1
|
Wynn EL, Browne AS, Clawson ML. Diversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle. Genome 2024; 67:204-209. [PMID: 38330385 DOI: 10.1139/gen-2023-0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle (n = 202) and bison (n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.
Collapse
Affiliation(s)
- Emily L Wynn
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS) US Meat Animal Research Center, Clay Center, NE, USA
| | - A Springer Browne
- USDA, Animal and Plant Health Inspection Service (APHIS), Center for Epidemiology and Animal Health, Fort Collins, CO, USA
| | - Michael L Clawson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS) US Meat Animal Research Center, Clay Center, NE, USA
| |
Collapse
|
2
|
Youk S, Kang M, Ahn B, Koo Y, Park C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes (Basel) 2023; 15:7. [PMID: 38275589 PMCID: PMC10815642 DOI: 10.3390/genes15010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.
Collapse
Affiliation(s)
- Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Yangmo Koo
- Genetic & Breeding Department, Korea Animal Improvement Association, Seocho, Seoul 06668, Republic of Korea;
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| |
Collapse
|
3
|
Uncovering novel MHC alleles from RNA-Seq data: expanding the spectrum of MHC class I alleles in sheep. BMC Genom Data 2023; 24:1. [PMID: 36597020 PMCID: PMC9809118 DOI: 10.1186/s12863-022-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I glycoproteins present selected peptides or antigens to CD8 + T cells that control the cytotoxic immune response. The MHC class I genes are among the most polymorphic loci in the vertebrate genome, with more than twenty thousand alleles known in humans. In sheep, only a very small number of alleles have been described to date, making the development of genotyping systems or functional studies difficult. A cost-effective way to identify new alleles could be to use already available RNA-Seq data from sheep. Current strategies for aligning RNA-Seq reads against annotated genome sequences or transcriptomes fail to detect the majority of class I alleles. Here, I combine the alignment of RNA-Seq reads against a specific reference database with de novo assembly to identify alleles. The method allows the comprehensive discovery of novel MHC class I alleles from RNA-Seq data (DinoMfRS). RESULTS Using DinoMfRS, virtually all expressed MHC class I alleles could be determined. From 18 animals 75 MHC class I alleles were identified, of which 69 were novel. In addition, it was shown that DinoMfRS can be used to improve the annotation of MHC genes in the sheep genome sequence. CONCLUSIONS DinoMfRS allows for the first time the annotation of unknown, more divergent MHC alleles from RNA-Seq data. Successful application to RNA-Seq data from 16 animals has approximately doubled the number of known alleles in sheep. By using existing data, alleles can now be determined very inexpensively for populations that have not been well studied. In addition, MHC expression studies or evolutionary studies, for example, can be greatly improved in this way, and the method should be applicable to a broader spectrum of other multigene families or highly polymorphic genes.
Collapse
|
4
|
Goh S, Kolakowski J, Holder A, Pfuhl M, Ngugi D, Ballingall K, Tombacz K, Werling D. Development of a Potential Yeast-Based Vaccine Platform for Theileria parva Infection in Cattle. Front Immunol 2021; 12:674484. [PMID: 34305904 PMCID: PMC8297500 DOI: 10.3389/fimmu.2021.674484] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/10/2021] [Indexed: 01/05/2023] Open
Abstract
East Coast Fever (ECF), caused by the tick-borne apicomplexan parasite Theileria parva, remains one of the most important livestock diseases in sub-Saharan Africa with more than 1 million cattle dying from infection every year. Disease prevention relies on the so-called "Infection and Treatment Method" (ITM), which is costly, complex, laborious, difficult to standardise on a commercial scale and results in a parasite strain-specific, MHC class I-restricted cytotoxic T cell response. We therefore attempted to develop a safe, affordable, stable, orally applicable and potent subunit vaccine for ECF using five different T. parva schizont antigens (Tp1, Tp2, Tp9, Tp10 and N36) and Saccharomyces cerevisiae as an expression platform. Full-length Tp2 and Tp9 as well as fragments of Tp1 were successfully expressed on the surface of S. cerevisiae. In vitro analyses highlighted that recombinant yeast expressing Tp2 can elicit IFNγ responses using PBMCs from ITM-immunized calves, while Tp2 and Tp9 induced IFNγ responses from enriched bovine CD8+ T cells. A subsequent in vivo study showed that oral administration of heat-inactivated, freeze-dried yeast stably expressing Tp2 increased total murine serum IgG over time, but more importantly, induced Tp2-specific serum IgG antibodies in individual mice compared to the control group. While these results will require subsequent experiments to verify induction of protection in neonatal calves, our data indicates that oral application of yeast expressing Theileria antigens could provide an affordable and easy vaccination platform for sub-Saharan Africa. Evaluation of antigen-specific cellular immune responses, especially cytotoxic CD8+ T cell immunity in cattle will further contribute to the development of a yeast-based vaccine for ECF.
Collapse
Affiliation(s)
- Shan Goh
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Jeannine Kolakowski
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Mark Pfuhl
- Faculty of Life Science and Medicine, King's College London, London, United Kingdom
| | - Daniel Ngugi
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Kata Tombacz
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| |
Collapse
|
5
|
Oliveira HR, Lourenco DAL, Masuda Y, Misztal I, Tsuruta S, Jamrozik J, Brito LF, Silva FF, Cant JP, Schenkel FS. Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle. J Dairy Sci 2019; 102:9995-10011. [PMID: 31477296 DOI: 10.3168/jds.2019-16821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/08/2019] [Indexed: 11/19/2022]
Abstract
Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression.
Collapse
Affiliation(s)
- H R Oliveira
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - Y Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - J Jamrozik
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - L F Brito
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F F Silva
- Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - J P Cant
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
6
|
The influence of BoLA-DRB3 alleles on incidence of clinical mastitis, cystic ovary disease and milk traits in Holstein Friesian cattle. Mol Biol Rep 2018; 45:917-923. [DOI: 10.1007/s11033-018-4238-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/04/2018] [Indexed: 11/25/2022]
|
7
|
Ballingall KT, Lantier I, Todd H, Lantier F, Rocchi M. Structural and functional diversity arising from intra- and inter-haplotype combinations of duplicated DQA and B loci within the ovine MHC. Immunogenetics 2017; 70:257-269. [PMID: 28889256 DOI: 10.1007/s00251-017-1029-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/03/2017] [Indexed: 11/27/2022]
Abstract
In sheep, the A and B loci encoding the α and β chains of the classical class II MHC molecules are DRA and DRB and DQA and DQB. Previous analyses described the duplication of the DQA and DQB genes. The majority of haplotypes include DQA1 and DQA2 loci, however, in a number of haplotypes, DQA1 appears absent and these haplotypes have been described as DQA1 null. In these haplotypes, the DQA2 locus is found in combination with a second locus which appeared more closely related to DQA2 than DQA1, hence the description of this locus as DQA2-like. Here we combine our previous analysis of the DQA transcripts with an analysis of the associated DQB transcripts in ten haplotypes from MHC homozygous animals. This allows the potential for surface expression of different haplotype combinations of DQA and B genes and the functional significance of DQA2-like and its predicted DQB partner to be determined. Atypical DQB transcripts (DQB2-like) were identified in haplotypes classified as DQA1-null and conserved DQB2-like orthologues were identified in other Bovidae indicating trans-species conservation of the allelic lineage. Functional combinations detected by co-transfection of DQ1, DQ2 and DQ2-like genes demonstrates the potential for a wide range of DQ molecules derived from both intra- and inter-haplotype as well as inter-locus combinations. We provide evidence that DQA2-like and B2-like genes form an evolutionary conserved pair which generates structurally distinct class II molecules that are likely to present a distinct range of peptides to CD4+ T cells.
Collapse
Affiliation(s)
- Keith T Ballingall
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK.
| | - Isabelle Lantier
- INRA-Centre Val de Loire, UMR 1282, Infectiologie et Santé Publique, 37380, Nouzilly, France
| | - Helen Todd
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK
| | - Frederic Lantier
- INRA-Centre Val de Loire, UMR 1282, Infectiologie et Santé Publique, 37380, Nouzilly, France
| | - Mara Rocchi
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, EH26 OPZ, Midlothian, UK
| |
Collapse
|
8
|
Hart J, MacHugh ND, Sheldrake T, Nielsen M, Morrison WI. Identification of immediate early gene products of bovine herpes virus 1 (BHV-1) as dominant antigens recognized by CD8 T cells in immune cattle. J Gen Virol 2017; 98:1843-1854. [PMID: 28671533 DOI: 10.1099/jgv.0.000823] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In common with other herpes viruses, bovine herpes virus 1 (BHV-1) induces strong virus-specific CD8 T-cell responses. However, there is a paucity of information on the antigenic specificity of the responding T-cells. The development of a system to generate virus-specific CD8 T-cell lines from BHV-1-immune cattle, employing Theileria-transformed cell lines for antigen presentation, has enabled us to address this issue. Use of this system allowed the study to screen for CD8 T-cell antigens that are efficiently presented on the surface of virus-infected cells. Screening of a panel of 16 candidate viral gene products with CD8 T-cell lines from 3 BHV-1-immune cattle of defined MHC genotypes identified 4 antigens, including 3 immediate early (IE) gene products (ICP4, ICP22 and Circ) and a tegument protein (UL49). Identification of the MHC restriction specificities revealed that the antigens were presented by two or three class I MHC alleles in each animal. Six CD8 T-cell epitopes were identified in the three IE proteins by screening of synthetic peptides. Use of an algorithm (NetMHCpan) that predicts the peptide-binding characteristics of restricting MHC alleles confirmed and, in some cases refined, the identity of the epitopes. Analyses of the epitope specificity of the CD8 T-cell lines showed that a large component of the response is directed against these IE epitopes. The results indicate that these IE gene products are dominant targets of the CD8 T-cell response in BHV-I-immune cattle and hence are prime-candidate antigens for the generation of a subunit vaccine.
Collapse
Affiliation(s)
- Jane Hart
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Niall D MacHugh
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Tara Sheldrake
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Morten Nielsen
- Department of Bio and Health Informatics, Centre for Biological Science Sequence Analysis, The Technical University, Lyngby, Denmark
| | - W Ivan Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Biotechnological Research Institute, National University of San Martin, San Martin, Buenos Aires, Argentina
| |
Collapse
|
9
|
Sørensen MR, Ilsøe M, Strube ML, Bishop R, Erbs G, Hartmann SB, Jungersen G. Sequence-Based Genotyping of Expressed Swine Leukocyte Antigen Class I Alleles by Next-Generation Sequencing Reveal Novel Swine Leukocyte Antigen Class I Haplotypes and Alleles in Belgian, Danish, and Kenyan Fattening Pigs and Göttingen Minipigs. Front Immunol 2017; 8:701. [PMID: 28670315 PMCID: PMC5472656 DOI: 10.3389/fimmu.2017.00701] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/30/2017] [Indexed: 11/13/2022] Open
Abstract
The need for typing of the swine leukocyte antigen (SLA) is increasing with the expanded use of pigs as models for human diseases and organ-transplantation experiments, their use in infection studies, and for design of veterinary vaccines. Knowledge of SLA sequences is furthermore a prerequisite for the prediction of epitope binding in pigs. The low number of known SLA class I alleles and the limited knowledge of their prevalence in different pig breeds emphasizes the need for efficient SLA typing methods. This study utilizes an SLA class I-typing method based on next-generation sequencing of barcoded PCR amplicons. The amplicons were generated with universal primers and predicted to resolve 68-88% of all known SLA class I alleles dependent on amplicon size. We analyzed the SLA profiles of 72 pigs from four different pig populations; Göttingen minipigs and Belgian, Kenyan, and Danish fattening pigs. We identified 67 alleles, nine previously described haplotypes and 15 novel haplotypes. The highest variation in SLA class I profiles was observed in the Danish pigs and the lowest among the Göttingen minipig population, which also have the highest percentage of homozygote individuals. Highlighting the fact that there are still numerous unknown SLA class I alleles to be discovered, a total of 12 novel SLA class I alleles were identified. Overall, we present new information about known and novel alleles and haplotypes and their prevalence in the tested pig populations.
Collapse
Affiliation(s)
| | - Mette Ilsøe
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Lenz Strube
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | - Richard Bishop
- International Livestock Research Institute, Nairobi, Kenya
| | - Gitte Erbs
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Gregers Jungersen
- National Veterinary Institute, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
10
|
Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TPL, Medrano JF, Hammond JA. The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation. Immunogenetics 2017; 69:255-269. [PMID: 28180967 PMCID: PMC5350243 DOI: 10.1007/s00251-017-0973-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/25/2017] [Indexed: 11/27/2022]
Abstract
Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is in part created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high-quality draft genome assemblies for cattle and goat; re-annotated sheep, pig, and horse genome assemblies; and the published human, rat, and mouse lemur NKC. The major NKC genes are largely in the equivalent positions in all eight species, with significant independent expansions and deletions between species, allowing us to propose a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ, and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between the NKC genes concentrated in the predicted extracellular ligand-binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting that this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination.
Collapse
Affiliation(s)
- John C Schwartz
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Mark S Gibson
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1150-082, Lisbon, Portugal
| | - Dorothea Heimeier
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | | | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, 95616, USA
| | - John A Hammond
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
| |
Collapse
|
11
|
Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations using next-generation sequencing. Immunogenetics 2016; 68:765-781. [PMID: 27516207 PMCID: PMC5056950 DOI: 10.1007/s00251-016-0945-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/19/2016] [Indexed: 12/12/2022]
Abstract
The major histocompatibility complex (MHC) region contains many genes that are key regulators of both innate and adaptive immunity including the polymorphic MHCI and MHCII genes. Consequently, the characterisation of the repertoire of MHC genes is critical to understanding the variation that determines the nature of immune responses. Our current knowledge of the bovine MHCI repertoire is limited with only the Holstein-Friesian breed having been studied in any depth. Traditional methods of MHCI genotyping are of low resolution and laborious and this has been a major impediment to a more comprehensive analysis of the MHCI repertoire of other cattle breeds. Next-generation sequencing (NGS) technologies have been used to enable high throughput and much higher resolution MHCI typing in a number of species. In this study we have developed a MiSeq platform approach and requisite bioinformatics pipeline to facilitate typing of bovine MHCI repertoires. The method was validated initially on a cohort of Holstein-Friesian animals and then demonstrated to enable characterisation of MHCI repertoires in African cattle breeds, for which there was limited or no available data. During the course of these studies we identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire.
Collapse
|
12
|
Parasar P, Wilhelm A, Rutigliano HM, Thomas AJ, Teng L, Shi B, Davis WC, Suarez CE, New DD, White KL, Davies CJ. Expression of bovine non-classical major histocompatibility complex class I proteins in mouse P815 and human K562 cells. Res Vet Sci 2016; 107:161-170. [PMID: 27473990 DOI: 10.1016/j.rvsc.2016.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/20/2016] [Accepted: 06/06/2016] [Indexed: 11/16/2022]
Abstract
Major histocompatibility complex class I (MHC-I) proteins can be expressed as cell surface or secreted proteins. To investigate whether bovine non-classical MHC-I proteins are expressed as cell surface or secreted proteins, and to assess the reactivity pattern of monoclonal antibodies with non-classical MHC-I isoforms, we expressed the MHC proteins in murine P815 and human K562 (MHC-I deficient) cells. Following antibiotic selection, stably transfected cell lines were stained with H1A or W6/32 antibodies to detect expression of the MHC-I proteins by flow cytometry. Two non-classical proteins (BoLA-NC1*00501 and BoLA-NC3*00101) were expressed on the cell surface in both cell lines. Surprisingly, the BoLA-NC4*00201 protein was expressed on the cell membrane of human K562 but not mouse P815 cells. Two non-classical proteins (BoLA-NC1*00401, which lacks a transmembrane domain, and BoLA-NC2*00102) did not exhibit cell surface expression. Nevertheless, Western blot analyses demonstrated expression of the MHC-I heavy chain in all transfected cell lines. Ammonium-sulfate precipitation of proteins from culture supernatants showed that BoLA-NC1*00401 was secreted and that all surface expressed proteins where shed from the cell membrane by the transfected cells. Interestingly, the surface expressed MHC-I proteins were present in culture supernatants at a much higher concentration than BoLA-NC1*00401. This comprehensive study shows that bovine non-classical MHC-I proteins BoLA-NC1*00501, BoLA-NC3*00101, and BoLA-NC4*00201 are expressed as surface isoforms with the latter reaching the cell membrane only in K562 cells. Furthermore, it demonstrated that BoLA-NC1*00401 is a secreted isoform and that significant quantities of membrane associated MHC-I proteins can be shed from the cell membrane.
Collapse
Affiliation(s)
- Parveen Parasar
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Amanda Wilhelm
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Heloisa M Rutigliano
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Lihong Teng
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Bi Shi
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - William C Davis
- Department of Veterinary Microbiology and Pathology, P.O. Box 647040, Washington State University, Pullman, WA, USA
| | - Carlos E Suarez
- USDA-ARS Animal Disease Research Unit, P.O. Box 646630, Washington State University, Pullman, WA, USA
| | - Daniel D New
- Department of Veterinary Microbiology and Pathology, P.O. Box 647040, Washington State University, Pullman, WA, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, 4815 Old Main Hill, Utah State University, Logan, UT, USA; School of Veterinary Medicine, 4815 Old Main Hill, Utah State University, Logan, UT, USA; Center for Integrated BioSystems, 4700 Old Main Hill, Utah State University, Logan, UT, USA.
| |
Collapse
|
13
|
Demasius W, Weikard R, Hadlich F, Buitkamp J, Kühn C. A novel RNAseq-assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease. BMC Genomics 2016; 17:365. [PMID: 27188848 PMCID: PMC4869273 DOI: 10.1186/s12864-016-2688-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/30/2016] [Indexed: 12/02/2022] Open
Abstract
Background MHC class I genotyping is essential for a wide range of biomedical, immunological and biodiversity applications. Whereas in human a comprehensive MHC class I allele catalogue is available, respective data in non-model species is scarce in spite of decades of research. Results Taking advantage of the new high-throughput RNA sequencing technology (RNAseq), we developed a novel RNAseq-assisted method (RAMHCIT) for MHC class I typing at nucleotide level. RAMHCIT is performed on white blood cells, which highly express MHC class I molecules enabling reliable discovery of new alleles and discrimination of closely related alleles due to the high coverage of alleles with reads. RAMHCIT is more comprehensive than previous methods, because no targeted PCR pre-amplification of MHC loci is necessary, which avoids preselection of alleles as usually encountered, when amplification with MHC class I primers is performed prior to sequencing. In addition to allele identification, RAMHCIT also enables quantification of MHC class I expression at allele level, which was remarkably consistent across individuals. Conclusions Successful application of RAMHCIT is demonstrated on a data set from cattle with different phenotype regarding a lethal, vaccination-induced alloimmune disease (bovine neonatal pancytopenia), for which MHC class I alleles had been postulated as causal agents. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2688-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wiebke Demasius
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Johannes Buitkamp
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586, Grub, Germany
| | - Christa Kühn
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
| |
Collapse
|
14
|
Sequence diversity between class I MHC loci of African native and introduced Bos taurus cattle in Theileria parva endemic regions: in silico peptide binding prediction identifies distinct functional clusters. Immunogenetics 2016; 68:339-52. [DOI: 10.1007/s00251-016-0902-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022]
|
15
|
Siva Subramaniam N, Morgan EF, Wetherall JD, Stear MJ, Groth DM. A comprehensive mapping of the structure and gene organisation in the sheep MHC class I region. BMC Genomics 2015; 16:810. [PMID: 26480943 PMCID: PMC4613773 DOI: 10.1186/s12864-015-1992-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
Background The major histocompatibility complex (MHC) is a chromosomal region that regulates immune responsiveness in vertebrates. This region is one of the most important for disease resistance because it has been associated with resistance or susceptibility to a wide variety of diseases and because the MHC often accounts for more of the variance than other loci. Selective breeding for disease resistance is becoming increasingly common in livestock industries, and it is important to determine how this will influence MHC polymorphism and resistance to diseases that are not targeted for selection. However, in sheep the order and sequence of the protein coding genes is controversial. Yet this information is needed to determine precisely how the MHC influences resistance and susceptibility to disease. Methods CHORI bacterial artificial chromosomes (BACs) known to contain sequences from the sheep MHC class I region were sub-cloned, and the clones partially sequenced. The resulting sequences were analysed and re-assembled to identify gene content and organisation within each BAC. The low resolution MHC class I physical map was then compared to the cattle reference genome, the Chinese Merino sheep MHC map published by Gao, et al. (2010) and the recently available sheep reference genome. Results Immune related class I genes are clustered into 3 blocks; beta, kappa and a novel block not previously identified in other organisms. The revised map is more similar to Bovidae maps than the previous sheep maps and also includes several genes previously not annotated in the Chinese Merino BAC assembly and others not currently annotated in the sheep reference chromosome 20. In particular, the organisation of nonclassical MHC class I genes is similar to that present in the cattle MHC. Sequence analysis and prediction of amino acid sequences of MHC class I classical and nonclassical genes was performed and it was observed that the map contained one classical and eight nonclassical genes together with three possible pseudogenes. Conclusions The comprehensive physical map of the sheep MHC class I region enhances our understanding of the genetic architecture of the class I MHC region in sheep and will facilitate future studies of MHC function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1992-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- N Siva Subramaniam
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - E F Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - J D Wetherall
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| | - M J Stear
- Department of Animal Production and Public Health, Faculty of Veterinary Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK. .,Institute of Biodiversity, Animal Health and Comparative Medicine, Garscube Estate, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, UK.
| | - D M Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, 6845, WA, Australia.
| |
Collapse
|
16
|
Corripio-Miyar Y, Hope J, McInnes CJ, Wattegedera SR, Jensen K, Pang Y, Entrican G, Glass EJ. Phenotypic and functional analysis of monocyte populations in cattle peripheral blood identifies a subset with high endocytic and allogeneic T-cell stimulatory capacity. Vet Res 2015; 46:112. [PMID: 26407849 PMCID: PMC4582714 DOI: 10.1186/s13567-015-0246-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/17/2015] [Indexed: 12/22/2022] Open
Abstract
Circulating monocytes in several mammalian species can be subdivided into functionally distinct subpopulations based on differential expression of surface molecules. We confirm that bovine monocytes express CD172a and MHC class II with two distinct populations of CD14+CD16low/-CD163+ and CD14−CD16++CD163low- cells, and a more diffuse population of CD14+CD16+CD163+ cells. In contrast, ovine monocytes consisted of only a major CD14+CD16+ subset and a very low percentage of CD14−CD16++cells. The bovine subsets expressed similar levels of CD80, CD40 and CD11c molecules and mRNA encoding CD115. However, further mRNA analyses revealed that the CD14−CD16++ monocytes were CX3CR1highCCR2low whereas the major CD14+ subset was CX3CR1lowCCR2high. The former were positive for CD1b and had lower levels of CD11b and CD86 than the CD14+ monocytes. The more diffuse CD14+CD16+ population generally expressed intermediate levels of these molecules. All three populations responded to stimulation with phenol-extracted lipopolysaccharide (LPS) by producing interleukin (IL)-1β, with the CD16++ subset expressing higher levels of IL-12 and lower levels of IL-10. The CD14−CD16++ cells were more endocytic and induced greater allogeneic T cell responses compared to the other monocyte populations. Taken together the data show both similarities and differences between the classical, intermediate and non-classical definitions of monocytes as described for other mammalian species, with additional potential subpopulations. Further functional analyses of these monocyte populations may help explain inter-animal and inter-species variations to infection, inflammation and vaccination in ruminant livestock.
Collapse
Affiliation(s)
- Yolanda Corripio-Miyar
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Jayne Hope
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Colin J McInnes
- Current address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK.
| | - Sean R Wattegedera
- Current address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK.
| | - Kirsty Jensen
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Yvonne Pang
- Current address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK.
| | - Gary Entrican
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK. .,Current address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK.
| | - Elizabeth J Glass
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| |
Collapse
|
17
|
Schwartz JC, Hammond JA. The assembly and characterisation of two structurally distinct cattle MHC class I haplotypes point to the mechanisms driving diversity. Immunogenetics 2015; 67:539-44. [PMID: 26227296 PMCID: PMC4539362 DOI: 10.1007/s00251-015-0859-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/20/2015] [Indexed: 12/11/2022]
Abstract
In cattle, there are six classical MHC class I genes that are variably present between different haplotypes. Almost all known haplotypes contain between one and three genes, with an allele of Gene 2 present on the vast majority. However, very little is known about the sequence and therefore structure and evolutionary history of this genomic region. To address this, we have refined the MHC class I region in the Hereford cattle genome assembly and sequenced a complete A14 haplotype from a homozygous Holstein. Comparison of the two haplotypes revealed extensive variation within the MHC class Ia region, but not within the flanking regions, with each gene contained within a conserved 63- to 68-kb sequence block. This variable region appears to have undergone block gene duplication and likely deletion at regular breakpoints, suggestive of a site-specific mechanism. Phylogenetic analysis using complete gene sequences provided evidence of allelic diversification via gene conversion, with breakpoints between each of the extracellular domains that were associated with high guanine-cytosine (GC) content. Advancing our knowledge of cattle MHC class I evolution will help inform investigations of cattle genetic diversity and disease resistance.
Collapse
Affiliation(s)
- John C Schwartz
- Livestock Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | | |
Collapse
|
18
|
Allan AJ, Sanderson ND, Gubbins S, Ellis SA, Hammond JA. Cattle NK Cell Heterogeneity and the Influence of MHC Class I. THE JOURNAL OF IMMUNOLOGY 2015. [PMID: 26216890 PMCID: PMC4543905 DOI: 10.4049/jimmunol.1500227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Primate and rodent NK cells form highly heterogeneous lymphocyte populations owing to the differential expression of germline-encoded receptors. Many of these receptors are polymorphic and recognize equally polymorphic determinants of MHC class I. This diversity can lead to individuals carrying NK cells with different specificities. Cattle have an unusually diverse repertoire of NK cell receptor genes predicted to encode receptors that recognize MHC class I. To begin to examine whether this genetic diversity leads to a diverse NK cell population, we isolated peripheral NK cells from cattle with different MHC homozygous genotypes. Cytokine stimulation differentially influenced the transcription of five receptors at the cell population level. Using dilution cultures, we found that a further seven receptors were differentially transcribed, including five predicted to recognize MHC class I. Moreover, there was a statistically significant reduction in killer cell lectin-like receptor mRNA expression between cultures with different CD2 phenotypes and from animals with different MHC class I haplotypes. This finding confirms that cattle NK cells are a heterogeneous population and reveals that the receptors creating this diversity are influenced by the MHC. The importance of this heterogeneity will become clear as we learn more about the role of NK cells in cattle disease resistance and vaccination.
Collapse
Affiliation(s)
- Alasdair J Allan
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | | | - Simon Gubbins
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - Shirley A Ellis
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - John A Hammond
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| |
Collapse
|
19
|
Bell CR, MacHugh ND, Connelley TK, Degnan K, Morrison WI. Haematopoietic depletion in vaccine-induced neonatal pancytopenia depends on both the titre and specificity of alloantibody and levels of MHC I expression. Vaccine 2015; 33:3488-96. [PMID: 26055292 DOI: 10.1016/j.vaccine.2015.05.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/05/2015] [Accepted: 05/26/2015] [Indexed: 01/13/2023]
Abstract
Bovine Neonatal Pancytopenia (BNP) is a disease of calves characterised by haematopoietic depletion, mediated by ingestion of alloantibodies in colostrum. It has been linked epidemiologically to vaccination of the dams of affected calves with a particular vaccine (Pregsure) containing a novel adjuvant. Evidence suggests that BNP-alloantibodies are directed against MHC I molecules, induced by contaminant bovine cellular material from Madin-Darby Bovine Kidney (MDBK) cells used in the vaccine's production. We aimed to investigate the specificity of BNP-alloantibody for bovine MHC I alleles, particularly those expressed by MDBK cells, and whether depletion of particular cell types is due to differential MHC I expression levels. A complement-mediated cytotoxicity assay was used to assess functional serum alloantibody titres in BNP-dams, Pregsure-vaccinated dams with healthy calves, cows vaccinated with an alternative product and unvaccinated controls. Alloantibody specificity was investigated using transfected mouse lines expressing the individual MHC I alleles identified from MDBK cells and MHC I-defined bovine leukocyte lines. All BNP-dams and 50% of Pregsure-vaccinated cows were shown to have MDBK-MHC I specific alloantibodies, which cross-reacted to varying degrees with other MHC I genotypes. MHC I expression levels on different blood cell types, assessed by flow cytometry, were found to correlate with levels of alloantibody-mediated damage in vitro and in vivo. Alloantibody-killed bone marrow cells were shown to express higher levels of MHC I than undamaged cells. The results provide evidence that MHC I-specific alloantibodies play a dominant role in the pathogenesis of BNP. Haematopoietic depletion was shown to be dependent on the titre and specificity of alloantibody produced by individual cows and the density of surface MHC I expression by different cell types. Collectively, the results support the hypothesis that MHC I molecules originating from MDBK cells used in vaccine production, coupled with a powerful adjuvant, are responsible for the generation of pathogenic alloantibodies.
Collapse
Affiliation(s)
- Charlotte R Bell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Niall D MacHugh
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Timothy K Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Kathryn Degnan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - W Ivan Morrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| |
Collapse
|
20
|
Jolles AE, Beechler BR, Dolan BP. Beyond mice and men: environmental change, immunity and infections in wild ungulates. Parasite Immunol 2015; 37:255-66. [PMID: 25354672 PMCID: PMC4414670 DOI: 10.1111/pim.12153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023]
Abstract
In the face of rapid environmental change, anticipating shifts in microparasite and macroparasite dynamics, including emergence events, is an enormous challenge. We argue that immunological studies in natural populations are pivotal to meeting this challenge: many components of environmental change--shifts in biotic assemblages, altered climate patterns and reduced environmental predictability--may affect host immunity. We suggest that wild ungulates can serve as model systems aiding the discovery of immunological mechanisms that link environmental change with parasite transmission dynamics. Our review of eco-immunological studies in wild ungulates reveals progress in understanding how co-infections affect immunity and parasite transmission and how environmental and genetic factors interact to shape immunity. Changes in bioavailability of micronutrients have been linked to immunity and health in wild ungulates. Although physiological stress in response to environmental change has been assessed, downstream effects on immunity have not been studied. Moreover, the taxonomic range of ungulates studied is limited to bovids (bighorn sheep, Soay sheep, chamois, musk oxen, bison, African buffalo) and a few cervids (red deer, black-tailed deer). We discuss areas where future studies in ungulates could lead to significant contributions in understanding the patterns of immunity and infection in natural populations and across species.
Collapse
Affiliation(s)
- Anna E. Jolles
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331
| | - Brianna R. Beechler
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331
| | - Brian P. Dolan
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331
| |
Collapse
|
21
|
Demasius W, Weikard R, Kromik A, Wolf C, Müller K, Kühn C. Bovine neonatal pancytopenia (BNP): novel insights into the incidence, vaccination-associated epidemiological factors and a potential genetic predisposition for clinical and subclinical cases. Res Vet Sci 2014; 96:537-42. [PMID: 24746449 DOI: 10.1016/j.rvsc.2014.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 01/27/2014] [Accepted: 03/28/2014] [Indexed: 01/20/2023]
Abstract
Bovine neonatal pancytopenia (BNP) is a haemorrhagic disease of newborn calves elicited by colostrum from specific cows. Two studies have indicated that BNP-inducing colostrum might be associated with alloantibodies directed against MHC class I in response to vaccination with a distinct inactivated viral vaccine. However, the proportion of alloantibody-producing individuals by far exceeds the proportion of clinical BNP cases in the vaccinated population. This raises the question about the incidence of subclinical, unrecognised cases and also suggests further factors involved in BNP pathogenesis, e.g., genetic predisposition. Our results on neonatal calves from a closely monitored resource population confirmed the hypothesis of a genetic predisposition for clinical BNP and suggest that the predisposition is also involved in subclinical BNP-cases. No indication was obtained for a higher frequency of subclinical BNP-cases compared with clinical cases. Neither time point nor frequency of vaccination was a relevant factor for BNP in our resource population.
Collapse
Affiliation(s)
- W Demasius
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - R Weikard
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - A Kromik
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - C Wolf
- State Office for Agriculture, Food Safety and Fishery Mecklenburg-Western Pommerania (LALLF M-V), Thierfelderstraße 18, 18059 Rostock, Germany
| | - K Müller
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, Königsweg 65, 14163 Berlin, Germany
| | - C Kühn
- Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| |
Collapse
|
22
|
Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
Collapse
Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| |
Collapse
|
23
|
Oomen RA, Gillett RM, Kyle CJ. Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage. Mol Ecol Resour 2012; 13:103-16. [PMID: 23095905 DOI: 10.1111/1755-0998.12027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 12/23/2022]
Abstract
Characterization and population genetic analysis of multilocus genes, such as those found in the major histocompatibility complex (MHC) is challenging in nonmodel vertebrates. The traditional method of extensive cloning and Sanger sequencing is costly and time-intensive and indirect methods of assessment often underestimate total variation. Here, we explored the suitability of 454 pyrosequencing for characterizing multilocus genes for use in population genetic studies. We compared two sample tagging protocols and two bioinformatic procedures for 454 sequencing through characterization of a 185-bp fragment of MHC DRB exon 2 in wolverines (Gulo gulo) and further compared the results with those from cloning and Sanger sequencing. We found 10 putative DRB alleles in the 88 individuals screened with between two and four alleles per individual, suggesting amplification of a duplicated DRB gene. In addition to the putative alleles, all individuals possessed an easily identifiable pseudogene. In our system, sequence variants with a frequency below 6% in an individual sample were usually artefacts. However, we found that sample preparation and data processing procedures can greatly affect variant frequencies in addition to the complexity of the multilocus system. Therefore, we recommend determining a per-amplicon-variant frequency threshold for each unique system. The extremely deep coverage obtained in our study (approximately 5000×) coupled with the semi-quantitative nature of pyrosequencing enabled us to assign all putative alleles to the two DRB loci, which is generally not possible using traditional methods. Our method of obtaining locus-specific MHC genotypes will enhance population genetic analyses and studies on disease susceptibility in nonmodel wildlife species.
Collapse
Affiliation(s)
- Rebekah A Oomen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.
| | | | | |
Collapse
|
24
|
Babik W, Kawałko A, Wójcik JM, Radwan J. Low Major Histocompatibility Complex Class I (MHC I) Variation in the European Bison (Bison bonasus). J Hered 2012; 103:349-59. [DOI: 10.1093/jhered/ess005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
25
|
Baltian LR, Ripoli MV, Sanfilippo S, Takeshima SN, Aida Y, Giovambattista G. Association between BoLA-DRB3 and somatic cell count in Holstein cattle from Argentina. Mol Biol Rep 2012; 39:7215-20. [DOI: 10.1007/s11033-012-1526-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 01/24/2012] [Indexed: 11/27/2022]
|
26
|
Codner GF, Birch J, Hammond JA, Ellis SA. Constraints on haplotype structure and variable gene frequencies suggest a functional hierarchy within cattle MHC class I. Immunogenetics 2012; 64:435-45. [DOI: 10.1007/s00251-012-0612-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/13/2012] [Indexed: 12/11/2022]
|
27
|
Cattle MHC nomenclature: is it possible to assign sequences to discrete class I genes? Immunogenetics 2012; 64:475-80. [PMID: 22419150 DOI: 10.1007/s00251-012-0611-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/02/2012] [Indexed: 12/12/2022]
Abstract
The cattle major histocompatibility complex (MHC) region contains a variable number of classical class I genes encoding polymorphic molecules involved in antigen presentation. Six classical class I genes have been described, but assigning sequences to these genes has proved problematic. We propose a refinement of the existing nomenclature, which currently names the 97 known classical class I sequences in a single series. Phylogenetic analysis of the 3' portion of the coding region allows segregation of these into six groups; thus, we have prefixed existing names with the appropriate number. Although it is clear that some of these groups correspond to discrete genes, it is currently not possible to state definitively that all do. However, the main groupings are consistent, and in conjunction with other evidence, we feel it is now appropriate to rename the sequences accordingly. Segregation of sequences into groups in this way will facilitate ongoing research and future use of the cattle MHC section of the Immuno Polymorphism Database.
Collapse
|
28
|
Theileria annulata-transformed cell lines are efficient antigen-presenting cells for in vitro analysis of CD8 T cell responses to bovine herpesvirus-1. Vet Res 2011; 42:119. [PMID: 22182243 PMCID: PMC3284437 DOI: 10.1186/1297-9716-42-119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 12/19/2011] [Indexed: 02/06/2023] Open
Abstract
Continuously growing cell lines infected with the protozoan parasite Theileria annulata can readily be established by in vitro infection of leukocytes with the sporozoite stage of the parasite. The aim of the current study was to determine whether such transformed cell lines could be used as antigen presenting cells to analyse the antigenic specificity of bovine CD8 T cell responses to viral infections. Bovine herpes virus 1 (BHV-1), which is known to induce CD8 T cell responses, was used as a model. T. annulata- transformed cells were shown to express high levels of CD40 and CD80 and were susceptible to infection with BHV-1, vaccinia and canarypox viruses. The capacity of the cells to generate antigen-specific CD8 T cell lines was initially validated using a recombinant canarypox virus expressing a defined immunodominant T. parva antigen (Tp1). Autologous T. annulata-transformed cells infected with BHV-1 were then used successfully to generate specific CD8 T cell lines and clones from memory T cell populations of BHV-1-immune animals. These lines were BHV-1-specific and class I MHC-restricted. In contrast to previous studies, which reported recognition of the glycoproteins gB and gD, the CD8 T cell lines generated in this study did not recognise these glycoproteins. Given the ease with which T. annulata-transformed cell lines can be established and maintained in vitro and their susceptibility to infection with poxvirus vectors, these cell lines offer a convenient and efficient in vitro system to analyse the fine specificity of virus-specific CD8 T cell responses in cattle.
Collapse
|
29
|
Codner GF, Stear MJ, Reeve R, Matthews L, Ellis SA. Selective forces shaping diversity in the class I region of the major histocompatibility complex in dairy cattle. Anim Genet 2011; 43:239-49. [DOI: 10.1111/j.1365-2052.2011.02239.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
|
31
|
Machugh ND, Burrells AC, Morrison WI. Demonstration of strain-specific CD8 T cell responses to Theileria annulata. Parasite Immunol 2011; 30:385-93. [PMID: 18498311 PMCID: PMC2592345 DOI: 10.1111/j.1365-3024.2008.01038.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The present study set out to examine the nature and specificity of the bovine CD8 T cell response at the clonal level in a group of eight animals immunized with a cloned population of Theileria annulata. The results demonstrated that immunized animals generated parasite-specific CD8 T cells that produced IFNγ in response to parasite stimulation but had highly variable levels of cytotoxicity for parasitized cells. The study also demonstrated that these parasite-specific CD8 T cells could be propagated and cloned in vitro from the memory T cell pool of cattle immunized with live T. annulata parasites. Within the small group of animals studied, there was evidence that responses were preferentially directed to antigens presented by an A10+ class I major histocompatibility complex (MHC) haplotype, suggesting that responses restricted by products of this haplotype may be dominant. The A10-restricted responses showed differential recognition of different parasite isolates and clones. By using a cloned population of parasites both for immunization of the animals and for in vitro analyses of the responses, we obtained unambiguous evidence that at least a proportion of CD8 T cells restricted by one MHC haplotype were parasite strain restricted.
Collapse
Affiliation(s)
- N D Machugh
- Division of Veterinary Clinical Sciences, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, UK.
| | | | | |
Collapse
|
32
|
Xu TJ, Sun YN, Chen SL. Allelic variation, balancing selection and positive selected sites detected from MHC class Iα gene of olive flounder. Genetica 2010; 138:1251-9. [DOI: 10.1007/s10709-010-9524-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
|
33
|
Macdonald IK, Harkiolaki M, Hunt L, Connelley T, Carroll AV, MacHugh ND, Graham SP, Jones EY, Morrison WI, Flower DR, Ellis SA. MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors. PLoS Pathog 2010; 6:e1001149. [PMID: 20976198 PMCID: PMC2954893 DOI: 10.1371/journal.ppat.1001149] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 09/10/2010] [Indexed: 01/07/2023] Open
Abstract
T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.
Collapse
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)
| |
Collapse
|
34
|
HPV-16 E5 down-regulates expression of surface HLA class I and reduces recognition by CD8 T cells. Virology 2010; 407:137-42. [PMID: 20813390 DOI: 10.1016/j.virol.2010.07.044] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Revised: 07/09/2010] [Accepted: 07/28/2010] [Indexed: 12/20/2022]
Abstract
HPV-16 is the major causes of cervical cancer. Persistence of infection is a necessary event for progression of the infection to cancer. Among other factors, virus persistence is due the viral proteins fighting the immune response. HPV-16 E5 down-regulates MHC/HLA class I, which is much reduced on the cell surface and accumulates in the Golgi apparatus in cells expressing E5. This effect is observed also in W12 cells, which mimic early cervical intraepithelial progression to cervical cancer. The functional effect of MHC I down-regulation on human CD8 T cells is not known, because of the need for HLA-matched, HPV-specific T cells that recognise E5 expressing-cells. Here we employ a heterologous cell/MHC I system which uses mouse cells expressing both E5 and HLA-A2, and A2-restricted CTLs; we show that the E5-induced reduction of HLA-A2 has a functional impact by reducing recognition of E5 expressing cells by HPV specific CD8+ T cells.
Collapse
|
35
|
Induction of a cross-reactive CD8(+) T cell response following foot-and-mouth disease virus vaccination. J Virol 2010; 84:12375-84. [PMID: 20861264 DOI: 10.1128/jvi.01545-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious infection in cloven-hoofed animals. Current inactivated FMDV vaccines generate short-term, serotype-specific protection, mainly through neutralizing antibody. An improved understanding of the mechanisms of protective immunity would aid design of more effective vaccines. We have previously reported the presence of virus-specific CD8(+) T cells in FMDV-vaccinated and -infected cattle. In the current study, we aimed to identify CD8(+) T cell epitopes in FMDV recognized by cattle vaccinated with inactivated FMDV serotype O. Analysis of gamma interferon (IFN-γ)-producing CD8(+) T cells responding to stimulation with FMDV-derived peptides revealed one putative CD8(+) T cell epitope present within the structural protein P1D, comprising residues 795 to 803 of FMDV serotype O UKG/2001. The restricting major histocompatibility complex (MHC) class I allele was N*02201, expressed by the A31 haplotype. This epitope induced IFN-γ release, proliferation, and target cell killing by αβ CD8(+) T cells, but not CD4(+) T cells. A protein alignment of representative samples from each of the 7 FMDV serotypes showed that the putative epitope is highly conserved. CD8(+) T cells from FMDV serotype O-vaccinated A31(+) cattle recognized antigen-presenting cells (APCs) loaded with peptides derived from all 7 FMDV serotypes, suggesting that CD8(+) T cells recognizing the defined epitope are cross-reactive to equivalent peptides derived from all of the other FMDV serotypes.
Collapse
|
36
|
Gene duplication and evidence for balancing selection acting on MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis). Mar Genomics 2010; 3:117-23. [PMID: 21798205 DOI: 10.1016/j.margen.2010.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 08/06/2010] [Accepted: 08/10/2010] [Indexed: 11/24/2022]
Abstract
Allelic polymorphism and evolution mechanism of major histocompatibility complex (MHC) genes has been investigated in many mammals, however, much less is known in teleost. In order to investigate the mechanisms creating and maintaining variability at the MHC class II DAA locus, we examined the polymorphism, gene duplication and balancing selection of MHC class II DAA gene of the half-smooth tongue sole (Cynoglossus semilaevis). We described 33 alleles in the C. semilaevis, recombination and gene duplication seems to play more important roles in the origin of new alleles. The rate of non-synonymous substitutions (d(N)) occurred at a significantly higher frequency than that of synonymous substitutions (d(S)) in peptide-binding region (PBR) and non-PBR, suggesting balancing selection for maintaining polymorphisms at the MHC II DAA locus. Many positive selection sites were found to act very intensively on antigen-binding sites. Our founding suggests a snapshot in an evolutionary process of MHC-DAA gene evolution of the C. semilaevis.
Collapse
|
37
|
Tallmadge RL, Campbell JA, Miller DC, Antczak DF. Analysis of MHC class I genes across horse MHC haplotypes. Immunogenetics 2010; 62:159-72. [PMID: 20099063 DOI: 10.1007/s00251-009-0420-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2009] [Accepted: 12/12/2009] [Indexed: 11/28/2022]
Abstract
The genomic sequences of 15 horse major histocompatibility complex (MHC) class I genes and a collection of MHC class I homozygous horses of five different haplotypes were used to investigate the genomic structure and polymorphism of the equine MHC. A combination of conserved and locus-specific primers was used to amplify horse MHC class I genes with classical and nonclassical characteristics. Multiple clones from each haplotype identified three to five classical sequences per homozygous animal and two to three nonclassical sequences. Phylogenetic analysis was applied to these sequences, and groups were identified which appear to be allelic series, but some sequences were left ungrouped. Sequences determined from MHC class I heterozygous horses and previously described MHC class I sequences were then added, representing a total of ten horse MHC haplotypes. These results were consistent with those obtained from the MHC homozygous horses alone, and 30 classical sequences were assigned to four previously confirmed loci and three new provisional loci. The nonclassical genes had few alleles and the classical genes had higher levels of allelic polymorphism. Alleles for two classical loci with the expected pattern of polymorphism were found in the majority of haplotypes tested, but alleles at two other commonly detected loci had more variation outside of the hypervariable region than within. Our data indicate that the equine major histocompatibility complex is characterized by variation in the complement of class I genes expressed in different haplotypes in addition to the expected allelic polymorphism within loci.
Collapse
Affiliation(s)
- Rebecca L Tallmadge
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | | | | |
Collapse
|
38
|
Doyle J, Ellis SA, O’Gorman GM, Aparicio Donoso IM, Lonergan P, Fair T. Classical and non-classical Major Histocompatibility Complex class I gene expression in in vitro derived bovine embryos. J Reprod Immunol 2009; 82:48-56. [DOI: 10.1016/j.jri.2009.06.125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 06/12/2009] [Accepted: 06/17/2009] [Indexed: 10/20/2022]
|
39
|
Babik W, Taberlet P, Ejsmond MJ, Radwan J. New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system. Mol Ecol Resour 2009; 9:713-9. [PMID: 21564729 DOI: 10.1111/j.1755-0998.2009.02622.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland, Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, Grenoble, France
| | | | | | | |
Collapse
|
40
|
Difference in number of loci of swine leukocyte antigen classical class I genes among haplotypes. Genomics 2008; 93:261-73. [PMID: 18996466 DOI: 10.1016/j.ygeno.2008.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 10/03/2008] [Accepted: 10/14/2008] [Indexed: 10/21/2022]
Abstract
The structure of the entire genomic region of swine leukocyte antigen (SLA)-the porcine major histocompatibility complex--was recently elucidated in a particular haplotype named Hp-1.0 (H01). However, it has been suggested that there are differences in the number of loci of SLA genes, particularly classical class I genes, among haplotypes. To clarify the between-haplotype copy number variance in genes of the SLA region, we sequenced the genomic region carrying SLA classical class I genes on two different haplotypes, revealing increments of up to six in the number of classical class I genes in a single haplotype. All of the SLA-1(-like) (SLA-1 and newly designated SLA-12) and SLA-3 genes detected in the haplotypes thus analyzed were transcribed in the individual. The process by which duplication of SLA classical class I genes was likely to have occurred was interpreted from an analysis of repetitive sequences adjacent to the duplicated class I genes.
Collapse
|
41
|
Genomic location and characterisation of nonclassical MHC class I genes in cattle. Immunogenetics 2008; 60:267-73. [DOI: 10.1007/s00251-008-0294-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 03/20/2008] [Indexed: 01/19/2023]
|
42
|
Guzman E, Taylor G, Charleston B, Skinner MA, Ellis SA. An MHC-restricted CD8+ T-cell response is induced in cattle by foot-and-mouth disease virus (FMDV) infection and also following vaccination with inactivated FMDV. J Gen Virol 2008; 89:667-675. [PMID: 18272757 DOI: 10.1099/vir.0.83417-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a highly contagious disease of cloven-hooved animals that carries enormous economic consequences. CD8(+) cytotoxic T lymphocytes play an important role in protection and disease outcome in viral infections but, to date, the role of the CD8(+) T-cell immune response to FMDV remains unclear. This study aimed to investigate major histocompatibility complex (MHC) class I-restricted CD8(+) T-cell responses to FMDV in vaccinated and in infected cattle. An in vitro assay was used to detect antigen-specific gamma interferon release by CD8(+) T cells in FMDV-infected cattle of known MHC class I genotypes. A significant MHC class I-restricted CD8(+) T-cell response was detected to both FMDV strain O1 BFS and a recombinant fowlpox virus expressing the structural proteins of FMDV. Antigen-specific MHC class I-restricted CD8(+) T-cell responses were also detected in cattle vaccinated with inactivated FMDV. These responses were shown to be directed, at least in part, to epitopes within the structural proteins (P12A region) of the virus. By using mouse cells expressing single cattle MHC class I alleles, it was possible to identify the restriction elements in each case. Identification of these epitopes will facilitate the quantitative and qualitative analysis of FMDV-specific memory CD8(+) T cells in cattle and help to ensure that potential vaccines induce a qualitatively appropriate CD8(+) T-cell response.
Collapse
Affiliation(s)
- Efrain Guzman
- Institute for Animal Health (IAH), Division of Immunology, Compton, Newbury RG20 7NN, UK
| | - Geraldine Taylor
- Institute for Animal Health (IAH), Division of Immunology, Compton, Newbury RG20 7NN, UK
| | - Bryan Charleston
- Institute for Animal Health (IAH), Division of Immunology, Compton, Newbury RG20 7NN, UK
| | - Michael A Skinner
- Department of Virology, Division of Investigative Science, Faculty of Medicine, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK
| | - Shirley A Ellis
- Institute for Animal Health (IAH), Division of Immunology, Compton, Newbury RG20 7NN, UK
| |
Collapse
|
43
|
Xu S, Sun P, Zhou K, Yang G. Sequence variability at three MHC loci of finless porpoises (Neophocaena phocaenoides). Immunogenetics 2007; 59:581-92. [PMID: 17486336 DOI: 10.1007/s00251-007-0223-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 03/31/2007] [Indexed: 11/29/2022]
Abstract
Major histocompatibility complex (MHC) class II DQB and DRA genes and class I gene of finless porpoises (Neophocaena phocaenoides) were investigated by single-strand conformation polymorphism and sequence analysis. The DRA, DQB, and MHC-I loci each contained 5, 14, and 34 unique sequences, respectively, and considerable sequence variation was found at the MHC-I and DQB loci. Gene duplication was manifested as three to five distinct sequences at each of the DQB and MHC-I loci from some individuals, and these sequences at each of the two loci separately clustered into four groups (cluster A, B, C, and D) based on the phylogenetic trees. Phylogenetic reconstruction revealed a trans-species pattern of evolution. Relatively high rates of non-synonymous (dN) vs synonymous (dS) substitution in the peptide-binding region (PBR) suggested balancing selection for maintaining polymorphisms at the MHC-I and DQB loci. In contrast, one single locus with little sequence variation was detected in the DRA gene, and no non-synonymous substitutions in the PBR indicated no balancing selection on this gene.
Collapse
Affiliation(s)
- Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 122 Ninghai Road, Nanjing 210097, China
| | | | | | | |
Collapse
|
44
|
Dobromylskyj M, Ellis S. Complexity in cattle KIR genes: transcription and genome analysis. Immunogenetics 2007; 59:463-72. [PMID: 17450354 DOI: 10.1007/s00251-007-0215-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 03/12/2007] [Indexed: 10/23/2022]
Abstract
Killer immunoglobulin (Ig)-like receptors (KIRs) are the major functional natural killer (NK) cell receptors in human. The presence of KIR genes has only recently been demonstrated in other (non-primate) species, and their expression, genomic arrangement, and function in these species have yet to be investigated. In this study, we describe the KIR gene family in cattle. KIR sequences were amplified from cDNA derived from four animals. Seventeen new sequences were identified in total. Some are alleles of two previously described genes, and the remainder are representative of at least four additional genes. These cDNA data, together with analysis of the cattle genome sequence, confirm that, as in humans, cattle have multiple inhibitory and activating KIR genes, with variable haplotype composition, and putative framework genes. In contrast to human, the majority of the cattle KIR genes encode three Ig-domain KIRs; most of the inhibitory genes encode only one immunoreceptor tyrosine-based inhibitory motif (ITIM), and the activating genes encode molecules with arginine rather than the more usual lysine in the transmembrane domain. A divergent gene, 2DL1, encodes a two Ig-domain KIR with an unusual D0-D2 structure, and a distinct signaling domain with two ITIMs. Similarity to pig and human two Ig-domain (D0-D2) KIRs suggest these may be more related to an ancestral gene than the other cattle KIR genes. Cattle have multiple NKG2A-related genes and at least one Ly49 gene; thus, the data presented here suggest that they have the potential to express more major histocompatibility complex-binding NK receptors than other species.
Collapse
|
45
|
Birch J, Ellis SA. Complexity in the cattle CD94/NKG2 gene families. Immunogenetics 2007; 59:273-80. [PMID: 17285285 DOI: 10.1007/s00251-006-0189-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Natural killer cell responses are controlled to a large extent by the interaction of an array of inhibitory and activating receptors with their ligands. The mostly nonpolymorphic CD94/NKG2 receptors in both humans and mice were shown to recognize a single nonclassical MHC class I molecule in each case. In this paper, we describe the CD94/NKG2 gene family in cattle. NKG2 and CD94 sequences were amplified from cDNA derived from four animals. Four CD94 sequences, ten NKG2A, and three NKG2C sequences were identified in total. In contrast to human, we show that cattle have multiple distinct NKG2A genes, some of which show minor allelic variation. All of the sequences designated NKG2A have two tyrosine-based inhibitory motifs in the cytoplasmic domain and one putative gene has, in addition, a charged residue in the transmembrane domain. NKG2C appears to be essentially monomorphic in cattle. All of the NKG2A sequences are similar apart from NKG2A-01, which, in contrast, shares the majority of its carbohydrate recognition domain with NKG2-C. Most of the genes appear to generate multiple alternatively spliced forms. These findings suggest that the CD94/NKG2A heterodimers in cattle, in contrast to other species, are binding several different ligands. Because NKG2C is not polymorphic, this raises questions as to the combined functional capacity of the CD94/NKG2 gene families in cattle.
Collapse
Affiliation(s)
- James Birch
- Immunology Division, Institute for Animal Health, Compton, RG20 7NN, UK
| | | |
Collapse
|
46
|
Babiuk S, Horseman B, Zhang C, Bickis M, Kusalik A, Schook LB, Abrahamsen MS, Pontarollo R. BoLA class I allele diversity and polymorphism in a herd of cattle. Immunogenetics 2007; 59:167-76. [PMID: 17206412 DOI: 10.1007/s00251-006-0173-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2006] [Accepted: 10/24/2006] [Indexed: 10/23/2022]
Abstract
Major histocompatibility complex class I genes are among the most polymorphic genes characterized. The high level of polymorphism is essential for generating host immune responses. In humans, three distinct genomic loci encode human leukocyte antigen (HLA) class I genes, allowing individuals to express up to six different HLA class I molecules. In cattle, the number of distinct genomic loci are currently at least six, and the number of different bovine leukocyte antigens (BoLA) class I molecules that are expressed in individual animals are variable. The extent of allele variation within the cattle population is unknown. In this study, the number and variety of BoLA class I sequences expressed by 36 individuals were determined from full-length BoLA class I cDNA clones. Twenty distinct BoLA class I alleles were identified, with only four being previously reported. The number of expressed BoLA class I alleles in individual animals ranged between one and four, with none of the animals having an identical complement of BoLA class I molecules. Variation existed in the number of BoLA class I alleles expressed as well as the composition of expressed alleles, however, several BoLA class I alleles were found in multiple individual animals. Polymorphic amino acid sites were analyzed for positive and negative selection using the ADAPTSITE program. In the antigen recognition sites (ARS), there were eight positions that were predicted to be under positive selection and three positions that were predicted to be under negative selection from 62 positions. In contrast, for non-antigen recognition sites (non-ARS), there were three positions that were predicted to be under positive selection and 20 that were predicted to be under negative selection from 278, indicating that positive selection of amino acids occurs at a greater frequency within the antigen recognition sites.
Collapse
Affiliation(s)
- Shawn Babiuk
- Pyxis Genomics Canada, Saskatoon, Saskatchewan, Canada.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Bhushan B, Patra BN, Das PJ, Dutt T, Kumar P, Sharma A, Umang, Dandapat S, Ahlawat SPS. Polymorphism of exon 2-3 of bovine major histocompatibility complex class I BoLa-A gene. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000400009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | | | | | | | - Umang
- Indian Veterinary Research Institute, India
| | | | | |
Collapse
|
48
|
Araibi EH, Marchetti B, Dornan ES, Ashrafi GH, Dobromylskyj M, Ellis SA, Campo MS. The E5 oncoprotein of BPV-4 does not interfere with the biosynthetic pathway of non-classical MHC class I. Virology 2006; 353:174-83. [PMID: 16806386 DOI: 10.1016/j.virol.2006.05.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 05/17/2006] [Accepted: 05/25/2006] [Indexed: 01/07/2023]
Abstract
The major histocompatibility complex (MHC) class I region in mammals contains both classical and non-classical MHC class I genes. Classical MHC class I molecules present antigenic peptides to cytotoxic T lymphocytes, whereas non-classical MHC class I molecules have a variety of functions. Both classical and non-classical MHC molecules interact with natural killer cell receptors and may under some circumstances prevent cell death by natural killer cytotoxicity. The E5 oncoprotein of BPV-4 down-regulates the expression of classical MHC class I on the cell surface and retains the complex in the Golgi apparatus. The inhibition of classical MHC class I to the cell surface results from both the impaired acidification of the Golgi, due to the interaction of E5 with subunit c of the H+ V-ATPase, and to the physical binding of E5 to the heavy chain of MHC class I. Despite the profound effect of E5 on classical MHC class I, E5 does not retain a non-classical MHC class I in the Golgi, does not inhibit its transport to the cell surface and does not bind its heavy chain. We conclude that, as is the case for HPV-16 E5, BPV-4 E5 does not down-regulate certain non-classical MHC class I, potentially providing a mechanism for the escape of the infected cell from attack by both cytotoxic T lymphocytes and NK cells.
Collapse
Affiliation(s)
- E H Araibi
- Division of Pathological Sciences, Institute of Comparative Medicine, University of Glasgow, Garscube Estate, Glasgow G61 1QH, Scotland, UK
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Theileria parva is a tick-borne intracellular protozoan of cattle, with obligate sequential differentiation stages in lymphocytes and erythrocytes. Immunity is mediated by cytotoxic T lymphocytes (CTL) that target and clear parasitized lymphocytes but allow persistence of infected erythrocytes, which are required for transmission to the tick. The life cycle of T. parva is haploid with the exception of a brief diploid stage in the tick vector during which sexual recombination occurs. There is evidence for antigenic diversity in field parasite populations, although broad immunity can be acquired following exposure to a limited number of strains. The CTL response in individual animals is tightly focused and its specificity is strongly influenced by major histocompatibility complex (MHC) phenotype. This review discusses the issue of how CTL immunity is likely to impact on parasite population structure in the light of available information on diversity of the parasite and its ability to recombine.
Collapse
Affiliation(s)
- D J McKeever
- Department of Veterinary Clinical Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian, UK.
| |
Collapse
|
50
|
Birch J, Murphy L, MacHugh ND, Ellis SA. Generation and maintenance of diversity in the cattle MHC class I region. Immunogenetics 2006; 58:670-9. [PMID: 16807744 DOI: 10.1007/s00251-006-0137-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Accepted: 05/31/2006] [Indexed: 10/24/2022]
Abstract
Major histocompatibility complex (MHC) class I genes play a crucial role in the immune defence against intracellular pathogens. An important evolutionary strategy is to generate and maintain a high level of diversity in these genes. Humans express three highly polymorphic classical MHC class I genes (HLA-A, HLA-B and HLA-C). In contrast, some species, for example rat and rhesus macaque, maintain diversity by generation of haplotypes that vary considerably with regard to the number and combination of transcribed genes. Cattle appear to use both strategies. We show that various combinations of six apparently classical genes, three of which are highly polymorphic, are transcribed on different haplotypes. Although additional sequences were identified in both cDNA and gDNA, it was not possible to assign them to any of these defined genes. Most were highly divergent or were non-classical class I genes. Thus, we found little evidence for frequent duplication and deletion of classical class I genes as reported in some other species. However, the maintenance of class I diversity in cattle may involve limited gene shuffling and deletion, possibly as a result of unequal crossing-over within the class I region.
Collapse
Affiliation(s)
- James Birch
- Immunology Division, Institute for Animal Health, Compton, RG20 7NN, UK
| | | | | | | |
Collapse
|