Heather G. Shilling

Human Diversity in Killer Cell Inhibitory Receptor Genes

The presence and expression of killer inhibitory receptor (KIR) and CD94:NKG2 genes from 68 donors were analyzed using molecular typing techniques. The genes encoding CD94:NKG2 receptors were present in each person, but KIR gene possession varied. Most individuals expressed inhibitory KIR for the three well-defined HLA-B and -C ligands, but noninhibitory KIR genes were more variable. Twenty different KIR phenotypes were defined. Two groups of KIR haplotypes were distinguished and occurred at relatively even frequency. Group A KIR haplotypes consist of six genes: the main inhibitory KIR, one noninhibitory KIR, and a structurally divergent KIR. Allelic polymorphism within five KIR genes was detected. Group B comprises more noninhibitory KIR genes and contains at least one additional gene not represented in group A. The KIR locus therefore appears to be polygenic and polymorphic within the human population.

Functionally and structurally distinct NK cell receptor repertoires in the peripheral blood of two human donors.

The expression of KIR and CD94:NKG2 receptors was determined for more than 100 natural killer (NK) cell clones obtained from two blood donors who differ in their HLA class I and KIR genes. More than 98% of the clones were inhibited by individual autologous class I allotypes, and every clone was inhibited by the combination of autologous allotypes. The patterns of inhibition correlate with expression of inhibitory receptors of defined specificity. One donor possesses three class I ligands for KIR, and a majority of NK cells use KIR as their inhibitory receptor; the second donor possesses only a single ligand for KIR, and a majority of NK cells use the more broadly reactive CD94:NKG2a as their inhibitory receptor. Because of these differences, the first donor has subpopulations of NK cells that kill cells of the second donor, whereas the NK cells of the second donor are universally tolerant of cells from the first donor.

Allelic Polymorphism Synergizes with Variable Gene Content to Individualize Human KIR Genotype

Killer Ig-like receptor (KIR) genes are a multigene family on human chromosome 19. KIR genes occur in various combinations on different haplotypes. Additionally, KIR genes are polymorphic. To examine how allelic polymorphism diversifies KIR haplotypes with similar or identical combinations of KIR genes, we devised methods for discriminating alleles of KIR2DL1, -2DL3, -3DL1, and -3DL2. These methods were applied to 143 individuals from 34 families to define 98 independent KIR haplotypes at the allele level. Three novel 3DL2 alleles and a chimeric 3DL1/3DL2 sequence were also identified. Among the A group haplotypes were 22 different combinations of 2DL1, 2DL3, 3DL1, and 3DL2 alleles. Among the B group haplotypes that were unambiguously determined were 15 distinct haplotypes involving 9 different combinations of KIR genes. A and B haplotypes both exhibit strong linkage disequilibrium (LD) between 2DL1 and 2DL3 alleles, and between 3DL1 and 3DL2 alleles. In contrast, there was little LD between the 2DL1/2DL3 and 3DL1/3DL2 pairs that define the two halves of the KIR gene complex. The synergistic combination of allelic polymorphism and variable gene content individualize KIR genotype to an extent where unrelated individuals almost always have different KIR types. This level of diversity likely reflects strong pressure from pathogens on the human NK cell response.

Different NK Cell Surface Phenotypes Defined by the DX9 Antibody Are Due to KIR3DL1 Gene Polymorphism

KIR3DL1 and KIR3DL2 are NK cell receptors for polymorphic HLA-B and -A determinants. The proportion of NK cells that bind anti-KIR3DL1-specific Ab DX9 and their level of binding vary between individuals. To determine whether these differences are due to KIR polymorphism, we assessed KIR3D gene diversity in unrelated individuals and families. Both KIR3DL1 and KIR3DL2 are highly polymorphic genes, with KIR3DS1 segregating like an allele of KIR3DL1. A KIR haplotype lacking KIR3DL1 and KIR3DS1 was defined. The two KIR3DL1 alleles of a heterozygous donor were expressed by different, but overlapping, subsets of NK cell clones. Sequence variation in KIR3DL1 and KIR3DL2 appear distinct; recombination is more evident in KIR3DL1, and point mutation is more evident in KIR3DL2. The KIR3DL1 genotype correlates well with levels of DX9 binding by NK cells, but not with the frequency of DX9-binding cells. Different KIR3DL1 alleles determine high, low, and no binding of DX9 Ab. Consequently, heterozygotes for high and low binding KIR3DL1 alleles have distinct subpopulations of NK cells that bind DX9 at high and low levels, giving characteristic bimodal distributions in flow cytometry. The Z27 Ab gave binding patterns similar to those of DX9. Four KIR3DL1 alleles producing high DX9 binding phenotypes were distinguished from four alleles producing low or no binding phenotypes by substitution at one or more of four positions in the encoded protein: 182 and 283 in the extracellular Ig-like domains, 320 in the transmembrane region, and 373 in the cytoplasmic tail.

Predominance of group A KIR haplotypes in Japanese associated with diverse NK cell repertoires of KIR expression.

Abstract. Genomic DNA from a panel of 41 healthy unrelated Japanese individuals was typed for the presence or absence of 16 KIR genes and pseudogenes. Only eight different KIR genotypes were found. Group A haplotypes outnumbered group B haplotypes in frequency by approximately 3:1, with individuals having two group A haplotypes accounting for 56% of the panel. The frequency of A haplotypes in the Japanese is higher than that observed in other populations. Flow cytometric comparison of KIR expression in 19 panel members showed considerable diversity in NK cell repertoire, which was also seen within the group of individuals having two A haplotypes. This diversity is likely due to allelic polymorphism in expressed genes of the A haplotype. In comparison to other populations, the Japanese appear less heterogeneous in KIR genotype as assessed by gene content.

Distinctive KIR and HLA diversity in a panel of north Indian Hindus.

HLA and KIR are diverse and rapidly evolving gene complexes that work together in human immunity mediated by cytolytic lymphocytes. Understanding their complex immunogenetic interaction requires study of both HLA and KIR diversity in the same human population. Here a panel of 72 unrelated north Indian Hindus was analyzed. HLA-A, B, C, DRB1, DQA1, and DQB1 alleles and their frequencies were determined by sequencing or high-resolution typing of genomic DNA; KIR genotypes were determined by gene-specific typing and by allele-level DNA typing for KIR2DL1, 2DL3, 2DL5, 3DL1, and 3DL2. From HLA analysis, the north Indian population is seen to have several characteristics shared either with Caucasian or East Asian populations, consistent with the demographic history of north India, as well as specific features, including several alleles at high frequency that are rare or absent in other populations. A majority of the north Indian KIR gene profiles have not been seen in Caucasian and Asian populations. Most striking is a higher frequency of the B group of KIR haplotypes, resulting in equal frequencies for A and B group haplotypes in north Indians. All 72 members of the north Indian panel have different HLA genotype and different KIR genotype.

Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002

During discussion at the WHO Nomenclature Committee for Factors of the HLA System meeting in Victoria, Canada in May 2002, it was decided to form a subcommittee to co-ordinate the naming of alleles of the genes encoding the killer-cell immunoglobulin-like receptors (KIR) (Marsh et al. 2002). These genes are encoded on chromosome 19 (19q13.4) and have varying degrees of polymorphism. The receptors encoded by the KIR genes are expressed by natural killer (NK) cells and a subset of T cells and some of them have been shown to have specificity for determinants of HLA class I molecules. The extracellular ligand-binding part of KIR consists of two or three immunoglobulin(Ig-) like domains. The discussions which took place in Victoria are further to earlier discussions on KIR nomenclature at the NK Polymorphism meeting (27–29 July 2001) in Cambridge, UK. In addition a request has been made by the International Union of Immunological Societies (IUIS) to provide a standardised nomenclature for the expressed protein products of the KIR genes.

Killer cell receptors : keeping pace with MHC class I evolution

Summary: NK cells express receptors that bind to polymorphic determinants of MHC class 1 heavy chains. MHC ligands vary greatly between mammalian species, and the use of distinct molecular families of NK ceil receptors by humans and mice suggests that the receptors too can be evolving rapidly. The KIR (killer cell inhibitory receptor) family of receptors are found in primates and recognize c lass I epitopes that are of relatively recent origin in primate evolution. Therefore. KIR molecules have probably evolved class I receptor function more recently than C type lectins, which are represented in both humans and mice. Individual humans express NK cell receptors for which they have no class I ligand. demonstrating a loose ness ill the coupling of expression between the receptors and their ligands. However, study of a single donor suggests that every NK cell expresses at least one inhibitory receptor for a self‐HLA class I allotype, consistent with the missing self hypothesis. Thus the NK‐cell receptor‐class I interaction appears to control the NK‐cell repertoire during ontogeny of the individual and has the potential to be a selective factor influencing both MHC class I and NK cell receptor diversity in the evolution of populations and species.

Killer-cell immunoglobulin-like receptor (KIR) nomenclature report, 2002.

During discussion at the WHO Nomenclature Committee for Factors of the HLA System meeting in Victoria, Canada in May 2002, it was decided to form a subcommittee to coordinate the naming of alleles of the genes encoding the killer-cell immunoglobulin-like receptors (KIRs) (Marsh et al., 2002). These genes are encoded on chromosome 19 (19q13.4) and have varying degrees of polymorphism. The receptors encoded by the KIR genes are expressed by natural killer (NK) cells and a subset of T cells, and some of them have been shown to have specificity for determinants of HLA class I molecules. The extracellular ligand-binding part of KIR consists of two or three immunoglobulin (Ig)-like domains. The discussions which took place in Victoria are further to earlier discussions on KIR nomenclature at the NK Polymorphism meeting (27-29 July 2001) in Cambridge, UK. In addition, a request has been made by the International Union of Immunological Societies (IUIS) to provide a standardized nomenclature for the expressed protein products of the KIR genes.