T lymphocytes expressing the T cell receptor β chain subgroup BV20 inhibit antigen recognition. Vet Immunol Immunopathol 2022; 246:110392. [DOI: 10.1016/j.vetimm.2022.110392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/28/2022]
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10
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Morrison WI, Aguado A, Sheldrake TA, Palmateer NC, Ifeonu OO, Tretina K, Parsons K, Fenoy E, Connelley T, Nielsen M, Silva JC. CD4 T Cell Responses to Theileria parva in Immune Cattle Recognize a Diverse Set of Parasite Antigens Presented on the Surface of Infected Lymphoblasts. J Immunol 2021; 207:1965-1977. [PMID: 34507950 DOI: 10.4049/jimmunol.2100331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/22/2021] [Indexed: 12/23/2022]
Abstract
Parasite-specific CD8 T cell responses play a key role in mediating immunity against Theileria parva in cattle (Bos taurus), and there is evidence that efficient induction of these responses requires CD4 T cell responses. However, information on the antigenic specificity of the CD4 T cell response is lacking. The current study used a high-throughput system for Ag identification using CD4 T cells from immune animals to screen a library of ∼40,000 synthetic peptides representing 499 T. parva gene products. Use of CD4 T cells from 12 immune cattle, representing 12 MHC class II types, identified 26 Ags. Unlike CD8 T cell responses, which are focused on a few dominant Ags, multiple Ags were recognized by CD4 T cell responses of individual animals. The Ags had diverse properties, but included proteins encoded by two multimember gene families: five haloacid dehalogenases and five subtelomere-encoded variable secreted proteins. Most Ags had predicted signal peptides and/or were encoded by abundantly transcribed genes, but neither parameter on their own was reliable for predicting antigenicity. Mapping of the epitopes confirmed presentation by DR or DQ class II alleles and comparison of available T. parva genome sequences demonstrated that they included both conserved and polymorphic epitopes. Immunization of animals with vaccine vectors expressing two of the Ags demonstrated induction of CD4 T cell responses capable of recognizing parasitized cells. The results of this study provide detailed insight into the CD4 T cell responses induced by T. parva and identify Ags suitable for use in vaccine development.
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Affiliation(s)
- W Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom;
| | - Adriana Aguado
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Tara A Sheldrake
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Nicholas C Palmateer
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Olukemi O Ifeonu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Kyle Tretina
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Keith Parsons
- Institute for Animal Health, Berkshire, United Kingdom
| | - Emilio Fenoy
- Biotechnological Research Institute, National University of San Martin, Buenos Aires, Argentina
| | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Morten Nielsen
- Biotechnological Research Institute, National University of San Martin, Buenos Aires, Argentina.,Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark; and
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD
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11
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Gillespie A, Gervasi MG, Sathiyaseelan T, Connelley T, Telfer JC, Baldwin CL. Gamma Delta TCR and the WC1 Co-Receptor Interactions in Response to Leptospira Using Imaging Flow Cytometry and STORM. Front Immunol 2021; 12:712123. [PMID: 34394114 PMCID: PMC8356672 DOI: 10.3389/fimmu.2021.712123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/06/2021] [Indexed: 01/04/2023] Open
Abstract
The WC1 cell surface family of molecules function as hybrid gamma delta (γδ) TCR co-receptors, augmenting cellular responses when cross-linked with the TCR, and as pattern recognition receptors, binding pathogens. It is known that following activation, key tyrosines are phosphorylated in the intracytoplasmic domains of WC1 molecules and that the cells fail to respond when WC1 is knocked down or, as shown here, when physically separated from the TCR. Based on these results we hypothesized that the colocalization of WC1 and TCR will occur following cellular activation thereby allowing signaling to ensue. We evaluated the spatio-temporal dynamics of their interaction using imaging flow cytometry and stochastic optical reconstruction microscopy. We found that in quiescent γδ T cells both WC1 and TCR existed in separate and spatially stable protein domains (protein islands) but after activation using Leptospira, our model system, that they concatenated. The association between WC1 and TCR was close enough for fluorescence resonance energy transfer. Prior to concatenating with the WC1 co-receptor, γδ T cells had clustering of TCR-CD3 complexes and exclusion of CD45. γδ T cells may individually express more than one variant of the WC1 family of molecules and we found that individual WC1 variants are clustered in separate protein islands in quiescent cells. However, the islands containing different variants merged following cell activation and before merging with the TCR islands. While WC1 was previously shown to bind Leptospira in solution, here we showed that Leptospira bound WC1 proteins on the surface of γδ T cells and that this could be blocked by anti-WC1 antibodies. In conclusion, γδ TCR, WC1 and Leptospira interact directly on the γδ T cell surface, further supporting the role of WC1 in γδ T cell pathogen recognition and cellular activation.
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Affiliation(s)
- Alexandria Gillespie
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, United States
| | - Maria Gracia Gervasi
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, United States
| | | | | | - Janice C Telfer
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, United States.,Program in Molecular & Cellular Biology, University of Massachusetts, Amherst, MA, United States
| | - Cynthia L Baldwin
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, United States.,Program in Molecular & Cellular Biology, University of Massachusetts, Amherst, MA, United States
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12
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Vasoya D, Oliveira PS, Muriel LA, Tzelos T, Vrettou C, Morrison WI, de Miranda Santos IKF, Connelley T. High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations. HLA 2021; 98:93-113. [PMID: 34102036 DOI: 10.1111/tan.14339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/13/2021] [Accepted: 06/02/2021] [Indexed: 01/16/2023]
Abstract
The major histocompatibility complex (MHC) contains many genes that play key roles in initiating and regulating immune responses. This includes the polymorphic MHCI and MHCII genes that present epitopes to CD8+ and CD4+ T-cells, respectively. Consequently, the characterisation of the repertoire of MHC genes is an important component of improving our understanding of the genetic variation that determines the outcomes of immune responses. In cattle, MHC (BoLA) research has predominantly focused on Holstein-Friesian animals (as the most economically important breed globally), although the development of high-throughput approaches has allowed the BoLA-DRB3 repertoire to be studied in a greater variety of breeds. In a previous study we reported on the development of a MiSeq-based method to enable high-throughput and high-resolution analysis of bovine MHCI repertoires. Herein, we report on the expansion of this methodology to incorporate analysis of the BoLA-DRB3 and its application to analyse MHC diversity in a large cohort of cattle from Brazil (>500 animals), including representatives from the three major Bos indicus breeds present in Brazil - Guzerat, Gir and Nelore. This large-scale description of paired MHCI-DRB3 repertoires in Bos indicus cattle has identified a small number of novel DRB3 alleles, a large number of novel MHCI alleles and haplotypes, and provided novel insights into MHCI-MHCII association - further expanding our knowledge of bovine MHC diversity.
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Affiliation(s)
- Deepali Vasoya
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Priscila Silva Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
| | - Laura Agundez Muriel
- Translational Synthetic Biology Department, Mammalian genome editing and gene therapy, Parque de Investigación Biomédica, Carrer del Dr, Barcelona, Spain
| | - Thomas Tzelos
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Christina Vrettou
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - W Ivan Morrison
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Timothy Connelley
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Edinburgh, UK
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13
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Makau MC, Powell J, Prendergast J, de Laté PL, Morrison LJ, Fisch A, Gathura P, Kitala P, Connelley T, Toye P. Corrigendum to "Inverted CD4 +/CD8+T cell ratio in Boran (Bos indicus) cattle" [Vet. Immunol. Immunopathol. 230 110126]. Vet Immunol Immunopathol 2021; 235:110219. [PMID: 33743998 PMCID: PMC8085732 DOI: 10.1016/j.vetimm.2021.110219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Maurine C Makau
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya.
| | - Jessica Powell
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - James Prendergast
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Perle Latré de Laté
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya
| | - Liam J Morrison
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Avenida dos Bandeirantes, 3900, 14040-902 Ribeirao Preto, Brazil
| | - Peter Gathura
- The University of Nairobi, Department of Public Health, Pharmacology and Toxicology, P.O Box 30197-00100, Nairobi, Kenya
| | - Phillip Kitala
- The University of Nairobi, Department of Public Health, Pharmacology and Toxicology, P.O Box 30197-00100, Nairobi, Kenya
| | - Timothy Connelley
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Philip Toye
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya
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14
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Gillespie A, Yirsaw A, Gunasekaran KP, Smith TP, Bickhart DM, Turley M, Connelley T, Telfer JC, Baldwin CL. Characterization of the domestic goat γδ T cell receptor gene loci and gene usage. Immunogenetics 2021; 73:187-201. [PMID: 33479855 DOI: 10.1007/s00251-021-01203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Goats and cattle diverged 30 million years ago but retain similarities in immune system genes. Here, the caprine T cell receptor (TCR) gene loci and transcription of its genes were examined and compared to cattle. We annotated the TCR loci using an improved genome assembly (ARS1) of a highly homozygous San Clemente goat. This assembly has already proven useful for describing other immune system genes including antibody and leucocyte receptors. Both the TCRγ (TRG) and TCRδ (TRD) loci were similarly organized in goats as in cattle and the gene sequences were highly conserved. However, the number of genes varied slightly as a result of duplications and differences occurred in mutations resulting in pseudogenes. WC1+ γδ T cells in cattle have been shown to use TCRγ genes from only one of the six available cassettes. The structure of that Cγ gene product is unique and may be necessary to interact with WC1 for signal transduction following antigen ligation. Using RT-PCR and PacBio sequencing, we observed the same restriction for goat WC1+ γδ T cells. In contrast, caprine WC1+ and WC1- γδ T cell populations had a diverse TCRδ gene usage although the propensity for particular gene usage differed between the two cell populations. Noncanonical recombination signal sequences (RSS) largely correlated with restricted expression of TCRγ and δ genes. Finally, caprine γδ T cells were found to incorporate multiple TRD diversity gene sequences in a single transcript, an unusual feature among mammals but also previously observed in cattle.
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Affiliation(s)
- Alexandria Gillespie
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Al Yirsaw
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Karthick P Gunasekaran
- College of Information and Computer Sciences, University of Massachusetts, 140 Governors Drive, Amherst, MA, 01003, USA
| | - Timothy P Smith
- United States Department of Agriculture, Agricultural Research Service, United States Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Derek M Bickhart
- United States Department of Agriculture, Agricultural Research Service, United States Dairy Forage Research Center, Madison, WI, 53706, USA
| | - Michael Turley
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | | | - Janice C Telfer
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - Cynthia L Baldwin
- Integrated Sciences Building, Department of Veterinary and Animal Sciences, University of Massachusetts, 661 N. Pleasant St, Amherst, MA, 01003, USA.
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15
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Benedictus L, Steinbach S, Holder T, Bakker D, Vrettou C, Morrison WI, Vordermeier M, Connelley T. Hydrophobic Mycobacterial Antigens Elicit Polyfunctional T Cells in Mycobacterium bovis Immunized Cattle: Association With Protection Against Challenge? Front Immunol 2020; 11:588180. [PMID: 33281817 PMCID: PMC7688591 DOI: 10.3389/fimmu.2020.588180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/20/2020] [Indexed: 01/09/2023] Open
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is a chronic disease of cattle with a detrimental impact on food quality and production. Research on bTB vaccines has predominantly been focused on proteinaceous antigens. However, mycobacteria have a thick and intricate lipid outer layer and lipids as well as lipopeptides are important for immune-evasion and virulence. In humans, lipid extracts of M. tuberculosis have been shown to elicit immune responses effective against M. tuberculosis in vitro. Chloroform-methanol extraction (CME) was applied to M. bovis BCG to obtain a hydrophobic antigen extract (CMEbcg) containing lipids and lipopeptides. CMEbcg stimulated IFN-γ+IL-2+ and IL-17A+IL-22+ polyfunctional T cells and elicited T cell responses with a Th1 and Th17 cytokine release profile in both M. bovis BCG vaccinated and M. bovis challenged calves. Lipopeptides were shown to be the immunodominant antigens in CMEbcg, stimulating CD4 T cells via MHC class II. CMEbcg expanded T cells killed CMEbcg loaded monocytes and the CMEbcg-specific CD3 T cell proliferative response following M. bovis BCG vaccination was the best predictor for reduced pathology following challenge with M. bovis. Although the high predictive value of CMEbcg-specific immune responses does not confirm a causal relationship with protection against M. bovis challenge, when taking into account the in vitro antimycobacterial phenotype of CMEbcg-specific T cells (e.g. Th1/Th17 cytokine profile), it is indicative that CMEbcg-specific immune responses could play a functional role in immunity against M. bovis. Based on these findings we conclude that lipopeptides of M. bovis are potential novel subunit vaccine candidates and that further studies into the functional characterization of lipopeptide-specific immune responses together with their role in protection against bovine tuberculosis are warranted.
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Affiliation(s)
- Lindert Benedictus
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Sabine Steinbach
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Thomas Holder
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Douwe Bakker
- Independent Researcher and Technical Consultant, Lelystad, Netherlands
| | - Christina Vrettou
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - W Ivan Morrison
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
| | - Martin Vordermeier
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,Centre for Bovine Tuberculosis, Institute for Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush, United Kingdom
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16
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Makau MC, Powell J, Prendergast J, Latré de Laté P, Morrison LJ, Fisch A, Gathura P, Kitala P, Connelley T, Toye P. Inverted CD4 +/CD8 + T cell ratio in Boran (Bos indicus) cattle. Vet Immunol Immunopathol 2020; 230:110126. [PMID: 33080530 PMCID: PMC7700890 DOI: 10.1016/j.vetimm.2020.110126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 10/26/2022]
Abstract
The CD4+/CD8+ ratio is used as a marker of the immune regulation of T cell balance. When the ratio in peripheral blood is less than 1, this is considered an indication of immune suppression in an individual. Previous work on bovine Peripheral Blood Mononuclear Cells (PBMC) has consistently reported a ratio ≥1 as seen in other mammalian hosts, i.e. higher circulating CD4+ cell numbers than CD8+ cell numbers. However, a consistent inverted CD4+/CD8+ ratio (<1) was observed in Boran cattle, an African Bos indicus breed. The T cell populations were characterized in Boran cattle (n = 52), revealing higher percentages of circulating CD8+ cells (31.9 % average) than CD4+ cells (19.1 % average), thus resulting in the inversion of the expected T cell homeostasis in these animals. The results show that this inversion is not an effect of age or relatedness of the cattle, rather, it was shared by almost all Boran cattle used in this study. Despite this inversion being a feature shared by both males and females, the female cattle had significantly higher CD4+/CD8+ ratios than the male Boran. This paper describes the characteristics of the T cell fractions in the study animals and compares the findings to those of other Boran cattle in Kenya, and four other cattle breeds representing African indicine, African taurine, Brazilian indicine and European taurine cattle. We demonstrate that the consistent observation of inverted CD4+/CD8+ cell ratio was restricted to the Boran.
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Affiliation(s)
- Maurine C Makau
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya.
| | - Jessica Powell
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - James Prendergast
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Perle Latré de Laté
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya
| | - Liam J Morrison
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Andressa Fisch
- Ribeirão Preto College of Nursing, University of Sao Paulo, Avenida dos Bandeirantes, 3900, 14040-902 Ribeirao Preto Brazil
| | - Peter Gathura
- The University of Nairobi, Department of Public Health, Pharmacology and Toxicology, P.O Box 30197-00100, Nairobi, Kenya
| | - Phillip Kitala
- The University of Nairobi, Department of Public Health, Pharmacology and Toxicology, P.O Box 30197-00100, Nairobi, Kenya
| | - Timothy Connelley
- The Roslin Institute and Centre for Tropical Livestock Genetics and Health, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Philip Toye
- International Livestock Research Institute (ILRI) and Centre for Tropical Livestock Genetics and Health, P.O. Box 30709, Nairobi 00100, Kenya
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17
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Bastos RG, Franceschi V, Tebaldi G, Connelley T, Morrison WI, Knowles DP, Donofrio G, Fry LM. Molecular and Antigenic Properties of Mammalian Cell-Expressed Theileria parva Antigen Tp9. Front Immunol 2019; 10:897. [PMID: 31110506 PMCID: PMC6501543 DOI: 10.3389/fimmu.2019.00897] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
East Coast Fever (ECF), caused by the tick-borne apicomplexan parasite Theileria parva, is a leading cause of morbidity and mortality in cattle of sub-Saharan Africa. The infection and treatment method (ITM) is currently the only vaccine available to control T. parva. Although ITM elicits levels of protection, its widespread adoption is limited by costs, laborious production process, and antibiotic co-treatment requirement, necessitating the development of a more sustainable vaccine. To this end, efforts have been concentrated in the identification of new T. parva vaccine antigens and in the development of suitable platforms for antigen expression. In this study, we investigated the molecular and antigenic properties of T. parva antigen Tp9 expressed by mammalian cells. Data indicate that Tp9 contains a signal peptide that is weakly functional in mammalian cells. Thus, Tp9 secretion from mammalian cells increased 10-fold after the native signal peptide was replaced with the human tissue plasminogen activator signal peptide (tPA). Sera from all T. parva-immune cattle recognized this recombinant, secreted Tp9. Additionally, PBMC from ITM-immunized cattle produced significant (p < 0.05) amounts of IFNγ following ex vivo exposure to Tp9, but this response varied between cattle of different MHC class I and class II genotypes. In addition, depletion experiments demonstrated that IFNγ to Tp9 was primarily produced by CD4+ T cells. Molecular analysis demonstrated that Tp9 presents a signal peptide that is weakly functional in mammalian cells, suggesting that it remains within lymphocytes during infection. Tp9 secretion from mammalian cells was substantially increased when the tPA secretion signal sequence was substituted for the native secretion signal sequence. Using full-length, recombinant Tp9 secreted from mammalian cells, we demonstrated that T. parva-immune cattle develop both humoral and cellular immune responses to this antigen. Collectively, these results provide rationale for further evaluation of Tp9 as a component of a T. parva subunit vaccine.
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Affiliation(s)
- Reginaldo G Bastos
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | | | - Giulia Tebaldi
- Department of Medical-Veterinary Science, University of Parma, Parma, Italy
| | - Timothy Connelley
- Royal School of Veterinary Sciences, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - W Ivan Morrison
- Royal School of Veterinary Sciences, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Donald P Knowles
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Gaetano Donofrio
- Department of Medical-Veterinary Science, University of Parma, Parma, Italy
| | - Lindsay M Fry
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States.,Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Pullman, WA, United States
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18
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Shaukat A, Ali Q, Connelley T, Khan MAU, Saleem MA, Evans M, Rashid I, Sargison ND, Chaudhry U. Selective sweep and phylogenetic models for the emergence and spread of pyrimethamine resistance mutations in Plasmodium vivax. Infect Genet Evol 2018; 68:221-230. [PMID: 30594654 DOI: 10.1016/j.meegid.2018.12.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/20/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
Abstract
Pyrimethamine resistance is a major concern for the control of human haemoprotozoa, especially Plasmodium species. Currently, there is little understanding of how pyrimethamine resistance developed in Plasmodium vivax in the natural field conditions. Here, we present for the first time evidence of positive selection pressure on a dihydrofolate reductase locus and its consequences on the emergence and the spread of pyrimethamine resistance in P. vivax in the Punjab province of Pakistan. First, we examined the dihydrofolate reductase locus in 38 P. vivax isolates to look for evidence of positive selection pressure in human patients. The S58R (AGA)/S117N (AAC) double mutation was most common, being detected in 10/38 isolates. Single mutation S117N (AAC), I173L (CTT) and S58R (AGA) SNPs were detected in 8/38, 2/38 and 1/38 isolates, respectively. The F57L/I (TTA/ATA) and T61M (ATG) SNPs were not detected in any isolates examined. Although both soft and hard selective sweeps have occurred with striking differences between isolates, there was a predominance of hard sweeps. A single resistance haplotype was present at high frequency in 9/14 isolates, providing a strong evidence for single emergence of resistance by the single mutation, characteristics of hard selective sweeps. In contrast, 5/14 isolates carried multiple resistance haplotypes at high frequencies, providing an evidence of the emergence of resistance by recurrent mutations, characteristics of soft selective sweeps. Our phylogenetic relationship analysis suggests that S58R (AGA)/S117N (AAC) and S117N (AAC) mutations arose multiple times from a single origin and spread to multiple different cities in the Punjab province through gene flow. Interestingly, the I173L (CTT) mutation was present on a single haplotype, suggesting that it arises rarely and has not spread between cities. Our work shows the need for responsible use of existing and new antimicrobial drugs and their combinations, control the movement of infected patients and mosquito vector control strategies.
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Affiliation(s)
- Ayaz Shaukat
- Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Qasim Ali
- Department of Parasitology, University of Veterinary and Animal Sciences Lahore, Pakistan
| | - Timothy Connelley
- University of Edinburgh, The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | | | - Mushtaq A Saleem
- Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | - Mike Evans
- University of Edinburgh, The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences Lahore, Pakistan
| | - Neil D Sargison
- University of Edinburgh, The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK
| | - Umer Chaudhry
- University of Edinburgh, The Roslin Institute, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, UK.
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Gillespie A, Connelley T, Telfer JC, Baldwin CL. Interaction of γδ TCR with the WC1 hybrid co-receptor/pathogen recognition receptor in cattle. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.226.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Ruminants have a larger proportion of γδ T lymphocytes in blood compared to mice and humans. These lymphocytes are first responders to pathogens such as Leptospira and Mycobacterium. Bovine γδ T cells that respond to these pathogens express members of a unique γδ T-cell specific molecular family WC1 that are hybrid pattern recognition receptors and signaling co-receptors. Only γδ T cells that express WC1 molecules that bind to the pathogens selectively respond by proliferation and cytokine production. WC1 molecules have also been shown to augment signaling when co-crosslinked with the TCR but cannot signal on their own. Silencing WC1 through shRNA results in inhibition of the response to leptospira. Together these data indicate that WC1 is crucial for activation of the cells and we wished to further understand how the TCR interacts with WC1. The TCR is transcribed from a recombination of variable, joining, and diversity genes resulting in hundreds to millions of different possible sequences while the WC1 family has only 137 different pathogen-binding SRCR domains coded for by 13 genes. Yet only γδ T cells that express particular WC1 family members respond to leptospira suggesting it has primacy. We hypothesize that WC1 molecules co-localize with the TCR following binding of the pathogen. To test this hypothesis we used Imaging flow cytometry. Using FRET analysis we are able to determine that not only are the TCR and WC1 co-localized in the synapse following activation but they also are interacting closely within 9nm of each other. To evaluate the role of the TCR in dictating specificity of the response we are using next generation sequencing of transcripts coding for the TCR gamma and delta chains in leptospira-responsive cells.
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Olsen L, Åkesson CP, Storset AK, Lacroix-Lamandé S, Boysen P, Metton C, Connelley T, Espenes A, Laurent F, Drouet F. The early intestinal immune response in experimental neonatal ovine cryptosporidiosis is characterized by an increased frequency of perforin expressing NCR1(+) NK cells and by NCR1(-) CD8(+) cell recruitment. Vet Res 2015; 46:28. [PMID: 25890354 PMCID: PMC4355373 DOI: 10.1186/s13567-014-0136-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/11/2014] [Indexed: 12/02/2022] Open
Abstract
Cryptosporidium parvum, a zoonotic protozoan parasite, causes important losses in neonatal ruminants. Innate immunity plays a key role in controlling the acute phase of this infection. The participation of NCR1+ Natural Killer (NK) cells in the early intestinal innate immune response to the parasite was investigated in neonatal lambs inoculated at birth. The observed increase in the lymphocyte infiltration was further studied by immunohistology and flow cytometry with focus on distribution, density, cellular phenotype related to cytotoxic function and activation status. The frequency of NCR1+ cells did not change with infection, while their absolute number slightly increased in the jejunum and the CD8+/NCR1- T cell density increased markedly. The frequency of perforin+ cells increased significantly with infection in the NCR1+ population (in both NCR1+/CD16+ and NCR1+/CD16- populations) but not in the NCR1-/CD8+ population. The proportion of NCR1+ cells co-expressing CD16+ also increased. The fraction of cells expressing IL2 receptor (CD25), higher in the NCR1+/CD8+ population than among the CD8+/NCR1- cells in jejunal Peyer’s patches, remained unchanged during infection. However, contrary to CD8+/NCR1- lymphocytes, the intensity of CD25 expressed by NCR1+ lymphocytes increased in infected lambs. Altogether, the data demonstrating that NK cells are highly activated and possess a high cytotoxic potential very early during infection, concomitant with an up-regulation of the interferon gamma gene in the gut segments, support the hypothesis that they are involved in the innate immune response against C. parvum. The early significant recruitment of CD8+/NCR1- T cells in the small intestine suggests that they could rapidly drive the establishment of the acquired immune response.
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Affiliation(s)
- Line Olsen
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
| | - Caroline Piercey Åkesson
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
| | - Anne K Storset
- Department of Food Safety & Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
| | - Sonia Lacroix-Lamandé
- Institut National de la Recherche Agronomique, UMR1282, Infectiologie et Santé Publique, Laboratoire Apicomplexes et Immunité Muqueuse, Nouzilly, France.
| | - Preben Boysen
- Department of Food Safety & Infection Biology, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
| | - Coralie Metton
- Institut National de la Recherche Agronomique, UMR1282, Infectiologie et Santé Publique, Laboratoire Apicomplexes et Immunité Muqueuse, Nouzilly, France.
| | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Arild Espenes
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway.
| | - Fabrice Laurent
- Institut National de la Recherche Agronomique, UMR1282, Infectiologie et Santé Publique, Laboratoire Apicomplexes et Immunité Muqueuse, Nouzilly, France.
| | - Françoise Drouet
- Institut National de la Recherche Agronomique, UMR1282, Infectiologie et Santé Publique, Laboratoire Apicomplexes et Immunité Muqueuse, Nouzilly, France.
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Affiliation(s)
- W. Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom;
| | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom;
| | | | - Niall D. MacHugh
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom;
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Olsen L, Boysen P, Åkesson CP, Gunnes G, Connelley T, Storset AK, Espenes A. Characterization of NCR1+ cells residing in lymphoid tissues in the gut of lambs indicates that the majority are NK cells. Vet Res 2013; 44:109. [PMID: 24219350 PMCID: PMC4176090 DOI: 10.1186/1297-9716-44-109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022] Open
Abstract
Natural killer (NK) cells are important for immune protection of the gut mucosa. Previous studies have shown that under pathologic conditions NK cells, T cells and dendritic cells are found co-localised in secondary lymphoid organs where their interaction coordinates immune responses. However, in the gut-associated lymphoid tissues (GALTs), there are few detailed reports on the distribution of NK cells. Sheep harbour several types of organised lymphoid tissues in the gut that have different functions. The ileal Peyer's patch (IPP) functions as a primary lymphoid tissue for B cell generation, while the jejunal Peyer's patches (JPPs) and colon patches (CPs) are considered secondary lymphoid tissues. In the present study, we analysed tissues from healthy lambs by flow cytometry and in situ multicolour immunofluorescence, using recently described NCR1 antibodies to identify ovine NK cells. Most NCR1+ cells isolated from all tissues were negative for the pan T cell marker CD3, and thus comply with the general definition of NK cells. The majority of NCR1+ cells in blood as well as secondary lymphoid organs expressed CD16, but in the GALT around half of the NCR1+ cells were negative for CD16. A semi-quantitative morphometric study on tissue sections was used to compare the density of NK cells in four compartments of the IPPs, JPP and CPs. NCR1+ cells were found in all gut segments. Statistical analysis revealed significant differences between compartments of the primary lymphoid organ IPP and the secondary lymphoid organs of the JPPs and CP. NK cells co-localised and made close contact with T cells, dendritic cells and other NK cells, but did not show signs of proliferation. We conclude that NK cells are present in all investigated segments of the sheep gut, but that presence of other innate lymphoid cells expressing NCR1 cannot be excluded.
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Affiliation(s)
- Line Olsen
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, Oslo, Norway.
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Wilson GJ, Seo KS, Cartwright RA, Connelley T, Chuang-Smith ON, Merriman JA, Guinane CM, Park JY, Bohach GA, Schlievert PM, Morrison WI, Fitzgerald JR. A novel core genome-encoded superantigen contributes to lethality of community-associated MRSA necrotizing pneumonia. PLoS Pathog 2011; 7:e1002271. [PMID: 22022262 PMCID: PMC3192841 DOI: 10.1371/journal.ppat.1002271] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 08/01/2011] [Indexed: 01/08/2023] Open
Abstract
Bacterial superantigens (SAg) stimulate T-cell hyper-activation resulting in immune modulation and severe systemic illnesses such as Staphylococcus aureus toxic shock syndrome. However, all known S. aureus SAgs are encoded by mobile genetic elements and are made by only a proportion of strains. Here, we report the discovery of a novel SAg staphylococcal enterotoxin-like toxin X (SElX) encoded in the core genome of 95% of phylogenetically diverse S. aureus strains from human and animal infections, including the epidemic community-associated methicillin-resistant S. aureus (CA-MRSA) USA300 clone. SElX has a unique predicted structure characterized by a truncated SAg B-domain, but exhibits the characteristic biological activities of a SAg including Vβ-specific T-cell mitogenicity, pyrogenicity and endotoxin enhancement. In addition, SElX is expressed by clinical isolates in vitro, and during human, bovine, and ovine infections, consistent with a broad role in S. aureus infections of multiple host species. Phylogenetic analysis suggests that the selx gene was acquired horizontally by a progenitor of the S. aureus species, followed by allelic diversification by point mutation and assortative recombination resulting in at least 17 different alleles among the major pathogenic clones. Of note, SElX variants made by human- or ruminant-specific S. aureus clones demonstrated overlapping but distinct Vβ activation profiles for human and bovine lymphocytes, indicating functional diversification of SElX in different host species. Importantly, SElX made by CA-MRSA USA300 contributed to lethality in a rabbit model of necrotizing pneumonia revealing a novel virulence determinant of CA-MRSA disease pathogenesis. Taken together, we report the discovery and characterization of a unique core genome-encoded superantigen, providing new insights into the evolution of pathogenic S. aureus and the molecular basis for severe infections caused by the CA-MRSA USA300 epidemic clone. Staphylococcus aureus is a global pathogen, responsible for an array of different illnesses in humans and animals. In particular, community-associated methicillin-resistant S. aureus (CA-MRSA) strains of the pandemic USA300 clone have the capacity to cause lethal human necrotizing pneumonia, but the molecular basis for the enhanced virulence remains unclear. Bacterial superantigens (SAg) stimulate T-cell hyper-activation resulting in severe systemic illnesses such as toxic shock syndrome (TSS). However, all S. aureus SAgs identified to date are encoded by mobile genetic elements found only in a proportion of clinical isolates. Here, we report the discovery of a unique core genome-encoded SAg (SElX) which was acquired by an ancestor of the S. aureus species and which has undergone genetic and functional diversification in pathogenic clones infecting humans and animals. Importantly, we report that SElX made by pandemic USA300 contributes to lethality in a rabbit model of human necrotizing pneumonia revealing a novel virulence determinant of severe CA-MRSA infection.
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Affiliation(s)
- Gillian J. Wilson
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Keun Seok Seo
- Department of Basic Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Robyn A. Cartwright
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Timothy Connelley
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Olivia N. Chuang-Smith
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Joseph A. Merriman
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Caitriona M. Guinane
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joo Youn Park
- Department of Basic Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Gregory A. Bohach
- Department of Basic Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
- Department of Biochemistry and Molecular Biology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Patrick M. Schlievert
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - W. Ivan Morrison
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - J. Ross Fitzgerald
- The Roslin Institute and Centre for Infectious Diseases, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
- * E-mail:
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Goldfinch N, Reinink P, Connelley T, Koets A, Morrison I, Van Rhijn I. Conservation of mucosal associated invariant T (MAIT) cells and the MR1 restriction element in ruminants, and abundance of MAIT cells in spleen. Vet Res 2010; 41:62. [PMID: 20507818 PMCID: PMC2896809 DOI: 10.1051/vetres/2010034] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 05/27/2010] [Indexed: 01/25/2023] Open
Abstract
MHC-related protein 1 (MR1) is a highly conserved MHC class I-like molecule. Human and murine mucosal associated invariant T (MAIT) cells are restricted by MR1 and express an invariant T cell receptor. Even though MR1 protein expression on the cell surface has not been demonstrated in vivo or ex vivo, it is assumed that MR1 presents a bacterial antigen from the intestinal lumen to MAIT cells because MAIT cells are present in the lamina propria and their expansion is dependent on the presence of intestinal micro flora. The existence of bovine MAIT cells and MR1 has been demonstrated recently although ovine MAIT cells and MR1 have not yet been described. We cloned bovine and ovine MR1 transcripts, including splice variants, and identified an anti human MR1 antibody that recognizes cells transfected with the bovine homolog. Using this antibody, no MR1 staining was detected using cells freshly isolated from blood, thymus, spleen, colon, ileum, and lymph node. MAIT cells are known to be enriched in the CD4/CD8 double negative peripheral blood T cell population, but their relative abundance in different tissues is not known. Comparison of the amount of MAIT cell-specific TCR transcript to the amount of constant α chain transcript revealed that numbers of MAIT cells are low in neonates and increase by 3-weeks of age. In 3-month old animals, MAIT cells are abundant in spleen and less so in ileum, peripheral blood, lymph node, colon, and thymus.
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Affiliation(s)
- Nick Goldfinch
- Infection and Immunity Division, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, Midlothian EH25 9RG, United Kingdom
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Dobromylskyj MJ, Connelley T, Hammond JA, Ellis SA. Cattle Ly49 is polymorphic. Immunogenetics 2009; 61:789-95. [DOI: 10.1007/s00251-009-0406-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 10/23/2009] [Indexed: 11/29/2022]
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MacHugh ND, Connelley T, Graham SP, Pelle R, Formisano P, Taracha EL, Ellis SA, McKeever DJ, Burrells A, Morrison WI. CD8+ T-cell responses to Theileria parva are preferentially directed to a single dominant antigen: Implications for parasite strain-specific immunity. Eur J Immunol 2009; 39:2459-69. [PMID: 19670382 PMCID: PMC3149124 DOI: 10.1002/eji.200939227] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although immunodominance of CD8+ T-cell responses is a well-recognised feature of viral infections, its role in responses to more antigenically complex pathogens is less clear. In previous studies we have observed that CD8+ T-cell responses to Theileria parva exhibit different patterns of parasite strain specificity in cattle of different MHC genotypes. In the current study, we demonstrated that animals homozygous for the A10 and A18 MHC haplotypes have detectable responses to only one of 5 T. parva antigens. Over 60% of the responding T cells from the A18+ and A10+ animals recognised defined epitopes in the Tp1 and Tp2 antigens, respectively. Comparison of T-cell receptor β chain expression profiles of CD8+ T-cell lines and CD8+ T cells harvested ex vivo confirmed that the composition of the T-cell lines was representative of the in vivo memory CD8+ T-cell populations. Analysis of the Tp1 and Tp2 antigens revealed sequence polymorphism, which was reflected by differential recognition by T-cell lines. In conclusion, we have demonstrated a profound immunodominance in the CD8+ T-cell response to T. parva, which we propose is a major determinant of the parasite strain specificity of the response and hence immune protection.
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Affiliation(s)
- Niall D MacHugh
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK
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Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FSL, Lau LPL, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CTA, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JGR, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJM, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo ARR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IKFDM, de Oliveira CJF, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JCM, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MFG, Olsaker I, Pant SD, Panzitta F, Pastor RCP, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BPVL, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009; 324:522-8. [PMID: 19390049 DOI: 10.1126/science.1169588] [Citation(s) in RCA: 806] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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Connelley T, Aerts J, Law A, Morrison WI. Genomic analysis reveals extensive gene duplication within the bovine TRB locus. BMC Genomics 2009; 10:192. [PMID: 19393068 PMCID: PMC2685407 DOI: 10.1186/1471-2164-10-192] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 04/24/2009] [Indexed: 12/18/2022] Open
Abstract
Background Diverse TR and IG repertoires are generated by V(D)J somatic recombination. Genomic studies have been pivotal in cataloguing the V, D, J and C genes present in the various TR/IG loci and describing how duplication events have expanded the number of these genes. Such studies have also provided insights into the evolution of these loci and the complex mechanisms that regulate TR/IG expression. In this study we analyze the sequence of the third bovine genome assembly to characterize the germline repertoire of bovine TRB genes and compare the organization, evolution and regulatory structure of the bovine TRB locus with that of humans and mice. Results The TRB locus in the third bovine genome assembly is distributed over 5 scaffolds, extending to ~730 Kb. The available sequence contains 134 TRBV genes, assigned to 24 subgroups, and 3 clusters of DJC genes, each comprising a single TRBD gene, 5–7 TRBJ genes and a single TRBC gene. Seventy-nine of the TRBV genes are predicted to be functional. Comparison with the human and murine TRB loci shows that the gene order, as well as the sequences of non-coding elements that regulate TRB expression, are highly conserved in the bovine. Dot-plot analyses demonstrate that expansion of the genomic TRBV repertoire has occurred via a complex and extensive series of duplications, predominantly involving DNA blocks containing multiple genes. These duplication events have resulted in massive expansion of several TRBV subgroups, most notably TRBV6, 9 and 21 which contain 40, 35 and 16 members respectively. Similarly, duplication has lead to the generation of a third DJC cluster. Analyses of cDNA data confirms the diversity of the TRBV genes and, in addition, identifies a substantial number of TRBV genes, predominantly from the larger subgroups, which are still absent from the genome assembly. The observed gene duplication within the bovine TRB locus has created a repertoire of phylogenetically diverse functional TRBV genes, which is substantially larger than that described for humans and mice. Conclusion The analyses completed in this study reveal that, although the gene content and organization of the bovine TRB locus are broadly similar to that of humans and mice, multiple duplication events have led to a marked expansion in the number of TRB genes. Similar expansions in other ruminant TR loci suggest strong evolutionary pressures in this lineage have selected for the development of enlarged sets of TR genes that can contribute to diverse TR repertoires.
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Affiliation(s)
- Timothy Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK.
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Connelley T, Aerts J, Law A, Morrison W. Genomic and cDNA analysis of the bovine TCRβ gene repertoire. Vet Immunol Immunopathol 2009. [DOI: 10.1016/j.vetimm.2008.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Connelley T, Burrells A, Machugh ND, Morrison WI. Use of a Pan-Vbeta primer permits the amplification and sequencing of TCRbeta chains expressed by bovine T-cell clones following a single semi-nested PCR reaction. Vet Immunol Immunopathol 2008; 126:156-62. [PMID: 18635266 DOI: 10.1016/j.vetimm.2008.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/23/2008] [Accepted: 05/30/2008] [Indexed: 11/17/2022]
Abstract
We report in this study the design and validation of a Pan-Vbeta primer that in combination with Cbeta-specific primers enables the amplification, in a single semi-nested PCR, of TCRbeta chains expressed by bovine T-cell clones irrespective of the expressed Vbeta sequence. Using the Pan-Vbeta primer we examined the TCRbeta chains expressed by 16 Theileria parva-specific clones that had not been previously analysed. TCRbeta chain sequence was obtained from 15 of the clones following direct sequencing of the PCR product, whilst the other clone appeared to express 2 different TCRbeta chains which were characterised following sub-cloning of the PCR product. We have also successfully used the Pan-Vbeta primer to amplify the TCRbeta chains expressed by 19 T-cell clones, on which previous analysis using Vbeta-subfamily-specific primers had failed to do. Sequencing of these TCRbeta chains has identified members of 2 novel bovine Vbeta subfamilies-Vbeta5 and VbetaX. This method offers a simple and rapid method of analyzing the TCRbeta chains of bovine T-cell clones that has many potential applications in the investigation of bovine T-cell responses.
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Affiliation(s)
- T Connelley
- Division of Veterinary Clinical Studies, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK.
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Connelley T, MacHugh ND, Burrells A, Morrison WI. Dissection of the clonal composition of bovine alphabeta T cell responses using T cell receptor Vbeta subfamily-specific PCR and heteroduplex analysis. J Immunol Methods 2008; 335:28-40. [PMID: 18436232 DOI: 10.1016/j.jim.2008.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 02/14/2008] [Accepted: 02/22/2008] [Indexed: 11/26/2022]
Abstract
Although techniques that permit analysis of the clonal composition of T cell populations have been used extensively to provide a better understanding of the mechanisms that influence efficacy of T cell responses in humans and mice, such methods are lacking for other animal species. In this paper we report the establishment and validation of a panel of Vbeta subfamily-specific semi-nested PCR assays, and a CDR3beta heteroduplex technique for analysing the clonal diversity of bovine alphabeta T cell responses. Development of these methods was based on available sequence data for 48 functional Vbeta genes classified within 17 subfamilies. These techniques were used to determine the clonal composition of parasite-reactive CD8(+) T cells obtained from two animals immunised with the protozoan parasite Theileria parva. Analyses of uncloned T cell lines as well as large panels of cloned T cells derived from each of these lines confirmed the specificity and sensitivity of the assays. Specific PCR products were obtained from 96% of the T cell clones examined, indicating that the currently identified Vbeta genes represent most of the functional Vbeta subfamilies in cattle. Heteroduplex analyses, coupled with sequencing of PCR products, identified over 20 clonal expansions within each of the T cell lines, distributed over a large number of Vbeta subfamilies, although a limited number of clonotypes numerically dominated the response in both animals. The development and validation of these methods provides for the first time a generic set of molecular tools that can be used to perform detailed analysis of the TCR diversity and clonal composition of bovine T cell responses.
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Affiliation(s)
- T Connelley
- Division of Veterinary Clinical Studies, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, UK.
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Houston EF, Connelley T, Parsons K, MacHugh ND, Morrison WI. Analysis of T-cell receptor BV gene sequences in cattle reveals extensive duplication within the BV9 and BV20 subgroups. Immunogenetics 2005; 57:674-81. [PMID: 16187058 DOI: 10.1007/s00251-005-0040-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 08/08/2005] [Indexed: 10/25/2022]
Abstract
We investigated the repertoire of functional T-cell receptor beta-chain variable genes (TRBV genes) in cattle by analysing the nucleotide sequences and predicted amino acid sequences of a set of cDNA clones isolated from lymph node T cells. Thirty-nine distinct TRBV sequences were identified, bringing the total number of recognised bovine TRBV gene segments to more than 40. Sixteen TRBV subgroups were defined based on their sequence homology to each other and to human TRBV genes. All of the main phylogenetic lineages of BV gene subgroups described in humans and mice were represented. Eight of the subgroups were found to contain more than one member. The most striking feature of the results was the large number of sequences (more than half of the sequenced clones) in the BV9 and BV20 subgroups, which were found to contain 12 and 8 distinct sequences, respectively. In contrast, the corresponding human TRBV subfamilies contain a single member. The results indicate that, as in humans, there has been extensive gene duplication within the TRBV locus during evolution. However, duplication of different BV subgroups in cattle has resulted in a TRBV gene repertoire distinct from that found in other species.
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Affiliation(s)
- E F Houston
- Institute for Animal Health, Compton, Newbury, Berkshire, RG20 7NN, UK
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