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Choi EJ, Baek IC, Park S, Kim HJ, Kim TG. Development of cost-effective and fast KIR genotyping by multiplex PCR-SSP. HLA 2024; 103:e15191. [PMID: 37688498 DOI: 10.1111/tan.15191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 09/11/2023]
Abstract
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.
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Affiliation(s)
- Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tai-Gyu Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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2
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Ahmadi SAY, Shahsavar F, Anbari K, Rezaian J. An introduction to the role of immunology in medical anthropology and molecular epidemiology. Biomed Pharmacother 2019; 109:2203-9. [DOI: 10.1016/j.biopha.2018.11.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
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3
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Amorim LM, van Tong H, Hoan NX, Vargas LDB, Ribeiro EMDSF, Petzl-Erler ML, Boldt ABW, Toan NL, Song LH, Velavan TP, Augusto DG. KIR-HLA distribution in a Vietnamese population from Hanoi. Hum Immunol 2017; 79:93-100. [PMID: 29191786 DOI: 10.1016/j.humimm.2017.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/14/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022]
Abstract
The KIR (killer cell immunoglobulin-like receptors) gene family codifies a group of receptors that recognize human leukocyte antigens (HLA) and modulate natural killer (NK) cells response. Genetic diversity of KIR genes and HLA ligands has not yet been deeply investigated in South East Asia. Here, we characterized KIR gene presence and absence polymorphism of 14 KIR genes and two pseudogenes, as well as the frequencies of the ligands HLA-Bw4, HLA-C1 and HLA-C2 in a Vietnamese population from Hanoi (n = 140). Genotyping was performed by polymerase chain reaction with specific sequence primers (PCR-SSP). We compared KIR frequencies and performed principal component analysis with 43 worldwide populations of different ancestries. KIR carrier frequencies in Vietnamese were similar to those reported for Thai and Chinese Han, but differed significantly from other geographically close populations such as Japanese and South Korean. This similarity was also observed in KIR gene-content genotypes and is in accordance with the origin from Southern China and Thailand proposed for the Vietnamese population. The frequencies of HLA ligands observed in Vietnamese did not differ from those reported for other East-Asian populations (p > .05). Studies regarding KIR-HLA in populations are of prime importance to understand their evolution, function and role in diseases.
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Affiliation(s)
| | - Hoang van Tong
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Viet Nam; Vietnamese - German Center for Excellence in Medical Research, Hanoi, Viet Nam
| | - Nghiem Xuan Hoan
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Vietnamese - German Center for Excellence in Medical Research, Hanoi, Viet Nam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Viet Nam
| | | | | | | | - Angelica B W Boldt
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Nguyen Linh Toan
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Viet Nam; Vietnamese - German Center for Excellence in Medical Research, Hanoi, Viet Nam
| | - Le Huu Song
- Vietnamese - German Center for Excellence in Medical Research, Hanoi, Viet Nam; Institute of Clinical Infectious Diseases, 108 Military Central Hospital, Hanoi, Viet Nam
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Viet Nam; Vietnamese - German Center for Excellence in Medical Research, Hanoi, Viet Nam.
| | - Danillo G Augusto
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil; Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil.
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4
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Bani M, Seket J, Kaabi H, Cherif G, Chaabane M, Bellali H, Hmida S. Killer cell immunoglobulin-like receptor (KIR) locus profiles in the Tunisian population. Hum Immunol 2015; 76:355-61. [DOI: 10.1016/j.humimm.2015.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 02/17/2015] [Accepted: 03/11/2015] [Indexed: 10/23/2022]
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5
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John E, Christiansen FT, Mueller I, Schofield L, Senitzer D, Siba P, Witt CS. Distinct distribution of killer-cell immunoglobulin-like receptor genes in the Mugil and Ilaita areas of Papua New Guinea. Tissue Antigens 2012; 79:263-71. [PMID: 22320834 DOI: 10.1111/j.1399-0039.2012.01848.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The frequency of the killer-cell immunoglobulin-like receptor (KIR) genes and transmembrane alleles of KIR2DL4 were studied in coastal (Mugil community) and inland (Ilaita community) communities in Papua New Guinea. Linkage disequilibria between KIR genes and between alleles of KIR2DL4 and the KIR genes were similar to those found in other populations suggesting conservation of the usual gene order in Papua New Guinean haplotypes. Significant differences in the frequency of KIR genes were found between the two populations despite being separated by only 300 km. Examples of individuals who lacked the KIR2DL4 gene and others whose KIR2DL4 allele appeared to have 11 adenines in the polyadenine tract in exon 6 were identified. A relatively low frequency of the KIR A haplotype was found in both populations and particularly in the inland community. The KIR gene frequencies were consistent with the inland Ilaita community being closely related to Australian Aborigines and southern Indians, whereas the KIR gene frequencies of the coastal Mugil community appeared to have been influenced either by recent or ancient admixture from populations with a higher frequency of the KIR A haplotype.
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Affiliation(s)
- E John
- Department of Clinical Immunology, PathWest, Royal Perth Hospital, Perth, WA, Australia
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Singh KM, Phung YT, Kohla MS, Lan BY, Chan S, Suen DL, Murad S, Rheault S, Davidson P, Evans J, Singh M, Dohil S, Osorio RW, Wakil AE, Page K, Feng S, Cooper SL. KIR genotypic diversity can track ancestries in heterogeneous populations: a potential confounder for disease association studies. Immunogenetics 2012; 64:97-109. [PMID: 21898189 DOI: 10.1007/s00251-011-0569-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 08/25/2011] [Indexed: 10/17/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIR) are encoded by highly polymorphic genes that regulate the activation of natural killer (NK) cells and other lymphocyte subsets and likely play key roles in innate and adaptive immunity. Association studies increasingly implicate KIR in disease predisposition and outcome but could be confounded by unknown KIR genetic structure in heterogeneous populations. To examine this, we characterized the diversity of 16 KIR genes in 712 Northern Californians (NC) stratified by self-assigned ethnicities and compared the profiles of KIR polymorphism with other US and global populations using a reference database. Sixty-eight distinct KIR genotypes were characterized: 58 in 457 Caucasians (NCC), 17 in 47 African Americans (NCAA), 21 in 80 Asians (NCA), 20 in 74 Hispanics (NCH), and 18 in 54 "other" ethnicities (NCO). KIR genotype patterns and frequencies in the 4 defined ethnicities were compared with each other and with 34 global populations by phylogenetic analysis. Although there were no population-specific genotypes, the KIR genotype frequency patterns faithfully traced the ancestry of NCC, NCAA, and NCA but not of NCH whose ancestries are known to be more heterogeneous. KIR genotype frequencies can therefore track ethnic ancestries in modern urban populations. Our data emphasize the importance of selecting ethnically matched controls in KIR-based studies to avert spurious associations.
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7
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Wang HD, Zhu BF, Shen CM, Fan AY, Song TN, Liu JL, Qin HX, Deng LB, Fan SL, Huang QZ, Guo YF, Fang J, Zhang P, Yan CX. Diversity distributions of killer cell immunoglobulin-like receptor genes and their ligands in the Chinese Shaanxi Han population. Hum Immunol 2011; 72:733-40. [DOI: 10.1016/j.humimm.2011.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 04/01/2011] [Accepted: 04/18/2011] [Indexed: 10/24/2022]
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8
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Augusto DG, Zehnder-Alves L, Pincerati MR, Martin MP, Carrington M, Petzl-Erler ML. Diversity of the KIR gene cluster in an urban Brazilian population. Immunogenetics 2012; 64:143-52. [PMID: 21850526 DOI: 10.1007/s00251-011-0565-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 07/30/2011] [Indexed: 10/17/2022]
Abstract
The activity of natural killer cells depends on the balance between activating and inhibitory signals coming from their receptors. Among these are the killer cell immunoglobulin-like receptors (KIR) that recognize specific HLA class I allotypes. Here we characterized KIR genetic diversity and their HLA ligands in the population of Curitiba, Paraná State (n = 164), and compared it with other worldwide populations. The distribution of 2DL4 alleles was also analyzed. The Curitiba population did not differ significantly from European and Euro-descendant populations, but as an admixed population showed higher genetic diversity. We found 27 KIR profiles, many of them uncommon in European populations, in agreement with the elevated historically recent gene flow in the study population. The frequencies of KIR genes and their respective HLA ligands were distributed independently and none of the analyzed individuals lacked functional KIR-HLA ligand combinations. KIR gene frequencies of 33 worldwide populations were consistent with geographic and ethnic distribution, in agreement with demography being the major factor shaping the observed gene content diversity of the KIR locus.
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9
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Alvarado-hernández DL, Hernández-ramírez D, Noyola DE, García-sepúlveda CA. KIR gene diversity in Mexican mestizos of San Luis Potosí. Immunogenetics 2011; 63:561-75. [DOI: 10.1007/s00251-011-0540-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 05/19/2011] [Indexed: 10/18/2022]
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10
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Velickovic M, Velickovic Z, Panigoro R, Dunckley H. Diversity of killer cell immunoglobulin-like receptor genes in Indonesian populations of Sumatra, Sulawesi and Moluccas Islands. ACTA ACUST UNITED AC 2011; 76:325-30. [PMID: 20670355 DOI: 10.1111/j.1399-0039.2010.01525.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Killer immunoglobulin-like receptors (KIRs) regulate the activity of natural killer and T cells through interaction with specific human leukocyte antigen (HLA) molecules on target cells. Like HLA class I genes that are characterised by extreme allelic polymorphism, KIR genes are diverse and vary in both gene content and allelic polymorphism. Population studies conducted over the last several years have showed that KIR gene frequencies (GF) and genotype content vary among different ethnic groups, indicating the extent of KIR diversity. Some studies have also shown the effect of the presence or absence of specific KIR genes in human disease. We have recently reported the distribution of KIR genes in populations from Java (Central Javanese and the Sundanese of West Java), East Timor (Timorese), Kalimantan provinces of Indonesian Borneo (Dayaks) and Irian Jaya (Western half of the island of New Guinea; Melanese). We here extend analysis of the KIR genes in populations from North Sulawesi (Minahasans), West Sumatra (Minangs) and Moluccas Islands. All 16 KIR genes were observed in all three populations. Variation in GF between populations was observed, except for the KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 genes, which were present in every individual tested. When comparing KIR GF between populations, both principal component analysis and phylogenetic tree analyses showed a close relationship between Minahasan and Moluccan populations that are clustered with Timorese in the same clade. The Minang tribe lies between the Javanese/Kalimantan and the Timorese/Minahasan/Moluccan clades, whereas Irianese show the greatest genetic distances from other Indonesian populations. The results correspond well with the history of migration in Indonesia and will contribute to the understanding of the genetic as well as the geographic history of the region.
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Affiliation(s)
- M Velickovic
- Molecular Genetics, Tissue Typing, Australian Red Cross Blood Service, Sydney, NSW, Australia.
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11
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Gourjon G, Boëtsch G, Degioanni A. Gender and population history: Sex bias revealed by studying genetic admixture of Ngazidja population (Comoro Archipelago). Am J Phys Anthropol 2011; 144:653-60. [PMID: 21312182 DOI: 10.1002/ajpa.21474] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Géraud Gourjon
- UMR 6578 Anthropologie bioculturelle, Université de la Méditerranée/CNRS/EFS, Faculté de Médecine-Secteur Nord Université de la Méditerranée, Bd. Pierre Dramard, Marseille Cedex 15, France
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12
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Zhu BF, Wang HD, Shen CM, Deng YJ, Yang G, Wu QJ, Xu P, Qin HX, Fan SL, Huang P, Deng LB, Lucas R, Wang ZY. Killer cell immunoglobulin-like receptor gene diversity in the Tibetan ethnic minority group of China. Hum Immunol 2010; 71:1116-23. [DOI: 10.1016/j.humimm.2010.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 06/24/2010] [Accepted: 07/12/2010] [Indexed: 11/30/2022]
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13
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Jobim M, Salim PH, Portela P, Wilson TJ, Fraportti J, Baronio D, Gil B, Penna LS, Roesler R, Jobim LF, Schwartsmann G. Killer cell immunoglobulin-like receptor gene diversity in a Caucasian population of Southern Brazil. Int J Immunogenet 2010; 37:83-9. [PMID: 20082646 DOI: 10.1111/j.1744-313x.2009.00894.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- M Jobim
- Department of Immunology, Hospital de Clínicas, Porto Alegre, Brazil.
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14
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Wu GQ, Zhao YM, Lai XY, Yang KL, Zhu FM, Zhang W, Wang W, Luo Y, Tan YM, Wang YJ, Cao WJ, Huang H. Distribution of killer-cell immunoglobulin-like receptor genes in Eastern mainland Chinese Han and Taiwanese Han populations. ACTA ACUST UNITED AC 2009; 74:499-507. [DOI: 10.1111/j.1399-0039.2009.01366.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Guinan KJ, Cunningham RT, Meenagh A, Dring MM, Middleton D, Gardiner CM. Receptor systems controlling natural killer cell function are genetically stratified in Europe. Genes Immun 2010; 11:67-78. [DOI: 10.1038/gene.2009.60] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Buhler S, Di Cristofaro J, Frassati C, Basire A, Galicher V, Chiaroni J, Picard C. High levels of molecular polymorphism at the KIR2DL4 locus in French and Congolese populations: impact for anthropology and clinical studies. Hum Immunol 2009; 70:953-9. [PMID: 19679155 DOI: 10.1016/j.humimm.2009.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/28/2009] [Accepted: 08/05/2009] [Indexed: 11/27/2022]
Abstract
To characterize KIR2DL4 molecular polymorphism, a cloning-sequencing protocol was performed in 49 French and 52 Teke Congolese individuals. These two populations exhibited high levels of genetic diversity for KIR2DL4, possibly under the influence of natural selection. The most frequent alleles in French individuals (i.e., *00801 and *00802 with a cumulated frequency of approximately 43%) were not the same in Congolese individuals (i.e., *00103 at 47%). In the latter population, four new allelic variants were detected, three of them harboring nonsynonymous substitutions leading to amino acid changes in the extracellular and cytoplasmic domains of the protein. Expression patterns of KIR2DL4 were tightly linked with 9 and 10 poly-adenine polymorphism in exon 7 (i.e., 9A and 10A type alleles). French individuals exhibited a majority of 9A alleles (62%), whereas Congolese individuals had a dominant subset of 10A alleles (72%), suggesting that KIR2DL4 polymorphism could be under the influence of various environmental and pathogenic backgrounds. We conclude that KIR2DL4 might be a good candidate to study for anthropology. In addition, the discovery of its intrinsic variability is shedding light on potential differences among human populations in relation to immunologic functions.
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Affiliation(s)
- Stéphane Buhler
- UMR 6578 (Anthropobiologie Bioculturelle), Université de la Méditerranée, CNRS, EFS, Marseille, France.
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17
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Rudnick CCC, Franceschi DSA, Marangon AV, Guelsin GAS, Sell AM, Visentainer JEL. Killer cell immunoglobulin-like receptor gene diversity in a Southern Brazilian population from the state of Paraná. Hum Immunol 2008; 69:872-6. [PMID: 18848853 DOI: 10.1016/j.humimm.2008.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 08/25/2008] [Accepted: 09/03/2008] [Indexed: 12/20/2022]
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18
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Martin MP, Single RM, Wilson MJ, Trowsdale J, Carrington M. KIR haplotypes defined by segregation analysis in 59 Centre d'Etude Polymorphisme Humain (CEPH) families. Immunogenetics 2008; 60:767-74. [PMID: 18972110 DOI: 10.1007/s00251-008-0334-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Accepted: 09/29/2008] [Indexed: 01/21/2023]
Abstract
The killer cell immunoglobulin-like receptor (KIR) gene cluster exhibits extensive allelic and haplotypic diversity. Variation at the locus is associated with an increasing number of human diseases, reminiscent of the HLA loci. Characterization of diversity at the KIR locus has progressed over the past several years, particularly since the sequence of entire KIR haplotypes have become available. To determine the extent of KIR haplotypic variability among individuals of northern European descent, we genotyped 59 CEPH families for presence/absence of all KIR genes and performed limited allelic subtyping at several KIR loci. A total of 20 unique haplotypes differing in gene content were identified, the most common of which was the previously defined A haplotype (f = 0.52). Several unusual haplotypes that probably arose as a consequence of unequal crossing over events were also identified. Linkage disequilibrium (LD) analysis indicated strong negative and positive LD between several pairs of genes, values that may be useful in determining haplotypic structure when family data are not available. These data provide a resource to aid in the interpretation of disease association data involving individuals of European descent.
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Affiliation(s)
- M P Martin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc, NCI-Frederick, Frederick, MD, 21702, USA
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Velickovic M, Velickovic Z, Panigoro R, Dunckley H. Diversity of killer cell immunoglobulin-like receptor genes in Indonesian populations of Java, Kalimantan, Timor and Irian Jaya. ACTA ACUST UNITED AC 2008; 73:9-16. [PMID: 19000141 DOI: 10.1111/j.1399-0039.2008.01149.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) regulate the activity of natural killer and T cells through interactions with specific human leucocyte antigen class I molecules on target cells. Population studies performed over the last several years have established that KIR gene frequencies (GFs) and genotype content vary considerably among different ethnic groups, indicating the extent of KIR diversity, some of which have also shown the effect of the presence or absence of specific KIR genes in human disease. We have determined the frequencies of 16 KIR genes and pseudogenes and genotypes in 193 Indonesian individuals from Java, East Timor, Irian Jaya (western half of the island of New Guinea) and Kalimantan provinces of Indonesian Borneo. All 16 KIR genes were observed in all four populations. Variation in GFs between populations was observed, except for KIR2DL4, KIR3DL2, KIR3DL3, KIR2DP1 and KIR3DP1 genes, which were present in every individual tested. When comparing KIR GFs between populations, both principal component analysis and a phylogenetic tree showed close clustering of the Kalimantan and Javanese populations, while Irianese populations were clearly separated from the other three populations. Our results indicate a high level of KIR polymorphism in Indonesian populations that probably reflects the large geographical spread of the Indonesian archipelago and the complex evolutionary history and population migration in this region.
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Affiliation(s)
- M Velickovic
- Department of Molecular Genetics, Tissue Typing, Australian Red Cross Blood Service, Sydney, New South Wales, Australia.
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Gonzalez A, Meenagh A, Sleator C, Middleton D. Investigation of killer cell immunoglobulin-like receptor (KIR) gene diversity: KIR2DL2, KIR2DL5 and KIR2DS5. ACTA ACUST UNITED AC 2008; 72:11-20. [PMID: 18498296 DOI: 10.1111/j.1399-0039.2008.01050.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human killer cell immunoglobulin-like receptor (KIR) genes are important for restraining natural killer cytotoxicity toward cells with autologous human leukocyte antigen (HLA) while targeting cells lacking or expressing low levels of self-HLA molecules. KIR gene content and alleles vary across individual genomes and populations, requiring specialized laboratory tools for their characterization. Here, we detail methods based on sequence-specific polymerase chain reaction amplification and oligonucleotide probe hybridization to identify alleles of KIR2DL2, KIR2DL5A, KIR2DL5B and KIR2DS5. Allele frequencies for a Northern Irish population of 354 individuals typed with this system are given, along with results from 132 cell lines from the International Histocompatibility Workshop that cover many world populations. This information complements published reports by our laboratory for allele-level typing of other KIR members, totaling 12 of the 17 known genes. These methods are allowing us to characterize KIR haplotypes in our population.
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Affiliation(s)
- A Gonzalez
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast, UK.
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Levinson RD, Du Z, Luo L, Monnet D, Tabary T, Brezin AP, Zhao L, Gjertson DW, Holland GN, Reed EF, Cohen JHM, Rajalingam R. Combination of KIR and HLA gene variants augments the risk of developing birdshot chorioretinopathy in HLA-A*29-positive individuals. Genes Immun 2008; 9:249-58. [PMID: 18340360 DOI: 10.1038/gene.2008.13] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Birdshot chorioretinopathy (BCR), a chronic ocular inflammatory disease with characteristic choroidal lymphocytic infiltrates, has been strongly associated with human leukocyte antigen (HLA)-A29. Although HLA-A29 occurs frequently in all populations, BCR affects only a small percentage of HLA-A29-positive Caucasians, indicating additional susceptibility factors for BCR. Discovery of HLA class I-specific killer cell immunoglobulin-like receptors (KIR) led to a series of epidemiological studies implicating KIR-HLA gene combinations in disease. Here, we characterized KIR-HLA pairs in BCR patients and controls carrying HLA-A*29 as well as controls lacking HLA-A*29. KIR-HLA pairs implicated for weak inhibition (KIR2DL2/3+HLA-C1 and KIR3DL1+HLA-Bw4(T80)) in combination with activating KIR genes associated with autoimmunity (KIR2DS2, 2DS3 and 2DS4) augment the risk of developing BCR in HLA-A*29-positive individuals. The reciprocal association of strong inhibitory pairs (KIR3DL1+HLA-Bw4(I80) and KIR2DL1+HLA-C2) in combination with those implicated in protection from infection (KIR3DS1+HLA-Bw4(I80) and KIR2DS1+HLA-C2) was observed in HLA-A*29-negative controls. These results suggest that a profound effect of KIR2DS2/S3/S4 in the absence of strong inhibition may enhance the activation of natural killer cells and T-cell subsets against intraocular self-antigens, thereby contributing to pathogenesis of BCR.
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Affiliation(s)
- R D Levinson
- Ocular Inflammatory Disease Center, Jules Stein Eye Institute, David Geffen School of Medicine at UCLA, University of California at Los Angeles, CA 90095-1652, USA
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Middleton D, Meenagh A, Moscoso J, Arnaiz-Villena A. Killer immunoglobulin receptor gene and allele frequencies in Caucasoid, Oriental and Black populations from different continents. ACTA ACUST UNITED AC 2007; 71:105-13. [PMID: 18069936 DOI: 10.1111/j.1399-0039.2007.00973.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Parallel to the growth in interest in the past few years in the killer immunoglobulin-like receptor (KIR) genes has been the elucidation of the presence/absence of these genes and to a very limited extent, the frequency of alleles of these genes in many populations. In the present study, we have chosen seven populations to investigate the presence/absence of the KIR genes and their alleles, i.e. Cuban, Brazilian, Oman, Hong Kong Chinese, Singapore Chinese, South African Xhosa and South African San. The populations were chosen to represent different continents of the world. We show the divergence in the frequencies of these genes, and their alleles, in the different populations. Many new sequence-specific oligonucleotide probe patterns represent new alleles, each occurred in only one of the populations. The KIR gene frequencies of these seven populations were calculated and genetic distances were represented by neighbour-joining dendrograms and correspondence analyses. Also, the presence or absence of 17 KIR loci in the presently studied populations was compared with the presence or absence of the same loci in 56 worldwide populations (available on the website www.allelefrequencies.net). In total, 5134 individuals were analysed and the populations grouped, with some exceptions, according to a geographical gradient.
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Affiliation(s)
- D Middleton
- Northern Ireland Regional Histocompatibility and Immunogenetics Laboratory, City Hospital, Belfast, Northern Ireland.
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Du Z, Gjertson DW, Reed EF, Rajalingam R. Receptor-ligand analyses define minimal killer cell Ig-like receptor (KIR) in humans. Immunogenetics 2006; 59:1-15. [PMID: 17103212 DOI: 10.1007/s00251-006-0168-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Accepted: 10/15/2006] [Indexed: 01/06/2023]
Abstract
Interactions between inhibitory killer cell immunoglobulin-like receptors (iKIR) and human leukocyte antigen (HLA) class I molecules regulate natural killer (NK) cell responses to eliminate infected and transformed cells while maintaining tolerance to healthy cells. Unlinked polymorphic gene families encode KIR receptors and HLA class I ligands and their independent segregation results in a variable number and type of iKIR + HLA pairs inherited in individuals. The diversity in the co-inheritance of iKIR + HLA pairs and activating KIR (aKIR) genes in 759 unrelated individuals from four ethnic populations was analyzed. Every individual studied inherited a minimum of one iKIR + HLA pair; suggesting that major histocompatibility complex class I-dependent inhibitory KIR signaling is essential for human NK cell function. In contrast, 13.4% of the study group lacked all aKIR genes. Twenty percent of the study group carried only one of the four iKIR + HLA pairs. Interestingly, 3% of the study group carrying only KIR2DL3 + HLA-C1 as an iKIR + HLA pair lacked aKIR genes. These data suggest that a single iKIR can constitute the minimal KIR repertoire for human NK cells. Genotypes carrying an equal number of iKIR + HLA pairs and aKIR genes represented 20% of the study group. The remaining individuals had either a dominant inhibitory KIR genotype (iKIR + HLA > aKIR) or a dominant activating KIR genotype (iKIR + HLA < aKIR). Genotypes encoding these imbalanced inhibitory and activating interactions may contribute to susceptibility or resistance to human diseases.
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Affiliation(s)
- Zeying Du
- UCLA Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, 1000 Veteran Avenue, Room No. 1-536, Los Angeles, CA 90095-1652, USA
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