Killer Cell Immunoglobulin-like Receptors Genes Research Articles

O-034 Specific KIR gene profiles and recurrent implantation failure

Abstract Study question Is there a link between killer cell immunoglobulin-like receptors (KIRs) genes, haplotypes, or genotypes and recurrent implantation failure (RIF)? Summary answer The KIRAA1 genotype significantly increases the risk of RIF. The presence of the full-length receptor KIR2DS4norm in KIRAA haplotype patients is indicative of RIF development. What is known already KIRs are expressed by a subset of uterine natural killer cells (uNK cells). The KIRs family consists of 16 genes with high polymorphism that are divided into two main haplotypes: KIRAA and KIRBx. The KIRAA haplotype consists mostly of inhibitory KIRs and only one activating receptor, KIR2DS4, whose function is uncertain, whereas the Bx haplotype has a diverse gene composition, with a focus on activating receptor genes. The primary difference is in the balance of KIRs, which can activate or inhibit uNKcells’ ability to produce components required for embryo-implantation, and hence they are thought to being implicated in RIF. Study design, size, duration A three-year observational cohort research was conducted at a private infertility centre. A total of 82 patients were genotyped for activating or inhibiting KIR genes. The study included 60 ovarian normo-responders under the age of 40, with 28 women with repeated implantation failure serving as the study group and 32 as controls. Participants/materials, setting, methods DNA was extracted from blood samples of all participants, including RIF patients and controls. The 16 KIR genes were investigated utilizing PCR with Sequence-Specific Primer (SSP) technique. Individual KIR gene profiles, KIRAA and KIRBx haplotypes, and their unique genotypes were detected by software analyses of the collected data based on the reaction pattern when compared to patterns associated with described KIR gene sequences. All data were statistically analysed with the Fisher Exact Test. Main results and the role of chance The frequencies of the two main haplotypes, KIR AA and KIR Bx, were 28% and 72%, respectively. Patients with more inhibitory KIR genes (haplotype KIR AA) had a higher rate of RIF (60% vs 40% in controls; P = 0.2) than those with KIR Bx phenotypes (37.5% RIF vs 62.5% controls; p = 0.026). Further analysis of KIR AA revealed two genotypes: KIR AA 1 (31.82%) and KIR AA195 (68.18%). The KIR2DS4 locus in the full-length receptor (KIR2DS4-norm) was only expressed in KIR AA1. The distribution of RIF occurrences in the two different genotypes demonstrates a significant increase in the number of RIF in the possessors of KIR AA1 (75% vs 15%, p = 0.01), with no significant difference between the two groups in the KIR AA195. Limitations, reasons for caution The study encompasses small samples but the association strength was noticeably high, which confers the findings more confidence. Wider implications of the findings These findings imply that women with a high proportion of inhibited KIR genes (haplotype KIR AA) and KIR2DS4norm are more likely to develop RIF. Trial registration number NA

Full resolution HLA and KIR gene annotations for human genome assemblies.

The Human leukocyte antigens (HLA) genes and the Killer cell immunoglobulin like receptors (KIR) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, they are hard to study with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a nontrivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotated 9,931 HLA and KIR genes and found that almost half of these genes, 4,068, had novel sequences compared to the current Immuno Polymorphism Database (IPD). These novel gene sequences were represented by 2,664 distinct alleles, some of which contained nonsynonymous variations resulting in 92 novel protein sequences. We demonstrated the complex haplotype structures at the two loci and reported the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.

The association of the killer cell immunoglobulin-like receptor (KIR) genotype distribution and HLA-C ligands in colorectal cancer in the eastern region of Saudi Arabia

Colorectal cancer (CRC) is the most common cause of cancer-related mortality globally. It ranks as the most common cancer among men and the third most prevalent among women in Saudi Arabia, especially in the eastern region. The immune system's response to cancer is significantly influenced by natural killer cells through their killer-cell immunoglobulin-like receptors (KIRs) interaction with human leukocyte antigen (HLA) molecules. Our research aimed to target a homogeneous ethnic group in the eastern region of Saudi Arabia, analyzing the distribution of 16 KIR genes and HLA-C1/C2 allotypes in 50 CRC patients and 63 healthy controls using the sequence-specific PCR amplification method. Findings revealed significantly lower frequencies of the 2DL2 and 3DL1 genes in CRC patients compared to controls (OR = 2.21; P = 0.04) and (OR = 7.46; P = 0.00009), respectively. Additionally, a higher prevalence of HLA-C2 was noted in CRC patients (84 %) versus controls (66.7 %) (OR = 2.26; P = 0.04). Conversely, the HLA-C1C2 combination showed a protective effect against CRC (OR = 0.38; P = 0.04). Our combinatorial analysis further identified specific gene combinations correlating with CRC risk or protection. Notably, the absence of KIR2DL2 combined with the presence of KIR2DS2 emerged as a significant risk factor, while various combinations involving KIR2DL2 and/or KIR2DS1 with HLA-C ligands were associated with either increased susceptibility or protection. The study underscores the protective role of KIR2DL2 against CRC in Saudi Arabia's eastern region and suggests that the absence of KIR2DL2, especially when KIR2DS2 is present, might increase CRC risk. This research contributes to understanding genetic influences on CRC susceptibility, emphasizing the potential of KIR and HLA interactions as biomarkers for CRC risk assessment.

Determination for KIR genotype and allele copy number via real-time quantitative PCR method.

Killer cell immunoglobulin-like receptor (KIR) and human leukocyte antigen (HLA) play crucial roles in regulating NK cell activity. Here, we report a real-time quantitative PCR (qPCR) to genotype all KIR genes and their copy numbers simultaneously. With 18 pairs of locus-specific primers, we identified KIR genes by Ct values and determined KIR copy number using the 2-∆Ct method. Haplotypes were assigned based on KIR gene copy numbers. The real-time qPCR results were consistent with the NGS method, except for one sample with KIR2DL5 discrepancy. qPCR is a multiplex method that can identify KIR copy number, which helps obtain a relatively accurate haplotype structure, facilitating increased KIR research in laboratories where NGS or other high-resolution methods are not available.

Association of KIR Genes with Middle East Respiratory Syndrome Coronavirus Infection in South Koreans.

Middle East respiratory syndrome (MERS) is a lower respiratory tract disease caused by a beta coronavirus (CoV) called MERS-CoV, characterized by a high mortality rate. We aimed to evaluate the association between genetic variation in killer cell immunoglobulin-like receptors (KIRs) and the risk of MERS in South Koreans. KIR genes were genotyped by multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP). A case-control study was performed to identify the odds ratios (OR) of KIR genes for MERS and the association of KIR genes and their ligands, human leukocyte antigens (HLA) genes. KIR2DS4D and KIR3DP1F showed higher frequencies in the group of all patients infected with MERS-CoV than in the control group (p = 0.023, OR = 2.4; p = 0.039, OR = 2.7). KIR2DL1, KIR2DP1, and KIR3DP1D were significantly associated with moderate/mild (Mo/Mi) cases. KIR2DL2, KIR2DS1, and KIR3DP1F were affected in severe cases. When we investigated the association between KIR genes and their ligands in MERS patient and control groups, KIR3DL1+/Bw4(80I)+, KIR3DL1+/Bw6+, KIR3DL1+/Bw6-, KIR2DS1+/C2+, and KIR3DS+/Bw4(80I)+ were associated with MERS. KIR3DL1+/Bw6- was found in Mo/Mi cases. KIR2DS1+/C2+ and KIR2DS2+/C1+ were found in severe cases. Further investigations are needed to prove the various immune responses of MERS-CoV-infected cells according to variations in the KIR gene and ligand gene. A treatment strategy based on current research on the KIR gene and MERS-CoV will suggest potential treatment targets.

High-resolution characterization of KIR genes polymorphism in healthy subjects from the Bulgarian population-A pilot study.

Although killer-cell immunoglobulin-like receptor (KIR) gene content has been widely studied in health and disease, with the advancement of next-generation sequencing (NGS) technology the high-resolution characterization of this complex gene region has become achievable. KIR allele-level diversity has lately been described across human populations. The present study aimed to analyze for the first time the allele-level polymorphism of nine KIR genes in 155 healthy, unrelated individuals from the Bulgarian population by applying NGS. The highest degree of polymorphism was detected for the KIR3DL3 gene with 40 observed alleles at five-digit resolution in total, 22 of which were common. On the other hand, the KIR3DS1 gene was found to have the lowest degree of polymorphism among the studied KIR genes with one common allele: KIR3DS1*01301 (31.6%). To better understand KIR allelic associations and patterns in Bulgarians, we have estimated the pairwise linkage disequilibrium (LD) for the 10 KIR loci, where KIR2DL3*00501 allele was found in strong LD with KIR2DL1*00101 (D' = 1.00, R2 = 0.742). This is the first study investigating KIR polymorphism at the allele level in a population from the South-East European region. Considering the effect of the populationally shaped KIR allelic polymorphism on NK cell function, this data could lead to a better understanding of the genetic heterogeneity of this region and can be carried into clinical practice by improvement of the strategies taken for NK-mediated diseases.

Killer cell immunoglobulin-like receptors in Thai patients with multiple myeloma.

Natural killer (NK) cells have been implicated in the immune response against multiple myeloma (MM) cells. Killer cell immunoglobulin-like receptors (KIRs) regulate NK cell activity by recognizing specific human leukocyte antigen (HLA) class I as ligands. To investigate the association of KIR genes and ligands with MM in the Thai population. KIR gene polymorphisms and their HLA ligands were investigated in 66 Thai patients with MM and 200 healthy controls. The frequencies of KIR3DL1 and 2DS4 were significantly lower in myeloma patients than in controls (P = 0.02). The frequencies of KIR3DL1, 2DS4, 2DL1 with C2, and 3DL1 with Bw4 were significantly higher in the patients achieving > very good partial response (VGPR) than those achieving ≤ VGPR after treatment with bortezomib (P = 0.009, 0.009, 0.01, and 0.02, respectively). This study suggests the association of KIR genes with the protection against MM and the association of inhibitory KIR and ligands with the response to treatment in MM.

The KIR repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation.

The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human KIR gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the KIR repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic KIR region configurations have been mapped, and seventeen additional ones were deduced by genotyping. Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length KIR transcriptome - in our MHC characterized pedigreed West African chimpanzee cohort - using SMRT sequencing (PacBio). In addition, the genomic organization of 14 KIR haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies. In the cohort, we discovered 35 undescribed and 15 already recorded Patr-KIR alleles, and a novel hybrid KIR gene. Some KIR transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the KIR region dynamics (location and order of genes) was obtained, however, only five new KIR region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2. Although the KIR region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the ancient selective sweep that affected the chimpanzee MHC class I region may also have impacted the KIR system.

Gene and genotype frequencies of immunoglobulin-like natural killer cell receptors in the population of Samara region

Background. The using of killer-cell immunoglobulin-like receptor (KIR) composition data is of increasing interest in clinical practice to select an optimal donor for allogeneic hematopoietic stem cell transplantation for treatment of hematologic malignancies to reduce graft versus host disease and the risk of relapse. It is also of interest to study the frequencies of KIR genes and genotypes in different populations. For the Russian Federation, KIR gene and genotype frequencies have been described for only a few relatively small samples and have not been fully studied. The study of KIR gene and genotype frequencies has not been conducted for the Samara region population to date.Aim. To study the frequencies of KIR genes and genotypes in the population of Samara region and to compare the data with previously described Russian populations.Materials and methods. To study the frequencies of KIR genes and genotypes, molecular genetic typing of 142 CBUs from the public cord blood bank of the Samara Regional Medical Centre “Dynasty” was performed. Molecular genetic typing of KIR genes was performed by polymerase chain reaction with sequence-specific primers with subsequent visualization of products in agarose gel. 16 KIR genes and pseudogenes were analyzed: 2DL1, 2DL2, 2DL3, 3DL1, 3DL2, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DS1, 2DP1, 3DL3, 2DL4, 2DL5, 3DP1. KIR gene frequencies were determined by direct counting. Genotypes were determined using Allele Frequencies database. A determination B-content group was performed using the Donor KIR B-content group calculator. Statistical analysis was performed using the χ2 test.Results. The highest frequency of KIR inhibitory genes was found for KIR2DL1 (98.6 %), KIR3DL1 (98.6 %), KIR2DL3 (96.5 %), KIR2DL5 (46.5 %), and KIR2DL2 (34.5 %). The most frequent among the activating receptor genes was KIR2DS4 (89.4 %), the frequencies of other KIR activating genes were KIR2DS2 – 45.1 %, KIR2DS1 – 35.9 %, KIR2DS3 33.8 %, and KIR2DS5 – 26.1 %. Comparative analysis of KIR gene frequencies in the population of Samara region and other Russian populations revealed certain differences. Significant differences in the frequencies of occurrence were found for KIR2DL3, KIR2DS4, KIR2DL2, KIR2DL5, KIR2DS3, KIR2DS5, as well as KIR2DP1 and KIR3DP1. Examination of 142 samples revealed 45 different genotypes: AA genotypes were detected in 30 % and Bx genotypes in 70 % of cases. AA genotype ID195 with a frequency of 5.6 % was detected, which has not been previously described in Russian populations. Among the Samara region population sample, only 3.5 % had the “best” status, 20.4 % had the “better” status, and 76.1 % had the “neutral” status of the B-content.Conclusion. The results obtained in this sample on the frequencies of KIR genes and genotypes differ from the previously published data for the Russian Federation. Of interest is the finding of a greater diversity of genotypes among a rather small study group, the detection of an atypical ID195 genotype, and the difference in the representation of B-content groups. The analysis of KIR genotypes in the population of Samara region can be used in the selection of optimal CBU and hematopoietic cell/bone marrow donors in addition to HLA typing. Studying the frequency distribution of KIR and HLA genes and genotypes can play a role in the study of fundamental aspects of human immunology and population genetics.

Donor NK Cell Education By KIR3DL1 and HLA-B Associates with Reduced Relapse in Unrelated Bone Marrow Transplantation for Adult T-Cell Leukemia

Background: Adult T-cell leukemia/lymphoma (ATL) derives from human T-cell leukemia virus-1 (HTLV-1)-infected T cells, and its prognosis is still dismal. Whereas allogeneic stem cell transplant (allo-HSCT) may lead to long-term remission, 1-year relapse rate is still high at 35-47% (Muranushi et al, Bone Marrow Transplant. 2021). As for NK cell modulation against ATL, polymorphisms of killer-cell immunoglobulin-like receptors (KIRs) are of interest. NK cell inhibition by donor KIR/patient HLA interaction and NK cell education status have been reported to affect the prognosis of allo-HSCT, but no consensus has been reached. Furthermore, the effects of entire KIR haplotypes have not been extensively studied. Aim: Using high-resolution genotyping of all 15 functional KIR genes based on long-range PCR and long-read sequencer, correlations between KIR/HLA polymorphisms and relapses in unrelated bone marrow transplantation (UR-BMT) for ATL were evaluated. Methods: DNAs and clinical data of 264 transplants performed between 2007 and 2016 were obtained. Alleles of 15 KIRs, HLA-A, B, C, DRB1, DPB1 and DQB1 were genotyped for patients and donors. Prognostic factors for relapse were evaluated using the Fine-Gray proportional-hazards models. Results: Donor KIR3DL1 and patient HLA-B combination predictive of strong interaction (n=74) showed a trend for a lower relapse rate than weak or non-interactive combinations (n=145) (HR, 0.64; p=0.100), raising the beneficial impact of donor NK cell education at KIR3DL1/HLA-B interaction. Comprehensive analysis focusing on amino acids of donors' KIRs/HLAs specified combinations of HLA-B isoleucine 80 (80I)/ KIR3DL2 aspartic acid 42 and HLA-B threonine 80 (80T)/ KIR3DL2 glutamic acid 42 (n=76) associated with decreased relapse (HR, 0.35; 95%CI, 0.19-0.65; p=0.00087). On the other hand, combinations of HLA-B glutamic acid 152 (152E)/ KIR2DL4 cysteine 30 and HLA-B valine 152 (152V)/ KIR2DL4 tyrosine 30 (n=27) were associated with increased relapse (HR, 11.79; 95%CI, 1.6-86.58; p=0.015). Given that KIR3DL2/ KIR2DL4 do not bind HLA-B and are closely linked to KIR3DL1/S1 in KIR haplotypes, specific KIR3DL1/S1 alleles were further explored by subgroup analyses. As a result, combinations of HLA-B 80I/ KIR3DL1*015& KIR3DL2*002 and HLA-B 80T/ KIR3DL1∗001, ∗005, ∗007, ∗020, ∗038, ∗097 (n=60) were defined as the group at low risk for relapse (adjusted HR, 0.21; 95%CI, 0.09-0.48; p=0.00026) (Figure 1A), and combinations of HLA-B 152E/ KIR3DS1 and HLA-B 152V/ KIR3DL1∗001, ∗007, ∗015, ∗020, ∗029, ∗038 (n=176) were defined as the group at high-risk for relapse (adjusted HR, 5.31; 95%CI, 1.72-16.39; p=0.0037) (Figure 1B). The cases in the low-risk group and/or not in the high-risk group (n=84) had a lower relapse rate (adjusted HR, 0.20; 95%CI, 0.10-0.40; p=0.0000059) (Figure 1C) and a higher overall survival (adjusted HR, 0.66; 95%CI, 0.46-0.95; p=0.0265389) (Figure 1D) than the remaining cases (n=130). In spite of reduced relapse rate, the former showed a lower rate of grades II-IV acute GVHD (HR 0.65; p=0.049). Finally, CD107a degranulation of NK cells was measured following coincubation of HLA-null K562 cells and PBMCs from healthy donors with or without genotypes of the low-risk group. KIR3DL1(+) NK cells showed increased CD107a degranulation compared with KIR3DL1(−) NK cells in healthy donors with the low-risk group genotype (p=0.031), but this difference was not apparent in healthy donors without the low-risk group genotype (p=0.28) (Figure 2). Conclusions: Allelic genotyping of KIRs enabled to specify donors associated with reduced relapses. Donor NK cell education status at HLA-B/KIR3DL1 interaction might confer enhanced GVT effects and better prognosis in UR-BMT against ATL.

Association study between killer immunoglobulin-like receptor polymorphisms and susceptibility to COVID-19 disease: a systematic review and meta-analysis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a known virus that leads to a respiratory disease called coronavirus disease 19 (COVID-19). Natural killer (NK) cells, as members of innate immunity, possess crucial roles in restricting viral infections, including COVID-19. Their functions and development depend on receiving signals through various receptors, of which killer cell immunoglobulin-like receptors (KIRs) belong to the most effective ones. Different studies investigated the association between KIR gene content and susceptibility to COVID-19. Since previous studies have yielded contradictory results, we designed this meta-analysis study to draw comprehensive conclusions about COVID-19 risk and KIR gene association. According to PRISMA guidelines, a systematic search was performed in the electronic databases to find all studies investigating KIR gene contents in COVID-19 patients before March 2023. Any association between KIR genes and COVID-19 risk was determined by calculating pooled odds ratio (OR) and 95% confidence interval (CI). After applying the inclusion and exclusion criteria, 1673 COVID-19 patients and 1526 healthy controls from eight studies were included in this meta-analysis. As the main results, we observed a positive association between the 2DL3 (OR = 1.48, 95% CI = 1.17-1.88, P < 0.001) and susceptibility to COVID-19 and a negative association between the 2DP1 and the risk for COVID-19 (OR = 0.48, 95% CI = 0.23-0.99, P = 0.049). This meta-analysis demonstrated that KIR2DL3, as a member of iKIRs, might be associated with an increased risk of COVID-19 disease.

Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP.

Killer-cell immunoglobulin-like receptors (KIR) control natural killer (NK) cell functions by recognizing HLA molecules and modulating the activity of NK cells. The KIR gene cluster contains polymorphic and highly homologous genes. Diversity of the KIR region is achieved through differences in gene content, allelic polymorphism, and gene copy number, which result in unrelated individuals having different KIR genotypes and individualized immune responses that are relevant to multiple aspects of human health and disease. Therefore, KIR genotyping is increasingly used in epidemiological studies. Here, we developed multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP) to compensate for the shortcomings of the conventional PCR-SSP method, which is most commonly used for KIR analysis. Multiplex PCR-SSP method involves six multiplex reactions that detect 16 KIR genes and distinguish variant types of some KIR genes by adding two reactions. The assay was evaluated in a blind survey using a panel of 40 reference DNA standards from the UCLA KIR Exchange Program. The results are 100% concordant with the genotype determined using Luminex-based reverse sequence-specific oligonucleotide typing systems. Additionally, we investigated the currently known 16 KIR genes and their common variants in 120 unrelated Korean individuals. The results were consistent with the KIR genotype previously reported by Hwang et al. This multiplex PCR-SSP is an efficient method for analyzing KIR genotypes in both small- and large-scale studies with minimal labor, reagents, and DNA. Furthermore, by providing a better definition of KIR polymorphisms it can contribute to developments in immunogenetics.

Correlationbetweenhumanleukocyteantigenligandsandkillercellimmunoglobulin-likereceptorsinaplasticanemiapatientsfromShaanxiHan.

Regulating natural killer (NK) cell responses in hematological malignancies largely depend on molecular interactions between killer cell immunoglobulin-like receptors (KIR) and human leukocyte antigen (HLA) class I ligands. The goal of the current study was to examine the key functions of KIR genes, gene combinations of KIR-HLA, and KIR genotypes in genetic predisposition to aplastic anemia (AA). Herein, the genotyping of 16 KIR genes and HLA-A, -B, and -C ligands were performed in 72 AA patients and 150 healthy controls using PCR evaluations with sequence-specific primers using standard assays. According to the obtained results, AA patients had an increased incidence of activating KIR and KIR2DS4 (P = 0.465 × 10-4, Pc = 0.837 × 10-3, OR = 20.81, 95% CI = 2.786-155.5) compared to controls. KIR/HLA class I ligand profile KIR2DS4/C1 (P = 0.350 × 10-4, Pc = 0.630 × 10-3, OR = 8.944, 95% CI = 2.667-29.993) was significantly elevated in AA patients compared to healthy controls. Genotype AA1 (P = 0.003, OR = 2.351, 95% CI = 1.325-4.172) were increased, and AA195 (P = 0.006, OR = 0.060, 95% CI = 0.004-1.023) was decreased among AA cases compared to controls. Our findings indicated that KIR2DS4 may play a role in the pathogenesis of AA. This study revealed the contribution of KIR genes in the etiology of AA cases.

Killer cell immunoglobulin-like receptor alleles influence susceptibility to occult hepatitis B infection in West African population.

Occult hepatitis B infection (OBI) is a public health problem in Burkina Faso. OBI represents a risk factor for the development of cirrhosis and hepatocellular carcinoma (HCC). OBI could be due to mutant viruses undetectable by HBsAg assays or a strong suppression of viral replication and gene expression under the pression of the host immune system. To investigate the role of killer cell immunoglobulin-like receptor (KIR) gene polymorphisms in patients with OBI in Burkina Faso compared to healthy and chronic hepatitis B subjects. A total of 286 participants was recruited, including 42 cases of OBI, 110 cases of chronic hepatitis B and 134 HBV negative subjects. SSP-PCR was performed to search for the presence of KIR genes. The HBV viral load was determined by qPCR. The frequencies of the activator gene KIR2DS5 (P=0.045) and the pseudogene KIR2DP1 (P<0.001) in patients with OBI were higher than those in patients with chronic hepatitis B. These genes are associated with susceptibility of occult hepatitis B infection. The frequencies of the inhibitory KIR gene KIR2DL3 (P=0.01) of patients with occult hepatitis B were lower than those in chronic hepatitis B patients. This gene KIR2DL3 is associated with protection against occult hepatitis B infection. Also, the frequencies of the inhibitory KIR genes KIR2DL2 (P<0.001), KIR2DL3 (P<0.001) and activators KIR2DS2 (P<0.001) in chronic hepatitis B patients were higher compared to the frequencies of the KIR genes in healthy subjects. These genes KIR2DL3, KIR2DL5 (A, B), KIR3DL3, KIR3DS1, KIR2DL2 and KIR2DS2 are thought to be genes associated with the susceptibility to OBI. The KIR2DS5 and KIR2DP1 genes could be associated with susceptibility to OBI. As for the KIR gene KIR2DL3 could be associated with protection against occult hepatitis B infection.

Role of the Killer Immunoglobulin-like Receptor and Human Leukocyte Antigen I Complex Polymorphisms in Kaposi Sarcoma-Associated Herpesvirus Infection.

Kaposi sarcoma, caused by the pathogen Kaposi sarcoma-associated herpesvirus (KSHV), is the most common neoplasm for patients with AIDS. Susceptibility to KSHV has been associated with several different genetic risk variants. The purpose of this study was to test whether variants of killer cell immunoglobulin-like receptors (KIRs) and their human leukocyte antigen (HLA-I) ligands influence the risk of KSHV infection. A case-control study was performed in Xinjiang, a KSHV-endemic region of China. We recruited 299 individuals with HIV, including 123 KSHV-seropositive persons and 176 KSHV-seronegative controls. We used logistic regression and the MiDAS package to evaluate the association between KIR/HLA-I polymorphisms and KSHV infection. HLA-A*31:01, HLA-C*03:04, and HLA-C*12:03 were found to be associated with KSHV infection, with A*31:01 showing a protective effect under 3 different models (dominant: 0.30 [95% confidence interval {CI}, .08-.82], P = .031; additive: 0.30 [95% CI, .09-.80], P = .030; overdominant: 0.31 [95% CI, .09-.88], P = .042). The effect of A*31:01 might cause the variants of amino acid at HLA-A position 56, with individuals carrying an arginine having a lower KSHV infection risk. The increased homozygous KIR2DL3 was associated with a relatively high KSHV viral load (16.30% vs 41.94%, P = .010). This study provides further insight into the link between HLA-I alleles and KIR genes and KSHV infection, highlighting KSHV-susceptible variants of HLA-I and KSHV replication caused by specific KIR genotype, and revealing a potential role of KIR-mediated natural killer cell activation in anti-KSHV infection.

Killer cell immunoglobulin-like receptor (KIR) genes and their HLA ligands in a Brazilian population.

Killer cell immunoglobulin-like receptors (KIR) exhibit extensive diversity, giving rise to different KIR profiles in populations worldwide. This study aimed to investigate the distribution of KIR genes and HLA ligands in a population from Campinas, southeastern Brazil (n = 292), and to compare their results with other populations. A comprehensive analysis of population-specific genes, genotype, and haplotype frequencies of KIR may facilitate a better understanding of their evolution and role in immunity. The genotyping of 16 KIR genes and HLA class I alleles was performed by the reverse sequence-specific oligonucleotide methodology using the Luminex platform (One Lambda, Inc., Canoga Park, CA). The framework genes were present in all individuals, with the most common non-framework KIR genes detected being KIR2DP1(96.6%), KIR2DL1(95.5%), KIR3DL1(94.5%), KIR2DS4(93.8%) and KIR2DL3(87.3%). KIR2DS1, KIR2DS3, KIR2DS5, and KIR3DS1 presented frequencies below 40%. KIR2DL2, KIR2DL5, and KIR2DS2 showed intermediate frequencies (between53% and 58%). The activating gene KIR2DS5 was the least common in this population (30.8%). Forty-five KIR profiles were found with the commonest being the homozygous A haplotype (27.4%). The distribution of KIR genes in the Brazilian population is similar to Caucasian European and Euro-descendant populations.

Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data.

Killer cell immunoglobulin like receptor (KIR) genes and human leukocyte antigen (HLA) genes play important roles in innate and adaptive immunity. They are highly polymorphic and cannot be genotyped with standard variant calling pipelines. Compared with HLA genes, many KIR genes are similar to each other in sequences and may be absent in the chromosomes. Therefore, although many tools have been developed to genotype HLA genes using common sequencing data, none of them work for KIR genes. Even specialized KIR genotypers could not resolve all the KIR genes. Here we describe T1K, a novel computational method for the efficient and accurate inference of KIR or HLA alleles from RNA-seq, whole-genome sequencing, or whole-exome sequencing data. T1K jointly considers alleles across all genotyped genes, so it can reliably identify present genes and distinguish homologous genes, including the challenging KIR2DL5A/KIR2DL5B genes. This model also benefits HLA genotyping, where T1K achieves high accuracy in benchmarks. Moreover, T1K can call novel single-nucleotide variants and process single-cell data. Applying T1K to tumor single-cell RNA-seq data, we found that KIR2DL4 expression was enriched in tumor-specific CD8+ T cells. T1K may open the opportunity for HLA and KIR genotyping across various sequencing applications.

Comparative genomics of the Leukocyte Receptor Complex in carnivores.

The mammalian Leukocyte Receptor Complex (LRC) chromosomal region may contain gene families for the killer cell immunoglobulin-like receptor (KIR) and/or leukocyte immunoglobulin-like receptor (LILR) collections as well as various framing genes. This complex region is well described in humans, mice, and some domestic animals. Although single KIR genes are known in some Carnivora, their complements of LILR genes remain largely unknown due to obstacles in the assembly of regions of high homology in short-read based genomes. As part of the analysis of felid immunogenomes, this study focuses on the search for LRC genes in reference genomes and the annotation of LILR genes in Felidae. Chromosome-level genomes based on single-molecule long-read sequencing were preferentially sought and compared to representatives of the Carnivora. Seven putatively functional LILR genes were found across the Felidae and in the Californian sea lion, four to five genes in Canidae, and four to nine genes in Mustelidae. They form two lineages, as seen in the Bovidae. The ratio of functional genes for activating LILRs to inhibitory LILRs is slightly in favor of inhibitory genes in the Felidae and the Canidae; the reverse is seen in the Californian sea lion. This ratio is even in all of the Mustelidae except the Eurasian otter, which has a predominance of activating LILRs. Various numbers of LILR pseudogenes were identified. The structure of the LRC is rather conservative in felids and the other Carnivora studied. The LILR sub-region is conserved within the Felidae and has slight differences in the Canidae, but it has taken various evolutionary paths in the Mustelidae. Overall, the process of pseudogenization of LILR genes seems to be more frequent for activating receptors. Phylogenetic analysis found no direct orthologues across the Carnivora which corroborate the rapid evolution of LILRs seen in mammals.

KIR2DS4 and Its Variant KIR1D in KIR-AA Genotype Donors Showed Differential Survival Impact in Patients with Lymphoid Disease after HLA-Matched Unrelated Hematopoietic Stem Cell Transplantation

Previous studies illustrated associations between presence of activating killer cell immunoglobulin-like receptor (KIR) genes and lower susceptibility to hematologic malignancies in humans. In addition, favorable hematopoietic stem cell transplantation (HSCT) outcomes were reported in patients, who received transplants from donors with KIR genotypes dominant for activating KIR receptors. However, the association of activating KIR genes on an allelic level with disease and their impact on HSCT outcome has been only scarcely investigated. To this end, we genotyped a large transplantation cohort for KIR two Ig domains and short cytoplasmic tail 4 (KIR2DS4) polymorphisms and investigated their association with disease. We next investigated the impact of KIR-AA genotype donor KIR2DS4 polymorphisms (AA/KIR2DS4 versus (vs.) AA/KIR1D), on clinical outcome of HSCT in patient subgroups (myeloid vs. lymphoid). Among 2810 transplant pairs, 68.8% (n=1934) were 10/10 human leukocyte antigen (HLA) matched and 31.2% (n=876) were 9/10 HLA-matched. The distribution of KIR one Ig domain (KIR1D) in patients vs. donors was equal (P value = 0.205). Multivariate analysis in 10/10 HLA-matched patients with lymphoid disease showed improved HSCT outcome (overall survival (OS): hazard ratio (HR) 0.62, P=0.002; disease free survival (DFS): HR 0.70, P=0.011; graft-versus-host disease free and relapse-free survival (GRFS): HR 0.67, P=0.002; non-relapse mortality (NRM): HR 0.55, P<0.001) when they received grafts from AA/KIR1D donors. This effect was not seen in either 9/10 HLA-matched patients with lymphoid disease or patients with myeloid disease. Our study indicates that the presence of KIR1D alleles is not associated with disease in patients and interestingly, using grafts from AA/KIR1D donors translated into a beneficial survival outcome in 10/10 HLA-matched patients with lymphoid disease.

KIR genotype and haplotype repertoire in Kuwaiti healthy donors, hematopoietic cell transplant recipients and healthy family members.

The gene complex located on chromosome 19q13.4 encodes the Killer-cell Immunoglobulin-like Receptors (KIRs), which exhibit remarkable polymorphism in both gene content and sequences. Further, the repertoire of KIR genes varies within and between populations, creating a diverse pool of KIR genotypes. This study was carried out to characterize KIR genotypes and haplotypes among 379 Arab Kuwaiti individuals including 60 subjects from 20 trio families, 49 hematopoietic cell transplantation (HCT) recipients and 270 healthy Kuwaiti volunteer HCT donors. KIR Genotyping was performed by a combination of reverse sequence specific oligonucleotide probes (rSSO) and/or Real Time PCR. The frequencies of KIR genes in 270 healthy Kuwaiti volunteer donors were compared to previously reported frequencies in other populations. In addition, we compared the differences in KIR repertoire of patients and healthy donors to investigate the reproducibility of previously reported significant differences between patients with hematological malignancies and healthy donors. The observed frequencies in our cohort volunteer HCT donors was comparable to those reported in neighboring Arab populations. The activating genes KIR2DS1, KIR2DS5 and KIR3DS1 and the inhibitory gene KIR2DL5 were significantly more frequent in patients compared to healthy donors, however, none of the previously reported differences were reproducible in our Kuwaiti cohort. This report is the first description of KIR gene carrier frequency and haplotype characterization in a fairly large cohort of the Kuwaiti population, which may have implications in KIR based HCT donor selection strategies.