Gene organization and polymorphism of the swine major histocompatibility complex

The recent availability of the full‐length sequence of one haplotype of the swine leukocyte antigen (SLA) complex, the swine major histocompatibility complex (MHC), and significant progress in the studies on gene expression and polymorphisms led to major advances in deciphering its role in resistance to diseases in animals. The present status of the genomic organization and polymorphism of the SLA complex is presented in this Review. Additionally, a comparative analysis with mammalian MHC has also been provided. The sequenced SLA‐H01 haplotype harbors 152 loci including genuine SLA genes, non‐MHC genes and pseudogenes. Although the numbers of expressed SLA genes could vary across haplotypes, three SLA class Ia, three SLA class Ib, four SLA class IIa and four SLA class IIb genes are currently expressed. Except for the class I genes, which have no clear orthologs, the gene organization of the loci was highly conserved between humans and pigs. Moreover, the human leukocyte antigen (HLA) complex lies on a single chromosomal segment, whereas a centromere at the class II and III junction splits the SLA complex into two segments, without disturbing gene organization or impeding functionality. Over 400 SLA class I and II allele sequences available in databases have been recently clustered and assigned to a specific SLA locus according to a newly defined nomenclature system.     

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense.     

Porcine MHC classical class I genes are coordinately expressed in superantigen-activated mononuclear cells

The expression of the major histocompatibility complex (MHC) classical class I genes is important for the adaptive immune response to target virus-infected cells and cancer cells. The up-regulation of the MHC is achieved by hormonal/cytokine signals including IFN-γ-inducible elements. The swine leukocyte antigen (SLA), the MHC class I region of pigs, consists of the duplicated classical class I genes, SLA-1, SLA-2 and SLA-3, but the molecular mechanisms involved in their up-regulation after T cell stimulation have not been fully elucidated. In order to better understand some of the putative regulatory mechanisms of SLA class I gene expression in activated T cells, we examined the coordinated expression of the SLA classical class I, IFN-γ and interferon regulatory factor-1 (IRF-1) genes in the peripheral blood mononuclear cells (PBMCs) of SLA homozygous Clawn miniature swine stimulated for 72h with either IFN-γ or an enterotoxin produced by Staphylococcus aureus. This enterotoxin, toxic shock syndrome-1 (TSST-1), is known to act as a superantigen (sAG) to activate the T cells in various vertebrate species. We showed by using mAbs and flow cytometry that the CD4(+)CD25(+) cell number of swine PBMCs was also increased by TSST-1 and to a lesser degree by IFN-γ. Time course analyses of the expression of the IFN-γ, IRF-1 and the three classical class I genes, SLA-1, SLA-2, and SLA-3, in PBMCs by quantitative real-time PCR revealed a transitory response to TSST-1 or IFN-γ stimulation. The IFN-γ mRNA levels in the PBMCs were continuously up-regulated over the first 48h by TSST-1 or IFN-γ. In contrast, SLA class I expression moderately increased at 24h and then decreased to a baseline level or less at 72h of IFN-γ or TSST-1 stimulation. The three classical SLA class I genes showed similar expression kinetics, although SLA-3 mRNA level was consistently lower than those of SLA-1 and -2. The expression of IRF-1, a modulator of SLA expression, showed similar kinetics to those of the three classical SLA class I genes. The expression profiles detected by flow cytometry of the SLA molecules on the cell surface of PBMCs were maintained at a consistently high level during cell stimulation with either TSST-1 or IFN-γ, which was distinct from the kinetics of mRNA expression. These results showed that miniature swine SLA class I mRNA expression was effectively and equally up-regulated among the three loci and coordinately with IRF-1 gene expression after stimulation of T cell activation by sAG or IFN-γ.     

The cattle major histocompatibility complex: is it unique?

Major histocompatibility complex (MHC) class I genes encode highly polymorphic molecules that are expressed on virtually every cell type, and have been identified in all but the most primitive vertebrates. They play a number of crucial roles in the immune response to infectious disease. Most information regarding MHC genes has been generated from humans and mice but, because of the great variability found in the MHC system, it is not always possible to extrapolate from these to other species. Many strategies have evolved to maximise the ability of the MHC to protect individuals and populations against pathogens. Cattle MHC class I genes exhibit a number of unusual features. Evidence from mapping studies, haplotype and phylogenetic analyses suggests the presence of six classical class I loci, in contrast to the more usual two or three, and these are expressed in various combinations of one, two or three on different haplotypes. Although it remains difficult to assign alleles to loci, it appears that none of the loci are expressed on all haplotypes. There is currently limited information relating to polymorphism, but various approaches suggest diversity is high, and may vary between breeds/populations. Functional consequences of variable MHC haplotype composition are discussed. Identifying unique features of the MHC in cattle will lead to new insights into evolution of the immune system.     

Structure and expression of class I MHC genes in the miniature swine

The genome of the miniature swine, unlike other species, contains a relatively small class I MHC gene family, consisting of only seven members. This provides an excellent system in which to identify and characterize the regulatory mechanisms which operate to both coordinately and differentially regulate the expression of a multi-gene family. The structure of class I SLA genes, like other class I genes, consists of eight exons encoding a leader sequence, three extracytoplasmic domains, a transmembrane domain and intracytoplasmic domains. Despite the common structure, two sub-families of class I genes can be distinguished within the SLA family. One, containing the closely related PD1 and PD14 genes, encodes the classical transplantation antigens. Another contains the highly divergent PD6; the functions of the products of this subfamily, if any, are not known. The class I SLA genes share some common regulatory mechanisms, as evidenced by the fact that all three genes analyzed are transcribed in mouse L cells. Furthermore, interferon treatment of transfected mouse L cells enhances expression of all three genes. Both PD1 and PD6 are transcribed in vivo, where the highest levels of expression are observed in lymphoid tissues. Superimposed on the common patterns of class I gene expression are distinct ones, as evidenced by the findings that PD1 is preferentially expressed in B cells, whereas PD6 is preferentially expressed in T cells. These differences may reflect the extensive divergence of the 5' flanking sequences of these genes. Future studies will be aimed at elucidating the precise molecular interactions and mechanisms which give rise to the observed differential expression.     

Expression kinetics of chicken β2-microglobulin and Class I MHC in vitro and in vivo during Marek’s disease viral infections

Marek’s disease virus (MDV) is a highly cell-associated herpesvirus that causes a disease in chickens characterized by tumor formation and immunosuppression. The changes of major histocompatibility complex (MHC) expression in different MDV-infected cells are not completely understood. In this study, we investigated the expression of the Class I MHC and β2-microglobulin (β2m) genes in response to MDV infection at different time points by real-time PCR. In both in vitro and in vivo, the expression levels of Class I MHC and β2m genes were upregulated during early MDV infections in comparison to control cells; We also found that the expression of Class I MHC gene was downregulated in BudR (5-bromo-2′-deoxyuridine)-treated MSB1 cells at 48 h and MDV-infected chicken embryo fibroblast cells (CEF) at 120 and 168 h post infection (hpi); Furthermore, compared to control groups, Class I MHC and β2m expression levels were downregulated in peripheral blood lymphocytes (PBLC) from MDV-infected chickens at 14 and 28 days post infection (dpi); Interestingly, both Class I MHC and β2m gene expression levels increased again in PBLC from MDV RB1B-infected chickens at 35 dpi, in which MDV was in the latent or transformed infection stages. In addition, Class I MHC expression was clearly decreased in MDV-infected CEF at 120 hpi although β2m expression was significantly increased. These changes in Class I MHC and β2m gene expression might provide more insights into host-virus interaction.     

The impact of MHC diversity on cattle T cell responses

Major histocompatibility complex (MHC) genes play a key role in immunity to infectious pathogens. Their high level of diversity is a functionally important characteristic. In cattle our knowledge of MHC diversity and the functional distinction between genes is limited. Recent studies in commercially important dairy cattle populations reveal that MHC class I diversity is relatively low, although it does not appear to be declining. The presence and frequency of some genes and alleles was markedly different between geographically distinct populations, and trait selection was implicated as an influential force. Functional studies suggest that some alleles may have a disproportionally high impact on T cell responses, thus it may be important to consider their role in both disease resistance and vaccine efficacy. It is clear that increasing our knowledge of the functional capabilities of different cattle MHC class I genes is essential to maintain healthy populations in the future.     

Genetic manipulation of the major histocompatibility complex

The genes of the major histocompatibility complex (MHC) are prime candidates for genetic engineering of domestic species because of their importance in many biological phenomena, including disease resistance and reproduction. One MHC-linked gene, the Ped gene in the mouse, has been shown to influence embryo development and survival. The Ped gene has mapped to the Qa-2 subregion of the mouse MHC, the H-2 complex. Future studies are aimed at determining, at the DNA and protein levels, the structure of the Ped gene and its gene product. There is preliminary evidence that there may be MHC-linked Ped-like genes that influence reproduction in other species. The search for Ped-like genes in domestic species has been hampered by the limited data available describing the molecular structure of the MHC of species other than mouse and man. This paper describes the use of restriction fragment length polymorphism analysis to study the MHC of two domestic species, the pig and the chicken. Major histocompatibility complex effects on reproduction have been reported for both the pig and the chicken. The long-range goal is to identify and isolate advantageous alleles that could then be injected into recipient embryos to create more reproductively efficient animals.     

Genes controlling vaccine responses and disease resistance to respiratory viral pathogens in cattle

Farm animals remain at risk of endemic, exotic and newly emerging viruses. Vaccination is often promoted as the best possible solution, and yet for many pathogens, either there are no appropriate vaccines or those that are available are far from ideal. A complementary approach to disease control may be to identify genes and chromosomal regions that underlie genetic variation in disease resistance and response to vaccination. However, identification of the causal polymorphisms is not straightforward as it generally requires large numbers of animals with linked phenotypes and genotypes. Investigation of genes underlying complex traits such as resistance or response to viral pathogens requires several genetic approaches including candidate genes deduced from knowledge about the cellular pathways leading to protection or pathology, or unbiased whole genome scans using markers spread across the genome. Evidence for host genetic variation exists for a number of viral diseases in cattle including bovine respiratory disease and anecdotally, foot and mouth disease virus (FMDV). We immunised and vaccinated a cattle cross herd with a 40-mer peptide derived from FMDV and a vaccine against bovine respiratory syncytial virus (BRSV). Genetic variation has been quantified. A candidate gene approach has grouped high and low antibody and T cell responders by common motifs in the peptide binding pockets of the bovine major histocompatibility complex (BoLA) DRB3 gene. This suggests that vaccines with a minimal number of epitopes that are recognised by most cattle could be designed. Whole genome scans using microsatellite and single nucleotide polymorphism (SNP) markers has revealed many novel quantitative trait loci (QTL) and SNP markers controlling both humoral and cell-mediated immunity, some of which are in genes of known immunological relevance including the toll-like receptors (TLRs). The sequencing, assembly and annotation of livestock genomes and is continuing apace. In addition, provision of high-density SNP chips should make it possible to link phenotypes with genotypes in field populations without the need for structured populations or pedigree information. This will hopefully enable fine mapping of QTL and ultimate identification of the causal gene(s). The research could lead to selection of animals that are more resistant to disease and new ways to improve vaccine efficacy.     

主要组织相容性复合体在鸟类保护生物学中的应用

在保护生物学研究中,主要组织相容性复合体（major histocompatibility complex,MHC）的遗传多样性越来越受到人们的重视。在研究比较广泛和深入的哺乳动物和鱼类中,MHC被认为与抗病能力、配偶选择和亲缘识别有关。然而,MHC基因对哺乳动物行为产生影响的机制是否适用于鸟类,特别是鸟类野生种群,尚不清楚。文章对MHC多态性机制、MHC基因分型方法及其与鸟类疾病抗性、配偶选择的关系等进行了综述,为研究人员对鸟类保护生物学的深入研究提供参考。     

翼手目保护生物学研究中的MHC分子标记

主要组织相容性复合体(major histocompatibility complex,MHC)是脊椎动物基因组中多态性最高的基因座位之一,是动物免疫相关基因。MHC进化机制主要是病原体选择机制,MHC多态性能够反映动物种群生活史的适应性进化和生存能力,MHC基因作为非中性分子标记,在翼手目保护生物学研究中具有重要意义和应用前景。     

主要组织相容性复合体（MHC）基因研究进展

主要组织相容性复合体(major histocompatibility complex,MHC)广泛存在于脊椎动物中,由于其高度多态性,使其在遗传育种和抗病性方面成为人们关注的热点。作者通过对国内外研究者近几十年在MHC基因多态性及该基因与疾病之间的关系等方面的研究做一回顾性总结,并将其中的一些内容作为参考进行下一步的相关性试验。     

Immunological basis of differences in disease resistance in the chicken

Genetic resistance to diseases is a multigenic trait governed mainly by the immune system and its interactions with many physiologic and environmental factors. In the adaptive immunity, T cell and B cell responses, the specific recognition of antigens and interactions between antigen presenting cells, T cells and B cells are crucial. It occurs through a network of mediator proteins such as the molecules of the major histocompatibility complex (MHC), T cell receptors, immunoglobulins and secreted proteins such as the cytokines and antibodies. The diversity of these proteins that mainly is due to an intrinsic polymorphism of the genes causes phenotypic variation in disease resistance. The well-known linkage of MHC polymorphism and Marek's disease resistance difference represents a classic model revealing immunological factors in resistance differences and diversity of mediator molecules. The molecular bases in any resistance variation to infectious pathogens are vaguely understood. This paper presents a review of the major immune mediators involved in resistance and susceptibility to infectious diseases and their functional mechanisms in the chicken. The genetic interaction of disease resistance with production traits and the environment is mentioned.     

鸡主要组织相容性复合体(MHC)研究进展

鸡主要组织相容性复合体(MHC)与排斥反应、淋巴细胞反应及抗原递呈有关,其编码基因簇位于16号染色体上,其上许多基因具有多态性,与疾病抗性或易感性密切相关.文章主要对鸡的16号染色体上基因分布、MHC-B区域基因、MHC单倍型检测方法及鸡MHC与常见疾病的关系等方面进行综述.     

我国地方鸡种TAP2基因SNP筛查及遗传结构分析

抗原处理相关转运体基因(TAP)位于主要组织相容性复合体区域,而由TAP1 和TAP2 组成的二聚体能够将抗原肽从细胞质转运入内质网腔,因此,其在免疫反应过程中发挥重要的呈递作用。[目的]检测26个鸡种TAP2基因全长的序列信息,分析TAP2基因单核苷酸多态性,并进一步研究TAP2不同SNPs位点对其蛋白结构的影响及其在不同鸡种中的遗传变异特点。[方法]采用目标捕获序列测序方法,检测26个鸡种的260个体的TAP2基因全长,利用DNAMAN软件对26个鸡品种的测序序列进行比对分析,筛选不同鸡种TAP2基因存在的SNP位置以及类型,并通过软件预测分析SNP对蛋白的影响,进一步构建系统进化树,探究不同鸡种同源性。[结果]TAP2基因总共有效测序长度为3 037 bp,在不同鸡种中一共发生了20个位点的突变,具有较为丰富的遗传多样性,其中9个SNP发生在外显子上,其余则存在于内含子,同时分析了对编码氨基酸产生影响的4个SNP(rs316795220、rs738706078、rs739725385、rs732937653)对蛋白结构的影响。[结论]鸡TAP2基因具有较高的多态性,这些丰富多态的基因的存在为进一步利用丰富的资源提供了原始材料。该研究为TAP2基因转运抗体功能关联研究候选SNPs的选择提供了科学依据。     

MHC class II is an important genetic risk factor for canine systemic lupus erythematosus (SLE)-related disease: implications for reproductive success

Major histocompatibility complex (MHC) class II genes are important genetic risk factors for development of immune-mediated diseases in mammals. Recently, the dog (Canis lupus familiaris) has emerged as a useful model organism to identify critical MHC class II genotypes that contribute to development of these diseases. Therefore, a study aimed to evaluate a potential genetic association between the dog leukocyte antigen (DLA) class II region and an immune-mediated disease complex in dogs of the Nova Scotia duck tolling retriever breed was performed. We show that DLA is one of several genetic risk factors for this disease complex and that homozygosity of the risk haplotype is disadvantageous. Importantly, the disease is complex and has many genetic risk factors and therefore we cannot provide recommendations for breeders exclusively on the basis of genetic testing for DLA class II genotype.     

Genetic variation and responses to vaccines

Disease is a major source of economic loss to the livestock industry. Understanding the role of genetic factors in immune responsiveness and disease resistance should provide new approaches to the control of disease through development of safe synthetic subunit vaccines and breeding for disease resistance. The major histocompatibility complex (MHC) has been an important candidate locus for immune responsiveness studies. However, it is clear that other loci play an important role. Identifying these and quantifying the relative importance of MHC and non-MHC genes should result in new insights into host-pathogen interactions, and information that can be exploited by vaccine designers. The rapidly increasing information available about the bovine genome and the identification of polymorphisms in immune-related genes will offer potential candidates that control immune responses to vaccines. The bovine MHC, BoLA, encodes two distinct isotypes of class II molecules, DR and DQ, and in about half the common haplotypes the DQ genes are duplicated and expressed. DQ molecules are composed of two polymorphic chains whereas DR consists of one polymorphic and one non-polymorphic chain. Although, it is clear that MHC polymorphism is related to immune responsiveness, it is less clear how different allelic and locus products influence the outcome of an immune response in terms of generating protective immunity in outbred animals. A peptide derived from foot-and-mouth disease virus (FMDV) was used as a probe for BoLA class II function. Both DR and DQ are involved in antigen presentation. In an analysis of T-cell clones specific for the peptide, distinct biases to particular restriction elements were observed. In addition inter-haplotype pairings of DQA and DQB molecules produced functional molecules, which greatly increases the numbers of possible restriction elements, compared with the number of genes, particularly in cattle with duplicated DQ genes. In a vaccine trial with several peptides derived from FMDV, BoLA class II DRB3 polymorphisms were correlated with both protection and non-protection. Although variation in immune responsiveness to the FMDV peptide between different individuals is partly explainable by BoLA class II alleles, other genetic factors play an important role. In a quantitative trait locus project, employing a second-generation cross between Charolais and Holstein cattle, significant sire and breed effects were also observed in T-cell, cytokine and antibody responses to the FMDV peptide. These results suggest that both MHC and non-MHC genes play a role in regulating bovine immune traits of relevance to vaccine design. Identifying these genes and quantifying their relative contributions is the subject of further studies.     

家禽主要组织相容性复合体结构的研究进展

主要组织相容性复合体(MHC)存在于所有高等脊椎动物的基因组中,表现为高度多态和多基因的特性。MHC在免疫应答和病毒抵御上发挥着重要作用,不同家禽的MHC结构差异一定程度上可以解释其抗病性的差异。本文对近年来在鸡、鹌鹑、火鸡、鸭、鹅和其他几种禽类MHC结构研究方面的进展进行综述,对不同家禽MHC结构进行对比分析,有利于了解不同家禽品种间的遗传关系,促进家禽抗病育种的研究。     

Functional expression of a bovine major histocompatibility complex class I gene in transgenic mice

Major histocompatibility complex (MHC) class I restricted cellular immune responses play an important role in immunity to intracellular pathogens. By binding antigenic peptides and presenting them to T cells, class I molecules impose significant selection on the targets of immune responses. Candidate vaccine antigens for cellular immune responses should therefore be analysed in the context of MHC class I antigen presentation. Transgenic mice expressing human MHC (HLA) genes provide a useful model for the identification of potential cytotoxic T lymphocyte (CTL) antigens. To facilitate the analysis of candidate CTL vaccines in cattle, we have produced transgenic mice expressing a common bovine MHC (BoLA) class I allele.The functional BoLA-A11 gene, carried on a 7 kb genomic DNA fragment, was used to make transgenic mice by pronuclear microinjection. Three transgenic mouse lines carrying the BoLA-A11 gene were established. Expression of the BoLA-A11 gene was found in RNA and the A11 product could be detected on the surface of spleen and blood cells. Functional analysis of the A11 transgene product, and its ability to act as an antigen presenting molecules in the mouse host will be discussed.     

Structure and function of the major histocompatibility complex in domestic animals

The major histocompatibility complex (MHC) is a genetic region that has been intensively studied for the past 2 decades. Interest in the MHC has been high because of (i) the particular involvement of the MHC in transplantation reactions, including organ allograft rejection in human beings; and (ii) the more general role of MHC gene products in the genetic control of immune responses in all mammals. The MHC has several remarkable properties that include a distinctive genetic structure which has been well-preserved through evolution, and the extreme plasticity of form of the principal MHC genes, which can coexist within a single species in 30 or more allelic forms. The genes of the MHC regulate cell-cell interactions of various types within the lymphoreticular system, and thus function as the so-called "immune response" genes that have been described in mice, rats, and guinea pigs. In human beings, the "disease associations" demonstrated between MHC alleles and various pathologic conditions are probably manifestations of abnormal functions of immune regulation governed by the MHC. Studies of the MHC in domestic species are still in their infancy. However, investigations of the MHC have been carried out in swine, cattle, horses, sheep, goats, dogs, and chickens. Further research on the MHC of domestic animals is merited, both for its contribution to the overall understanding of the biological significance of the MHC and for its practical application in clinical veterinary medicine.