The peptide motif of the single dominantly expressed class I molecule of the chicken MHC can explain the response to a molecular defined vaccine of infectious bursal disease virus (IBDV)

Discovery of novel MHC-B haplotypes in Chantecler chickens

The major histocompatibility complex (MHC) is a highly polymorphic cluster of genes which contribute to immune response. Located on chromosome 16, the chicken MHC has great influence over disease resistance and susceptibility. Through the use of a high-density SNP panel which encompasses the MHC-B region, haplotypes can be easily identified. This study aims to use an MHC-B SNP panel to evaluate the MHC-B variability in the Chantecler breed. This breed is native to Quebec, Canada, and is a dual-purpose breed known for its strong resistance to extreme cold temperatures. The Chantecler breed faced a near extinction event in the 1970s, which most likely resulted in a genetic bottleneck and loss of diversity. Despite this, SNP haplotype diversity was observed among 4 Chantecler populations. A total of 8 haplotypes were observed. Of these haplotypes, 6 were previously defined in other breeds, and the other 2 were unique to the Chantecler. Within the populations, the number of haplotypes ranged from 4 to 7, with 3 haplotypes, including the novel BSNP-Chant01, being present in all the groups. This study shows existence of reasonable diversity in the MHC-B region of the Chantecler breed and our results further contribute to understanding the variability of this region in chickens.

New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system

The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.

Infectious bursal disease virus' interferences with host immune cells: What do we know?

AbstractInfectious bursal disease virus (IBDV) induces one of the most important immunosuppressive diseases in chickens leading to high economic losses due increased mortality and condemnation rates, secondary infections and the need for antibiotic treatment. Over 400 publications have been listed in PubMed.gov in the last five years pointing out the research interest in this disease and the development of improved preventive measures. While B cells are the main target cells of the virus, also other immune and non-immune cell populations are affected leading a multifaceted impact on the normally well orchestrated immune system in IBDV-infected birds. Recent studies clearly revealed the contribution of innate immune cells as well as T cells to a cytokine storm and subsequent death of affected birds in the acute phase of the disease. Transcriptomics identified differential regulation of immune related genes between different chicken genotypes as well as virus strains, which may be associated with a variable disease outcome. The recent availability of primary B cell culture systems allowed a closer look into virus-host interactions during IBDV-infection. The new emerging field of research with transgenic chickens will open up new opportunities to understand the impact of IBDV on the host also under in vivo conditions, which will help to understand the complex virus-host interactions further.

Exonic SNP in MHC-DMB2 is associated with gene expression and humoral immunity in Japanese quails

The DMB2 gene is widely expressed at high levels in avian. This gene plays an important role in humoral immunity. The aim of this study was to investigate the effects of 361 G > C Single nucleotide polymorphism (SNP) on DMB2 protein structure and gene expression to determine how the 361 G > C SNP affects humoral immune response in Japanese quails. 0.2 mL of 5% sheep red blood cell (SRBC) was injected into breast muscle of 130 Japanese quails on 28 days. After DNA extraction, PCR was carried out to amplify a 333-base pair DNA fragment from the exon 2 of DMB2 gene. The pattern of all samples was determined through RFLP technique. PCR-RFLP results identified two alleles segregating (C, G) as three genotypes (CC, CG and GG) in Japanese Quails. The antibody response to SRBC with CC genotype was significantly higher than the CG and GG genotypes (P < 0.01). In silico analysis showed that the 361 G > C SNP has no effect on the physicochemical properties and 3D structure. The results of RT-qPCR indicated that the effect of genotype on gene expression is significant, so that the expression of CC genotype is more than CG and GG genotype. It can be inferred that the 361 G > C SNP in the exon 2 of MHC-DMB2 gene is not desirable. This mutation decreases humoral immune response by reducing DMB2 gene expression.

Chickens as a simple system for scientific discovery: The example of the MHC

Chickens have played many roles in human societies over thousands of years, most recently as an important model species for scientific discovery, particularly for embryology, virology and immunology. In the last few decades, biomedical models like mice have become the most important model organism for understanding the mechanisms of disease, but for the study of outbred populations, they have many limitations. Research on humans directly addresses many questions about disease, but frank experiments into mechanisms are limited by practicality and ethics. For research into all levels of disease simultaneously, chickens combine many of the advantages of humans and of mice, and could provide an independent, integrated and overarching system to validate and/or challenge the dogmas that have arisen from current biomedical research. Moreover, some important systems are simpler in chickens than in typical mammals. An example is the major histocompatibility complex (MHC) that encodes the classical MHC molecules, which play crucial roles in the innate and adaptive immune systems. Compared to the large and complex MHCs of typical mammals, the chicken MHC is compact and simple, with single dominantly-expressed MHC molecules that can determine the response to infectious pathogens. As a result, some fundamental principles have been easier to discover in chickens, with the importance of generalist and specialist MHC alleles being the latest example.

The Chicken MHC: Insights into Genetic Resistance, Immunity, and Inflammation Following Infectious Bronchitis Virus Infections

The chicken immune system has provided an immense contribution to basic immunology knowledge by establishing major landmarks and discoveries that defined concepts widely used today. One of many special features on chickens is the presence of a compact and simple major histocompatibility complex (MHC). Despite its simplicity, the chicken MHC maintains the essential counterpart genes of the mammalian MHC, allowing for a strong association to be detected between the MHC and resistance or susceptibility to infectious diseases. This association has been widely studied for several poultry infectious diseases, including infectious bronchitis. In addition to the MHC and its linked genes, other non-MHC loci may play a role in the mechanisms underlying such resistance. It has been reported that innate immune responses, such as macrophage function and inflammation, might be some of the factors driving resistance or susceptibility, consequently influencing the disease outcome in an individual or a population. Information about innate immunity and genetic resistance can be helpful in developing effective preventative measures for diseases such as infectious bronchitis, to which a systemic antibody response is often not associated with disease protection. In this review, we summarize the importance of the chicken MHC in poultry disease resistance, particularly to infectious bronchitis virus (IBV) infections and the role played by innate immunity and inflammation on disease outcome. We highlight how future studies focusing on the MHC and non-MHC genes can potentially bring clarity to observed resistance in some chicken B haplotype lines.

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of duck MHC class I complexed with a TUMV viral peptide

The CTL immune response mediated by MHC I plays an important role in duck anti-TMUV infection. This study reports the expression, purification and crystallization of a complex of duck MHC class I molecules Anpl-UAA*SD, duck β2-microglobulin (Anpl-β2m) and the polypeptide LRKRQLTVL (LRK9) derived from Tembusu virus (TMUV) NS3. The crystal diffraction resolution is 1.50 Å and belongs to the P6₂ space group, and the unit cell parameters are a = 82.468, b = 82.468, c = 112.507. The Matthew's constant is calculated to be 2.32 Å³ Da ^-1, and an asymmetric unit contains a complex molecule with a solvent content of 47%. The research lays the foundation for the structure of immune molecules about duck anti-TMUV research.

Divergent Peptide Presentations of HLA-A*30 Alleles Revealed by Structures With Pathogen Peptides

Human leukocyte antigen (HLA) alleles have a high degree of polymorphism, which determines their peptide-binding motifs and subsequent T-cell receptor recognition. The simplest way to understand the cross-presentation of peptides by different alleles is to classify these alleles into supertypes. A1 and A3 HLA supertypes are widely distributed in humans. However, direct structural and functional evidence for peptide presentation features of key alleles (e.g., HLA-A^*30:01 and -A^*30:03) are lacking. Herein, the molecular basis of peptide presentation of HLA-A^*30:01 and -A^*30:03 was demonstrated by crystal structure determination and thermostability measurements of complexes with T-cell epitopes from influenza virus (NP44), human immunodeficiency virus (RT313), and Mycobacterium tuberculosis (MTB). When binding to the HIV peptide, RT313, the PΩ-Lys anchoring modes of HLA-A^*30:01, and -A^*30:03 were similar to those of HLA-A^*11:01 in the A3 supertype. However, HLA-A^*30:03, but not -A^*30:01, also showed binding with the HLA^*01:01-favored peptide, NP44, but with a specific structural conformation. Thus, different from our previous understanding, HLA-A^*30:01 and -A^*30:03 have specific peptide-binding characteristics that may lead to their distinct supertype-featured binding peptide motifs. Moreover, we also found that residue 77 in the F pocket was one of the key residues for the divergent peptide presentation characteristics of HLA-A^*30:01 and -A^*30:03. Interchanging residue 77 between HLA-A^*30:01 and HLA-A^*30:03 switched their presented peptide profiles. Our results provide important recommendations for screening virus and tumor-specific peptides among the population with prevalent HLA supertypes for vaccine development and immune interventions.

Progress on chicken T cell immunity to viruses

Avian virus infection remains one of the most important threats to the poultry industry. Pathogens such as avian influenza virus (AIV), avian infectious bronchitis virus (IBV), and infectious bursal disease virus (IBDV) are normally controlled by antibodies specific for surface proteins and cellular immune responses. However, standard vaccines aimed at inducing neutralizing antibodies must be administered annually and can be rendered ineffective because immune-selective pressure results in the continuous mutation of viral surface proteins of different strains circulating from year to year. Chicken T cells have been shown to play a crucial role in fighting virus infection, offering lasting and cross-strain protection, and offer the potential for developing universal vaccines. This review provides an overview of our current knowledge of chicken T cell immunity to viruses. More importantly, we point out the limitations and barriers of current research and a potential direction for future studies.

An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I

MHC molecules are found in all jawed vertebrates and are known to present peptides to T lymphocytes. In mammals, peptides can hang out either end of the peptide-binding groove of classical class II molecules, whereas the N and C termini of peptides are typically tightly bound to specific pockets in classical class I molecules. The chicken MHC, like many nonmammalian vertebrates, has a single dominantly expressed classical class I molecule encoded by the BF2 locus. We determined the structures of BF2*1201 bound to two peptides and found that the C terminus of one peptide hangs outside of the groove with a conformation much like the peptides bound to class II molecules. We found that BF2*1201 binds many peptides that hang out of the groove at the C terminus, and the sequences and structures of this MHC class I allele were determined to investigate the basis for this phenomenon. The classical class I molecules of mammals have a nearly invariant Tyr (Tyr⁸⁴ in humans) that coordinates the peptide C terminus, but all classical class I molecules outside of mammals have an Arg in that position in common with mammalian class II molecules. We find that this invariant Arg residue switches conformation to allow peptides to hang out of the groove of BF2*1201, suggesting that this phenomenon is common in chickens and other nonmammalian vertebrates, perhaps allowing the single dominantly expressed class I molecule to bind a larger repertoire of peptides.

Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens

In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens.

A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles.

Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases.

Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression.

Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.

LEI0258 microsatellite variability and its association with humoral and cell mediated immune responses in broiler chickens

Major histocompatibility complex (MHC) has a profound influence on disease resistance or susceptibility, productivity and important economic traits in chicken. Association of the MHC with a wide range of immune responses makes it a valuable predictive factor for the disease pathogenesis and outcome. The tandem repeat LEI0258 is a genetic marker which is located within the B locus of chicken MHC and strongly associated with serologically defined haplotypes. LEI0258 microsatellite marker was applied to investigate the MHC polymorphism in Ross 308 broiler chicken (N=104). Association of LEI0258 alleles with humoral and cell mediated immune responses to Newcastle disease (ND), Infectious bursal disease (IBD) and Avian influenza (AI) vaccines were also examined. LEI0258 polymorphism was determined by PCR-based fragment analysis, and association of LEI0258 alleles with immune responses were evaluated using multivariate regression analysis and GLM procedures. A total of seven alleles ranging from 195 to 448bp were found, including two novel alleles (263 and 362bp) that were unique in Ross 308 broiler population. Association study revealed a significant influence of MHC alleles on humoral and cellular immune responses in Ross population (P<0.05). Alleles 385 and 448bp were associated with increased peripheral blood lymphocyte proliferation response. Alleles 300, 362 and 448bp had a positive effect on immune responses to Infectious bursal disease vaccine, and allele 263bp was significantly correlated with elevated antibody titer against Newcastle disease vaccine. Results obtained from this study confirmed the important role of MHC as a candidate gene marker for immune responses that could be used in genetic improvement of disease-resistant traits and resource conservation in broiler population.

What chickens might tell us about the MHC class II system

Almost all knowledge about the structure and function of MHC class II molecules outside of mammals comes from work with chickens. Most of the genes implicated in the class II system are present in chickens, so it is likely that the machinery of antigen processing and peptide-loading is similar to mammals. However, there is only one isotype (lineage) of classical class II genes, with one monomorphic DR-like BLA gene and two polymorphic BLB genes, located near one DMA and two DMB genes. The DMB2 and BLB2 genes are widely expressed at high levels, whereas the DMB1 and BLB1 genes are only expressed at highest levels in spleen and intestine, suggesting the possibility of two class II systems in chickens.

Cytokine response to the RSV antigen delivered by dendritic cell-directed vaccination in congenic chicken lines

Systems of antigen delivery into antigen-presenting cells represent an important novel strategy in chicken vaccine development. In this study, we verified the ability of Rous sarcoma virus (RSV) antigens fused with streptavidin to be targeted by specific biotinylated monoclonal antibody (anti-CD205) into dendritic cells and induce virus-specific protective immunity. The method was tested in four congenic lines of chickens that are either resistant or susceptible to the progressive growth of RSV-induced tumors. Our analyses confirmed that the biot-anti-CD205-SA-FITC complex was internalized by chicken splenocytes. In the cytokine expression profile, several significant differences were evident between RSV-challenged progressor and regressor chicken lines. A significant up-regulation of IL-2, IL-12, IL-15, and IL-18 expression was detected in immunized chickens of both regressor and progressor groups. Of these cytokines, IL-2 and IL-12 were most up-regulated 14 days post-challenge (dpc), while IL-15 and IL-18 were most up-regulated at 28 dpc. On the contrary, IL-10 expression was significantly down-regulated in all immunized groups of progressor chickens at 14 dpc. We detected significant up-regulation of IL-17 in the group of immunized progressors. LITAF down-regulation with iNOS up-regulation was especially observed in the progressor group of immunized chickens that developed large tumors. Based on the increased expression of cytokines specific for activated dendritic cells, we conclude that our system is able to induce partial stimulation of specific cell types involved in cell-mediated immunity.

Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I

Canines represent a crucial animal model for studying human diseases and organ transplantation, as well as the evolution of domestic animals. MHCs, with a central role in cellular immunity, are commonly used in the study of dog population genetics and genome evolution. However, the molecular basis for the peptide presentation of dog MHC remains largely unknown. In this study, peptide presentation by canine MHC class I DLA-88*50801 was structurally determined, revealing diversified anchoring modes of the binding peptides. Flexible and large pockets composed of both hydrophobic and hydrophilic residues can accommodate pathogen-derived peptides with diverse anchor residues, as confirmed by thermostability measurements. Furthermore, DLA-88*50801 contains an unusual α2 helix with a large coil in the TCR contact region. These results further our understanding of canine T cell immunity through peptide presentation of MHC class I and shed light on the molecular basis for vaccine development for canine infectious diseases, for example, canine distemper virus.

Host genetics determine susceptibility to avian influenza infection and transmission dynamics

Host-genetic control of influenza virus infection has been the object of little attention. In this study we determined that two inbred lines of chicken differing in their genetic background , Lines 0 and C-B12, were respectively relatively resistant and susceptible to infection with the low pathogenicity influenza virus A/Turkey/England/647/77 as defined by substantial differences in viral shedding trajectories. Resistant birds, although infected, were unable to transmit virus to contact birds, as ultimately only the presence of a sustained cloacal shedding (and not oropharyngeal shedding) was critical for transmission. Restriction of within-bird transmission of virus occurred in the resistant line, with intra-nares or cloacal infection resulting in only local shedding and failing to transmit fully through the gastro-intestinal-pulmonary tract. Resistance to infection was independent of adaptive immune responses, including the expansion of specific IFNγ secreting cells or production of influenza-specific antibody. Genetic resistance to a novel H9N2 virus was less robust, though significant differences between host genotypes were still clearly evident. The existence of host-genetic determination of the outcome of influenza infection offers tools for the further dissection of this regulation and also for understanding the mechanisms of influenza transmission within and between birds.

Co-evolution with chicken class I genes

The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC.

Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance

Nearly all genes presently mapped to chicken chromosome 16 (GGA 16) have either a demonstrated role in immune responses or are considered to serve in immunity by reason of sequence homology with immune system genes defined in other species. The genes are best described in regional units. Among these, the best known is the polymorphic major histocompatibility complex-B (MHC-B) region containing genes for classical peptide antigen presentation. Nearby MHC-B is a small region containing two CD1 genes, which encode molecules known to bind lipid antigens and which will likely be found in chickens to present lipids to specialized T cells, as occurs with CD1 molecules in other species. Another region is the MHC-Y region, separated from MHC-B by an intervening region of tandem repeats. Like MHC-B, MHC-Y is polymorphic. It contains specialized class I and class II genes and c-type lectin-like genes. Yet another region, separated from MHC-Y by the single nucleolar organizing region (NOR) in the chicken genome, contains olfactory receptor genes and scavenger receptor genes, which are also thought to contribute to immunity. The structure, distribution, linkages and patterns of polymorphism in these regions, suggest GGA 16 evolves as a microchromosome devoted to immune defense. Many GGA 16 genes are polymorphic and polygenic. At the moment most disease associations are at the haplotype level. Roles of individual MHC genes in disease resistance are documented in only a very few instances. Provided suitable experimental stocks persist, the availability of increasingly detailed maps of GGA 16 genes combined with new means for detecting genetic variability will lead to investigations defining the contributions of individual loci and more applications for immunogenetics in breeding healthy poultry.