SLA typing using the PCR-SSP method and establishment of the SLA homozygote line in pedigreed SNU miniature pigs

Allogeneic and xenogeneic lymphoid reconstitution in a RAG2 -/- IL2RG y/- severe combined immunodeficient pig: A preclinical model for intrauterine hematopoietic transplantation

Mice with severe combined immunodeficiency are commonly used as hosts of human cells. Size, longevity, and physiology, however, limit the extent to which immunodeficient mice can model human systems. To address these limitations, we generated RAG2^−/−IL2RG^y/− immunodeficient pigs and demonstrate successful engraftment of SLA mismatched allogeneic D42 fetal liver cells, tagged with pH2B-eGFP, and human CD34⁺ hematopoietic stem cells after in utero cell transplantation. Following intrauterine injection at day 42–45 of gestation, fetuses were allowed to gestate to term and analyzed postnatally for the presence of pig (allogeneic) and human (xenogeneic) B cells, T-cells and NK cells in peripheral blood and other lymphoid tissues. Engraftment of allogeneic hematopoietic cells was detected based on co-expression of pH2B-eGFP and various markers of differentiation. Analysis of spleen revealed robust generation and engraftment of pH2B-eGFP mature B cells (and IgH recombination) and mature T-cells (and TCR-β recombination), T helper (CD3⁺CD4⁺) and T cytotoxic (CD3⁺CD8⁺) cells. The thymus revealed engraftment of pH2B-eGFP double negative precursors (CD4⁻CD8⁻) as well as double positive (CD4⁺, CD8⁺) precursors and single positive T-cells. After intrauterine administration of human CD34⁺ hematopoietic stem cells, analysis of peripheral blood and lymphoid tissues revealed the presence of human T-cells (CD3⁺CD4⁺ and CD3⁺CD8⁺) but no detectable B cells or NK cells. The frequency of human CD45⁺ cells in the circulation decreased rapidly and were undetectable within 2 weeks of age. The frequency of human CD45⁺ cells in the spleen also decreased rapidly, becoming undetectable at 3 weeks. In contrast, human CD45⁺CD3⁺T-cells comprised >70% of cells in the pig thymus at birth and persisted at the same frequency at 3 weeks. Most human CD3⁺ cells in the pig's thymus expressed CD4 or CD8, but few cells were double positive (CD4⁺ CD8⁺). In addition, human CD3⁺ cells in the pig thymus contained human T-cell excision circles (TREC), suggesting de novo development. Our data shows that the pig thymus provides a microenvironment conducive to engraftment, survival and development of human T-cells and provide evidence that the developing T-cell compartment can be populated to a significant extent by human cells in large animals.

SLA-1 Genetic Diversity in Pigs: Extensive Analysis of Copy Number Variation, Heterozygosity, Expression, and Breed Specificity

Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large number of foreign antigens and thus, their genetic diversity plays a critical role in their functions. In this study, we developed a new high-resolution typing method for pig SLA-1 and successfully typed 307 individuals from diverse genetic backgrounds including 11 pure breeds, 1 cross bred, and 12 cell lines. We identified a total of 52 alleles including 18 novel alleles and 9 SLA-1 duplication haplotypes, including 4 new haplotypes. We observed significant differences in the distribution of SLA-1 alleles among the different pig breeds, including the breed specific alleles. SLA-1 duplication was observed in 33% of the chromosomes and was especially high in the biomedical model breeds such as SNU (100%) and NIH (76%) miniature pigs. Our analysis showed that SLA-1 duplication is associated with the increased level of SLA-1 mRNA expression in porcine cells compared to that of the single copy haplotype. Therefore, we provide here the results of the most extensive genetic analysis on pig SLA-1.

Importance of the Major Histocompatibility Complex (Swine Leukocyte Antigen) in Swine Health and Biomedical Research

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.

Molecular genetic characterization and haplotype diversity of swine leukocyte antigen in Chinese Rongshui miniature pigs

The Rongshui miniature pig is an important model animal for studying livestock disease prevention and control in China. The highly polymorphic swine leukocyte antigen (SLA) has been the focus of considerable interest because of the strong, reproducible associations between particular SLA haplotypes and infectious diseases. In this study, we identified 42 alleles at eight polymorphic SLA loci (SLA-1, SLA-3, SLA-2, SLA-6, DRA, DRB1, DQA, and DQB1) representing seven class I and six class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers in Rongshui miniature pigs. The official names were designated by the SLA Nomenclature Committee of the International Society for Animal Genetics. Seven class I haplotypes, Hp-5b.0, 86.0, 87.0, 88.0, 89.0, 90.0 and 91.0, and four class II haplotypes, Hp-0.18b, 0.19c, 0.41 and 0.47, had not previously been reported in other pig breeds. We also comprehensively analyzed the molecular genetic characterization and phylogenies of the identified alleles and the SLA haplotype diversity in Rongshui miniature pigs. SLA-1 and SLA-6 genes were under positive selection, while SLA-2 was under neutral selection, and the other five genes were under purifying selection. The highly polymorphic new alleles may be derived by nucleotide mutations, insertions and deletions, and fragment recombination, and alleles segregated based on sequence differences and peptide-binding motifs, rather than on pig breed. SLA haplotype diversity was generated by allele/gene conversion and recombination. These results will be helpful for elucidating the molecular genetic mechanisms influencing differential disease resistance among pigs with different SLA haplotypes.

Influence of swine leukocyte antigen haplotype on serum antibody titers against swine erysipelas vaccine and reproductive and meat production traits of SLA-defined selectively bred Duroc pigs

We investigated possible associations of SLA class II haplotypes with serum antibody titers against a swine erysipelas vaccine, reproductive and meat production traits using a population of selective breeding Duroc pigs. In the selective breeding Duroc pigs, four SLA class II-DRB1 and -DQB1 alleles were assigned by using PCR-sequence specific primer technique. Low-resolution haplotype (Lr)-0.30 and/or Lr-0.13 were deduced from the SLA class II alleles in the population of SLA-defined Duroc pigs. SLA-homozygous piglets with the Lr-0.30 haplotype had relatively lower serum antibody titers against the vaccine compared to those with Lr-0.13. In contrast, there were no statistically significant differences in reproductive performance between the SLA-defined pigs with two SLA class II haplotypes. Weaning and rearing rates until the body weight of 105 kg was reached in homozygous piglets with Lr-0.30 were significantly lower than those in homozygous piglets with Lr-0.13. The SLA-defined pigs had lower birth and weaning weights, body weights at 60 days of age, and daily weight gains than non-selective breeding Duroc pigs. Furthermore, the SLA-defined pigs had slightly lower back fat thickness compared to the non-selective breeding pigs. The rib eye areas of homozygous or heterozygous pigs with Lr-0.13 were larger than those of homozygous pigs with Lr-0.30 and non-selective breeding pigs. These data suggested that SLA haplotypes had the potential as useful genetic markers for selective breeding in the population of SLA-defined Duroc pigs.

Swine Leukocyte Antigen Diversity in Canadian Specific Pathogen-Free Yorkshire and Landrace Pigs

The highly polymorphic swine major histocompatibility complex (MHC), termed swine leukocyte antigen (SLA), is associated with different levels of immunologic responses to infectious diseases, vaccines, and transplantation. Pig breeds with known SLA haplotypes are important genetic resources for biomedical research. Canadian Yorkshire and Landrace pigs represent the current specific pathogen-free (SPF) breeding stock maintained in the isolation environment at the Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences. In this study, we identified 61 alleles at five polymorphic SLA loci (SLA-1, SLA-2, SLA-3, DRB1, and DQB1) representing 17 class I haplotypes and 11 class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers methods in 367 Canadian SPF Yorkshire and Landrace pigs. The official designation of the alleles has been assigned by the SLA Nomenclature Committee of the International Society for Animal Genetics and released in updated Immuno Polymorphism Database-MHC SLA sequence database [Release 2.0.0.3 (2016-11-03)]. The submissions confirmed some unassigned alleles and standardized nomenclatures of many previously unconfirmed alleles in the GenBank database. Three class I haplotypes, Hp-37.0, 63.0, and 73.0, appeared to be novel and have not previously been reported in other pig populations. One crossover within the class I region and two between class I and class II regions were observed, resulting in three new recombinant haplotypes. The presence of the duplicated SLA-1 locus was confirmed in three class I haplotypes Hp-28.0, Hp-35.0, and Hp-63.0. Furthermore, we also analyzed the functional diversities of 19 identified frequent SLA class I molecules in this study and confirmed the existence of four supertypes using the MHCcluster method. These results will be useful for studying the adaptive immune response and immunological phenotypic differences in pigs, screening potential T-cell epitopes, and further developing the more effective vaccines.

Sequence variations of the locus-specific 5' untranslated regions of SLA class I genes and the development of a comprehensive genomic DNA-based high-resolution typing method for SLA-2

The genetic diversity of the major histocompatibility complex (MHC) class I molecules of pigs has not been well characterized. Therefore, the influence of MHC genetic diversity on the immune-related traits of pigs, including disease resistance and other MHC-dependent traits, is not well understood. Here, we attempted to develop an efficient method for systemic analysis of the polymorphisms in the epitope-binding region of swine leukocyte antigens (SLA) class I genes. We performed a comparative analysis of the last 92 bp of the 5' untranslated region (UTR) to the beginning of exon 4 of six SLA classical class I-related genes, SLA-1, -2, -3, -4, -5, and -9, from 36 different sequences. Based on this information, we developed a genomic polymerase chain reaction (PCR) and direct sequencing-based comprehensive typing method for SLA-2. We successfully typed SLA-2 from 400 pigs and 8 cell lines, consisting of 9 different pig breeds, and identified 49 SLA-2 alleles, including 31 previously reported alleles and 18 new alleles. We observed differences in the composition of SLA-2 alleles among different breeds. Our method can be used to study other SLA class I loci and to deepen our knowledge of MHC class I genes in pigs.

Molecular characterization of swine leukocyte antigen class I genes by sequence-based and PCR-SSP method in Guizhou minipigs

The highly polymorphic swine leucocyte antigen (SLA) genes play an important role in swine immune responses to infectious diseases, vaccines and production performance. The pig resource with well defined SLA genes is useful for xenotransplantation and immunological studies. In this study, we have characterized three SLA class I genes (SLA-1, SLA-3, SLA-2) of 22 founder Guizhou minipigs using sequence-based typing method. Thirteen alleles were detected in this population, compared with the SLA allele sequences in GenBank, 11 of 13 SLA class I alleles were novel in Guizhou minipigs. There are four SLA I haplotypes, none of them previously reported in other pigs. Based on these alleles sequences information, we developed a simple method implemented to SLA-typing for unknown offsprings of Guizhou minipigs, relying on designed 13 sequence specific primers that could discriminate each one among which located in each locus using PCR in a SLA typing assay. According the combination methods of sequence-based typing and PCR-SSP, we were able to rapidly conduct SLA typing for Guizhou breeding stock and identify four SLA haplotypes present in the herd. This resource population of SLA-defined Guizhou minipigs will be useful as animal models for xenotransplantation and further immunological research.

Identification of peptides from foot-and-mouth disease virus structural proteins bound by class I swine leukocyte antigen (SLA) alleles, SLA-1*0401 and SLA-2*0401

Characterization of the peptide-binding specificity of swine leukocyte antigen (SLA) class I and II molecules is critical to the understanding of adaptive immune responses of swine toward infectious pathogens. Here, we describe the complete binding motif of the SLA-2*0401 molecule based on a positional scanning combinatorial peptide library approach. By combining this binding motif with data achieved by applying the NetMHCpan peptide prediction algorithm to both SLA-1*0401 and SLA-2*0401, we identified high-affinity binding peptides. A total of 727 different 9mer and 726 different 10mer peptides within the structural proteins of foot-and-mouth disease virus (FMDV), strain A24 were analyzed as candidate T-cell epitopes. Peptides predicted by the NetMHCpan were tested in ELISA for binding to the SLA-1*0401 and SLA-2*0401 major histocompatibility complex class I proteins. Four of the 10 predicted FMDV peptides bound to SLA-2*0401, whereas five of the nine predicted FMDV peptides bound to SLA-1*0401. These methods provide the characterization of T-cell epitopes in response to pathogens in more detail. The development of such approaches to analyze vaccine performance will contribute to a more accelerated improvement of livestock vaccines by virtue of identifying and focusing analysis on bona fide T-cell epitopes.