Bi-Functional Chicken Immunoglobulin-Like Receptors With a Single Extracellular Domain (ChIR-AB1): Potential Framework Genes Among a Relatively Stable Number of Genes Per Haplotype

Abstract

The leukocyte receptor complex (LRC) in humans encodes many receptors with immunoglobulin-like (Ig-like) extracellular domains, including the killer Ig-like receptors (KIRs) expressed on natural killer (NK) cells among others, the leukocyte Ig-like receptors (LILRs) expressed on myeloid and B cells, and an Fc receptor (FcR), all of which have important roles in the immune response. These highly-related genes encode activating receptors with positively-charged residues in the transmembrane region, inhibitory receptors with immuno-tyrosine based motifs (ITIMs) in the cytoplasmic tail, and bi-functional receptors with both. The related chicken Ig-like receptors (ChIRs) are almost all found together on a microchromosome, with over 100 activating (A), inhibitory (B), and bi-functional (AB) genes, bearing either one or two extracellular Ig-like domains, interspersed over 500–1,000 kB in the genome of an individual chicken. Sequencing studies have suggested rapid divergence and little overlap between ChIR haplotypes, so we wished to begin to understand their genetics. We chose to use a hybridization technique, reference strand-mediated conformational analysis (RSCA), to examine the ChIR-AB1 family, with a moderate number of genes dispersed across the microchromosome. Using fluorescently-labeled references (FLR), we found that RSCA and sequencing of ChIR-AB1 extracellular exon gave two groups of peaks with mobility correlated with sequence relationship to the FLR. We used this system to examine widely-used and well-characterized experimental chicken lines, finding only one or a few simple ChIR haplotypes for each line, with similar numbers of peaks overall. We found much more complicated patterns from a broiler line from a commercial breeder and a flock of red junglefowl, but trios of parents and offspring from another commercial chicken line show that the complicated patterns are due to heterozygosity, indicating a relatively stable number of peaks within haplotypes of these birds. Some ChIR-AB1 peaks were found in all individuals from the commercial lines, and some of these were shared with red junglefowl and the experimental lines derived originally from egg-laying chickens. Overall, this analysis suggests that there are some simple features underlying the apparent complexity of the ChIR locus.

Development and optimization of a hybridization technique to type the classical class I and class II B genes of the chicken MHC

“…Hybridization methods were originally developed to type human MHC genes and have been widely used to type MHC alleles, although they are being replaced by SNP typing and/or direct next generation sequencing (NGS). We have used RSCA successfully to type red junglefowl and commercial populations, not just for MHC (Worley et al 2008; Potts 2016) but also for chicken immunoglobulin-like receptors (CHIR-AB1) genes (Meziane et al 2019). However, there are various disadvantages to typing by RSCA.…”

Beware of Mycoplasma Anti-immunoglobulin Strategies

“…The LILRA2/MIB-MIP interplay could provide an explanation for the inflammatory nature of most mycoplasma disease ( 8 ), with antibody degradation being one of the root causes of the hyperstimulation of the innate immune response. In addition to human, families of genes encoding LILR receptors have been identified in murine, caprine, bovine, swine, and avian species ( 94 – 98 ). Characterization of these receptors is ongoing, and the human LILRA2 function has not yet been demonstrated in other species, although it is highly probable.…”

From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles

“…Sequencing studies suggest there can be haplotypes with few ChIR genes in common, suggesting both copy number variation and polymorphism (74)(75)(76). However, a gene typing method for 1D domains suggested relatively stable haplotypes, with only some examples of recombination during matings (77). The only molecules that have clear functions are many ChIR-AB molecules that bind IgY, the antibody isotype that acts somewhat like IgG in mammals (78)(79)(80).…”