Characterization of bovine MHC class II polymorphism using three typing methods: serology, RFLP and IEF.

Various methods, with different strengths and weaknesses, are currently used to define polymorphism of the bovine major histocompatibility complex (MHC) class II genes. A more complete characterization of bovine lymphocyte antigen (BoLA) haplotypes can be achieved by combining several of these methods. In this study BoLA class II polymorphism was characterized using three typing methods: serology, restriction fragment length polymorphism (RFLP), and isoelectric focusing (IEF). Twenty six Holstein-Friesian and 15 Angus cattle that carried an array of serologically defined BoLA haplotypes were selected for the study. The panel included 12 BoLA complex homozygotes. The three class II typing methods recognized polymorphism associated with the same or very tightly linked genes in the DQ-DR class II subregion. In total 25 BoLA-A locus (class I)--DQ-DR subregion (class II) haplotypes were defined. Three of the serological class II specificities, Dx1, Dx3, and Dx4, were associated with more than one RFLP defined DQ-DR haplotype. The other 4 class II specificities behaved as private specificities. One BoLA haplotype was found in both Holstein and Angus cattle. Two other BoLA haplotypes defined here have previously been described in other breeds. This suggests that these haplotypes exist in strong linkage disequilibrium.     

CHARACTERIZATION OF BOVINE MHC CLASS II POLYMORPHISM USING THREE TYPING METHODS: SEROLOGY,RFLP AND IEF

Various methods, with different strengths and weaknesses, are currently used to define polymorphism of the bovine major histocompatibility complex (MHC) class II genes. A more complete characterization of bovine lymphocyte antigen (BoLA) haplotypes can be achieved by combining several of these methods. In this study BoLA class II polymorphism was characterized using three typing methods: serology, restriction fragment length polymorphism (RFLP), and isoelectric focusing (IEF). Twenty six Holstein-Friesian and 15 Angus cattle that carried an array of serologically defined BoLA haplotypes were selected for the study. The panel included 12 BoLA complex homozygotes. The three class II typing methods recognized polymorphism associated with the same or very tightly linked genes in the DQ-DR class II subregion. In total 25 BoLA-A locus (class I) —DQ-DR subregion (class II) haplotypes were defined. Three of the serological class II specificities, Dx1, Dx3, and Dx4, were associated with more than one RFLP defined DQ-DR haplotype. The other 4 class II specificities behaved as private specificities. One BoLA haplotype was found in both Holstein and Angus cattle. Two other BoLA haplotypes defined here have previously been described in other breeds. This suggests that these haplotypes exist in strong linkage disequilibrium.     

Induction of active immunological hypo/non-responsiveness to C5 in adult C5-deficient DBA/2 mice.

A recently established, one-dimensional isoelectric focusing (IEF) method for distinguishing major histocompatibility complex (MHC) class II polymorphisms in an outbred species, cattle, has allowed us to analyse the involvement of the MHC in the recognition of antigen by bovine T cells. Bovine T-cell lines of Th cell phenotype (BoCD4+) specific for ovalbumin were generated from six individual high responder animals. These animals were bovine MHC (BoLA) class II typed using the IEF technique which detects bovine DR-like products. Four of the animals were shown to be heterozygous and two were homozygous for the IEF specificities. Six out of the 13 IEF specificities (EDF types) detected so far were represented by this group of animals. The cell lines were tested against a panel of IEF-typed antigen-presenting cells (APC) from unrelated donors. The lines only responded to antigen in proliferation assays when the APC shared at least one MHC class II EDF specificity with the BoCD4+ cell line. The responses did not correlate with BoLA class I specificities. However, lines from one of the animals were consistently generated to one of the two haplotypes only. This suggests that there are non-responder alleles to a multi-epitope antigen, present in the cattle population. The results demonstrate that IEF of bovine MHC class II products defines haplotypes of functional relevance, and may indeed be identifying the actual restriction elements involved in presentation of ovalbumin. These results have important implications for future vaccine design in an outbred species, particularly in terms of immune response gene effects and disease associations.     

MHC class II restricted recognition of FMDV peptides by bovine T cells.

A putative synthetic vaccine for foot-and-mouth disease (FMDV15) has proved less successful in a host species, cattle, than predicted by results in a small-animal model. Possible reasons for this include non-recognition by T cells influenced by major histocompatibility complex (MHC)-linked immune response gene control. It is now possible to type for human leucocyte antigen (HLA) DR-like bovine MHC (BoLA) class II polymorphisms with a one-dimensional isoelectric focusing (IEF) technique. Using this method 14 unrelated cattle were selected with eight different BoLA class II IEF types. After immunization with FMDV15, 13 cattle generated a T-cell response to FMDV15. However, the fine specificity and magnitude of the response was related to BoLA class II type. The non-response by one animal and low response by two other animals were associated with two of the BoLA class II types. Response to the region 149-158 was immunodominant and animals which did not respond to this region had low responses to the whole peptide. Using FMDV-specific T-cell lines five BoLA class II types associated with responder animals were able to present FMDV15 in an MHC class II-restricted fashion, indicating that this peptide is capable of binding to different MHC class II molecules and may account for the broad response observed. The restriction patterns of the lines indicated that the IEF method does not distinguish all functional polymorphisms. At least two of the IEF-defined types could each be split into two distinct specificities and revealed that the three sets of animals with identical IEF types in fact expressed distinct restriction elements.     

Distribution and origin of bovine major histocompatibility complex class II DQA1 genes in Japan

We sequenced the major histocompatibility complex (MHC) class II DQA1 gene in 352 Japanese cattle (95 Japanese Black, 91 Holstein, 102 Japanese Shorthorn and 64 Jersey cattle) using a new sequence-based typing method. In total, 19 bovine MHC ( BoLA )- DQA1 alleles, of which two were novel alleles, were detected. The Holstein, Jersey, Japanese Shorthorn and Japanese Black breeds had 13, 12, 10 and 15 alleles, respectively. The dendrogram that was constructed by the neighbor-joining method on the basis of the DQA1 gene allele frequencies of the four Japanese cattle breeds showed that the Holstein and Japanese Black breeds were closest to each other, with Jersey being farther from these two breeds than Japanese Shorthorn. In addition, Wu–Kabat analysis showed that the DQA1 alleles of the Holstein and Japanese Black were the most and least polymorphic, respectively. Phylogenetic analyses indicated that the DQA1 gene of Bovidae such as cattle, sheep, bison and goat were more similar to pig SLA-DQA genes than to human HLA-DQA1 and dog DLA-DQA genes. The cattle, goat, bison, sheep, human and pig DQA1 molecules had similar rates of amino acid sequence polymorphism, but the distribution of their polymorphic residues differed from that in the dog DQA1 protein. However, the Bovidae DQA1 molecule had more polymorphic residues than the human, pig and dog DQA molecules at two regions, namely positions 52–53 and 65–66. This indicates that the Bovidae DQA1 locus is more polymorphic than the DQA loci of other species.     

Genotyping BoLA‐DRB3 alleles in Brazilian Dairy Gir cattle (Bos indicus) by temperature‐gradient gel electrophoresis (TGGE) and direct sequencing

BoLA‐DRB3 is a gene of the major histocompatibility complex (MHC) in cattle. The product of the BoLA‐DRB3 gene is a beta chain of an MHC class II molecule, a glycoprotein expressed on the surface of antigen‐presenting cells (APCs). Responses of CD4⁺ T lymphocytes to peptides are dependent on the presentation of peptide ligands bound to class II molecules on APCs. Genotyping of the BoLA‐DRB3 gene is relatively complex due to the extensive polymorphism of this locus. Current techniques for assignment of genotypes are polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP), direct sequencing of PCR products, cloning‐sequencing, polymerase chain reaction using sequence‐specific oligonucleotide probes (PCR‐SSOP), and denaturant‐gradient gel electrophoresis. These techniques are time‐consuming, do not discriminate all possible alleles, or are not readily reproducible. The objective of this study was to genotype BoLA‐DRB3 using temperature‐gradient gel electrophoresis (TGGE) to separate alleles before sequencing. PCRs using 28 DNA samples from Gir Dairy cattle (a Brazilian breed of Bos indicus) were submitted to TGGE. New PCR products were generated from separated alleles, purified, and sequenced. Allele separation was possible in 21 out of 26 heterozygote samples (81%). Results indicate that two sequence reads (forward and reverse) were sufficient for accurate genotyping of BoLA‐DRB3 alleles. Separation of alleles by TGGE provides high‐throughput, reliable typing of BoLA‐DRB3, which is critical in disease association studies in cattle.     

Comparative organization and function of the major histocompatibility complex of domesticated cattle

Summary: This review focuses on recent advances in research on the bovine major histocompatibility complex ( BoLA ), with specific reference to the genetic organization, polymorphism and function of the class II genes. The BoLA region is unlike the MHC of humans and mice in that a large inversion has moved several class II genes, including the TAP/LMP cluster, close to the centromere of bovine chromosome 23. Therefore, dose linkage of MHC genes and other genes associated with the MHC in humans and mice does not appear to be required for normal immunological function. In cattle, polymorphism in the class IIa genes influences both the magnitude and the epitope specificity of antigen-specific T-cell responses to foot-and-mouth disease virus peptides. Disease association studies have demonstrated that BoLA alleles affect the subclinical progression of bovine leukemia virus ( BLV ) infection. This association is strongly correlated with the presence of specific amino acid motifs within the DRB3 antigen-binding domain. In addition to the practical significance of these findings, the association between BoLA and BLV provides a unique model to study host resistance to retrovirus infection in a non-inbred species. These studies contribute to our understanding of the evolution of the MHC in mammals, to the development of broadly effective vaccines, and to breeding strategies aimed at improving resistance to infectious diseases.     

Polymorphism of the BoLA System

The bovine lymphocyte antigen system (BoLA) was studied by serological methods. Evidence for the existence of one locus was established and six codominant alleles were found to segregate at this first locus. The frequency varied considerably among these genes, and the presence of a null allele suggests that new BoLA specificities are likely to be found in the cattle population.     

Cytotoxic T cell epitope in cattle from the attachment glycoproteins of rinderpest and peste des petits ruminants viruses

The surface glycoproteins of rinderpest virus (RPV) confer protective immunity in cattle. We demonstrated that cattle immunized with a recombinant extracellular baculovirus expressing the hemagglutinin (H) protein of RPV (rECV-H) generate virus neutralizing antibody responses, bovine leukocyte antigen (BoLA) class II restricted helper T cell responses and BoLA class I restricted cytotoxic T cell (CTL) responses against RPV-H and hemagglutinin-neuraminidase (HN) glycoprotein of closely related Peste des petits ruminants virus (PPRV). In this study, employing autologous skin fibroblasts transiently expressing truncations of H and HN in a BoLA class I restricted lymphoproliferation assay, we have mapped a highly homologous domain (amino acids 400-423) on these proteins harboring a CTL epitope. Subsequently, based on sequence comparison with available BoLA class I binding motifs, we have identified a BoLA-A11 binding motif (amino acids 408-416) in the stimulatory domain. Autologous cells pulsed with a synthetic peptide corresponding to this sequence stimulated CTLs from rECV-H immunized as well as tissue culture attenuated RPV vaccinated cattle of different breeds and parentage. This is the first epitope identified in cattle on the attachment glycoproteins of RPV and PPRV.     

POLYMORPHISM OF BOVINE MHC CLASS I GENES. JOINT REPORT OF THE FIFTH INTERNATIONAL BOVINE LYMPHOCYTE ANTIGEN (BoLA) WORKSHOP,INTERLAKEN, SWITZERLAND, 1 AUGUST 1992

The objectives of the Fifth International BoLA Workshop were to: standardize nomenclature, compare typing methods, and characterize BoLA haplotypes. The workshop was based on the distribution of blood samples (cells) from 60 selected cattle to 14 laboratories. Results for the class I (BoLA-A) region are presented in this paper while results for the class II regions are presented in a separate report. Thirty-six of the 50 previously established serological class I specificities were represented in the cell panel. However, only 30 specificities could be confirmed. Two specificities, A16 and A32, were upgraded from provisional, workshop (w) specificities to BoLA-A locus specificities and three new specificities, w51(w28), w52 and w53(w28), were defined. The 39 specificities distinguished 30 class I haplotypes in the 60 animals. Class I isoelectric focusing proved to be a useful adjunct to the serology. Isoelectric focusing confirmed several serologically defined splits and detected splits of A15(A8), A18(A6) and A22(w49) that had not been detected by serology. Subsequently, serological support for splits of A15(A8) and A22(w49) was found.     

An allele-specific,stochastic gene expression process controls the expression of multiple Ly49family genes and generates a diverse,MHC-specific NK cell receptor repertoire

Mouse NK cells express MHC class I-specific inhibitory Ly49 receptors. Since these receptors display distinct ligand specificities and are clonally distributed, their expression generates a diverse NK cell receptor repertoire specific for MHC class I molecules. We have previously found that the D ^d (or D^k )-specific Ly49A receptor is usually expressed from a single allele. However, a small fraction of short-term NK cell clones expressed both Ly49A alleles, suggesting that the two Ly49A alleles are independently and randomly expressed. Here we show that the genes for two additional Ly49 receptors (Ly49C and Ly49G2) are also expressed in a (predominantly) mono-allelic fashion. Since single NK cells can co-express multiple Ly49 receptors, we also investigated whether mono-allelic expression from within the tightly linked Ly49 gene cluster is coordinate or independent. Our clonal analysis suggests that the expression of alleles of distinct Ly49 genes is not coordinate. Thus Ly49 alleles are apparently independently and randomly chosen for stable expression, a process that directly restricts the number of Ly49 receptors expressed per single NK cell. We propose that the Ly49 receptor repertoire specific for MHC class I is generated by an allele-specific, stochastic gene expression process that acts on the entire Ly49 gene cluster.     

Killer immunoglobulin-like receptor expression on single cells: a cautionary note

Natural killer (NK) cells keep the surface expression of major histocompatibility complex (MHC) class I molecules under surveillance using killer immunoglobulin-like receptors (KIR). Virus-infected or aberrant cells are frequently characterized by a reduced surface expression of MHC class I antigens and may therefore be removed by cytolysis. NK cells are heterogeneous with regard to the expression of KIR genes. The resulting subpopulations show distinguishable specificities allowing the recognition of cells lacking varying combinations of MHC class I antigens. The KIR expression pattern in single NK cells has previously been analyzed by Husain and colleagues by cDNA preamplification of CD3- CD56+ single cells and subsequent gene-specific polymerase chain reaction. We show here that the data of this study contain inconsistencies. These inconsistencies are discussed in the context of KIR mRNA abundance and single-cell cDNA amplification efficiency.     

Strain specificity of bovine Theileria parva-specific cytotoxic T cells is determined by the phenotype of the restricting class I MHC

To determine whether the major histocompatibility complex (MHC) phenotype of cattle could affect the parasite strain specificity of immunity to Theileria parva by influencing the antigenic specificity of Theileria-specific cytotoxic T lymphocytes (CTL), we investigated the parasite strain specificity of Theileria-specific CTL clones derived from cattle of different class I MHC phenotypes. Thirty-one class I-restricted CTL clones were generated from four cattle immunized with the Muguga stock of T. parva. The MHC restriction and parasite strain specificities were determined for each clone utilizing as targets, parasitized cell lines of different MHC phenotypes and cloned cell lines containing different parasite strains. CTL clones restricted by the same MHC determinant had similar parasite strain specificities. On the other hand, clones restricted by different MHC determinants exhibited different parasite strain specificities. This was true whether the clones were generated from the same animal or from different cattle and tested on a target cell line expressing both MHC determinants. These results provide strong evidence that differences in the strain specificities of CTL derived from animals immunized with the same parasite stock, are determined by the class I MHC phenotype of the immunized animal.     

Establishment of a sequence-based typing system for BoLA-DQA1 exon 2

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for bovine diseases and immunological traits. Here, we developed a rapid, high-resolution sequence-based typing (SBT) system for BoLA-DQA1. We amplified 355 bp of BoLA-DQA1 by fully nested polymerase chain reaction (PCR) using the newly constructed primers and then performed direct sequencing of each product. Using this method, we investigated the locus in 51 animals whose BoLA haplotypes had been characterized at the Fifth International BoLA Workshop. We identified 15 distinct DQA1 alleles, and there is no conflict between the typing result of PCR-SBT and restriction fragment length polymorphism analysis. Together with the previously developed method for typing BoLA-DRB3, the PCR-SBT for BoLA-DQA1 clearly provides a useful tool for detailed class IIa haplotype analysis.     

An unusual insertion in intron 2 of apparently functional MHC class I alleles in rhesus macaques

Here we describe a nucleotide insertion in intron 2 of two rhesus major histocompatibility complex (MHC) class I alleles, Mamu-A*05 and Mamu-A*07. This resulted in an intron 2 that was nearly twice the length of any other intron 2 of primate MHC class I genes sequenced to date. This insertion was most similar (93% identity) to the beginning of intron 3 of HLA-A alleles. It was also similar to intron 3 of several human MHC class I pseudogenes and MHC class I pseudogenes from cotton top tamarin and cat. The finding of this insertion in two rhesus MHC class I genes is surprising given the uniformity in length and sequence of introns of functional HLA-A, -B and -C genes.     

Molecular characterization of classical and nonclassical MHC class I genes from the golden pheasant (Chrysolophus pictus)

Classical major histocompatibility complex (MHC) class I allelic polymorphism is essential for competent antigen presentation. To improve the genotyping efforts in the golden pheasant, it is necessary to differentiate more accurately between classical and nonclassical class I molecules. In our study, all MHC class I genes were isolated from one golden pheasant based on two overlapping PCR amplifications. In total, six full‐length class I nucleotide sequences (A–F) were identified, and four were novel. Two (A and C) belonged to the IA1 gene, two (B and D) were alleles derived from the IA2 gene through transgene amplification, and two (E and F) comprised a third novel locus, IA3 that was excluded from the core region of the golden pheasant MHC‐B. IA1 and IA2 exhibited the broad expression profiles characteristic of classical loci, while IA3 showed no expression in multiple tissues and was therefore defined as a nonclassical gene. Phylogenetic analysis indicated that the three IA genes in the golden pheasant share a much closer evolutionary relationship than the corresponding sequences in other galliform species. This observation was consistent with high sequence similarity among them, which likely arises from the homogenizing effect of recombination. Our careful distinction between the classical and nonclassical MHC class I genes in the golden pheasant lays the foundation for developing locus‐specific genotyping and establishing a good molecular marker system of classical MHC I loci.     

MHC Class II epitope predictive algorithms

Major histocompatibility complex class II (MHC‐II) molecules sample peptides from the extracellular space, allowing the immune system to detect the presence of foreign microbes from this compartment. To be able to predict the immune response to given pathogens, a number of methods have been developed to predict peptide–MHC binding. However, few methods other than the pioneering TEPITOPE/ProPred method have been developed for MHC‐II. Despite recent progress in method development, the predictive performance for MHC‐II remains significantly lower than what can be obtained for MHC‐I. One reason for this is that the MHC‐II molecule is open at both ends allowing binding of peptides extending out of the groove. The binding core of MHC‐II‐bound peptides is therefore not known a priori and the binding motif is hence not readily discernible. Recent progress has been obtained by including the flanking residues in the predictions. All attempts to make ab initio predictions based on protein structure have failed to reach predictive performances similar to those that can be obtained by data‐driven methods. Thousands of different MHC‐II alleles exist in humans. Recently developed pan‐specific methods have been able to make reasonably accurate predictions for alleles that were not included in the training data. These methods can be used to define supertypes (clusters) of MHC‐II alleles where alleles within each supertype have similar binding specificities. Furthermore, the pan‐specific methods have been used to make a graphical atlas such as the MHCMotifviewer, which allows for visual comparison of specificities of different alleles.