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Huang K, Zhang P, Dunn DW, Wang T, Mi R, Li B. Assigning alleles to different loci in amplifications of duplicated loci. Mol Ecol Resour 2019; 19:1240-1253. [DOI: 10.1111/1755-0998.13036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
| | - Derek W. Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
| | - Tongcheng Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
| | - Rui Mi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences Northwest University Xi'an China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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Prakash S, Ranjan P, Ghoshal U, Agrawal S. KIR-like activating natural killer cell receptors and their association with complicated malaria in north India. Acta Trop 2018; 178:55-60. [PMID: 29111138 DOI: 10.1016/j.actatropica.2017.10.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 02/01/2023]
Abstract
Killer immunoglobulin-like receptors (KIRs) genomic regions have been suggested to influence malaria pathogenesis and infection susceptibility. KIRs are known as activating natural killer (NK) cell receptors, which upon binding to their corresponding human leukocyte antigen (HLA) ligands cause lysis of any infected cell. We have examined the potential association of KIR genes with complicated malaria (CM) among north Indians in this study and further evaluated the KIR receptor-HLA ligand association on the severity of the disease considering the uncomplicated malaria (UCM) subjects as control. Molecular profiling of KIR and HLA was carried out using the PCR-SSP method. Susceptible association was found for individuals possessing KIR2DS2 (OR=1.76, p-value=0.0390), KIR2DL1 (OR=2.87, p-value=0.0005) and KIR2DL3 (OR=2.74, p-value=0.0011) genes with CM. This was supported by the strong linkage disequilibrium observed for 2DS2-2DL2 (D́=0.87, r2=0.54) with CM. Whereas the receptor-ligand association has revealed risk association against KIR2DS2-HLAC1 (OR=2.08, p-value=0.0229), KIR2DL3-HLAC1 (OR=1.79, p-value=0.0301), and KIR2DL1-HLAC2 (OR=2.10, p-value=0.0175) combinations for complicated malaria. The frequency of different KIR genes are more or less similar to that observed in African population showing not much genetic diversity at KIR level in context to malarial infection. In conclusion, our data indicates KIR gene loci differentially influenced the malarial outcome in north Indians and in particular the KIR2DS2 gene appeared to be associated with disease severity.
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Prakash S, Sarangi AN, Alam S, Sonawane A, Sharma RK, Agrawal S. Putative role of KIR3DL1/3DS1 alleles and HLA-Bw4 ligands with end stage renal disease and long term renal allograft survival. Gene 2017; 637:219-229. [PMID: 28942035 DOI: 10.1016/j.gene.2017.09.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Killer immunoglobulin receptors (KIR) are highly polymorphic in nature. KIR3DL1/3DS1 genes are known to affect HLA-B antigen binding affinity causing natural killer (NK) cell inhibition, which results into successful renal transplantation. In this study we have examined whether alleles of KIR3DL1/3DS1 play any role in changing the binding affinity with HLA-Bw4 antigen and if so then how are they associated with long term renal allograft survival. We have also evaluated plausible association of KIR3DL1 with HLA-A23/A24/A32 with renal pathophysiology. MATERIALS AND METHODS KIR3DL1/3DS1 allelic diversity was examined in 501 renal transplant cases and 507 controls. PCR-SSP was used to determine the incidence of KIR3DL1/3DS1 genes and HLA class-I antigens. KIR3DL1/3DS1 alleles were determined by sequencing. Expression at transcription level for KIR3DL1/3DS1 genes was evaluated in the presence of HLA-Bw4. Different statistical analyses were performed using SPSS v 22.0. p≤0.05 was considered significant. Sequence based variant effect was predicted using Variant Effect Predictor. To evaluate whether variation in KIR3DL1 and HLA interaction changes the binding affinity structure based effect prediction was carried out using MutaBind and BindProf software. RESULTS For KIR3DL1*0010101, no-risk and low mRNA expression was seen among antibody mediated acute rejection (ABMR) and chronic rejection (CR) cases. Whereas, 3DS1*01301, 3DL1*00401, and 3DL1*00402 showed susceptibility and elevated mRNA expression with ABMR and CR. Two mutations c.320C>T (rs143159382) and c.911G>T (rs35974949), present in alleles 3DL1*00402 and 3DL1*00401 were predicted to be deleterious. Reduced renal allograft survival was observed for individuals possessing KIR3DL1*00401-HLA-Bw4+. In relation to HLA-A locus no significance was observed with ESRD, ABMR, and CR. DISCUSSION The experimental and computational data corroborated with each other suggesting susceptibility for renal allograft in presence of 3DL1*00402 and 3DL1*00401 alleles.
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Affiliation(s)
- Swayam Prakash
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh, India
| | - Aditya Narayan Sarangi
- Biomedical Informatics Centre, School of Telemedicine and Biomedical Informatics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh, India
| | - Shahnawaz Alam
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh, India
| | - Avinash Sonawane
- School of Biotechnology, Kalinga Institute of Industrial Technology University, Bhubaneswar, Odisha, India
| | - Raj Kumar Sharma
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh, India
| | - Suraksha Agrawal
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh, India.
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Genetic associations of killer immunoglobulin like receptors and class I human leukocyte antigens on childhood acute lymphoblastic leukemia among north Indians. Hum Immunol 2015; 77:41-46. [PMID: 26472014 DOI: 10.1016/j.humimm.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 10/06/2015] [Accepted: 10/11/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND Molecular 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). METHODS Genotyping 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. RESULTS We 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. CONCLUSION Our data suggests the role for KIR genes and their HLA ligands in aetiology of childhood ALL.
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Alam S, Rangaswamy D, Prakash S, Sharma RK, Khan MI, Sonawane A, Agrawal S. Impact of killer immunoglobulin-like receptor-human leukocyte antigens ligand incompatibility among renal transplantation. Indian J Nephrol 2015; 25:27-33. [PMID: 25684869 PMCID: PMC4323909 DOI: 10.4103/0971-4065.134655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Killer immunoglobulin-like receptor (KIR) gene shows a high degree of polymorphism. Natural killer cell receptor gets activated once they bind to self-human leukocyte antigens (HLAs) with specific ligand. KIR gene and HLA ligand incompatibility due to the presence/absence of KIR in the recipient and the corresponding HLA ligand in the allograft may impact graft survival in solid organ transplantation. This study evaluates the effect of matches between KIR genes and known HLA ligands. KIR genotypes were determined using sequence specific primer polymerase chain reaction. Presence of certain KIR in a recipient, where the donor lacked the corresponding HLA ligand was considered a mismatch. The allograft was considered matched when both KIR receptor and HLA alloantigen reveald compatibility among recipient and donor. The data revealed better survival among individuals with matched inhibitory KIR receptors and their corresponding HLA ligands (KIR2DL2/DL3-HLAC2, KIR3DL1-HLABw4). On the contrary, no adverse effect was seen for matched activating KIR receptors and their corresponding HLA ligands. One of the activating gene KIR2DS4 showed risk (P = 0.0413, odds ratio = 1.91, 95% confidence interval = 1.02-3.57) association with renal allograft rejection. We conclude that the presence of inhibitory KIR gene leads to better survival; whereas activating motifs show no significant role in renal allograft survival.
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Affiliation(s)
- S Alam
- Department of Biosciences, Integral University, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India ; Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - D Rangaswamy
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - S Prakash
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India ; Department of Immunobiology Laboratory, School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - R K Sharma
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - M I Khan
- Department of Biosciences, Integral University, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - A Sonawane
- Department of Immunobiology Laboratory, School of Biotechnology, KIIT University, Bhubaneswar, Odisha, India
| | - S Agrawal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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Prakash S, Alam S, Bharadwaj U, Aggarwal A, Mishra RN, Agrawal S. Associations of killer cell immunoglobulin like receptors with rheumatoid arthritis among North Indian population. Hum Immunol 2014; 75:802-7. [PMID: 24912006 DOI: 10.1016/j.humimm.2014.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/11/2014] [Accepted: 05/29/2014] [Indexed: 11/16/2022]
Abstract
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, r(2) = 0.36), KIR3DL1-3DS1 (D' = 1, r(2) = 0.58) and KIR2DL1-2DL2 (D' = 1, r(2)=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.
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Affiliation(s)
- Swayam Prakash
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareily Road, Lucknow, Uttar Pradesh, India
| | - Shahnawaz Alam
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareily Road, Lucknow, Uttar Pradesh, India
| | - Uddalak Bharadwaj
- Margaret M. and Albert B. Alkek Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
| | - Amita Aggarwal
- Department of Immunology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareily Road, Lucknow, Uttar Pradesh, India
| | - Ram Nath Mishra
- Department of Immunology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareily Road, Lucknow, Uttar Pradesh, India
| | - Suraksha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raibareily Road, Lucknow, Uttar Pradesh, India.
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Prakash S, Alam S, Faridi RM, Sonawane A, Agrawal S. Killer immunoglobulin like receptor gene content diversity among Northern Indian population. Ann Hum Biol 2014; 41:540-7. [PMID: 24689793 DOI: 10.3109/03014460.2014.899624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Genes encoding KIR receptors are clustered in one of the most variable regions of the human genome. KIR gene frequencies vary in worldwide populations and reveal high probability of individuals differing in their gene content. AIM This study aimed to investigate KIR diversity among the northern Indian population who share features with either Western Eurasian or East Asian populations. It sought to decipher how northern Indians are associated phylogenetically with global populations whilst also focusing on differentiation of populations. SUBJECTS AND METHODS This paper studied 867 northern Indians using PCR-SSP. Gene and genotypic frequencies were calculated, using statistical analyses. Findings were compared against 76 global populations of differing ethnicities. RESULTS This northern Indian population shared characteristics with Western Eurasian or Asian Indian populations, as is evident from genetic distance, clustered heatmap, phylogenetic assessment and principal component analysis. The findings are consistent with the demographic history of northern India, including specific features, such as presence of comparatively high KIR B-haplotype as compared to A-haplotype. CONCLUSION KIR frequencies and profiles of northern Indians were more similar to Western Eurasians, Africans and Asian Indians. This may suggest that KIR genes are under constant evolutionary pressures and selection, which may be linked to different invading pathogens.
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Affiliation(s)
- Swayam Prakash
- School of Biotechnology, Kalinga Institute of Industrial Technology University , Bhubaneswar, Odisha , India
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Prakash S, Alam S, Sharma RK, Sonawane A, Imran M, Agrawal S. Distribution of Killer cell immunoglobulin like receptor genes in end stage renal disease among North Indian population. Hum Immunol 2013; 74:1339-45. [PMID: 23777934 DOI: 10.1016/j.humimm.2013.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 05/01/2013] [Accepted: 06/07/2013] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Swayam Prakash
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India; School of Biotechnology, KIIT University, Bhubaneswar, India
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Hou L, Chen M, Steiner N, Kariyawasam K, Ng J, Hurley CK. Killer cell immunoglobulin-like receptors (KIR) typing by DNA sequencing. Methods Mol Biol 2012; 882:431-68. [PMID: 22665249 DOI: 10.1007/978-1-61779-842-9_25] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
DNA sequencing is a powerful technique for identifying allelic variation within the natural killer cell immunoglobulin-like receptor genes. Because of the relatively large size of the KIR genes, each locus is amplified in two or more overlapping segments. Sanger sequencing of each gene from a preparation containing one or two alleles yields a sequence that is used to identify the alleles by comparison with a reference database.
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Affiliation(s)
- Lihua Hou
- Department of Pediatrics, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University Medical Centre, Washington, DC, USA
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Bao X, Hou L, Sun A, Chen M, Chen Z, He J. An allelic typing method for 2DS4 variant used in study of haplotypes of killer cell immunoglobulin-like receptor gene. Int J Lab Hematol 2011; 32:625-32. [PMID: 20456519 DOI: 10.1111/j.1751-553x.2010.01234.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The KIR2DS4 variants differ in exon 5 and play a role in hematopoietic stem cells transplantation (HSCT). A sequence-based testing (SBT) and TOPO TA cloning system identifying and distinguishing alleles of the KIR2DS4 gene was established and applied to a total of 150 Chinese-Han individuals: 75 patients received T-cell-depleted HSCT and their unrelated donors. The majority (139) of the 150 samples (92.7%) were positive for KIR2DS4. Four of the nine known KIR2DS4 alleles, KIR2DS4 *00101, *003,*004, and *007, were identified. In the haplotype A/A group, a higher risk of acute graft-versus-host disease (aGVHD) was seen when the donor carried two full-length KIR2DS4 alleles (RR 9.0 [95% CI 1.2-66.9], P = 0.010). Our findings suggested that the expression of full-length 2DS4 (*001) in A/A group may contribute to a worse clinical outcome after URD-HSCT. These data would be beneficial for the selection of suitable donors.
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Affiliation(s)
- X Bao
- Key Laboratory of Thrombosis and Hemostasis, Ministry of Health, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Hou L, Chen M, Jiang B, Ng J, Hurley CK. African Americans exhibit a predominant allele in the midst of extensive KIR2DL1 allelic diversity. ACTA ACUST UNITED AC 2010; 76:31-4. [PMID: 20210923 DOI: 10.1111/j.1399-0039.2010.01460.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
KIR2DL1 alleles were identified by DNA sequencing of the coding region from amplified genomic DNA from 100 random African Americans. The majority of individuals (97%) carried a KIR2DL1 locus. Allele KIR2DL1*00302 was found in 68% of individuals but KIR2DL1*00401, *002, *00303, *006, and *007 were also frequent. Eleven new alleles were described: KIR2DL1*00403, *01101, *01102, *012, *013N, *014, *015, *016, *017, *018, and *019. Nine of the novel alleles encoded amino acid substitutions located throughout the receptor; one allele carried a stop codon in the exon encoding the first extracellular domain.
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Affiliation(s)
- L Hou
- Departments of Pediatrics and Oncology, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University Medical Center, Washington, D.C. 20057, USA
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Bao X, Hou L, Sun A, Qiu Q, Yuan X, Chen M, Chen Z, He J. Distribution of killer cell immunoglobulin-like receptor genes and 2DS4 alleles in the Chinese Han population. Hum Immunol 2010; 71:289-92. [PMID: 20034528 DOI: 10.1016/j.humimm.2009.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2009] [Revised: 11/23/2009] [Accepted: 12/12/2009] [Indexed: 11/26/2022]
Abstract
Killer cell immunoglobulinlike receptors (KIRs) are a diverse family of receptors on natural killer cells. The KIR2DS4-deleted variant differs from the normal KIR2DS4 sequence by a 22-bp deletion in exon 5, which causes a frame shift, yielding a truncated KIR2DS4 protein with loss of the transmembrane and cytoplasmic domains of the full-length KIR2DS4 protein. A sequence-based testing and TOPO TA cloning system identifying and distinguishing alleles of the KIR2DS4 gene was established. The method was applied to 150 Chinese Han individuals: 75 patients who received T-depleted hematopoietic stem cells transplantation and their unrelated donors, establishing frequencies of 2DS4 allele and KIR gene within the local population. A majority (139) of the 150 samples (92.7%) were positive for KIR2DS4. The ratio of deleted to nondeleted versions of KIR2DS4 was approximately 1:2. Three KIR2DS4 novel alleles were identified. Forty-four percent individuals carried two group A haplotypes. The 17 KIR gene loci were found in 21.3%-100% in the population. Our findings suggest that the Chinese Han population is distinct in KIR gene frequencies and 2DS4 allele frequencies in comparison with some other populations.
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Affiliation(s)
- Xiaojing Bao
- The Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People's Republic of China
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Hou L, Chen M, Jiang B, Kariyawasam K, Ng J, Hurley CK. In contrast to other stimulatory natural killer cell immunoglobulin-like receptor loci, several KIR2DS5 alleles predominate in African Americans. Hum Immunol 2009; 70:733-7. [PMID: 19410616 DOI: 10.1016/j.humimm.2009.04.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 04/24/2009] [Accepted: 04/27/2009] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- LiHua Hou
- Departments of Pediatrics and Oncology, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University Medical Center, Washington, DC 20057, USA
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Faridi RM, Das V, Tripthi G, Talwar S, Parveen F, Agrawal S. Influence of activating and inhibitory killer immunoglobulin-like receptors on predisposition to recurrent miscarriages. Hum Reprod 2009; 24:1758-64. [PMID: 19279038 DOI: 10.1093/humrep/dep047] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Understanding of the immune events and mechanisms occurring at the feto-maternal interface is likely to help in understanding the ability of the fetus to survive within the maternal body. Evidence supporting extensive roles of natural killer cells during pregnancy gives rise to a possibility that these NK cells can be mis-regulated and involved in fetal allograft rejection. Killer immunoglobulin-like receptors (KIR) play an important role in regulating the NK cell activity through their activating and inhibiting isoforms. Since there exists a considerable, genetically determined variation in the repertoire of KIR receptors between different individuals, a particular maternal KIR repertoire may predispose to recurrent miscarriages (RMs). METHODS Gene-specific PCR amplification (PCR-SSP) was used to determine the individual KIR genotypes in women experiencing RM and controls. RESULTS A higher prevalence of activating KIR genes was seen in patients than in controls. Among women experiencing RM, the BB genotypes were more prevalent (P < 0.0001, OR = 4.4, 95% CI = 2.89-6.69) compared with controls. CONCLUSIONS Our results indicate that the balance between inhibitory and activating receptor-mediated signals present in natural killer cells is inclined toward a more activating state that may contribute to pregnancy loss.
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Affiliation(s)
- R M Faridi
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareli Road, Lucknow, Uttar Pradesh 226014, India
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Vilches C, Castaño J, Gómez-Lozano N, Estefanía E. Facilitation of KIR genotyping by a PCR-SSP method that amplifies short DNA fragments. ACTA ACUST UNITED AC 2007; 70:415-22. [PMID: 17854430 DOI: 10.1111/j.1399-0039.2007.00923.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Detection of killer-cell immunoglobulin-like receptors (KIR) genes by polymerase chain reaction with sequence-specific primers (PCR-SSP) led in 1997 to the discovery that human genomes diverge largely in the KIR they encode. While only a few KIR genes are conserved in all humans, most individuals lack several those genes, which tend to associate in diverse haplotypic combinations. The PCR-SSP technique, updated to detect the more recently identified KIR genes and alleles, is still used widely to analyze the diversity of human populations, and to study the influence of KIR-gene variability on human health. Several published PCR-SSP methods for KIR genotyping, although simple and robust, have the drawback of relying on the amplification of DNA fragments spanning 0.5-2.0 kbp, which tends to fail in low-quality DNAs. Valuable collections of DNAs often include such poor quality samples, which lead to loss of data and resources. Even worse, undetected falsely negative or positive reactions may result in erroneous gene frequencies and in odd gene combinations. To address those problems, we have redesigned our previously published KIR genotyping method so that it produces short amplicons (less than 200 bp for most genes). This modification minimizes amplification failures, thus conferring greater consistency and reliability to KIR genotyping. In addition, the new PCR-SSP method detects recently described alleles of several KIR genes, and allows for discrimination between the major structural variants of KIR2DS4 and KIR3DP1 without increasing the number of reactions.
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Affiliation(s)
- C Vilches
- Department of Immunology, Hospital Universitario Puerta de Hierro, Madrid, Spain.
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