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Schwartz JC, Farrell CP, Freimanis G, Sewell AK, Phillips JD, Hammond JA. A genome assembly and transcriptome atlas of the inbred Babraham pig to illuminate porcine immunogenetic variation. Immunogenetics 2024; 76:361-380. [PMID: 39294478 PMCID: PMC11496355 DOI: 10.1007/s00251-024-01355-7] [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: 07/03/2024] [Accepted: 09/05/2024] [Indexed: 09/20/2024]
Abstract
The inbred Babraham pig serves as a valuable biomedical model for research due to its high level of homozygosity, including in the major histocompatibility complex (MHC) loci and likely other important immune-related gene complexes, which are generally highly diverse in outbred populations. As the ability to control for this diversity using inbred organisms is of great utility, we sought to improve this resource by generating a long-read whole genome assembly and transcriptome atlas of a Babraham pig. The genome was de novo assembled using PacBio long reads and error-corrected using Illumina short reads. Assembled contigs were then mapped to the porcine reference assembly, Sscrofa11.1, to generate chromosome-level scaffolds. The resulting TPI_Babraham_pig_v1 assembly is nearly as contiguous as Sscrofa11.1 with a contig N50 of 34.95 Mb and contig L50 of 23. The remaining sequence gaps are generally the result of poor assembly across large and highly repetitive regions such as the centromeres and tandemly duplicated gene families, including immune-related gene complexes, that often vary in gene content between haplotypes. We also further confirm homozygosity across the Babraham MHC and characterize the allele content and tissue expression of several other immune-related gene complexes, including the antibody and T cell receptor loci, the natural killer complex, and the leukocyte receptor complex. The Babraham pig genome assembly provides an alternate highly contiguous porcine genome assembly as a resource for the livestock genomics community. The assembly will also aid biomedical and veterinary research that utilizes this animal model such as when controlling for genetic variation is critical.
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Affiliation(s)
| | - Colin P Farrell
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - John D Phillips
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - John A Hammond
- The Pirbright Institute, Ash Road, Woking, GU24 0NF, UK.
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2
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Banabazi MH, Freimanis G, Goatley LC, Netherton CL, de Koning DJ. The transcriptomic insight into the differential susceptibility of African Swine Fever in inbred pigs. Sci Rep 2024; 14:5944. [PMID: 38467747 PMCID: PMC10928096 DOI: 10.1038/s41598-024-56569-2] [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: 10/09/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
African swine fever (ASF) is a global threat to animal health and food security. ASF is typically controlled by strict biosecurity, rapid diagnosis, and culling of affected herds. Much progress has been made in developing modified live virus vaccines against ASF. There is host variation in response to ASF infection in the field and under controlled conditions. To better understand the dynamics underlying this host differential morbidity, whole transcriptome profiling was carried out in twelve immunized and five sham immunized pigs. Seventeen MHC homozygous inbred Large white Babraham pigs were sampled at three time points before and after the challenge. The changes in the transcriptome profiles of infected animals were surveyed over time. In addition, the immunization effect on the host response was studied as well among the contrasts of all protection subgroups. The results showed two promising candidate genes to distinguish between recovered and non-recovered pigs after infection with a virulent African swine fever virus (ASFV) pre-infection: HTRA3 and GFPT2 (padj < 0.05). Variant calling on the transcriptome assemblies showed a two-base pair insertion into the ACOX3 gene closely located to HTRA3 that may regulate its expression as a putative genomic variant for ASF. Several significant DGEs, enriched gene ontology (GO) terms, and KEGG pathways at 1 day and 7 days post-infection, compared to the pre-infection, indicate a significant inflammation response immediately after ASF infection. The presence of the virus was confirmed by the mapping of RNA-Seq reads on two whole viral genome sequences. This was concordant with a higher virus load in the non-recovered animals 7 days post-infection. There was no transcriptome signature on the immunization at pre-infection and 1 day post-infection. More samples and data from additional clinical trials may support these findings.
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Affiliation(s)
- Mohammad Hossein Banabazi
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | | | | | | | - Dirk-Jan de Koning
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden.
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3
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Hammer SE, Duckova T, Gociman M, Groiss S, Pernold CPS, Hacker K, Kasper L, Sprung J, Stadler M, Jensen AE, Saalmüller A, Wenzel N, Figueiredo C. Comparative analysis of swine leukocyte antigen gene diversity in Göttingen Minipigs. Front Immunol 2024; 15:1360022. [PMID: 38469309 PMCID: PMC10925748 DOI: 10.3389/fimmu.2024.1360022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Worldwide, pigs represent economically important farm animals, also representing a preferred preclinical large animal model for biomedical studies. The need for swine leukocyte antigen (SLA) typing is increasing with the expanded use of pigs in translational research, infection studies, and for veterinary vaccine design. Göttingen Minipigs (GMP) attract increasing attention as valuable model for pharmacological studies and transplantation research. This study represents a first-time assessment of the SLA gene diversity in Göttingen Minipigs in combination with a comparative metadata analysis with commercial pig lines. As Göttingen Minipigs could harbor private as well as potential novel SLA allele combinations, future research projects would benefit from the characterization of their SLA background. In 209 Göttingen Minipigs, SLA class I (SLA-1, SLA-2, SLA-3) and class II (DRB1, DQB1, DQA) genes were characterized by PCR-based low-resolution (Lr) haplotyping. Criteria and nomenclature used for SLA haplotyping were proposed by the ISAG/IUIS-VIC SLA Nomenclature Committee. Haplotypes were assigned based on the comparison with already known breed or farm-specific allele group combinations. In total, 14 SLA class I and five SLA class II haplotypes were identified in the studied cohort, to manifest in 26 SLA class I but only seven SLA class II genotypes. The most common SLA class I haplotypes Lr-24.0 (SLA-1*15XX or Blank-SLA-3*04:04-SLA-2*06:01~02) and Lr-GMP-3.0 (SLA-1*16:02-SLA-3*03:04-SLA-2*17:01) occurred at frequencies of 23.44 and 18.66%, respectively. For SLA class II, the most prevalent haplotypes Lr-0.21 (DRB1*01XX-DQB1*05XX-DQA*04XX) and Lr-0.03 (DRB1*03:02-DQB1*03:01-DQA*01XX) occurred at frequencies of 38.28 and 30.38%. The comparative metadata analysis revealed that Göttingen Minipigs only share six SLA class I and two SLA class II haplotypes with commercial pig lines. More importantly, despite the limited number of SLA class I haplotypes, the high genotype diversity being observed necessitates pre-experimental SLA background assessment of Göttingen Minipigs in regenerative medicine, allo-transplantation, and xenograft research.
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Affiliation(s)
- Sabine E. Hammer
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tereza Duckova
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Monica Gociman
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sandra Groiss
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Clara P. S. Pernold
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karolin Hacker
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | | | - Julia Sprung
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Maria Stadler
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Armin Saalmüller
- Department of Pathobiology, Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Nadine Wenzel
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
| | - Constanca Figueiredo
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Germany
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4
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Tng PYL, Al-Adwani L, Pauletto E, Hui JYK, Netherton CL. Capsid-Specific Antibody Responses of Domestic Pigs Immunized with Low-Virulent African Swine Fever Virus. Vaccines (Basel) 2023; 11:1577. [PMID: 37896980 PMCID: PMC10611099 DOI: 10.3390/vaccines11101577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
African swine fever (ASF) is a lethal disease in pigs that has grave socio-economic implications worldwide. For the development of vaccines against the African swine fever virus (ASFV), immunogenic antigens that generate protective immune responses need to be identified. There are over 150 viral proteins-many of which are uncharacterized-and humoral immunity to ASFV has not been closely examined. To profile antigen-specific antibody responses, we developed luciferase-linked antibody capture assays (LACAs) for a panel of ASFV capsid proteins and screened sera from inbred and outbred animals that were previously immunized with low-virulent ASFV before challenge with virulent ASFV. Antibodies to B646L/p72, D117L/p17, M1249L, and E120R/p14.5 were detected in this study; however, we were unable to detect B438L-specific antibodies. Anti-B646L/p72 and B602L antibodies were associated with recovery from disease after challenges with genotype I OUR T88/1 but not genotype II Georgia 2007/1. Antibody responses against M1249L and E120R/p14.5 were observed in animals with reduced clinical signs and viremia. Here, we present LACAs as a tool for the targeted profiling of antigen-specific antibody responses to inform vaccine development.
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Affiliation(s)
- Priscilla Y. L. Tng
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (L.A.-A.); (E.P.); (J.Y.K.H.)
| | - Laila Al-Adwani
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (L.A.-A.); (E.P.); (J.Y.K.H.)
| | - Egle Pauletto
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (L.A.-A.); (E.P.); (J.Y.K.H.)
- The Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Joshua Y. K. Hui
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (L.A.-A.); (E.P.); (J.Y.K.H.)
| | - Christopher L. Netherton
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (L.A.-A.); (E.P.); (J.Y.K.H.)
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5
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Schmidt A, Paudyal B, Villanueva-Hernández S, Mcnee A, Vatzia E, Carr BV, Schmidt S, Mccarron A, Martini V, Schroedel S, Thirion C, Waters R, Salguero FJ, Gerner W, Tenbusch M, Tchilian E. Effect of mucosal adjuvant IL-1β on heterotypic immunity in a pig influenza model. Front Immunol 2023; 14:1181716. [PMID: 37153548 PMCID: PMC10159270 DOI: 10.3389/fimmu.2023.1181716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
T cell responses directed against highly conserved viral proteins contribute to the clearance of the influenza virus and confer broadly cross-reactive and protective immune responses against a range of influenza viruses in mice and ferrets. We examined the protective efficacy of mucosal delivery of adenoviral vectors expressing hemagglutinin (HA) and nucleoprotein (NP) from the H1N1 virus against heterologous H3N2 challenge in pigs. We also evaluated the effect of mucosal co-delivery of IL-1β, which significantly increased antibody and T cell responses in inbred Babraham pigs. Another group of outbred pigs was first exposed to pH1N1 as an alternative means of inducing heterosubtypic immunity and were subsequently challenged with H3N2. Although both prior infection and adenoviral vector immunization induced strong T-cell responses against the conserved NP protein, none of the treatment groups demonstrated increased protection against the heterologous H3N2 challenge. Ad-HA/NP+Ad-IL-1β immunization increased lung pathology, although viral load was unchanged. These data indicate that heterotypic immunity may be difficult to achieve in pigs and the immunological mechanisms may differ from those in small animal models. Caution should be applied in extrapolating from a single model to humans.
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Affiliation(s)
- Anna Schmidt
- Virologisches Institut-Klinische und Molekulare Virologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Basudev Paudyal
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Adam Mcnee
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Eleni Vatzia
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Selma Schmidt
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Amy Mccarron
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | | | | | | | - Ryan Waters
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Wilhelm Gerner
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
| | - Matthias Tenbusch
- Virologisches Institut-Klinische und Molekulare Virologie, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- Medical Immunology Campus Erlangen (MICE), Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Elma Tchilian
- Host Responses, The Pirbright Institute, Pirbright, United Kingdom
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6
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Goatley LC, Nash RH, Andrews C, Hargreaves Z, Tng P, Reis AL, Graham SP, Netherton CL. Cellular and Humoral Immune Responses after Immunisation with Low Virulent African Swine Fever Virus in the Large White Inbred Babraham Line and Outbred Domestic Pigs. Viruses 2022; 14:v14071487. [PMID: 35891467 PMCID: PMC9322176 DOI: 10.3390/v14071487] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 12/15/2022] Open
Abstract
African swine fever virus is currently present in all of the world’s continents apart from Antarctica, and efforts to control the disease are hampered by the lack of a commercially available vaccine. The Babraham large white pig is a highly inbred line that could represent a powerful tool to improve our understanding of the protective immune responses to this complex pathogen; however, previous studies indicated differential vaccine responses after the African swine fever virus challenge of inbred minipigs with different swine leukocyte antigen haplotypes. Lymphocyte numbers and African swine fever virus-specific antibody and T-cell responses were measured in inbred and outbred animals after inoculation with a low virulent African swine fever virus isolate and subsequent challenge with a related virulent virus. Surprisingly, diminished immune responses were observed in the Babraham pigs when compared to the outbred animals, and the inbred pigs were not protected after challenge. Recovery of Babraham pigs after challenge weakly correlated with antibody responses, whereas protective responses in outbred animals more closely correlated with the T-cell response. The Babraham pig may, therefore, represent a useful model for studying the role of antibodies in protection against the African swine fever virus.
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7
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Yıldız B, Megens H, Hvilsom C, Bosse M. Genomic consequences of a century of inbreeding and isolation in the Danish wild boar population. Evol Appl 2022; 15:954-966. [PMID: 35782012 PMCID: PMC9234630 DOI: 10.1111/eva.13385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/26/2022] [Accepted: 03/07/2022] [Indexed: 11/30/2022] Open
Abstract
Demographic events such as series of bottlenecks impact the genetic variation and adaptive potential of populations. European megafauna, such as wild boars (Sus scrofa), have experienced severe climatic and size fluctuations that have shaped their genetic variation. Habitat fragmentation and human-mediated translocations have further contributed to the complex demographic history of European wild boar. Danish wild boars represent an extreme case of a small and isolated population founded by four wild boars from Germany. Here, we explore the genetic composition of the Danish wild boar population in Klelund. We genotyped all 21 Danish wild boars that were recently transferred from the source population in Lille Vildmose into the Klelund Plantation to establish a novel wild boar population. We compared the Danish wild boars with high-density single-nucleotide polymorphism genotypes from a comprehensive reference set of 1263 wild and domesticated pigs, including 11 individuals from Ulm, one of two presumed founder locations in Germany. Our findings support the European wild background of the Danish population, and no traces of gene flow with wild or domesticated pigs were found. The narrow genetic origin of the Danish wild boars is illustrated by extremely long and frequent runs of homozygous stretches in their genomes, indicative of recent inbreeding. This study provides the first insights into one of the most inbred wild boar populations globally established a century ago from a narrow base of only four founders.
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Affiliation(s)
- Beril Yıldız
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Hendrik‐Jan Megens
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | | | - Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
- Amsterdam Institute for Life and Environment (A‐LIFE)Section Ecology & EvolutionVrije Universiteit AmsterdamAmsterdamThe Netherlands
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8
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Martini V, Edmans M, Gubbins S, Jayaraman S, Paudyal B, Morgan S, McNee A, Morin T, Rijal P, Gerner W, Sewell AK, Inoue R, Bailey M, Connelley T, Charleston B, Townsend A, Beverley P, Tchilian E. Spatial, temporal and molecular dynamics of swine influenza virus-specific CD8 tissue resident memory T cells. Mucosal Immunol 2022; 15:428-442. [PMID: 35145208 PMCID: PMC9038527 DOI: 10.1038/s41385-021-00478-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023]
Abstract
For the first time we have defined naïve, central memory, effector memory and differentiated effector porcine CD8 T cells and analyzed their distribution in lymphoid and respiratory tissues after influenza infection or immunization, using peptide-MHC tetramers of three influenza nucleoprotein (NP) epitopes. The hierarchy of response to the three epitopes changes during the response in different tissues. Most NP-specific CD8 T cells in broncho-alveolar lavage (BAL) and lung are tissue resident memory cells (TRM) that express CD69 and downregulate CD45RA and CCR7. NP-specific cells isolated from BAL express genes characteristic of TRM, but gene expression differs at 7, 21 and 63 days post infection. In all tissues the frequency of NP-specific CD8 cells declines over 63 days almost to background levels but is best maintained in BAL. The kinetic of influenza specific memory CD8 T cell in this natural host species differs from that in small animal models.
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Affiliation(s)
- Veronica Martini
- The Pirbright Institute, Pirbright, UK.
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Institute for Research in Biomedicine, Bellinzona, Switzerland.
| | | | | | | | | | | | | | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Pramila Rijal
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Ryo Inoue
- Laboratory of Animal Science, Setsunan University, Osaka, Japan
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Langford, UK
| | | | | | - Alain Townsend
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter Beverley
- National Heart and Lung Institute, St Mary's Campus, Imperial College, London, UK
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9
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Le Page L, Gillespie A, Schwartz JC, Prawits LM, Schlerka A, Farrell CP, Hammond JA, Baldwin CL, Telfer JC, Hammer SE. Subpopulations of swine γδ T cells defined by TCRγ and WC1 gene expression. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104214. [PMID: 34329647 DOI: 10.1016/j.dci.2021.104214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/24/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
γδ T cells constitute a major portion of lymphocytes in the blood of both ruminants and swine. Subpopulations of swine γδ T cells have been distinguished by CD2 and CD8α expression. However, it was not clear if they have distinct expression profiles of their T-cell receptor (TCR) or WC1 genes. Identifying receptor expression will contribute to understanding the functional differences between these subpopulations and their contributions to immune protection. Here, we annotated three genomic assemblies of the swine TCRγ gene locus finding four gene cassettes containing C, J and V genes, although some haplotypes carried a null TRGC gene (TRGC4). Genes in the TRGC1 cassette were homologs of bovine TRGC5 cassette while the others were not homologous to bovine genes. Here we evaluated three principal populations of γδ T cells (CD2+/SWC5-, CD2-/SWC5+, and CD2-/SWC5-). Both CD2- subpopulations transcribed WC1 co-receptor genes, albeit with different patterns of gene expression but CD2+ cells did not. All subpopulations transcribed TCR genes from all four cassettes, although there were differences in expression levels. Finally, the CD2+ and CD2- γδ T-cell populations differed in their representation in various organs and tissues, presumably at least partially reflective of different ligand specificities for their receptors.
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Affiliation(s)
- Lauren Le Page
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Alexandria Gillespie
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | | | - Lisa-Maria Prawits
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Angela Schlerka
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Colin P Farrell
- Division of Hematology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Cynthia L Baldwin
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Janice C Telfer
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria.
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10
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Uehlein S, Ding X, Flößer J, Schmidt S, Steitz J, Bille M, Schnitter F, Baltes S, Saalmüller A, Gerner W, Herrmann T, Frey A, Kerkau T, Hofmann U, Beyersdorf N. Human-like Response of Pig T Cells to Superagonistic Anti-CD28 Monoclonal Antibodies. THE JOURNAL OF IMMUNOLOGY 2021; 207:2473-2488. [PMID: 34625520 DOI: 10.4049/jimmunol.2100174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/13/2021] [Indexed: 01/07/2023]
Abstract
Because of its size, anatomical similarities, and now also accessibility to genetic manipulations, pigs are used as animal models for human diseases and immune system development. However, expression and function of CD28, the most important costimulatory receptor expressed by T cells, so far is poorly understood in this species. Using a newly generated mAb (mAb 3D11) with specificity for pig CD28, we detected CD28 on CD8+ and CD4+ αβ T cells. Among γδ T cells, CD28 expression was restricted to a small CD2+ subpopulation of phenotypically naive cells. Functionally, CD28 ligation with mAb 3D11-costimulated porcine T cells, enhanced proliferation and cytokine secretion in vitro. We used a second, likewise newly generated but superagonistic, anti-CD28 mAb (CD28-SA; mAb 4D12) to test the function of CD28 on porcine T cells in a pilot study in vivo. Injection of the CD28-SA into pigs in vivo showed a very similar dose-response relationship as in humans (i.e., 100 µg/kg body weight [BW]) of CD28-SA induced a cytokine release syndrome that was avoided at a dose of 10 µg/kg BW and below. The data further suggest that low-dose (10 µg/kg BW) CD28-SA infusion was sufficient to increase the proportion of Foxp3+ regulatory T cells among CD4+ T cells in vivo. The pig is thus a suitable animal model for testing novel immunotherapeutics. Moreover, data from our pilot study in pigs further suggest that low-dose CD28-SA infusion might allow for selective expansion of CD4+ regulatory T cells in humans.
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Affiliation(s)
- Sabrina Uehlein
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Xin Ding
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Janina Flößer
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Selma Schmidt
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Julia Steitz
- Faculty of Medicine, Institute for Laboratory Animal Science, RWTH Aachen University, Aachen, Germany
| | - Maya Bille
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany; and
| | - Florian Schnitter
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany; and.,Department of Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Steffen Baltes
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany; and
| | - Armin Saalmüller
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Wilhelm Gerner
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Herrmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Anna Frey
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany; and.,Department of Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Thomas Kerkau
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Ulrich Hofmann
- Comprehensive Heart Failure Center, University Hospital Würzburg, Würzburg, Germany; and.,Department of Medicine I, University Hospital Würzburg, Würzburg, Germany
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany;
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11
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Gerner W, Mair KH, Schmidt S. Local and Systemic T Cell Immunity in Fighting Pig Viral and Bacterial Infections. Annu Rev Anim Biosci 2021; 10:349-372. [PMID: 34724393 DOI: 10.1146/annurev-animal-013120-044226] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
T cells are an essential component of the adaptive immune system. Over the last 15 years, a constantly growing toolbox with which to study T cell biology in pigs has allowed detailed investigations on these cells in various viral and bacterial infections. This review provides an overview on porcine CD4, CD8, and γδ T cells and the current knowledge on the differentiation of these cells following antigen encounter. Where available, the responses of these cells to viral infections like porcine reproductive and respiratory syndrome virus, classical swine fever virus, swine influenza A virus, and African swine fever virus are outlined. In addition, knowledge on the porcine T cell response to bacterial infections like Actinobacillus pleuropneumoniae and Salmonella Typhimurium is reviewed. For CD4 T cells, the response to the outlined infections is reflected toward the Th1/Th2/Th17/Tfh/Treg paradigm for functional differentiation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Wilhelm Gerner
- The Pirbright Institute, Pirbright, Woking, United Kingdom; ,
| | - Kerstin H Mair
- Christian Doppler Laboratory for Optimized Prediction of Vaccination Success in Pigs, Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria; .,Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Selma Schmidt
- The Pirbright Institute, Pirbright, Woking, United Kingdom; ,
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12
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Huo JL, Zhang LQ, Zhang X, Wu XW, Ye XH, Sun YH, Cheng WM, Yang K, Pan WR, Zeng YZ. Genome-wide single nucleotide polymorphism array and whole-genome sequencing reveal the inbreeding progression of Banna minipig inbred line. Anim Genet 2021; 53:146-151. [PMID: 34658041 DOI: 10.1111/age.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2021] [Indexed: 01/28/2023]
Abstract
Inbred pigs are promising animal models for biomedical research and xenotransplantation. Established in 1980, the Banna minipig inbred (BMI) line originated from a sow and its own male offspring. It was selected from a small backcountry minority Lahu village, where records show that no other pig breed has ever been introduced. During the inbreeding process, we perfomed extreme inbreeding over 23 consecutive generations using full-sibling or parent-offspring mating. In order to investigate the inbreeding effects in BMI pigs across generations over the past 40 years, in this study we conducted a genome-wide SNP genotyping of the last 10 generations, representing generations 14-23. In total, we genotyped 57,746 SNPs, corresponding to an average decrease in heterozygosity rate of 0.0078 per generation. Furthermore, we were only able to identify 18,216 polymorphic loci with a MAF larger than 0.05, which is substantially lower than the values in previous reports on other pig breeds. In addition, we sequenced the genome of the first pig in the twenty-third generation (inbreeding coefficient 99.28%) to an average coverage of 12.4× to evaluate at the genome level the impact of advanced inbreeding. ROH analysis indicates that BMI pigs have longer ROHs than Wuzhishan and Duroc pigs. Those long ROH regions in BMI pigs are enriched for distinct functions compared with the highly polymorphic regions. Our study reveals a genome-wide allele diversity loss during the progress of inbreeding in BMI pigs and characterizes ROH and polymorphic regions as a result of inbreeding. Overall, our results indicate the successful establishment of the BMI line, which paves the way for further in-depth studies.
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Affiliation(s)
- J L Huo
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China.,Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - L Q Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X Zhang
- College of Life Science, Lvliang University, Lvliang, 033001, China
| | - X W Wu
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - X H Ye
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Y H Sun
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - W M Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - K Yang
- Department of Computer Science, Virginia Tech, Blacksburg, VA, 24061, USA
| | - W R Pan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Y Z Zeng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.,Key Laboratory of Banna Mini-pig Inbred Line of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
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13
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Hammer SE, Duckova T, Groiss S, Stadler M, Jensen-Waern M, Golde WT, Gimsa U, Saalmueller A. Comparative analysis of swine leukocyte antigen gene diversity in European farmed pigs. Anim Genet 2021; 52:523-531. [PMID: 34028065 PMCID: PMC8362188 DOI: 10.1111/age.13090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/01/2023]
Abstract
In Europe, swine represent economically important farm animals and furthermore have become a preferred preclinical large animal model for biomedical studies, transplantation and regenerative medicine research. 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 and their use in infection studies and for design of veterinary vaccines. In this study, we characterised the SLA class I (SLA‐1, SLA‐2, SLA‐3) and class II (DRB1, DQB1, DQA) genes of 549 farmed pigs representing nine commercial pig lines by low‐resolution (Lr) SLA haplotyping. In total, 50 class I and 37 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotypes Lr‐04.0 (SLA‐1*04XX‐SLA‐3*04XX(04:04)‐SLA‐2*04XX) and Lr‐32.0 (SLA‐1*07XX‐SLA‐3*04XX(04:04)‐SLA‐2*02XX) occurred at frequencies of 11.02 and 8.20% respectively. For SLA class II, the most prevalent haplotypes Lr‐0.15b (DRB1*04XX(04:05/04:06)‐DQB1*02XX(02:02)‐DQA*02XX) and Lr‐0.12 (DRB1*06XX‐DQB1*07XX‐DQA*01XX) occurred at frequencies of 14.37 and 12.46% respectively. Meanwhile, our laboratory has contributed to several vaccine correlation studies (e.g. Porcine Reproductive and Respiratory Syndrome Virus, Classical Swine Fever Virus, Foot‐and‐Mouth Disease Virus and Swine Influenza A Virus) elucidating the immunodominance in the T‐cell response with antigen specificity dependent on certain SLA‐I and SLA‐II haplotypes. Moreover, these SLA–immune response correlations could facilitate tailored vaccine development, as SLA‐I Lr‐04.0 and Lr‐32.0 as well as SLA‐II Lr‐0.15b and Lr‐0.12 are highly abundant haplotypes in European farmed pigs.
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Affiliation(s)
- S E Hammer
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, 1210, Austria
| | - T Duckova
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, 1210, Austria
| | - S Groiss
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, 1210, Austria
| | - M Stadler
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, 1210, Austria
| | - M Jensen-Waern
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, PO Box 7054, Uppsala, 750 07, Sweden
| | - W T Golde
- Moredun Research Institute, Edinburgh, EH26 OPZ, UK
| | - U Gimsa
- Institute of Behavioural Physiology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany
| | - A Saalmueller
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, Vienna, 1210, Austria
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14
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Techakriengkrai N, Nedumpun T, Golde WT, Suradhat S. Diversity of the Swine Leukocyte Antigen Class I and II in Commercial Pig Populations. Front Vet Sci 2021; 8:637682. [PMID: 33996967 PMCID: PMC8121083 DOI: 10.3389/fvets.2021.637682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Among swine genetic markers, the highly polymorphic swine leukocyte antigen (SLA) is one of the key determinants, associated with not only immune responses but also reproductive performance and meat quality. The objective of this study was to characterize the SLA class I and II diversities in the commercial pig populations. In this study, a total number of 158 pigs (126 gilts and 32 boars) were randomly selected from different breeding herds of five major pig-producing companies, which covered ~70% of Thai swine production. The results indicate that a moderate level of SLA diversity was maintained in the Thai swine population, despite the performance-oriented breeding scheme. The highly common SLA class I alleles were SLA-1*08:XX, SLA-2*02:XX, and SLA-3*04:XX at a combined frequency of 30.1, 18.4, and 34.5%, respectively, whereas DRB1*04:XX, DQB1*02:XX and DQA*02:XX were the common class II alleles at 22.8, 33.3, and 38.6%, respectively. The haplotype Lr-32.0 (SLA-1*07:XX, SLA-2*02:XX, and SLA-3*04:XX) and Lr-0.23 (DRB1*10:XX, DQB1*06:XX, DQA* 01:XX) was the most common SLA class I and II haplotype, at 15.5 and 14.6%, respectively. Common class I and II haplotypes were also observed, which Lr-22.15 was the most predominant at 11.1%, followed by Lr-32.12 and Lr-4.2 at 10.8 and 7.9%, respectively. To our knowledge, this is the first report of SLA class I and II diversities in the commercial pigs in Southeast Asia. The information of the common SLA allele(s) in the population could facilitate swine genetic improvement and future vaccine design.
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Affiliation(s)
- Navapon Techakriengkrai
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Diagnosis and Monitoring of Animal Pathogens Research Unit, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - Teerawut Nedumpun
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
| | - William T Golde
- Department of Vaccines and Diagnostics, Moredun Research Institute, Penicuik, United Kingdom
| | - Sanipa Suradhat
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellence in Emerging Infectious Diseases in Animals, Chulalongkorn University (CU-EIDAs), Bangkok, Thailand
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15
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A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations. Sci Rep 2021; 11:4340. [PMID: 33619347 PMCID: PMC7900169 DOI: 10.1038/s41598-021-83637-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
Analysing pig class II mayor histocompatibility complex (MHC) molecules is mainly related to antigen presentation. Identifying frequently-occurring alleles in pig populations is an important aspect to be considered when developing peptide-based vaccines. Colombian creole pig populations have had to adapt to local conditions since entering Colombia; a recent census has shown low amounts of pigs which is why they are considered protected by the Colombian government. Commercial hybrids are more attractive regarding production. This research has been aimed at describing the allele distribution of Colombian pigs from diverse genetic backgrounds and comparing Colombian SLA-DRB1 locus diversity to that of internationally reported populations. Twenty SLA-DRB1 alleles were identified in the six populations analysed here using sequence-based typing. The amount of alleles ranged from six (Manta and Casco Mula) to nine (San Pedreño). Only one allele (01:02) having > 5% frequency was shared by all three commercial line populations. Allele 02:01:01 was shared by five populations (around > 5% frequency). Global FST indicated that pig populations were clearly structured, as 20.6% of total allele frequency variation was explained by differences between populations (FST = 0.206). This study’s results confirmed that the greatest diversity occurred in wild boars, thereby contrasting with low diversity in domestic pig populations.
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16
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Edmans M, McNee A, Porter E, Vatzia E, Paudyal B, Martini V, Gubbins S, Francis O, Harley R, Thomas A, Burt R, Morgan S, Fuller A, Sewell A, Charleston B, Bailey M, Tchilian E. Magnitude and Kinetics of T Cell and Antibody Responses During H1N1pdm09 Infection in Inbred Babraham Pigs and Outbred Pigs. Front Immunol 2021; 11:604913. [PMID: 33603740 PMCID: PMC7884753 DOI: 10.3389/fimmu.2020.604913] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
We have used the pig, a large natural host animal for influenza with many physiological similarities to humans, to characterize αβ, γδ T cell and antibody (Ab) immune responses to the 2009 pandemic H1N1 virus infection. We evaluated the kinetic of virus infection and associated response in inbred Babraham pigs with identical MHC (Swine Leucocyte Antigen) and compared them to commercial outbred animals. High level of nasal virus shedding continued up to days 4 to 5 post infection followed by a steep decline and clearance of virus by day 9. Adaptive T cell and Ab responses were detectable from days 5 to 6 post infection reaching a peak at 9 to 14 days. γδ T cells produced cytokines ex vivo at day 2 post infection, while virus reactive IFNγ producing γδ T cells were detected from day 7 post infection. Analysis of NP tetramer specific and virus specific CD8 and CD4 T cells in blood, lung, lung draining lymph nodes, and broncho-alveolar lavage (BAL) showed clear differences in cytokine production between these tissues. BAL contained the most highly activated CD8, CD4, and γδ T cells producing large amounts of cytokines, which likely contribute to elimination of virus. The weak response in blood did not reflect the powerful local lung immune responses. The immune response in the Babraham pig following H1N1pdm09 influenza infection was comparable to that of outbred animals. The ability to utilize these two swine models together will provide unparalleled power to analyze immune responses to influenza.
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Affiliation(s)
- Matthew Edmans
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Adam McNee
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Emily Porter
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Eleni Vatzia
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Basu Paudyal
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Veronica Martini
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Simon Gubbins
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Ore Francis
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Ross Harley
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Amy Thomas
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Rachel Burt
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Sophie Morgan
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Bryan Charleston
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Langford, United Kingdom
| | - Elma Tchilian
- The Pirbright Institute, Enhanced Host Responses, Pirbright, United Kingdom
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17
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Baratelli M, Morgan S, Hemmink JD, Reid E, Carr BV, Lefevre E, Montaner-Tarbes S, Charleston B, Fraile L, Tchilian E, Montoya M. Identification of a Newly Conserved SLA-II Epitope in a Structural Protein of Swine Influenza Virus. Front Immunol 2020; 11:2083. [PMID: 33042120 PMCID: PMC7524874 DOI: 10.3389/fimmu.2020.02083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/30/2020] [Indexed: 11/30/2022] Open
Abstract
Despite the role of pigs as a source of new Influenza A Virus viruses (IAV) potentially capable of initiating human pandemics, immune responses to swine influenza virus (SwIV) in pigs are not fully understood. Several SwIV epitopes presented by swine MHC (SLA) class I have been identified using different approaches either in outbred pigs or in Babraham large white inbred pigs, which are 85% identical by genome wide SNP analysis. On the other hand, some class II SLA epitopes were recently described in outbred pigs. In this work, Babraham large white inbred pigs were selected to identify SLA II epitopes from SwIV H1N1. PBMCs were screened for recognition of overlapping peptides covering the NP and M1 proteins from heterologous IAV H1N1 in IFNγ ELISPOT. A novel SLA class II restricted epitope was identified in NP from swine H1N1. This conserved novel epitope could be the base for further vaccine approaches against H1N1 in pigs.
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Affiliation(s)
- Massimiliano Baratelli
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | | | | | - Sergio Montaner-Tarbes
- Innovex Therapeutics S.L., Badalona, Spain.,Animal Health Department, Universidad de Lleida, Lleida, Spain
| | | | - Lorenzo Fraile
- Animal Health Department, Universidad de Lleida, Lleida, Spain
| | | | - Maria Montoya
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Universitat Autònoma de Barcelona, Bellaterra, Spain.,The Pirbright Institute, Surrey, United Kingdom.,Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
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18
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Entrican G, Lunney JK, Wattegedera SR, Mwangi W, Hope JC, Hammond JA. The Veterinary Immunological Toolbox: Past, Present, and Future. Front Immunol 2020; 11:1651. [PMID: 32849568 PMCID: PMC7399100 DOI: 10.3389/fimmu.2020.01651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/22/2020] [Indexed: 12/02/2022] Open
Abstract
It is well-recognized that research capability in veterinary species is restricted by a lack of immunological reagents relative to the extensive toolboxes for small rodent biomedical model species and humans. This creates a barrier to the strategic development of disease control solutions for livestock, companion animals and wildlife that not only affects animal health but can affect human health by increasing the risk of transmission of zoonotic pathogens. There have been a number of projects aimed at reducing the capability gaps in the veterinary immunological toolbox, the majority of these focusing on livestock species. Various approaches have been taken to veterinary immunological reagent development across the globe and technological advances in molecular biology and protein biochemistry have accelerated toolbox development. While short-term funding initiatives can address specific gaps in capability, they do not account for long-term sustainability of reagents and databases that requires a different funding model. We review the past, present and future of the veterinary immunological toolbox with specific reference to recent developments discussed at the International Union of Immunological Societies (IUIS) Veterinary Immunology Committee (VIC) Immune Toolkit Workshop at the 12th International Veterinary Immunology Symposium (IVIS) in Seattle, USA, 16–19 August 2019. The future availability of these reagents is critical to research for improving animal health, responses to infectious pathogens and vaccine design as well as for important analyses of zoonotic pathogens and the animal /human interface for One Health initiatives.
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Affiliation(s)
- Gary Entrican
- The Roslin Institute at The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD, United States
| | - Sean R Wattegedera
- Moredun Research Institute, Pentlands Science Park, Edinburgh, United Kingdom
| | | | - Jayne C Hope
- The Roslin Institute at The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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19
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Goatley LC, Reis AL, Portugal R, Goldswain H, Shimmon GL, Hargreaves Z, Ho CS, Montoya M, Sánchez-Cordón PJ, Taylor G, Dixon LK, Netherton CL. A Pool of Eight Virally Vectored African Swine Fever Antigens Protect Pigs Against Fatal Disease. Vaccines (Basel) 2020; 8:E234. [PMID: 32443536 PMCID: PMC7349991 DOI: 10.3390/vaccines8020234] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
Classical approaches to African swine fever virus (ASFV) vaccine development have not been successful; inactivated virus does not provide protection and use of live attenuated viruses generated by passage in tissue culture had a poor safety profile. Current African swine fever (ASF) vaccine research focuses on the development of modified live viruses by targeted gene deletion or subunit vaccines. The latter approach would be differentiation of vaccinated from infected animals (DIVA)-compliant, but information on which viral proteins to include in a subunit vaccine is lacking. Our previous work used DNA-prime/vaccinia-virus boost to screen 40 ASFV genes for immunogenicity, however this immunization regime did not protect animals after challenge. Here we describe the induction of both antigen and ASFV-specific antibody and cellular immune responses by different viral-vectored pools of antigens selected based on their immunogenicity in pigs. Immunization with one of these pools, comprising eight viral-vectored ASFV genes, protected 100% of pigs from fatal disease after challenge with a normally lethal dose of virulent ASFV. This data provide the basis for the further development of a subunit vaccine against this devastating disease.
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Affiliation(s)
- Lynnette C. Goatley
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Ana Luisa Reis
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Raquel Portugal
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Hannah Goldswain
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Gareth L. Shimmon
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Zoe Hargreaves
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Chak-Sum Ho
- Gift of Hope Organ and Tissue Donor Network, Itasca, IL 60143, USA;
| | - María Montoya
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Pedro J. Sánchez-Cordón
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Geraldine Taylor
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Linda K. Dixon
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
| | - Christopher L. Netherton
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (L.C.G.); (A.L.R.); (R.P.); (H.G.); (G.L.S.); (Z.H.); (M.M.); (P.J.S.-C.); (G.T.); (L.K.D.)
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20
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Lane MC, Gordon JL, Jiang C, Leitner WW, Pickett TE, Stemmy E, Bozick BA, Deckhut-Augustine A, Embry AC, Post DJ. Workshop report: Optimization of animal models to better predict influenza vaccine efficacy. Vaccine 2020; 38:2751-2757. [PMID: 32145879 DOI: 10.1016/j.vaccine.2020.01.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/17/2020] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
Animal models that can recapitulate the human immune system are essential for the preclinical development of safe and efficacious vaccines. Development and optimization of representative animal models are key components of the NIAID strategic plan for the development of a universal influenza vaccine. To gain insight into the current landscape of animal model usage in influenza vaccine development, NIAID convened a workshop in Rockville, Maryland that brought together experts from academia, industry and government. Panelists discussed the benefits and limitations of the field's most widely-used animal models, identified currently available and critically needed resources and reagents, and suggested areas for improvement based on inadequacies of existing models. Although appropriately-selected animal models can be useful for evaluating safety, mechanism-of-action, and superiority over existing vaccines, workshop participants concluded that multiple animal models will likely be required to sufficiently test all aspects of a novel vaccine candidate. Refinements are necessary for all current model systems, for example, to better represent special human populations, and will be facilitated by the development and broader availability of new reagents. NIAID continues to support progress towards increasing the predictive value of animal models.
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Affiliation(s)
- M Chelsea Lane
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
| | - Jennifer L Gordon
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Chao Jiang
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Wolfgang W Leitner
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Thames E Pickett
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Erik Stemmy
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Brooke A Bozick
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alison Deckhut-Augustine
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alan C Embry
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Diane J Post
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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21
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Hammer SE, Ho CS, Ando A, Rogel-Gaillard C, Charles M, Tector M, Tector AJ, Lunney JK. Importance of the Major Histocompatibility Complex (Swine Leukocyte Antigen) in Swine Health and Biomedical Research. Annu Rev Anim Biosci 2019; 8:171-198. [PMID: 31846353 DOI: 10.1146/annurev-animal-020518-115014] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In pigs, the major histocompatibility complex (MHC), or swine leukocyte antigen (SLA) complex, maps to Sus scrofa chromosome 7. It consists of three regions, the class I and class III regions mapping to 7p1.1 and the class II region mapping to 7q1.1. The swine MHC is divided by the centromere, which is unique among mammals studied to date. The SLA complexspans between 2.4 and 2.7 Mb, depending on haplotype, and encodes approximately 150 loci, with at least 120 genes predicted to be functional. Here we update the whole SLA complex based on the Sscrofa11.1 build and annotate the organization for all recognized SLA genes and their allelic sequences. We present SLA nomenclature and typing methods and discuss the expression of SLA proteins, as well as their role in antigen presentation and immune, disease, and vaccine responses. Finally, we explore the role of SLA genes in transplantation and xenotransplantation and their importance in swine biomedical models.
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Affiliation(s)
- Sabine E Hammer
- Institute of Immunology, Department of Pathobiology, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria
| | - Chak-Sum Ho
- Gift of Hope Organ & Tissue Donor Network, Itasca, Illinois 60143, USA
| | - Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan
| | | | - Mathieu Charles
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Matthew Tector
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,Current address: Makana Therapeutics, Wilmington, Delaware 19801, USA
| | - A Joseph Tector
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,Current address: Department of Surgery, University of Miami, Miami, Florida 33136, USA
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, Maryland 20705, USA;
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22
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Holzer B, Martini V, Edmans M, Tchilian E. T and B Cell Immune Responses to Influenza Viruses in Pigs. Front Immunol 2019; 10:98. [PMID: 30804933 PMCID: PMC6371849 DOI: 10.3389/fimmu.2019.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/14/2019] [Indexed: 01/31/2023] Open
Abstract
Influenza viruses are an ongoing threat to humans and are endemic in pigs, causing considerable economic losses to farmers. Pigs are also a source of new viruses potentially capable of initiating human pandemics. Many tools including monoclonal antibodies, recombinant cytokines and chemokines, gene probes, tetramers, and inbred pigs allow refined analysis of immune responses against influenza. Recent advances in understanding of the pig innate system indicate that it shares many features with that of humans, although there is a larger gamma delta component. The fine specificity and mechanisms of cross-protective T cell immunity have yet to be fully defined, although it is clear that the local immune response is important. The repertoire of pig antibody response to influenza has not been thoroughly explored. Here we review current understanding of adaptive immune responses against influenza in pigs and the use of the pig as a model to study human disease.
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Affiliation(s)
- Barbara Holzer
- Department of Mucosal Immunology, The Pirbright Institute (BBSRC), Pirbright, United Kingdom
| | - Veronica Martini
- Department of Mucosal Immunology, The Pirbright Institute (BBSRC), Pirbright, United Kingdom
| | - Matthew Edmans
- Department of Mucosal Immunology, The Pirbright Institute (BBSRC), Pirbright, United Kingdom
| | - Elma Tchilian
- Department of Mucosal Immunology, The Pirbright Institute (BBSRC), Pirbright, United Kingdom
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23
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Netherton CL, Goatley LC, Reis AL, Portugal R, Nash RH, Morgan SB, Gault L, Nieto R, Norlin V, Gallardo C, Ho CS, Sánchez-Cordón PJ, Taylor G, Dixon LK. Identification and Immunogenicity of African Swine Fever Virus Antigens. Front Immunol 2019; 10:1318. [PMID: 31275307 PMCID: PMC6593957 DOI: 10.3389/fimmu.2019.01318] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/23/2019] [Indexed: 12/22/2022] Open
Abstract
African swine fever (ASF) is a lethal haemorrhagic disease of domestic pigs for which there is no vaccine. Strains of the virus with reduced virulence can provide protection against related virulent strains of ASFV, but protection is not 100% and there are concerns about the safety profile of such viruses. However, they provide a useful tool for understanding the immune response to ASFV and previous studies using the low virulent isolate OUR T88/3 have shown that CD8+ cells are crucial for protection. In order to develop a vaccine that stimulates an effective anti-ASFV T-cell response we need to know which of the >150 viral proteins are recognized by the cellular immune response. Therefore, we used a gamma interferon ELIspot assay to screen for viral proteins recognized by lymphocytes from ASF-immune pigs using peptides corresponding to 133 proteins predicted to be encoded by OUR T88/3. Eighteen antigens that were recognized by ASFV-specific lymphocytes were then incorporated into adenovirus and MVA vectors, which were used in immunization and challenge experiments in pigs. We present a systematic characterization of the cellular immune response to this devastating disease and identify proteins capable of inducing ASFV-specific cellular and humoral immune responses in pigs. Pools of viral vectors expressing these genes did not protect animals from severe disease, but did reduce viremia in a proportion of pigs following ASFV challenge.
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Affiliation(s)
| | | | | | | | | | | | - Lynden Gault
- Gift of Life Michigan Histocompatibility Laboratory, Ann Arbor, MI, United States
| | - Raquel Nieto
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Veronica Norlin
- Gift of Life Michigan Histocompatibility Laboratory, Ann Arbor, MI, United States
| | - Carmina Gallardo
- European Union Reference Laboratory for ASF, Centro de Investigación en Sanidad Animal-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Chak-Sum Ho
- Gift of Life Michigan Histocompatibility Laboratory, Ann Arbor, MI, United States
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24
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Schwartz JC, Hammond JA. The unique evolution of the pig LRC, a single KIR but expansion of LILR and a novel Ig receptor family. Immunogenetics 2018; 70:661-669. [PMID: 29931472 PMCID: PMC6182393 DOI: 10.1007/s00251-018-1067-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/07/2018] [Indexed: 12/13/2022]
Abstract
The leukocyte receptor complex (LRC) encodes numerous immunoglobulin (Ig)-like receptors involved in innate immunity. These include the killer-cell Ig-like receptors (KIR) and the leukocyte Ig-like receptors (LILR) which can be polymorphic and vary greatly in number between species. Using the recent long-read genome assembly, Sscrofa11.1, we have characterized the porcine LRC on chromosome 6. We identified a ~ 197-kb region containing numerous LILR genes that were missing in previous assemblies. Out of 17 such LILR genes and fragments, six encode functional proteins, of which three are inhibitory and three are activating, while the majority of pseudogenes had the potential to encode activating receptors. Elsewhere in the LRC, between FCAR and GP6, we identified a novel gene that encodes two Ig-like domains and a long inhibitory intracellular tail. Comparison with two other porcine assemblies revealed a second, nearly identical, non-functional gene encoding a short intracellular tail with ambiguous function. These novel genes were found in a diverse range of mammalian species, including a pseudogene in humans, and typically consist of a single long-tailed receptor and a variable number of short-tailed receptors. Using porcine transcriptome data, both the novel inhibitory gene and the LILR were highly expressed in peripheral blood, while the single KIR gene, KIR2DL1, was either very poorly expressed or not at all. These observations are a prerequisite for improved understanding of immune cell functions in the pig and other species.
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Affiliation(s)
| | - John A Hammond
- The Pirbright Institute, Pirbright, Surrey, GU24 0NF, UK.
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25
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Schwartz JC, Hemmink JD, Graham SP, Tchilian E, Charleston B, Hammer SE, Ho C, Hammond JA. The major histocompatibility complex homozygous inbred Babraham pig as a resource for veterinary and translational medicine. HLA 2018; 92:40-43. [PMID: 29687612 PMCID: PMC6099331 DOI: 10.1111/tan.13281] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023]
Abstract
The Babraham pig is a highly inbred breed first developed in the United Kingdom approximately 50 years ago. Previous reports indicate a very high degree of homozygosity across the genome, including the major histocompatibility complex (MHC) region, but confirmation of homozygosity at the specific MHC loci was lacking. Using both direct sequencing and PCR-based sequence-specific typing, we confirm that Babraham pigs are essentially homozygous at their MHC loci and formalise their MHC haplotype as Hp-55.6. This enhances the utility of the Babraham pig as a useful biomedical model for studies in which controlling for genetic variation is important.
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Affiliation(s)
| | - J. D. Hemmink
- The Pirbright InstitutePirbrightSurreyUK
- The Roslin Institute, Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
- Livestock GeneticsThe International Livestock Research InstituteNairobiKenya
| | | | | | | | - S. E. Hammer
- Institute of Immunology, Department of PathobiologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - C.‐S. Ho
- Gift of Life MichiganAnn ArborMichigan
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