Identification of peptides associated with chicken major histocompatibility complex class II molecules of B21 and B19 haplotypes

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.

The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek's disease virus peptides by using an unprecedented binding motif

Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek's disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek's disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek's disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek's disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.

Interleukin-dependent modulation of the expression of MHC class I and MHC class II genes in chicken HD11 cells

Interleukins (ILs) regulate cell surface antigens known as activation markers, which have distinct functional roles. However, the regulation of major histocompatibility complex (MHC) class I, MHC class II, and related genes by cytokines in chickens is not well understood. In the present study, we evaluated the influence of certain recently discovered chicken interleukins-i.e., IL-11, IL-12B, IL-17A, IL-17B, IL-26, and IL-34-on the expression and regulation of genes related to MHC class I, MHC class II, and the associated proteins in an HD11 chicken macrophage cell line. We used quantitative reverse transcription polymerase chain reaction (qRT-PCR), immunocytochemical, and flow cytometric analyses to assess dose- and time-dependent expression in the HD11 cell line and found that the ILs induced MHC class I, MHC class II, and associated protein. As NF-κB is actively involved in cell activation and is constitutively activated in many immune cells, we also determined whether NF-κB regulates MHC class I, MHC class II, and related gene expression in the HD11 cell line. The NF-κB inhibitor sulfasalazine (Sz) dose-dependently inhibited MHC class I and MHC class II in the HD11 cell line. Sz also downregulated the expression of MHC class I, MHC class II, and the associated proteins in the IL-induced HD11 cell line. The expression of MHC class I, MHC class II, and associated genes was accompanied by the Sz-sensitive degradation of the p65 (RelA) and p50 subunits of NF-κB and IκBα. Our results indicate that the different effects of each IL on the expression of genes related to MHC class I, MHC class II, and the associated proteins are involved with the regulation of the dose and duration of antigenic peptide presentation and, thus, also influence Th1, Th2, and Th17 production.

Revisiting cellular immune response to oncogenic Marek's disease virus: the rising of avian T-cell immunity

Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that causes deadly T-cell lymphomas and serves as a natural virus-induced tumor model in chickens. Although Marek's disease (MD) is well controlled by current vaccines, the evolution of MDV field viruses towards increasing virulence is concerning as a better vaccine to combat very virulent plus MDV is still lacking. Our understanding of molecular and cellular immunity to MDV and its immunopathogenesis has significantly improved, but those findings about cellular immunity to MDV are largely out-of-date, hampering the development of more effective vaccines against MD. T-cell-mediated cellular immunity was thought to be of paramount importance against MDV. However, MDV also infects macrophages, B cells and T cells, leading to immunosuppression and T-cell lymphoma. Additionally, there is limited information about how uninfected immune cells respond to MDV infection or vaccination, specifically, the mechanisms by which T cells are activated and recognize MDV antigens and how the function and properties of activated T cells correlate with immune protection against MDV or MD tumor. The current review revisits the roles of each immune cell subset and its effector mechanisms in the host immune response to MDV infection or vaccination from the point of view of comparative immunology. We particularly emphasize areas of research requiring further investigation and provide useful information for rational design and development of novel MDV vaccines.

A Newly Recognized Pairing Mechanism of the α- and β-Chains of the Chicken Peptide-MHC Class II Complex

MHC class II (MHC-II) molecules play a crucial role in cellular and humoral immunity by forming peptide-MHC-II (pMHC-II) complexes. The three-dimensional structures of pMHC-II complexes have been well resolved in humans and mice. However, there is no structural information for pMHC-II complexes in nonmammals. In chickens, there are two closely related and highly polymorphic β-chains and one monomorphic α-chain, and the mechanism by which one monomorphic α-chain combines with two polymorphic β-chains to form a functional heterodimer remains unknown. In this study, we report the crystal structure of a chicken pMHC-II complex (pBL2*019:01) at 1.9-Å resolution as the first nonmammalian structure of a pMHC-II complex. The structure reveals an increase in hydrogen bonding between the α and β main chains at the central interface that is introduced by the insertion of four residues in the α-chain. The residues in the β-chain that form hydrogen bonds with the α-chain are conserved among all β alleles. These structural characteristics explain the phenomenon of only one BLA allele without sequence variation pairing with highly diverse BLB alleles from two loci in the genome. Additionally, the characteristics of the peptide in the peptide-binding groove were confirmed. These results provide a new understanding of the pairing mechanism of the α- and β-chains in a pMHC-II complex and establish a structural principle to design epitope-related vaccines for the prevention of chicken diseases.

Genetic variation at the MHC in a population of introduced wild turkeys

Genetic variation in the major histocompatibility complex (MHC) is known to affect disease resistance in many species. Investigations of MHC diversity in populations of wild species have focused on the antigen presenting class IIβ molecules due to the known polymorphic nature of these genes and the role these molecules play in pathogen recognition. Studies of MHC haplotype variation in the turkey ( Meleagris gallopavo ) are limited. This study was designed to examine MHC diversity in a group of Eastern wild turkeys ( Meleagris gallopavo silvestris ) collected during population expansion following reintroduction of the species in southern Wisconsin, USA. Southern blotting with BG and class IIβ probes and single nucleotide polymorphism (SNP) genotyping was used to measure MHC variation. SNP analysis focused on single copy MHC genes flanking the highly polymorphic class IIβ genes. Southern blotting identified 27 class IIβ phenotypes, whereas SNP analysis identified 13 SNP haplotypes occurring in 28 combined genotypes. Results show that genetic diversity estimates based on RFLP (Southern blot) analysis underestimate the level of variation detected by SNP analysis. Sequence analysis of the mitochondrial D-loop identified 7 mitochondrial haplotypes (mitotypes) in the sampled birds. Results show that wild turkeys located in southern Wisconsin have a genetically diverse MHC and originate from several maternal lineages.

Immunity to Marek's disease: where are we now?

Marek's disease (MD) in chickens was first described over a century ago and the causative agent of this disease, Marek's disease virus (MDV), was first identified in the 1960's. There has been extensive and intensive research over the last few decades to elucidate the underlying mechanisms of the interactions between the virus and its host. We have also made considerable progress in terms of developing efficacious vaccines against MD. The advent of the chicken genetic map and genome sequence as well as development of approaches for chicken transcriptome and proteome analyses, have greatly facilitated the process of illuminating underlying genetic mechanisms of resistance and susceptibility to disease. However, there are still major gaps in our understanding of MDV pathogenesis and mechanisms of host immunity to the virus and to the neoplastic events caused by this virus. Importantly, vaccines that can disrupt virus transmission in the field are lacking. The current review explores mechanisms of host immunity against Marek's disease and makes an attempt to identify the areas that are lacking in this field.

Immune responses against Marek's disease virus

It is more than a century since Marek's disease (MD) was first reported in chickens and since then there have been concerted efforts to better understand this disease, its causative agent and various approaches for control of this disease. Recently, there have been several outbreaks of the disease in various regions, due to the evolving nature of MD virus (MDV), which necessitates the implementation of improved prophylactic approaches. It is therefore essential to better understand the interactions between chickens and the virus. The chicken immune system is directly involved in controlling the entry and the spread of the virus. It employs two distinct but interrelated mechanisms to tackle viral invasion. Innate defense mechanisms comprise secretion of soluble factors as well as cells such as macrophages and natural killer cells as the first line of defense. These innate responses provide the adaptive arm of the immune system including antibody- and cell-mediated immune responses to be tailored more specifically against MDV. In addition to the immune system, genetic and epigenetic mechanisms contribute to the outcome of MDV infection in chickens. This review discusses our current understanding of immune responses elicited against MDV and genetic factors that contribute to the nature of the response.

Mass spectral data for 64 eluted peptides and structural modeling define peptide binding preferences for class I alleles in two chicken MHC-B haplotypes associated with opposite responses to Marek's disease

In the chicken, resistance to lymphomas that form following infection with oncogenic strains of Marek's herpesvirus is strongly linked to the major histocompatibility complex (MHC)-B complex. MHC-B21 haplotype is associated with lower tumor-related mortality compared to other haplotypes including MHC-B13. The single, dominantly expressed class I gene (BF2) is postulated as responsible for the MHC-B haplotype association. We used mass spectrometry to identify peptides and structural modeling to define the peptide binding preferences of BF2 2101 and BF2 1301 proteins. Endogenous peptides (8-12 residues long) were eluted from affinity-purified BF2 2101 and BF2 1301 proteins obtained from transduced cDNA expressed in RP9 cells, hence expressed in the presence of heterologous TAP. Sequences of individual peptides were identified by mass spectrometry. BF2 2101 peptides appear to be tethered at the binding groove margins with longer peptides arching out but selected by preferred residues at positions P3, P5, and P8: X-X-[AVILFP]-X((1-5))-[AVLFWP]-X((2-3))-[VILFM]. BF2 1301 peptides appear selected for residues at P2, P3, P5, and P8: X-[DE]-[AVILFW]-X((1-2))-[DE]-X-X-[ED]-X((0-4)). Some longer BF2 1301 peptides likely also arch out, but others are apparently accommodated by repositioning of Arg83 so that peptides extend beyond the last preferred residue at P8. Comparisons of these peptides with earlier peptides derived in the presence of homologous TAP transport revealed the same side chain preferences. Scanning of Marek's and other viral proteins with the BF2 2101 motif identified many matches, as did the control human leukocyte antigen A 0201 motif. The BF2 1301 motif is more restricting suggesting that this allele may confer a selective advantage only in infections with a subset of viral pathogens.

Using Proteomics to Understand Avian Systems Biology and Infectious Disease

The proteome is defined as the protein complement to the genome. Proteomics is the study of the proteome. Several techniques are frequently used in proteomics; these include 2-hybrid systems, 2-dimensional gel electrophoresis, and mass spectrometry. Systems biology is a scientific approach that takes into account the complex relationships among and between genes and proteins and determines how all of these interactions come together to form a functional organism. Proteomic tools can simultaneously probe the properties of numerous proteins and thus are a great aid to the emerging field of systems biology, in which the functional interactions of numerous proteins are studied instead of studying individual proteins as isolated entities. In the field of avian biology, proteomics has been used to study everything from the development and function of organs and systems to the interactions of infectious agents and the altered states that they induce in their hosts.

Chicken major histocompatibility complex class II molecules of the B haplotype present self and foreign peptides

The chicken major histocompatibility complex (MHC), or B-complex, mediates genetic resistance and susceptibility to infectious disease. For example, the B19 haplotype is associated with susceptibility to Marek's disease. Here, we describe the sequencing and analysis of peptides presented by B19 MHC class II molecules. A B19/B19 B-cell line was used for the immunoaffinity purification of MHC class II molecules, which was followed by acid elution of the bound peptides. The eluted peptides were then analysed using tandem mass spectrometry. Thirty peptide sequences were obtained, ranging from 11 to 25 amino acids in length. Source protein cellular localization included the plasma membrane, cytosol and endosomal pathway. In addition, five peptides from the envelope glycoprotein of chicken syncytial virus (CSV) were identified. Chicken syncytial virus had been used as a helper virus along with reticuloendotheliosis virus strain T for transformation of B19/B19B cells. Alignment and analysis of the peptide sequence pool provided a putative peptide-binding motif for the B19 MHC class II.

Synthesis of chicken major histocompatibility complex class II oligomers using a baculovirus expression system

Chicken major histocompatibility complex (MHC) B21 and B19 haplotypes are associated with resistance and susceptibility to Marek's disease (MD), respectively. T-cell-mediated immune response is crucial in coordinating protection against Marek's disease virus (MDV) infection, but it has been difficult to identify and characterize antigen-specific T-cells. MHC class II tetramers and oligomers have been widely used for characterization of antigen-specific T-cells in the context of infectious and autoimmune diseases. Thus, the objective of this study was to synthesize chicken MHC class II oligomers of B21 and B19 haplotypes for the future identification of antigen-specific T-cells. To achieve this objective, full-length coding sequences of chicken MHC class II B21 and B19 molecules were amplified and the molecules were expressed as fusion proteins, carrying Fos and Jun leucine zipper (LZ), histidine-tag and biotin ligase recognition site sequences, using a baculovirus expression system. Recombinant MHC-II were loaded with self-peptides, which stabilized the heterodimer in SDS-PAGE and allowed the detection of these molecules in Western blots with a conformation-specific anti-chicken MHC class II antibody. Biotinylated MHC molecules were conjugated to streptavidin to form oligomers, which were resolved under the transmission electron microscope through immuno-gold labelling, thus confirming success of oligomerization. In conclusion, chicken MHC class II oligomers may be used in the future to study the antigen-specific CD4+ T-cell compartment.