Characterization of rhesus macaque KIR genotypes and haplotypes

Abstract

Certain combinations of the killer immunoglobulin-like receptors (KIR) and major histocompatibility complex class I ligands in humans predispose carriers to a variety of diseases, requiring sophisticated genotyping of the highly polymorphic and diverse KIR and HLA genes. Particularly, KIR genotyping is challenging due to polymorphisms (allelic substitutions), genomic diversity (presence/absence of genes), and frequent duplications. Rhesus macaques are often used as important animal models of human diseases such as, e.g. AIDS. However, typing of rhesus macaque KIR genes has not been described so far. In this study, we report the identification of additional novel rhesus macaque KIR cDNA sequences and a sequence-specific KIR genotyping assay. From a cohort of four rhesus macaque families with a total of 70 individuals, we identified 25 distinct KIR genotypes. Segregation analyses of KIR genes and of two polymorphic microsatellite markers allowed the identification of 21 distinct KIR haplotypes in these families, with five to 11 segregating KIR genes per haplotype. Our analyses confirmed and extended knowledge on differential gene KIR gene content in macaques and indicate that rhesus macaque and human KIR haplotypes show a comparable level of diversity and complexity.

The extreme plasticity of killer cell Ig‐like receptor (KIR) haplotypes differentiates rhesus macaques from humans

“…2). However, based on our observations, no clearcut division between inhibitory or activating haplotypes, as observed in humans, exists in rhesus macaques, which is a confirmation of previous findings [36,37]. Indeed, if placentation is a strong selective force in humans [44], in rhesus macaques this influence may be less because the trophoblast-maternal interface is much smaller [45].…”

“…Sampling animals from other areas will undoubtedly reveal more KIR genotype variation. Indeed, this high number of genotypes may only represent the tip of the iceberg, since a comparison with 25 previously reported genotypes [37] showed only a very limited level of overlap.…”

“…Additionally, a group of previously described primers [37] was evaluated on their application for quantitative PCR (qPCR), however, because many of these primers could amplify only specific alleles, only the primer pair specific for Mamu-KIR3DS03 was used. Although all currently described alleles of Mamu-KIR3DL02 are covered by a reported primer pair [37], some false positives were observed in our qPCR system. In this instance, a novel primer pair for -KIR2DL02 was designed, which however does not cover all alleles.…”

“…Segregation analysis of these KIR genotypes revealed at least 18 unique haplotypes [36]. The existing knowledge on haplotype data is based on a relatively small number of animals (n 5 9 [36], n 5 11 [37]), which displays, however, a complexity similar to that found in humans. This begs the question as to how much of the KIR system variability is actually present in rhesus macaques.…”

“…This begs the question as to how much of the KIR system variability is actually present in rhesus macaques. Furthermore, a trend is apparent that no similar distinction of group A and B haplotypes, as observed in humans, can be made [36,37]. Therefore, to further investigate these questions, an extensive KIR gene content analysis has been performed on an outbred colony of rhesus macaques.…”