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.     

Compound KIR-HLA genotype analyses in the Iranian population by a novel PCR–SSP assay

Natural killer (NK) cells eliminate infected and transformed cells while still are self-tolerant. Interactions of the independently segregating Killer cell immunoglobulin-like receptors (KIR) and human leucocyte antigens (HLA) loci play a critical role in NK cell regulation. Different compound KIR-HLA genotypes can impart different thresholds of activation to the NK-cell repertoire and such genotypic variation has been found to confer altered risk in a number of human diseases including viral infections, autoimmune disorders, reproduction abnormalities and cancers. In this study, we presented a novel combined KIR-HLA polymerase chain reaction–sequence-specific primers genotyping assay for simultaneous determination of KIR genes and their three major HLA class I ligand groups (C1, C2, and Bw4). Moreover, known inhibitory and activating KIR + HLA (iKIR + HLA: 2DL2/3 + C1, 2DL1 + C2, 3DL1 + Bw4; and aKIR + HLA: 2DS2 + C1, 2DS1 + C2, 3DS1 + Bw4) combinations as well as co-inheritance of aKIR genes and iKIR + HLA pairs were analysed in a total of 200 unrelated healthy Iranian individuals. All tested subjects had at least one of the three iKIR + HLA pairs and the frequencies of various inhibitory combinations in the study group were: 31.5%, three iKIR + HLA pairs, 53.5%, two iKIR + HLA pairs, and 15%, 0ne iKIR + HLA pair. Furthermore, we revealed that majority of Iranians (69%) carry compound genotypes with greater number of inhibitory pairings than activating combinations (iKIR + HLA > aKIR + HLA). Conversely, iKIR + HLA < aKIR (45%) was dominant genotype in the study group. We conclude that selective evolutionary pressure has propensity to maintain KIR-HLA genotypes with more inhibitory combinations to guarantee self-tolerance. In contrast, existence of activating KIR genes without normal endogenous ligands, potentially arms the NK population for competent immunosurveillance and stronger defense against infections.     

KIR‐HLA‐A and B alleles of the Bw4 epitope against HIV infection in discordant heterosexual couples in Chaco Argentina

Activating and inhibitory killer immunoglobulin‐like receptors (KIR) and their ligands HLA‐Bw4 (loci A and B) were studied by way of establishing whether they can contribute to protection against HIV‐1 infection in highly exposed and persistently seronegative (HESN) patients. Twenty‐three HIV‐1 serodiscordant heterosexual couples, 100 HIV‐1⁺ patients and 200 healthy individuals were included in this retrospective case–control study. HLA typing was performed by means of PCR followed by sequence‐specific oligonucleotide probe reverse hybridization. KIR3DL1 and KIR3DS1 were studied by PCR sequence‐specific primers. The frequency of KIR3DS1(3DS1/3DL1)‐Bw4 combination was significantly higher in HESN patients versus the discordant couples (P = 0·0003) and HIV‐1⁺ patients (P = 0·0001). Conversely, the KIR3DL1/KIR3DL1 homozygosity was significantly decreased in HESN patients versus the discordant couples (P = 0·00003), and HIV‐1⁺ patients (P = 0·00066). The frequency of HLA‐A*32 and HLA‐B*44 was higher in HESN versus their discordant couples (P = 0·009; P = 0·049), and HIV‐1⁺ patients (P = 0·00002; P = 0·0001). This had greater significance in combination with KIR3DS1 (3DS1/3DL1). KIR3DS1(3DS1/3DL1) could have a greater effect on protection against HIV‐1 infection in HESN patients when bound to a specific HLA allele, in this case HLA‐A*32 and HLA‐B*44, both Bw4 alleles. The differences probably arise both in the HLA alleles and in the subtypes of KIR receptors depending on the ethnic group studied.     

Distribution of Killer cell immunoglobulin like receptor genes in end stage renal disease among North Indian population

Introduction

NK cell function is regulated by cell surface inhibitory and activating receptors including the C-type lectin receptors and Killer Immunoglobulin-like receptors (KIR). The effect of immune modulating cytokines produced by NK cells in the pathogenesis of end stage renal disease (ESRD) remained intriguing. In this regard the present study assesses the combinatorial association of KIR gene content and KIR receptor–HLA ligand in the North Indian ESRD patients.

Material and methods

KIR gene polymorphism as a susceptible marker in ESRD among 512 patients and 512 ethnically matched controls was analyzed. PCR-SSP based genotyping for KIR gene content and HLA-A, B, C typing was carried out.

Results

Significant difference in frequencies of KIR2DS1–HLA-C2 (p ? 0.0001, OR = 1.98, CI = 1.50–2.61), KIR2DS2–HLAC1 (p ? 0.0001, OR = 1.87, CI = 1.42–2.46), KIR3DS1–HLA-Bw4 (p = 0.0038, OR = 1.46, CI = 1.13–1.88) combinations for ESRD was found. In the combinatorial analysis Bw4⁺/3DL1⁻/3DS1⁺ (p ? 0.0001, OR = 4.90, CI = 2.75–8.71) and C1⁺/2DL2⁻/2DL3⁻/2DS2⁺/2DS3⁺ (p = 0.0037, OR = 2.50, CI = 1.35–4.63) showed risk association. KIR3DS1 was observed to be susceptible for all four primary kidney disease groups.

Conclusion

NK cell de-regulation due to HLA ligand binding KIR receptors may be involved in the patho-physiology of ESRD. Upon analyzing the data in this context it was found that C2/C2 donor might improve the clinical outcome of patients having C2 ligands.     

Diversity and association of HLA/KIR receptors with type 2 diabetes in South India

The present study was undertaken to delineate the association(s) of KIR–HLA combination in South Indian Type 2 diabetes mellitus (T2DM) patients. The T2DM patients (n = 343) and healthy controls (n = 309) were genotyped for KIR/HLA ligands by PCR‐SSP method. The increased frequency of activatory KIR (aKIR) 2DS2 (OR = 1.91; p < 2.91 × 10^?4) was observed in patients suggesting a susceptible association. The frequencies of iKIR 2DL2 (OR = 0.38; p < 1.55 × 10^?5) and aKIRs 2DS1 (OR = 0.60; p < 0.001) and 3DS1 (OR = 0.52; p < 5.83 × 10^?5) were decreased in patients suggesting protective associations. The C1/C2 combinatorial analysis has revealed an increased frequency of C1⁺/C2^? in T2DM patients (OR = 1.62; p < 0.014). The KIR “AB” genotype (OR = 2.41; p < 3.87 × 10^?5) was observed to be higher in patients. However, the “BB” genotype (OR = 0.32; p < 4.71 × 10^?7) was increased in controls. The KIR motifs, “Tel‐B/B” (OR = 1.84; p < 0.007), were observed higher among patients. However, the frequency of “Tel‐A/B” motif genotype was decreased in patients (OR = 0.56; p < 3.13 × 10^?4). The iKIR/HLA combinations such as 2DL2/3 +C1 and 3DL2+A3/A11 were increased in patients (OR = 3.90; p < 7.5 × 10^?5) suggesting susceptible associations. On the contrary, the aKIR+HLA combinations such as 2DS2+C1, 2DS1+C2 and 3DS1+Bw4 were less frequent in patients (OR = 0.32; p < 4.2 × 10^?4) suggesting protective associations. Thus, the present study clearly establishes the positive and negative associations of different KIR–HLA receptor combinations with T2DM in South India.     

Clinical and histopathological changes in different KIR gene profiles in chronic HCV Romanian patients

Hepatitis C virus (HCV)‐infected individuals may have a faster progression of liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC) development when influenced by host, viral and environmental factors. Hepatitis C virus disease progression is also associated with genetic variants of specific killer cell immunoglobulin‐like receptors (KIRs) and genes of the major histocompatibility complex (MHC). The aim of the present study was to correlate clinical, virologic and biochemical parameters and to evaluate the possible influence of KIR genes and their HLA class I ligands in patients infected with hepatitis C virus. The present study analysed a total of 127 chronic HCV‐infected patients for various biochemical and genetics factors that can influence disease progression and prognosis. Liver function parameters such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma‐glutamyl transferase (GGT), direct bilirubin (DB), alpha‐fetoprotein (AFP), HCV RNA levels and fibrosis indices were analysed using well‐established biochemical methods. At the same time, KIR and HLA genotyping was performed using a polymerase chain reaction sequence‐specific primer technique. Analysis of HLA class I and HLA ligands revealed that HLA‐C*12:02 and HLA‐A3 and HLA‐A11 were positively associated with the F3‐F4 fibrosis group (p = .026; OR = 8.717, CI = 1.040–73.077; respectively, p = .047; OR = 2.187; 95% CI = 1.066–4.486). KIR2DL2‐positive patients had high median levels of AST after treatment and direct bilirubin levels when compared to KIR2DL2‐negative patients (p = .013, respectively, p = .028). KIR2DL2/KIR2DL2‐C1C1 genotype was associated with increased AST, ALT and GGT levels. A higher GGT level was also observed in KIR2DS2‐C1‐positive patients when compared to KIR2DS2‐C1‐negative patients. The present research demonstrates several links between specific clinical, virologic and biochemical parameters and the expression of KIR genes and their HLA ligands in HCV‐infected patients. These connections should be taken into account when considering disease development and treatment.     

Genetic associations of killer immunoglobulin like receptors and class I human leukocyte antigens on childhood acute lymphoblastic leukemia among north Indians

BackgroundMolecular interactions between KIRs and their cognate HLA class-I ligands, play a central role in the regulation of natural killer (NK) cell responses in malignancies. We aimed to determine the role of KIR genes and their HLA ligands in genetic predisposition of childhood acute lymphoblastic leukemia (ALL).MethodsGenotyping of 16 KIR genes, along with HLA class-I groups C1/C2 and Bw4 super-type ligands, was carried-out in 137 childhood ALL cases and 274 healthy controls.ResultsWe observed an increased incidence of activating KIRs namely; 2DS2 (OR = 2.23, p = <0.001), 2DS3 (OR = 1.74, p = 0.011), 3DS1 (OR = 2.22, p = <0.001), 2DS5 (OR = 2.10, p = 0.001), 2DS1 (OR = 4.42, p = <0.001) and 2DS4 (OR = 2.88, p = <0.001) genes in childhood ALL cases compared to controls. Frequency of BB genotype that possess 2–6 activating KIR genes was predominant in cases compared to controls (OR = 2.55, p = <0.001). KIR-receptor/HLA-ligand combinations analysis revealed a moderate risk of almost 2-fold for activating KIR-ligand combinations namely; KIR2DS1-HLAC2, KIR2DS2-HLAC1 and KIR3DS1-HLABw4 in childhood ALL cases.ConclusionOur data suggests the role for KIR genes and their HLA ligands in aetiology of childhood ALL.     

Are Killer Cell Immunoglobulin-Like Receptor Genes Important for the Prediction of Kidney Graft Rejection?

Killer cell immunoglobulin-like receptors (KIRs) are expressed on natural killer cells and minor subpopulations of thymus-derived (T) lymphocytes. KIRs may have a long cytoplasmic tail and inhibit cell activation upon ligand (HLA class I) binding, or they may have a short cytoplasmic tail and activate a cell after ligand binding. They are encoded by up to 14 genes present in different individuals in different combinations, whence their associations with several human diseases. KIR involvement in the fate of kidney allograft has not been extensively studied; nevertheless some associations had already been noticed. Their results are not concordant: some authors found no effect of KIR genotype, whereas others detected protective effect of KIR2DL2/KIR2DS2 or KIR–KIR ligand mismatch. We found an association of KIR2DS4 gene with acute rejection and a protective effect of KIR2DS5 gene. Interestingly, in patients, whose end-stage renal disease was caused by glomerulonephritis, the effect of KIR2DS4 was stronger than HLA mismatch, whereas opposite was true for recipients with other causes of renal failure.     

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.     

Associations of killer cell immunoglobulin like receptors with rheumatoid arthritis among North Indian population

Introduction

Rheumatoid arthritis (RA) is an autoimmune and chronic inflammatory disease of unknown etiology. Killer cell immunoglobulin-like receptors (KIR) expressed on surface of natural killer cells and CD28 null T-cells which are present in synovial membrane of RA. The present study has evaluated associations of KIR genes with RA among North Indian population from Uttar Pradesh.

Materials and methods

KIR genotypes were determined in 100 RA cases and 100 healthy controls using sequence specific primer polymerase chain reaction (PCR-SSP) method.

Results

RA cases positive for KIR3DS1 (OR = 1.17, p-value = 0.0498) and KIR2DS2 (OR = 2.21, p-value = 0.0120) showed risk associations. While, KIR2DL2 (OR = 0.40, p-value = 0.0026), KIR2DL3 (OR = 0.44, p-value = 0.0283) and KIR3DL1 (OR = 0.32, p-value = 0.0012) showed protective associations. Increased incidence of BB genotype (45%) was revealed among cases. Risk association was noted against telomeric region (OR = 2.12, p = 0.0120) genes for RA. Pair-wise linkage disequilibrium (LD) analysis among RA cases revealed KIR2DS1-2DL1 (D′ = 0.83, r² = 0.36), KIR3DL1-3DS1 (D′ = 1, r² = 0.58) and KIR2DL1-2DL2 (D′ = 1, r² = 0.61) to be in significant LD. KIR3DS1 and KIR2DS3 genes showed significant risk associations among RA patients with extra-articular manifestations (OR = 5.14, p-value = 0.0018; OR = 3.79, p-value = 0.0106) and in limited range of motion in affected joints (OR = 14.91, p-value = 0.0001; OR = 2.95, p-value = 0.0126).

Conclusion

The KIR activating genes have risk association with RA in the present study.     

Human leucocyte antigen but not KIR alleles and haplotypes associated with chronic HCV infection in a Chinese Han population

The host immune system plays a key role in the elimination of infected cells which depend on killer‐cell immunoglobulin‐like receptors (KIR), human leucocyte antigen (HLA) class I molecules and their combinations. To evaluate the roles of HLAclass I, KIR genes and their combination in Chronic hepatitis C virus (HCV) infection (CHC), a total of 301 CHCs and 239 controls in a Chinese Han population were included for HLA and KIR genotyping using next‐generation sequencing and multiplex PCR sequence‐specific priming, respectively. The allele frequency of HLA‐C*08:01 was significantly higher in the CHCs than that of the controls (0.088 vs. 0.040, OR = 2.332, 95%CI: 1.361–3.996, p = 0.022), while the frequencies of B*13:01 (0.032 vs. 0.084, OR = 0.357, 95%CI: 0.204–0.625, p = 0.009) and C*08:04 (0.008 vs. 0.038, OR = 0.214, 95%CI: 0.079–0.581, p = 0.022) were significantly lower in the CHCs. The frequencies of haplotype A*11:01‐C*08:01 were higher in the CHCs (0.058 vs. 0.019, OR = 3.096, 95%CI: 1.486–6.452, p = 0.026), while haplotype B*13:01‐C*03:04 were lower in the CHCs compared to the controls (0.028 vs. 0.071, OR = 0.377, 95%CI: 0.207–0.685, p = 0.012). No association of CHC with KIR genes, genotypes, or haplotypes, as well as HLA/KIR combinations was observed. Our results indicated that HLA‐C*08:01 was a risk factor for CHC, while HLA‐C*08:04 and HLA‐B*13:01 were protective factors against CHC. Haplotypes HLA‐A*11:01‐C*08:01 could increase susceptibility to CHC, while HLA‐B*13:01‐C*03:04 could be protective against CHC in the Chinese Han population.     

A deep look at KIR–HLA in Amerindians: Comprehensive meta-analysis reveals limited diversity of KIR haplotypes

Killer-cell immunoglobulin-like receptors (KIR) are highly polymorphic and have been associated to several diseases. Their ligands are specific human leukocyte antigens (HLA) molecules, expressed on the majority of cells. Only few genetically isolated populations have been characterized for the frequency of KIR–HLA combinations. The aim of this work was summarize and reanalyze the data described in recent publications regarding KIR and HLA in Amerindians. In total, 1258 individuals from 23 Amerindian populations were analyzed. All population samples were previously genotyped for KIR presence/absence polymorphism; KIR allelic content was poorly described. Only 9 of the 23 populations were genotyped for HLA class I. Based on the KIR gene-content profiles, we estimated the most common Amerindian KIR gene-content haplotypes, information never reported before for many of these populations. When the HLA genes started to be analyzed in many of these groups, KIR genes were still not well characterized. Therefore, they have never been analyzed in a joint context. We thoroughly examined the HLA haplotypes of these populations; for the first time, we are showing the frequencies of the known HLA ligands of most of these populations, which had been separately studied for both KIR and HLA. Amerindians exhibits a low diversity of KIR gene-content haplotypes when compared to most worldwide population. We compared the KIR–HLA diversity within and between Amerindian groups trying to understand the natural causes of variation. This study corroborates the hypothesis that demographic factors such as founder effect played a major role in shaping KIR diversity in Amerindians and may contribute to understand the importance of KIR–HLA for human health and disease.     

Association of killer cell immunoglobulin-like receptor and human leucocyte antigen-Cw gene combinations with systemic lupus erythematosus

Killer cell immunoglobulin-like receptors (KIRs) are a diverse family of activating and inhibitory receptors expressed on natural killer (NK) cells and T cells, the genes of which show extreme polymorphism. Some KIRs bind to human leucocyte antigen (HLA) class I subgroups, and genetic interactions between KIR genes and their ligand HLA have been shown to be associated with several autoimmune diseases. The present study aimed to investigate whether the combinations of KIR genes and HLA-Cw ligands associate with the susceptibility of systemic lupus erythematosus (SLE). Polymerase chain reaction using sequence-specific primers was used to determine the genotypes of KIR genes and HLA-Cw alleles. We found that the frequencies of HLA-Cw07 were statistically significantly higher in the patient group than those in the control group (P = 0·009). KIR2DS1⁺HLA⁻Cw^Lys was more common in subjects with SLE compared to control subjects (P = 0·015). In addition, the frequency of KIR2DS1 was increased in SLE when KIR2DL1/HLA-Cw are absent, and the difference was significant (P = 0·001). KIR genotype and HLA ligand interaction may potentially influence the threshold for NK (and/or T) cell activation mediated through activating receptors, thereby contributing to the pathogenesis of SLE.     

Killer cell immunoglobulin-like receptor gene diversity in a Southern Brazilian population from the state of Paraná

Killer cell immunoglobulin-like receptors (KIR) are encoded by polymorphic genes and have as binding human leukocyte antigen (HLA) class I molecules. The aim of this study was to investigate the distribution of KIR genes and inhibitory KIR/HLA pairs in a population from Southern Brazil, in the state of Paraná, and to compare the results with results from other populations. The genotyping of 16 KIR genes and HLA class I alleles of 289 unrelated individuals was accomplished by reverse sequence-specific oligonucleotide Luminex (One Lambda, Inc., Canoga Park, CA). This Brazilian population demonstrated several similarities to Caucasian populations with regard to the frequency of KIR genes. Thirty-eight genotypes were defined in which the most frequent was the homozygous haplotype A (33.2%). Therefore, it was possible to define two new genotypes. Most of the individuals demonstrated at least one inhibitory KIR/HLA pair. Two pairs were the most frequent (40.4%), followed by three pairs (38.2%), one pair (14.6%), and four pairs (6.4%). The KIR2DL2/3 + HLA-C1 pair was the most frequent (79.9%) and the least frequent pair was KIR3DL2 + HLA-A3/11 (25.0%). This study demonstrated the diversity of KIR genes in a population of Paraná, as well as the characteristic pattern of Caucasians with racial admixture, which enabled the definition of two new genotypes and the identification of one individual without the inhibitory KIR/HLA pair.     

Next-generation sequencing technology a new tool for killer cell immunoglobulin-like receptor allele typing in hematopoietic stem cell transplantation

Killer cell Immunoglobulin-like Receptor (KIR) genes are a family of genes located together within the leukocyte receptor cluster on human chromosome 19q13.4. To date, 17 KIR genes have been identified including nine inhibitory genes (2DL1/L2/L3/L4/L5A/L5B, 3DL1/L2/L3), six activating genes (2DS1/S2/S3/S4/S5, 3DS1) and two pseudogenes (2DP1, 3DP1) classified into group A (KIR A) and group B (KIR B) haplotypes. The number and the nature of KIR genes vary between the individuals. In addition, these KIR genes are known to be polymorphic at allelic level (907 alleles described in July 2017). KIR genes encode for receptors which are predominantly expressed by Natural Killer (NK) cells. KIR receptors recognize HLA class I molecules and are able to kill residual recipient leukemia cells, and thus reduce the likelihood of relapse. KIR alleles of Hematopoietic Stem Cell (HSC) donor would require to be known (Alicata et al. Eur J Immunol 2016) because the KIR allele polymorphism may affect both the KIR⁺ NK cell phenotype and function (Gagne et al. Eur J Immunol 2013; Bari R, et al. Sci Rep 2016) as well as HSCT outcome (Boudreau et al. JCO 2017). The introduction of the Next Generation Sequencing (NGS) has overcome current conventional DNA sequencing method limitations, known to be time consuming. Recently, a novel NGS KIR allele typing approach of all KIR genes was developed by our team in Nantes from 30 reference DNAs (Maniangou et al. Front in Immunol 2017). This NGS KIR allele typing approach is simple, fast, reliable, specific and showed a concordance rate of 95% for centromeric and telomeric KIR genes in comparison with high-resolution KIR typing obtained to those published data using exome capture (Norman PJ et al. Am J Hum Genet 2016). This NGS KIR allele typing approach may also be used in reproduction and to better study KIR⁺ NK cell implication in the control of viral infections.     

Allele diversity of the killer cell immunoglobulin-like receptors KIR3DL1/S1 and the combination with their HLA ligands in Mexican Mestizos from Mexico City

Killer cell immunoglobulin-like receptors (KIRs), expressed on Natural Killer (NK) cells, activate/inhibit NK cell function through interactions with their HLA–A, B and C ligands. KIR3DL1 is one of the most polymorphic genes and its effect varies depending on the interaction of the specific allotype with its Bw4 ligand. We investigated the allelic diversity of KIR3DL1/S1 using sequence based typing and we typed as well, their Bw4 ligands in Mexican Mestizos of Mexico City. The results showed that this population has a great KIR3DL1 allelic diversity with ¹01502 (19.9%), ¹00101 (13.2%) and ¹00501 (12.8%) being the most common alleles, while KIR3DS1 showed predominance of ¹01301 (86%); these data agree with the diversity found in most populations studied. At least one KIR3DL1-HIGH surface expression allele was present in 67.5% of the subjects. Phylogenetic comparisons between Mestizos and 28 different populations showed that allelic diversity of KIR3DL1/S1 was similar in Mexican Mestizos from Mexico and in Hispanics from USA. Knowledge of KIR and MHC diversity worldwide is fundamental for understanding the impact of KIR and KIR-ligand polymorphism on NK cell effector functions and is relevant in genetic anthropology, disease association and transplantation.     

Functional advantage of educated KIR2DL1+ natural killer cells for anti‐HIV‐1 antibody‐dependent activation

Evidence from the RV144 HIV‐1 vaccine trial implicates anti‐HIV‐1 antibody‐dependent cellular cytotoxicity (ADCC) in vaccine‐conferred protection from infection. Among effector cells that mediate ADCC are natural killer (NK) cells. The ability of NK cells to be activated in an antibody‐dependent manner is reliant upon several factors. In general, NK cell‐mediated antibody‐dependent activation is most robust in terminally differentiated CD57⁺ NK cells, as well as NK cells educated through ontological interactions between inhibitory killer immunoglobulin‐like receptors (KIR) and their major histocompatibility complex class I [MHC‐I or human leucocyte antigen (HLA‐I)] ligands. With regard to anti‐HIV‐1 antibody‐dependent NK cell activation, previous research has demonstrated that the epidemiologically relevant KIR3DL1/HLA‐Bw4 receptor/ligand combination confers enhanced activation potential. In the present study we assessed the ability of the KIR2DL1/HLA–C2 receptor/ligand combination to confer enhanced activation upon direct stimulation with HLA‐I‐devoid target cells or antibody‐dependent stimulation with HIV‐1 gp140‐pulsed CEM.NKr‐CCR5 target cells in the presence of an anti‐HIV‐1 antibody source. Among donors carrying the HLA‐C2 ligand for KIR2DL1, higher interferon (IFN)‐γ production was observed within KIR2DL1⁺ NK cells than in KIR2DL1^– NK cells upon both direct and antibody‐dependent stimulation. No differences in KIR2DL1⁺ and KIR2DL1^– NK cell activation were observed in HLA‐C1 homozygous donors. Additionally, higher activation in KIR2DL1⁺ than KIR2DL1^– NK cells from HLA–C2 carrying donors was observed within less differentiated CD57^– NK cells, demonstrating that the observed differences were due to education and not an overabundance of KIR2DL1⁺ NK cells within differentiated CD57⁺ NK cells. These observations are relevant for understanding the regulation of anti‐HIV‐1 antibody‐dependent NK cell responses.     

Association of HLA class II (-DRB1,-DQB1,-DPB1) alleles and haplotypes on susceptibility to aplastic anemia in northern Chinese Han

The Human Leukocyte Antigen (HLA) genes, playing key roles in mediating the immune response, especially HLA class II alleles were suggested to play a role in the activation of autoreactive T-cells in aplastic anemia (AA). Previous studies in different ethnic groups have indicated that some of HLA-A,-B,-DRB1 alleles had a protective or susceptive association with the prevalence, pathogenesis and development of AA. HLA class II genes, especially HLA-DQB1 and -DPB1 alleles or haplotypes at high-resolution level associated with AA have not been fully identified in northern Chinese Han populations. The aim of this study was to identify association of the variations in HLA class II region with AA in northern Chinese Han population. A recent case-control study, including 96 AA patients and 824 healthy controls was performed. The high-resolution HLA genotyping was conducted by PCR-SBT, -SSO and NGS-ION S5^TM platform. Based on genotypic data of the three loci, haplotype estimation was carried out. HLA-DRB1*15:01 (Pc = 2.87 × 10^-3; OR = 2.11, 95% CI = 1.45–3.07) and HLA-DQB1*06:02 (Pc = 1.86 × 10^-2; OR = 2.01, 95% CI = 1.32–3.06) were the risk and predisposition alleles to AA in northern Chinese Han after considering multiple testing. Moreover, the HLA-DRB1*15:01-DQB1*06:02 (Pc = 4.90 × 10^-3; OR = 2.09, 95% CI = 1.37–3.19) and HLA-DRB1*14:05-DQB1*05:03 (Pc = 2.65 × 10^-2; OR = 2.82, 95%CI = 1.45–5.50) haplotypes had direct strong relevance to AA and were the susceptible haplotypes. HLA-DPB1 alleles and 23 polymorphic amino acid residues spanning exon 2 ~ 4 of DPβ1 molecules have showed no statistically significant associations between AA and controls. The present findings establish a novel link between inherited HLA-DRB1,-DQB1,-DPB1 risk alleles and haplotypes in northern Chinese Han with AA, and open new avenues for development of targeted therapies to prevent or redirect immunopathology in AA.     

Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop

The goals of the KIR component of the 17th International HLA and Immunogenetics Workshop (IHIW) were to encourage and educate researchers to begin analyzing KIR at allelic resolution, and to survey the nature and extent of KIR allelic diversity across human populations. To represent worldwide diversity, we analyzed 1269 individuals from ten populations, focusing on the most polymorphic KIR genes, which express receptors having three immunoglobulin (Ig)-like domains (KIR3DL1/S1, KIR3DL2 and KIR3DL3). We identified 13 novel alleles of KIR3DL1/S1, 13 of KIR3DL2 and 18 of KIR3DL3. Previously identified alleles, corresponding to 33 alleles of KIR3DL1/S1, 38 of KIR3DL2, and 43 of KIR3DL3, represented over 90% of the observed allele frequencies for these genes. In total we observed 37 KIR3DL1/S1 allotypes, 40 for KIR3DL2 and 44 for KIR3DL3. As KIR allotype diversity can affect NK cell function, this demonstrates potential for high functional diversity worldwide. Allelic variation further diversifies KIR haplotypes. We determined KIR3DL3?～?KIR3DL1/S1?～?KIR3DL2 haplotypes from five of the studied populations, and observed multiple population-specific haplotypes in each. This included 234 distinct haplotypes in European Americans, 191 in Ugandans, 35 in Papuans, 95 in Egyptians and 86 in Spanish populations. For another 35 populations, encompassing 642,105 individuals we focused on KIR3DL2 and identified another 375 novel alleles, with approximately half of them observed in more than one individual. The KIR allelic level data gathered from this project represents the most comprehensive summary of global KIR allelic diversity to date, and continued analysis will improve understanding of KIR allelic polymorphism in global populations. Further, the wealth of new data gathered in the course of this workshop component highlights the value of collaborative, community-based efforts in immunogenetics research, exemplified by the IHIW.     

Human leukocyte antigen-C and killer cell immunoglobulin-like receptor gene polymorphisms among patients with syphilis in a Chinese Han population

Syphilis is a sexually transmitted infection caused by the Treponema pallidum subspecies pallidum spirochete bacterium. The killer cell immunoglobulin‐like receptors (KIR), interacting with human leukocyte antigens (HLA), regulate the activations of natural killer (NK) cells and certain T‐cell subsets in response to microbe infection. The objective of this study was to explore whether KIR and HLA‐C gene polymorphisms were associated with syphilis in a Chinese Han population. Polymerase chain reaction with sequence‐specific primers (PCR‐SSP) method was used to genotype KIR and HLA‐C genes in 231 syphilis patients and 247 healthy controls. Framework genes KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 were present in all individuals. The frequencies of KIR2DS3 and KIR3DS1 were higher in syphilis patients than in healthy controls (p = 0.030 and p = 0.038, respectively), while the frequency of KIR2DS5 was higher in healthy controls than in syphilis patients (p = 0.015; OR = 0.575). The homozygote for HLA‐C1 allele (HLA‐C1C1) was more common in controls compared with syphilis patients (p = 0.030; OR = 0.667). The frequency of individuals with HLA‐C1C1 and KIR2DL3 genotype was higher in control group relative to syphilis patient group (p = 0.018; OR = 0.647). These data indicated that KIR2DS3 and KIR3DS1 were more prevalent in syphilis patients than in controls, and that KIR2DS5, HLA‐C1C1 and HLA‐C1C1‐KIR2DL3 were more prevalent in controls than in syphilis patients, respectively. These will require further investigation using functional studies.