Killer cell immunoglobulin-like receptor (KIR) locus profiles in the Tunisian population

Killer cell immunoglobulin-like receptors (KIRs) are a family of inhibitory and activatory receptors that are expressed by most natural killer (NK) cells. The KIR gene family is polymorphic: genomic diversity is achieved through differences in gene content and allelic polymorphism. The number of KIR loci has been reported to vary among individuals, resulting in different KIR haplotypes. In this study we report the genotypic structure of KIRs in 267 unrelated and healthy Tunisian subjects by polymerase chain reaction-sequence-specific primer (PCR-SSP) method.All 16 KIR genes were observed in the population with different frequencies; framework genes KIR3DP1 and KIR3DL2 and the nonframework genes KIR2DL1 and KIR2DP1 were present in all individuals. A total of 26 different KIR gene profiles and 54 subgenotypes were observed in the tested population samples. Genotype 1, with a frequency of 36.6%, is the most commonly observed in the Tunisian population.Our results showed that the Tunisian population possesses the previously reported general features of the Caucasian as well as African populations, with some additional interesting differences.Such knowledge of the KIR gene distribution in populations is very useful in the study of associations with diseases and in selection of donors for haploidentical bone marrow transplantation.     

Variation within the human killer cell immunoglobulin-like receptor (KIR) gene family

The killer cell immunoglobulin-like receptors (KIR) form a family of highly homologous immune receptors that regulate the response of natural killer (NK) cells and some T cells. The genetics of the human KIR family is reviewed in this article. In human populations, diversity in KIR genotype arises from variations in gene content and allelic polymorphism. Comparisons of 81 human KIR sequences reveal past events ofgene duplication and recombination, and indicate that individual KIR genes have diversified from the influence of natural selection. Comparison and compilation of population studies reveal extensive KIR genotype variability within human populations and among them. Genomic analysis shows the KIR genes to be close to each other and separated by homologous sequences that promote haplotype diversification through assymetric recombination. In contrast, homologous recombination appears favored at a unique sequence in the center of the KIR locus, and much haplotypic diversity can be explained by recombination between a limited number of gene-content motifs in the centromeric and telomeric halves of the locus. The importance of NK cells for early defenses against infection suggests that human KIR genotype diversity is the accumulated consequence of a history of numerous and successive selective episodes by different pathogens on human NK-cell responses.     

Killer-cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) class I genetic diversity in four South African populations

Killer-cell Immunoglobulin-like Receptor (KIR) and Human Leukocyte Antigen (HLA) genotypes vary considerably between individuals and populations due to KIR/HLA allelic variation and variable haplotype configurations of KIR. HLA mediate natural killer cell activity by serving as KIR ligands. KIR/HLA polymorphisms associate with both disease susceptibility and severity. We determined the frequencies of KIR, KIR genotypes and KIR-HLA combinations in 364 healthy individuals from four South African populations. Study participants included black African (n = 167), Caucasian (n = 97), Mixed ancestry (n = 50) and Indian (n = 50) individuals. We identified 48 KIR genotypes that included two genotypes not previously reported. Based on KIR gene content, Indian individuals represented the most distinct group, showing the highest frequencies of KIR2DL2, KIR2DL5, KIR2DS1, KIR2DS2, KIR2DS3 and KIR3DS1, the lowest frequencies of KIR2DL3, KIR2DS4 and KIR3DL1; and a KIR2DL4-negative individual. KIR2DS1 and KIR3DS1 were infrequent in black African populations. HLA-C2 was more common in black African individuals, while HLA-C1 predominated in the other populations. Indian individuals were more likely to possess KIR2DL2 paired with HLA-C1, while Caucasian individuals exhibited the highest frequencies of KIR2DL3 paired with HLA-C1. This report provides comprehensive reference data for further study of the roles of KIR/HLA in non-communicable and infectious diseases in South African populations.     

Killer cell immunoglobulin-like receptor (KIR) genes in systemic sclerosis

A previous study has suggested that the combination KIR2DS2⁺/KIR2DL2^‐ was related to increased risk for systemic sclerosis (SSc), while others have failed to reproduce this finding. Our objective was to study this matter further and test the association of other KIR genes with SSc. One hundred and ten SSc patients and 115 healthy bone marrow donors were enrolled in a case–control study. Blood was collected for DNA extraction; typing of 15 KIR genes and human leucocyte antigen‐C (HLA‐C) was made by polymerase chain reaction with sequence specific primers (PCR–SSP), followed by electrophoresis on agarose gel. Patients underwent clinical evaluation, serology, Doppler echocardiography and chest high‐resolution computed tomography. The frequency of the inhibitory KIR2DL2 was significantly lower in patients [29·1% versus 65·2% in controls, P < 0·0001; odds ratio (OR) = 0·22, 95% confidence interval 0·12–0·40]. When combinations of activating and inhibitory KIR genes were analysed, the presence of KIR2DS2 in the absence of KIR2DL2 (KIR2DS2⁺/KIR2DL2^‐) was more frequent in patients than in controls (25·5% versus 1·7%, respectively; P < 0·0001; OR = 19·29, 4·24–122·26). However, the presence of both KIR2DS2 and KIR2DL2 (KIR2DS2⁺/KIR2DL2⁺) was more frequent in controls (57·4%) than in patients (28·2%, P < 0·0001), suggesting a preponderant protective effect of KIR2DL2 over KIR2DS2. Stratification for HLA‐C1 status did not change these results. No statistically significant associations were found between KIR phenotypes and clinical and laboratory features of SSc. Our results suggest a protective role of KIR2DL2⁺ phenotype and confirmed the association of the combination KIR2DS2⁺/KIR2DL2^‐ with increased risk for SSc.     

The killer cell immunoglobulin-like receptor (KIR) genomic region: gene-order, haplotypes and allelic polymorphism

Summary: Recent genetic studies have established that the killer cell immunoglobulin‐like receptor (KIR) genomic region displays extensive diversity through variation in gene content and allelic polymorphism within individual KIR genes. It is demonstrated by family segregation analysis, genomic sequencing, and gene order determination that genomic diversity by gene content alone gives rise to more than 20 different KIR haplotypes and at least 40–50 KIR genotypes. In the most reductionist format, KIR haplotypes can be accommodated within one of 10 different prototypes, each with multiple permutations. Our haplotype model considers the KIR haplotype as two separate halves: the centromeric half bordered upstream by KIR3DL3 and downstream by 2DL4, and the telomeric half bordered upstream by 2DL4 and downstream by 3DL2. There are rare KIR haplotypes that do not fit into this model. Recombination, gene duplication, and inversion can however, readily explain these haplotypes. Additional allelic polymorphism imposes extensive individual variability. Accordingly, this segment of the human genome displays a level of diversity similar to the one observed for the human major histocompatibility complex. Recent application of immunogenetic analysis of KIR genes in patient populations implicates these genes as important genetic disease susceptibility factors.     

Investigation of killer cell immunoglobulin-like receptor (KIR) gene diversity: KIR2DL2, KIR2DL5 and KIR2DS5

Human killer cell immunoglobulin-like receptor (KIR) genes are important for restraining natural killer cytotoxicity toward cells with autologous human leukocyte antigen (HLA) while targeting cells lacking or expressing low levels of self-HLA molecules. KIR gene content and alleles vary across individual genomes and populations, requiring specialized laboratory tools for their characterization. Here, we detail methods based on sequence-specific polymerase chain reaction amplification and oligonucleotide probe hybridization to identify alleles of KIR2DL2, KIR2DL5A, KIR2DL5B and KIR2DS5. Allele frequencies for a Northern Irish population of 354 individuals typed with this system are given, along with results from 132 cell lines from the International Histocompatibility Workshop that cover many world populations. This information complements published reports by our laboratory for allele-level typing of other KIR members, totaling 12 of the 17 known genes. These methods are allowing us to characterize KIR haplotypes in our population.     

Killer cell immunoglobulin-like receptor (KIR) genes in 4 distinct populations and 51 families in mainland China

In this study, we investigated the killer cell immunoglobulin-like receptor (KIR) genes and HLA-C1/C2 dimorphism in 819 healthy, unrelated individuals composed of two southern Chinese Han populations (Hunan Han and Guangdong Han) and two northern Chinese populations (Inner Mongolia Han and Inner Mongolia Mongol), using polymerase chain reaction-sequence-specific priming (PCR-SSP) method. Fifty-one Chinese families were used to determine KIR haplotypic configuration. Our data showed that KIR2DL4, KIR3DL2, KIR3DL3, and KIR3DP1 genes were present in all of the 819 individuals. However, KIR2DL4 and KIR3DP1 genes were not detected in two members of a northern Chinese family. None of the KIR genes showed significant difference between the four populations. Thirty-five different KIR gene profiles were identified, one of which has not been previously reported in the Allele Frequencies KIR database. Eleven distinct KIR haplotypic configurations were determined through family analysis. Individuals with KIR2DLl and KIR2DL3 genes but lacking KIR2DSl and KIR2DS2 genes, coupled with HLA-C1 (Asn(80)) homozygosity, predominated in each population. At least one known inhibitory KIR-HLA pair was detected in each individual. The findings shown here are valuable for future studies of the potential role of KIR genes as well as KIR-HLA interaction in disease susceptibility in related ethnic groups.     

Investigation of killer cell immunoglobulin-like receptor gene diversity, KIR2DL1 and KIR2DS1

Polymorphism in the alleles of the killer cell immunoglobulin-like receptor 2DL1 and 2DS1 genes has been investigated by the development of polymerase chain reaction-sequence-specific oligonucleotide probing systems. The methods have been applied to 77 Northern Irish families, establishing allele frequencies from the unrelated parents. Additionally, cell line DNA from individuals and CEPH families of the 13th International Histocompatibility Workshop panel were investigated. Eight of the reported KIR2DL1 alleles and only the KIR2DS1*002 allele were identified in the groups studied. Two individuals were positive for three alleles of KIR2DL1, and a putative variant of KIR2DL1*001 was observed. Results also indicated an inherited KIR2DL1/2DS1 splice variant present in a haplotype with several core loci absent, in two families.     

Investigation of killer cell immunoglobulin-like receptor gene diversity III. KIR2DL3

The allelic variation of one of the chromosome 19 KIR genes, KIR2DL3, has been investigated using a polymerase chain reaction sequence-specific oligonucleotide probe-based methodology. The procedure has been applied to a healthy Northern Irish control group in order to establish phenotype and genotype frequencies in this Caucasian population. In addition, cell line DNA and Centre d'Etude du Humaine (CEPH) families, both from the 13th International Histocompatibility Workshop have been investigated, establishing control data for this gene.     

Investigation of killer cell immunoglobulin-like receptor gene diversity V. KIR3DL2

Allelic definition within the killer cell immunoglobulin-like receptor gene, KIR3DL2, has been achieved through a sequence-specific oligonucleotide probe methodology, designed around the specific amplification of the D0 and D1 domains and a section of the cytoplasmic tail of this gene. The system has been applied to a healthy Northern Irish control group, establishing frequencies for this Caucasian population. Additionally, the KIR3DL2 allele status of cell line DNA and Centre d'Etude du Polymorphisme Humain (CEPH) families, both from the 13th International Histocompatibility Workshop, has been established. A high level of KIR3DL2 allelic polymorphism has been identified.     

Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates

The human killer immunoglobulin-like receptors (KIR) are encoded within the Leukocyte Receptor Complex (LRC) on chromosome 19q13.4. Here we report the comparative genomic analysis of single KIR haplotypes in two other primates. In the common chimpanzee (Pan troglodytes), seven KIR genes (ptKIRnewI, ptKIRnewII, ptKIR2DL5, ptKIRnewIII, ptKIR3DP1, ptKIR2DL4, ptKIR3DL1/2) have been identified, and five KIR genes (mmKIRnewI, mmKIR1D, mmKIR2DL4, mmKIR3DL10, mmKIR3DL1) are present in the haplotype sequenced for the rhesus macaque (Macaca mulatta). Additional cDNA analysis confirms the genes predicted from the genomic sequence and reveals the presence of a fifth novel KIR gene (mmKIRnewII) in the second haplotype of the rhesus macaque. While all known human haplotypes contain both activating and inhibitory KIR genes, only inhibitory KIR genes (characterized by long cytoplasmic tails) were found by in silico and cDNA analyses in the two primate haplotypes studied here. Comparison of the two human and the two non-human primate haplotypes demonstrates rapid diversification of the KIR gene family members, many of which have diverged in a species-specific manner. An analysis of the intronic regions of the two non-human primates reveals the presence of ancient repeat elements, which are indicative of the duplication events that have taken place since the last common ancestor.     

Activating killer cell immunoglobulin-like receptor gene KIR2DS1 is associated with psoriatic arthritis

Killer cell immunoglobulin-like receptor genotyping was performed on a cohort of American Caucasian patients with psoriasis to investigate any possible relationship between these chromosome 19 genes and autoimmune-linked disease. This patient cohort also contained a subgroup of patients who had been additionally diagnosed as positive for psoriatic arthritis (PsA). Because of the known association of human leucocyte antigen (HLA)-Cw*06 with psoriasis, the study concentrated on the five KIR genes that have HLA-C as their recognized ligand (i.e., KIR2DL1, -2DL2, -2DL3, -2DS1, and -2DS2). An increase in the frequency of the activating KIR2DS1 gene was detected in the PsA patients, compared with psoriasis patients negative for PsA and an unaffected American Caucasian control group.     

Investigation of killer cell immunoglobulin-like receptor gene diversity: II. KIR2DS4

A polymerase chain reaction sequence-specific oligonucleotide probe typing method identifying and distinguishing alleles of the KIR2DS4 gene has been established. The system is based on the specific amplification of a region of this gene, followed by hybridization with 11 sequence-specific oligonucleotide probes. The method has been applied to a healthy group of Northern Irish caucasian individuals, establishing frequencies of alleles of this locus within the local population. Furthermore, cell line DNA and families from the 13th International Histocompatibility Workshop, in addition to local families, have also been allele typed at the KIR2DS4 locus. Haplotype segregation, with respect to KIR2DS4 alleles, has been examined by using the local family data. Within all sample groups investigated, four KIR2DS4 alleles were identified, two of which are novel to this investigation.     

Diversity of the killer cell immunoglobulin-like receptor gene KIR2DS4 in the Chinese population

Human killer cell immunoglobulin-like receptors are a subfamily of the immunoglobulin superfamily, which map to the leukocyte receptor complex on chromosome 19. Here, we established polymerase chain reaction-sequence-based typing (PCR-SBT) procedures to identify alleles of the KIR2DS4 gene. The method was designed around the specific amplification of exons 4-5 of the KIR2DS4 gene. Genomic DNA from 105 healthy unrelated Chinese Han individuals were typed for the KIR2DS4 alleles. Each sample was assigned the KIR2DS4 alleles combination, consistent with the pairwise combinations of sequences of all the known KIR2DS4 alleles. We observed eleven different genotypes and four KIR2DS4 alleles in the population, with the KIR2DS4*00101 having the highest frequency, 0.576, and also confirmed the new KIR2DS4*007 allele. Our data demonstrated that the established PCR-SBT method for the KIR2DS4 allele typing was reliable.     

In contrast to other stimulatory natural killer cell immunoglobulin-like receptor loci, several KIR2DS5 alleles predominate in African Americans

The five two-domain stimulatory KIR genes carried by 100 random African Americans were characterized by DNA sequencing of genomic DNA covering the majority of coding exons. The frequency of individual loci was similar to that found in European Americans, with the exception of a reduced frequency for KIR2DS1 in African Americans. New alleles were identified at the KIR2DS1 (*008), KIR2DS2 (*006), KIR2DS3 (*00104, *00105, *00106, *004), KIR2DS4 (*00103, *00104, *009, *011, *012, *013), and KIR2DS5 (*006, *007, *00801, *00802, *009) loci. The distribution of alleles at each locus was similar to that found in a European American population except for KIR2DS5. KIR2DS5 exhibits a single allele in European Americans; the same allele is found at a reduced frequency (41% of gene-positive individuals), accompanied by KIR2DS5*006 (18%), KIR2DS5*007 (26%), and six other alleles (25%), in African Americans.     

Homogenous expression of killer cell immunoglobulin-like receptors (KIR) on polyclonal natural killer cells detected by a monoclonal antibody to KIR2D

The activity of human natural killer (NK) cells is in part regulated by the expression of killer cell immunoglobulin (Ig)-like receptors (KIR) that recognize major histocompatibility complex (MHC) class I and can inhibit NK cell cytotoxicity. A monoclonal anti-KIR antibody was established and designated Lig1. Lig1 was shown to be specific for KIR in cell-surface staining and to react with all KIR2D, except KIR2DL4 which lacks a D1 domain, but not with KIR3D molecules in an enzyme-linked immunoadsorbent assay (ELISA) and Western blotting. Unlike other anti-KIR antibodies, Lig1 did not inhibit binding of KIR-Ig-fusion proteins to MHC-class I expressing cells nor did it interfere with KIR-mediated inhibition of NK cell cytotoxicity in a functional assay. Lig1 reacted with all NK cells in polyclonal NK populations from different donors, demonstrating that all NK cells express at least one KIR2D receptor.     

Investigation of killer cell immunoglobulin-like receptor gene diversity in KIR3DL1 and KIR3DS1 in a transplant population

Several overlapping amplicons were used to obtain the sequence of genomic DNA covering most of the coding regions of KIR3DL1 and KIR3DS1 from a family and 77 bone marrow transplant patients and their unrelated donors. Alleles 3DL1*00101 and *002 were most frequently observed in addition to 12 other known 3DL1 alleles. A single 3DS1 allele, 3DS1*01301, was identified in the 31 of 32 individuals carrying this gene. Two new alleles, 3DL1*01702 and 3DS1*058, were characterized. Three samples appeared to carry the duplicated killer cell immunoglobulin-like receptor (KIR) haplotype observed in other studies based on the presence of 3DS1 and two 3DL1 alleles. Additionally, one sample appeared to carry a novel KIR haplotype containing one 3DL1 and two 3DS1 alleles.     

Investigation of killer cell immunoglobulin-like receptor KIR2DL4 diversity by sequence-based typing in Chinese population

Human killer cell immunoglobulin-like receptors (KIRs) play an important role in controlling natural killer (NK) cell function. Here, polymerase chain reaction sequence-based typing (PCR-SBT) procedures identifying alleles of the KIR2DL4 gene have been established. The method was designed around the specific amplification of exon 3 to exon 5 and exon 7 to exon 9 of the KIR2DL4 gene and produce discrimination of KIR2DL4 alleles. Genomic DNAs from 83 healthy unrelated Chinese Han individuals were typed for KIR2DL4 alleles by this method. Each sample was assigned to the putative KIR2DL4 allele combination according to the nucleotide polymorphism profiles of all KIR2DL4 alleles. Twenty-one different genotypes and seven KIR2DL4 alleles were observed in the population, with KIR2DL4*00102 having the highest frequency, 0.5. Five individuals bear a recombinant allele KIR3DP*004 that associated with three putative KIR2DL4 alleles. Our data demonstrated that the established PCR-SBT method for KIR2DL4 allele typing was reliable, and Chinese Han population is distinct in KIR2DL4 allele frequencies in comparison to some other populations.