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Perce-da-Silva DDS, Joaquim TE, Aleixo ALQDC, Motta JPR, Lima-Junior JDC, Ribeiro-Alves M, de Oliveira-Ferreira J, Porto LCDMS, Banic DM, Amendoeira MRR. Influence of killer immunoglobulin-like receptors genes on the recurrence rate of ocular toxoplasmosis in Brazil. Mem Inst Oswaldo Cruz 2023; 118:e220203. [PMID: 37018796 PMCID: PMC10065411 DOI: 10.1590/0074-02760220203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/14/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Recurrence is a hallmark of ocular toxoplasmosis (OT), and conditions that influence its occurrence remain a challenge. Natural killer cells (NK) are effectors cells whose primary is cytotoxic function against many parasites, including Toxoplasma gondii. Among the NK cell receptors, immunoglobulin-like receptors (KIR) deserve attention due to their high polymorphism. OBJECTIVES This study aimed to analyse the influence of KIR gene polymorphism in the course of OT infection and its association with recurrences after an active episode. METHODS Ninety-six patients from the Ophthalmologic Clinic of the National Institute of Infectology Evandro Chagas were followed for up to five years. After DNA extraction, genotyping of the patients was performed by polymerase chain reaction sequence-specific oligonucleotide (PCR-SSO) utilising Luminex equipment for reading. During follow-up, 60.4% had a recurrence. FINDINGS We identified 25 KIR genotypes and found a higher frequency of genotype 1 (31.7%) with worldwide distribution. We note that the KIR2DL2 inhibitor gene and the gene activator KIR2DS2 were more frequent in patients without recurrence. Additionally, we observed that individuals who carry these genes progressed recurrence episodes slowly compared to individuals who do not carry these genes. MAIN CONCLUSIONS The KIR2DL2 and KIR2DS2 are associated as possible protection markers against ocular toxoplasmosis recurrence (OTR).
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Affiliation(s)
- Daiana de Souza Perce-da-Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunologia Clínica, Rio de Janeiro, RJ, Brasil
- Centro Universitário Arthur Sá Earp Neto, Faculdade de Medicina de Petrópolis, Laboratório de Imunologia Básica e Aplicada, Petrópolis, RJ, Brasil
- + Corresponding authors: /
| | - Thays Euzebio Joaquim
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Toxoplasmose e outras Protozooses, Rio de Janeiro, RJ, Brasil
| | - Ana Luisa Quintella do Couto Aleixo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em Oftalmologia Infecciosa, Rio de Janeiro, RJ, Brasil
| | | | - Josué da Costa Lima-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunoparasitologia, Rio de Janeiro, RJ, Brasil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Centro de Pesquisa Clínica HIV/AIDS, Rio de Janeiro, RJ, Brasil
| | - Joseli de Oliveira-Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunoparasitologia, Rio de Janeiro, RJ, Brasil
| | | | - Dalma Maria Banic
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunologia Clínica, Rio de Janeiro, RJ, Brasil
| | - Maria Regina Reis Amendoeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Toxoplasmose e outras Protozooses, Rio de Janeiro, RJ, Brasil
- + Corresponding authors: /
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Gunavathy N, Asirvatham A, Chitra A, Jayalakshmi M. Association of Killer Cell Immunoglobulin-Like Receptors and Their HLA-Ligands with Type 1 Diabetes Among South Indian Population. Immunol Invest 2023; 52:270-285. [PMID: 36705596 DOI: 10.1080/08820139.2023.2165940] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Type 1 diabetes (T1D) is a multifactorial autoimmune disease, involving strong genetic components with familial predisposition. Killer cell immunoglobulin-like receptors (KIRs) found on the surface of NK cells have ligands of human leukocyte antigen (HLA) class I that are associated with T1D. The present study evaluates the influence of KIR genes and their HLA-ligands in the aetiology of T1D among the South Indian population. METHODS A total of 125 T1D patients, along with their parents (n = 126) and siblings (n = 52) were recruited. PCR-based genotyping was performed for KIR genes and HLA class I ligands. The gene frequencies were compared between patients and siblings/parents. Linkage-disequilibrium (LD) analysis was performed to assess the genetic association between KIR gene pairs. RESULTS The results show significant differences in HLA-ligands of KIR genes between patients and parents. The HLA-C1C1 homozygosity was found to be a predisposing risk factor, and HLA-C1C2 heterozygosity was protective towards T1D along with either the activating KIR2DS2 or inhibitory KIRs 2DL1, 2DL2, 2DL3. However, the frequency of inhibitory KIR3DL1 significantly increased in the presence of HLA-B Bw4 Ile80 in parents when compared to patients showing a protective effect on T1D. Two pairs of KIR genes, 2DS4-3DL1 and 2DS1-2DL5, showed strong LD in patients, siblings and parents. CONCLUSION The KIR-HLA ligand combinations have a significant effect on T1D aetiology among the South Indian population. This study defines a pattern for family-based association studies with genotypic information about KIR genes and their HLA-ligands, providing the first evidence towards T1D among the South Indian population.
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Affiliation(s)
- Nagarajan Gunavathy
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Arthur Asirvatham
- Department of Diabetology, Government Rajaji Hospital, Madurai, India
| | - Ayyappan Chitra
- Institute of Child Health and Research Centre, Government Rajaji Hospital, Madurai, India
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Killer-Cell Immunoglobulin-like Receptor Diversity in an Admixed South American Population. Cells 2022; 11:cells11182776. [PMID: 36139351 PMCID: PMC9496851 DOI: 10.3390/cells11182776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Natural Killer (NK) cells are innate immune cells that mediate antiviral and antitumor responses. NK cell activation and induction of effector functions are tightly regulated by the integration of activating and inhibitory receptors such as killer immunoglobulin-like receptors (KIR). KIR genes are characterized by a high degree of diversity due to presence or absence, gene copy number and allelic polymorphism. The aim of this study was to establish the distribution of KIR genes and genotypes, to infer the most common haplotypes in an admixed Colombian population and to compare these KIR gene frequencies with some Central and South American populations and worldwide. A total of 161 individuals from Medellin, Colombia were included in the study. Genomic DNA was used for KIR and HLA genotyping. We analyzed only KIR gene-content (presence or absence) based on PCR-SSO. The KIR genotype, most common haplotypes and combinations of KIR and HLA ligands frequencies were estimated according to the presence or absence of KIR and HLA genes. Dendrograms, principal component (PC) analysis and Heatmap analysis based on genetic distance were constructed to compare KIR gene frequencies among Central and South American, worldwide and Amerindian populations. The 16 KIR genes analyzed were distributed in 37 different genotypes and the 7 most frequent KIR inferred haplotypes. Importantly, we found three new genotypes not previously reported in any other ethnic group. Our genetic distance, PC and Heatmap analysis revealed marked differences in the distribution of KIR gene frequencies in the Medellin population compared to worldwide populations. These differences occurred mainly in the activating KIR isoforms, which are more frequent in our population, particularly KIR3DS1. Finally, we observed unique structural patterns of genotypes, which evidences the potential diversity and variability of this gene family in our population, and the need for exhaustive genetic studies to expand our understanding of the KIR gene complex in Colombian populations.
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Vargas LDB, Beltrame MH, Ho B, Marin WM, Dandekar R, Montero-Martín G, Fernández-Viña MA, Hurtado AM, Hill KR, Tsuneto LT, Hutz MH, Salzano FM, Petzl-Erler ML, Hollenbach JA, Augusto DG. Remarkably low KIR and HLA diversity in Amerindians reveals signatures of strong purifying selection shaping the centromeric KIR region. Mol Biol Evol 2021; 39:6388041. [PMID: 34633459 PMCID: PMC8763117 DOI: 10.1093/molbev/msab298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The killer-cell immunoglobulin-like receptors (KIR) recognize human leukocyte antigen (HLA) molecules to regulate the cytotoxic and inflammatory responses of natural killer cells. KIR genes are encoded by a rapidly evolving gene family on chromosome 19 and present an unusual variation of presence and absence of genes and high allelic diversity. Although many studies have associated KIR polymorphism with susceptibility to several diseases over the last decades, the high-resolution allele-level haplotypes have only recently started to be described in populations. Here, we use a highly innovative custom next-generation sequencing method that provides a state-of-art characterization of KIR and HLA diversity in 706 individuals from eight unique South American populations: five Amerindian populations from Brazil (three Guarani and two Kaingang); one Amerindian population from Paraguay (Aché); and two urban populations from Southern Brazil (European and Japanese descendants from Curitiba). For the first time, we describe complete high-resolution KIR haplotypes in South American populations, exploring copy number, linkage disequilibrium, and KIR-HLA interactions. We show that all Amerindians analyzed to date exhibit the lowest numbers of KIR-HLA interactions among all described worldwide populations, and that 83-97% of their KIR-HLA interactions rely on a few HLA-C molecules. Using multiple approaches, we found signatures of strong purifying selection on the KIR centromeric region, which codes for the strongest NK cell educator receptors, possibly driven by the limited HLA diversity in these populations. Our study expands the current knowledge of KIR genetic diversity in populations to understand KIR-HLA coevolution and its impact on human health and survival.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Brenda Ho
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wesley M Marin
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ravi Dandekar
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Gonzalo Montero-Martín
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, 94304, USA
| | | | - A Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85287, USA
| | - Luiza T Tsuneto
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, PR, 87020-900, Brazil
| | - Mara H Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94158, USA
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
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Castro MDS, Issler HC, Gelmini GF, de Miranda BLM, Calonga-Solís V, Schmidt AH, Stein A, Bicalho MDG, Petzl-Erler ML, Augusto DG. High-resolution characterization of 12 classical and non-classical HLA loci in Southern Brazilians. HLA 2020; 93:80-88. [PMID: 30740929 DOI: 10.1111/tan.13488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 11/28/2022]
Abstract
The human leukocyte antigen (HLA) are the most polymorphic genes in the human genome. Because of their importance for antigen recognition, HLA molecules play a central role in host defense and graft rejection upon transplantation. The aim of this study was to characterize allelic diversity of the classical HLA genes HLA-A, -B, -C, -DRA, -DRB1, -DQA1, -DQB1, -DPA1, -DPB1, and the non-classical class I genes HLA-E, -F and -G at high-resolution for a population of predominantly European ancestry from Curitiba, Brazil. Genotyping of 108 individuals was performed by next-generation sequencing on the MiSeq platform and also by Sanger sequencing. The genotype distributions of all loci were in accordance with Hardy-Weinberg equilibrium (P > 0.05) and a total of 202 HLA variants at second field resolution were observed for the 12 loci. The strongest linkage disequilibrium (r2 = 1.0, P < 10-5 ) was observed for the following pairs of alleles: HLA-B*42:01:01 ~ HLA-DRB1*03:02:01; HLA-B*14:02:01 ~ HLA-C*08:02:01; B*42:01:01 ~ HLA-C*17:01:01; HLA-DRB1*03:01:01 ~ HLA-DQB1*02:01:01 ~ DRB1*03:01:01 ~ HLA-DQB1*02:01:01; DRB1*13:01:01~ HLA-DQB1*06:03:01 and HLA-DRB1*09:01:02 ~ HLA-DQA1*03:02. This is the first study to characterize all 12 HLA genes at high resolution in a single population. On the basis of the allelic frequencies of worldwide populations and principal component analysis, we confirmed the similarity of the study population to European and other Euro-descendant populations.
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Affiliation(s)
- Mariana de Sousa Castro
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen C Issler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Geórgia F Gelmini
- Laboratório de Imunogenética e Histocompatibilidade, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Bruna L M de Miranda
- Laboratório de Imunogenética e Histocompatibilidade, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Verónica Calonga-Solís
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Maria da Graça Bicalho
- Laboratório de Imunogenética e Histocompatibilidade, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G Augusto
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
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de Sá NBR, Ribeiro-Alves M, da Silva TP, Pilotto JH, Rolla VC, Giacoia-Gripp CBW, Scott-Algara D, Morgado MG, Teixeira SLM. Clinical and genetic markers associated with tuberculosis, HIV-1 infection, and TB/HIV-immune reconstitution inflammatory syndrome outcomes. BMC Infect Dis 2020; 20:59. [PMID: 31959123 PMCID: PMC6971853 DOI: 10.1186/s12879-020-4786-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 01/09/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) and AIDS are the leading causes of infectious disease death worldwide. In some TB-HIV co-infected individuals treated for both diseases simultaneously, a pathological inflammatory reaction termed immune reconstitution inflammatory syndrome (IRIS) may occur. The risk factors for IRIS are not fully defined. We investigated the association of HLA-B, HLA-C, and KIR genotypes with TB, HIV-1 infection, and IRIS onset. METHODS Patients were divided into four groups: Group 1- TB+/HIV+ (n = 88; 11 of them with IRIS), Group 2- HIV+ (n = 24), Group 3- TB+ (n = 24) and Group 4- healthy volunteers (n = 26). Patients were followed up at INI/FIOCRUZ and HGNI (Rio de Janeiro/Brazil) from 2006 to 2016. The HLA-B and HLA-C loci were typed using SBT, NGS, and KIR genes by PCR-SSP. Unconditional logistic regression models were performed for Protection/risk estimation. RESULTS Among the individuals with TB as the outcome, KIR2DS2 was associated with increased risk for TB onset (aOR = 2.39, P = 0.04), whereas HLA-B*08 and female gender were associated with protection against TB onset (aOR = 0.23, P = 0.03, and aOR = 0.33, P = 0.01, respectively). Not carrying KIR2DL3 (aOR = 0.18, P = 0.03) and carrying HLA-C*07 (aOR = 0.32, P = 0.04) were associated with protection against TB onset among HIV-infected patients. An increased risk for IRIS onset was associated with having a CD8 count ≤500 cells/mm3 (aOR = 18.23, P = 0.016); carrying the KIR2DS2 gene (aOR = 27.22, P = 0.032), the HLA-B*41 allele (aOR = 68.84, P = 0.033), the KIR2DS1 + HLA-C2 pair (aOR = 28.58, P = 0.024); and not carrying the KIR2DL3 + HLA-C1/C2 pair (aOR = 43.04, P = 0.034), and the KIR2DL1 + HLA-C1/C2 pair (aOR = 43.04, P = 0.034), CONCLUSIONS: These results suggest the participation of these genes in the immunopathogenic mechanisms related to the conditions studied. This is the first study demonstrating an association of HLA-B*41, KIR2DS2, and KIR + HLA-C pairs with IRIS onset among TB-HIV co-infected individuals.
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Affiliation(s)
- Nathalia Beatriz Ramos de Sá
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil
| | - Marcelo Ribeiro-Alves
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectious Diseases Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Tatiana Pereira da Silva
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil
| | - Jose Henrique Pilotto
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil
- Nova Iguaçu General Hospital, Nova Iguaçu, Rio de Janeiro, Brazil
| | - Valeria Cavalcanti Rolla
- Clinical Research Laboratory on Mycobacteria, National Institute of Infectious Diseases Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carmem B W Giacoia-Gripp
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil
| | - Daniel Scott-Algara
- Unité de Biologie Cellulaire des Lymphocytes, Institut Pasteur, Paris, France
| | - Mariza Gonçalves Morgado
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil.
| | - Sylvia Lopes Maia Teixeira
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ. Av. Brasil 4365, Leonidas Deane Building, room 401, Rio de Janeiro, 21040-360, Brazil
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Bao X, Zhang T, Wu X, Yuan X, Li Y, Chen L, He J. Population‐specific criterion to distinguish killer cell immunoglobulin‐like receptor genotypes and haplotypes in a large Eastern Han population. HLA 2019; 95:15-22. [PMID: 31496074 DOI: 10.1111/tan.13686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/14/2019] [Accepted: 09/04/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Xiaojing Bao
- Department of HLA Laboratory, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Tengteng Zhang
- Department of HLA Laboratory, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Xiaojin Wu
- Department of Hematology, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Xiaoni Yuan
- Department of HLA Laboratory, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Yang Li
- Department of HLA Laboratory, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Luyao Chen
- Department of HLA Laboratory, Jiangsu Institute of Hematology First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
| | - Jun He
- Department of HLA Laboratory, Jiangsu Institute of Hematology Center for Clinical Laboratory, Collaborative Innovation Center of Hematology, First Affiliated Hospital of Soochow University Suzhou Jiangsu PR China
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Amorim LM, Santos THS, Hollenbach JA, Norman PJ, Marin WM, Dandekar R, Ribeiro EMSF, Petzl-Erler ML, Augusto DG. Cost-effective and fast KIR gene-content genotyping by multiplex melting curve analysis. HLA 2019; 92:384-391. [PMID: 30468002 DOI: 10.1111/tan.13430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 11/05/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022]
Abstract
Killer cell immunoglobulin-like receptor (KIR) genes encode cell surface molecules that recognize HLA molecules and modulate the activity of natural killer (NK) cells. KIR genes exhibit presence and absence polymorphism, which generates a variety of gene-content haplotypes in worldwide populations. KIR gene-content variation is implicated in many diseases and is also important for placentation and transplantation. Because of the complexity of KIR polymorphism, variation in this family is still mostly studied at the gene-content level, even with the advent of next-generation sequencing (NGS) methods. Gene-content determination is generally expensive and/or time-consuming. To overcome these difficulties, we developed a method based on multiplex polymerase chain reaction with specific sequence primers (PCR-SSP) followed by melting curve analysis that allows cost-effective, precise and fast generation of results. Our method was 100% concordant with a gel-based method and 99.9% concordant with presence and absence determination by NGS. The limit of detection for accurate typing was 30 ng of DNA (0.42 μM) with 260/230 and 260/280 ratios as low as 0.19 and of 0.44. In addition, we developed a user-friendly Java-based computational application called killerPeak that interprets the raw data generated by Viia7 or QuantStudio 7 quantitative PCR machines and reliably exports the final genotyping results in spreadsheet file format. The combination of a reliable method that requires low amount of DNA with an automated interpretation of results allows scaling the KIR genotyping in large cohorts with reduced turnaround time.
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Affiliation(s)
- Leonardo M Amorim
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Tiago H S Santos
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, California
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado, Denver
| | - Wesley M Marin
- Department of Neurology, University of California San Francisco, San Francisco, California
| | - Ravi Dandekar
- Department of Neurology, University of California San Francisco, San Francisco, California
| | - Enilze M S F Ribeiro
- Laboratório de Citogenética Humana e Oncogenética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria L Petzl-Erler
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G Augusto
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Neurology, University of California San Francisco, San Francisco, California.,Setor de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
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Chinniah R, Vijayan M, Sivanadham R, Ravi P, Panneerselvam D, Kannan A, Karuppiah B. Diversity and association of HLA/KIR receptors with type 2 diabetes in South India. Int J Immunogenet 2019; 46:166-178. [PMID: 30809938 DOI: 10.1111/iji.12417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 12/08/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022]
Abstract
The present study was undertaken to delineate the association(s) of KIR-HLA combination in South Indian Type 2 diabetes mellitus (T2DM) patients. The T2DM patients (n = 343) and healthy controls (n = 309) were genotyped for KIR/HLA ligands by PCR-SSP method. The increased frequency of activatory KIR (aKIR) 2DS2 (OR = 1.91; p < 2.91 × 10-4 ) was observed in patients suggesting a susceptible association. The frequencies of iKIR 2DL2 (OR = 0.38; p < 1.55 × 10-5 ) and aKIRs 2DS1 (OR = 0.60; p < 0.001) and 3DS1 (OR = 0.52; p < 5.83 × 10-5 ) were decreased in patients suggesting protective associations. The C1/C2 combinatorial analysis has revealed an increased frequency of C1+ /C2- in T2DM patients (OR = 1.62; p < 0.014). The KIR "AB" genotype (OR = 2.41; p < 3.87 × 10-5 ) was observed to be higher in patients. However, the "BB" genotype (OR = 0.32; p < 4.71 × 10-7 ) was increased in controls. The KIR motifs, "Tel-B/B" (OR = 1.84; p < 0.007), were observed higher among patients. However, the frequency of "Tel-A/B" motif genotype was decreased in patients (OR = 0.56; p < 3.13 × 10-4 ). The iKIR/HLA combinations such as 2DL2/3 +C1 and 3DL2+A3/A11 were increased in patients (OR = 3.90; p < 7.5 × 10-5 ) suggesting susceptible associations. On the contrary, the aKIR+HLA combinations such as 2DS2+C1, 2DS1+C2 and 3DS1+Bw4 were less frequent in patients (OR = 0.32; p < 4.2 × 10-4 ) suggesting protective associations. Thus, the present study clearly establishes the positive and negative associations of different KIR-HLA receptor combinations with T2DM in South India.
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Affiliation(s)
- Rathika Chinniah
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Murali Vijayan
- Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Ramgopal Sivanadham
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Padmamalini Ravi
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | | | - Arun Kannan
- Endocrinology and Diabetology, Madurai Institute of Diabetes and Endocrine Practice and Research, Madurai, Tamil Nadu, India
| | - Balakrishnan Karuppiah
- Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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10
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Misra MK, Augusto DG, Martin GM, Nemat-Gorgani N, Sauter J, Hofmann JA, Traherne JA, González-Quezada B, Gorodezky C, Bultitude WP, Marin W, Vierra-Green C, Anderson KM, Balas A, Caro-Oleas JL, Cisneros E, Colucci F, Dandekar R, Elfishawi SM, Fernández-Viña MA, Fouda M, González-Fernández R, Große A, Herrero-Mata MJ, Hollenbach SQ, Marsh SGE, Mentzer A, Middleton D, Moffett A, Moreno-Hidalgo MA, Mossallam GI, Nakimuli A, Oksenberg JR, Oppenheimer SJ, Parham P, Petzl-Erler ML, Planelles D, Sánchez-García F, Sánchez-Gordo F, Schmidt AH, Trowsdale J, Vargas LB, Vicario JL, Vilches C, Norman PJ, Hollenbach JA. Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2018; 79:825-833. [PMID: 30321631 DOI: 10.1016/j.humimm.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
Abstract
The goals of the KIR component of the 17th International HLA and Immunogenetics Workshop (IHIW) were to encourage and educate researchers to begin analyzing KIR at allelic resolution, and to survey the nature and extent of KIR allelic diversity across human populations. To represent worldwide diversity, we analyzed 1269 individuals from ten populations, focusing on the most polymorphic KIR genes, which express receptors having three immunoglobulin (Ig)-like domains (KIR3DL1/S1, KIR3DL2 and KIR3DL3). We identified 13 novel alleles of KIR3DL1/S1, 13 of KIR3DL2 and 18 of KIR3DL3. Previously identified alleles, corresponding to 33 alleles of KIR3DL1/S1, 38 of KIR3DL2, and 43 of KIR3DL3, represented over 90% of the observed allele frequencies for these genes. In total we observed 37 KIR3DL1/S1 allotypes, 40 for KIR3DL2 and 44 for KIR3DL3. As KIR allotype diversity can affect NK cell function, this demonstrates potential for high functional diversity worldwide. Allelic variation further diversifies KIR haplotypes. We determined KIR3DL3 ∼ KIR3DL1/S1 ∼ KIR3DL2 haplotypes from five of the studied populations, and observed multiple population-specific haplotypes in each. This included 234 distinct haplotypes in European Americans, 191 in Ugandans, 35 in Papuans, 95 in Egyptians and 86 in Spanish populations. For another 35 populations, encompassing 642,105 individuals we focused on KIR3DL2 and identified another 375 novel alleles, with approximately half of them observed in more than one individual. The KIR allelic level data gathered from this project represents the most comprehensive summary of global KIR allelic diversity to date, and continued analysis will improve understanding of KIR allelic polymorphism in global populations. Further, the wealth of new data gathered in the course of this workshop component highlights the value of collaborative, community-based efforts in immunogenetics research, exemplified by the IHIW.
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Affiliation(s)
- Maneesh K Misra
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Danillo G Augusto
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA; Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gonzalo Montero Martin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Betsy González-Quezada
- Department of Immunology and Immunogenetics, InDRE, Secretary of Health, Francisco P. Miranda #177, Colonia Lomas de Plateros, Del. Álvaro Obregón, CP 01480, Mexico City, Mexico; Fundación Comparte Vida, A.C. Galileo #92, Col. Polanco, Del. Miguel Hidalgo, CP 11550 Mexico City, Mexico
| | - Clara Gorodezky
- Department of Immunology and Immunogenetics, InDRE, Secretary of Health, Francisco P. Miranda #177, Colonia Lomas de Plateros, Del. Álvaro Obregón, CP 01480, Mexico City, Mexico; Fundación Comparte Vida, A.C. Galileo #92, Col. Polanco, Del. Miguel Hidalgo, CP 11550 Mexico City, Mexico
| | - Will P Bultitude
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, Pond Street, London NW3 2QG, UK
| | - Wesley Marin
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Kirsten M Anderson
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Antonio Balas
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Jose L Caro-Oleas
- Histocompatibility and Immunogenetics, Banc de Sang i Teixits, Barcelona, Spain
| | - Elisa Cisneros
- Immunogenetics and Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro, Madrid, Spain
| | - Francesco Colucci
- Department of Obstetrics and Gynaecology, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge School of Clinical Medicine, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Ravi Dandekar
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | | | | | - Merhan Fouda
- National Cancer Institute, Cairo University, Cairo, Egypt
| | | | | | | | | | - Steven G E Marsh
- Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, Pond Street, London NW3 2QG, UK
| | - Alex Mentzer
- Wellcome Trust Centre for Human Genetics, and Jenner Institute, University of Oxford, Oxford, UK
| | | | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research, Cambridge, UK
| | | | | | - Annettee Nakimuli
- Department of Obstetrics and Gynecology, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | | | | | | | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luciana B Vargas
- Department of Genetics, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jose L Vicario
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Carlos Vilches
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado, Denver, CO 80045, United States
| | - Jill A Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.
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11
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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] [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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12
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Caniatti MCDCL, Borelli SD, Guilherme ALF, Franzener SB, Tsuneto LT. Association between KIR genes and dust mite sensitization in a Brazilian population. Hum Immunol 2017; 79:51-56. [PMID: 29100942 DOI: 10.1016/j.humimm.2017.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Killer cell immunoglobulin-like receptors (KIRs), found on the surface of natural killer (NK) cells, play a key role in controlling the innate response. Such response depends on a series of cellular interactions between these receptors and HLA activating/inhibiting ligands. Atopic diseases have been associated with genes that regulate cytokine production and HLA genes, which may either protect or predispose to hypersensitivity. OBJECTIVE To verify an association study of KIR genes with sensitization to the following mites: Dermatophagoides farinae, Dermatophagoides pteronyssinus, and Blomia tropicalis. METHODS A total of 341 children aged up to 14 years, were classified as mite-sensitive or mite-insensitive after undergoing a skin prick test for immediate allergic reactions. The presence/absence of KIR genes and their human leukocyte antigen (HLA) ligands was determined by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) with the commercial kit LabType™ using Luminex™. RESULTS The frequencies of KIR genes and their respective class I HLA ligands and the frequency of haplotypes were performed in sensitive and insensitive individuals, and no significant differences were found. CONCLUSION Our results suggest no influence of KIR genes on resistance/susceptibility to sensitization to dust mites.
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Affiliation(s)
| | - Sueli Donizete Borelli
- Department of Basic Health Sciences, Universidade Estadual de Maringá (UEM), Maringá, Paraná, Brazil
| | | | | | - Luiza Tamie Tsuneto
- Department of Basic Health Sciences, Universidade Estadual de Maringá (UEM), Maringá, Paraná, Brazil
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13
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Augusto DG. The Impact of KIR Polymorphism on the Risk of Developing Cancer: Not as Strong as Imagined? Front Genet 2016; 7:121. [PMID: 27446203 PMCID: PMC4923111 DOI: 10.3389/fgene.2016.00121] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 06/14/2016] [Indexed: 11/13/2022] Open
Abstract
The polymorphism of killer cell immunoglobulin-like receptors (KIR) has been associated with several diseases, including infection, autoimmunity and cancer. KIR molecules are a family of receptors expressed on the surface of natural killer cells (NK), frontline defense of innate immunity against microorganisms and neoplastic cells. Some studies have shown conflicting results concerning the role that KIR polymorphism plays in tumor susceptibility, particularly in leukemia and lymphoma. Interestingly, the presence of HLA ligands is sometimes strongly associated with several types of cancer and apparently is not related with their interaction with KIR. This manuscript briefly reviews the uncommon polymorphism of KIR and critically summarizes the recent findings with regards of the importance of KIR variation for cancer susceptibility.
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Affiliation(s)
- Danillo G Augusto
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná Curitiba, Brazil
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14
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Vojvodić S, Ademović-Sazdanić D. KIR and HLA haplotype analysis in a family lacking the KIR 2DL1-2DP1 genes. Balkan J Med Genet 2016; 18:55-64. [PMID: 26929906 PMCID: PMC4768826 DOI: 10.1515/bjmg-2015-0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The killer cell immunoglobulin-like receptor (KIR) gene cluster exhibits extensive allelic and haplotypic diversity that is observed as presence/absence of genes, resulting in expansion and contraction of KIR haplotypes and by allelic variation of individual KIR genes. We report a case of KIR pseudogene 2DP1 and 2DL1 gene absence in members of one family with the children suffering from acute myelogenous leukemia (AML). Killer cell immunoglobulin-like receptor low resolution genotyping was performed by the polymerase chain reaction (PCR)-sequence-specific primers (SSP)/sequence-specific oligonucleotide (SSO) method and haplotype assignment was done by gene content analysis. Both parents and the maternal grandfather, shared the same Cen-B2 KIR haplotype, containing KIR 3DL3, -2DS2, -2DL2 and -3DP1 genes. The second haplotype in the KIR genotype of the mother and grandfather was Tel-A1 with KIR 2DL4 (normal and deleted variant), -3DL1, -22 bp deletion variant of the 2DS4 gene and -3DL2, while the second haplotype in the KIR genotype of the father was Tel-B1 with 2DL4 (normal variant), -3DS1, -2DL5, -2DS5, -2DS1 and 3DL2 genes. Haplotype analysis in all three offsprings revealed that the children inherited the Cen-B2 haplotype with the same gene content but two of the children inherited a deleted variant of the 2DL4 gene, while the third child inherited a normal one. The second haplotype of all three offspring contained KIR 2DL4, -2DL5, -2DS1, -2DS4 (del 22bp variant), -2DS5, -3DL1 and -3DL2 genes, which was the basis of the assumption that there is a hybrid haplotype and that the present 3DL1 gene is a variant of the 3DS1 gene. Due to consanguinity among the ancestors, the results of KIR segregation analysis showed the existence of a very rare KIR genotype in the offspring. The family who is the subject of this case is even more interesting because the father was 10/10 human leukocyte antigen (HLA)-matched to his daughter, all members of the family have the “best” donor KIR-B content and the presence of a rare KIR genotype with KIR 2DP1-2DL1 genes absence.
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Affiliation(s)
- S Vojvodić
- Tissue Typing Compartment, Institute for Blood Transfusion of Vojvodina, Novi Sad, Serbia
| | - D Ademović-Sazdanić
- Tissue Typing Compartment, Institute for Blood Transfusion of Vojvodina, Novi Sad, Serbia
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15
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Augusto DG, Amorim LM, Farias TDJ, Petzl-Erler ML. KIR and HLA genotyping of Japanese descendants from Curitiba, a city of predominantly European ancestry from Southern Brazil. Hum Immunol 2016; 77:336-7. [PMID: 26805458 DOI: 10.1016/j.humimm.2016.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/16/2016] [Accepted: 01/18/2016] [Indexed: 01/16/2023]
Abstract
We hereby report the KIR gene frequencies and the frequencies of HLA ligands of KIR for Brazilians of Japanese ancestry. A total of 51 individuals were genotyped for presence/absence of KIR (killer cell immunoglobulin-like receptors) genes and presence of HLA (human leukocyte antigens) ligands. KIR was genotyped using two pairs of sequence-specific primers (PCR-SSP) and HLA ligands were typed by LABType® SSO reagent kits (One Lambda, USA). These data are fully available in Allele Frequencies Net Database, under the population name "Brazil Curitiba Japanese KIR".
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Affiliation(s)
- Danillo G Augusto
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba CEP 81531-980, Brazil.
| | - Leonardo M Amorim
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba CEP 81531-980, Brazil
| | - Ticiana D J Farias
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba CEP 81531-980, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba CEP 81531-980, Brazil.
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16
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Differential gene expression levels might explain association of LAIR2 polymorphisms with pemphigus. Hum Genet 2015; 135:233-44. [PMID: 26721477 DOI: 10.1007/s00439-015-1626-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/11/2015] [Indexed: 12/11/2022]
Abstract
The leukocyte-associated immunoglobulin-like receptor 1 (LAIR-1) is a collagen-binding inhibitory receptor important for the regulation of immune responses, expressed on the majority of peripheral blood mononuclear cells (PBMC). LAIR-2 is a soluble homolog that antagonizes LAIR-1 inhibitory function by binding the same ligands. We sought to investigate whether LAIR1 and LAIR2 single nucleotide polymorphisms (SNP) are associated with differential mRNA expression levels. We analyzed 14 SNPs of LAIR1 (6) and LAIR2 (8) by mass spectrometry-based genotyping and extracted mRNA from PBMC of 177 healthy subjects, followed by quantitative assays. Four SNPs of LAIR1 and two SNPs of LAIR2 mark differential mRNA levels in healthy individuals. To verify the biological relevance of these findings, we analyzed additional 515 individuals (282 patients and 233 controls) to check if LAIR1 and LAIR2 differential mRNA expression could be related to susceptibility to pemphigus foliaceus (PF), an autoimmune blistering skin disease endemic in Brazil. Two LAIR1 variants (rs56802430 G, OR = 1.52, p = 0.0329; rs11084332 C, OR = 0.57, p = 0.0022) and one LAIR2 (rs2287828 T+, OR = 1.9, p = 0.0097) contribute to differential susceptibility to PF. Furthermore, we demonstrate interactions among four LAIR2 SNPs (rs2042287, rs2287828, rs2277974 and rs114834145). A haplotype harboring these SNPs is strongly associated with higher LAIR2 mRNA levels (4.5-fold, p = 0.0069) and with higher susceptibility to PF (OR = 4.02, p = 0.0008). We suggest that LAIR1 and LAIR2 genetic variants are associated with regulation of gene expression and variable PF susceptibility, and show indirect association of LAIR2 differential mRNA expression with PF pathogenesis. Our data demonstrate how this relatively unknown disease can add invaluable knowledge regarding the role of LAIR1 and LAIR2 in immune responses.
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17
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Augusto DG, O’Connor GM, Lobo-Alves SC, Bass S, Martin MP, Carrington M, McVicar DW, Petzl-Erler ML. Pemphigus is associated with KIR3DL2 expression levels and provides evidence that KIR3DL2 may bind HLA-A3 and A11 in vivo. Eur J Immunol 2015; 45:2052-60. [PMID: 25867094 PMCID: PMC4530613 DOI: 10.1002/eji.201445324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/03/2015] [Accepted: 04/09/2015] [Indexed: 12/18/2022]
Abstract
Although HLA-A3 and A11 have been reported to be ligands for KIR3DL2, evidence for any in vivo relevance of this interaction is still missing. To explore the functional importance of KIR3DL2 allelic variation, we analyzed the autoimmune disease pemphigus foliaceus, previously associated (lower risk) with activating KIR genes. KIR3DL2*001 was increased in patients (odds ratio (OR) = 2.04; p = 0.007). The risk was higher for the presence of both KIR3DL2*001 and HLA-A3 or A11 (OR = 3.76, p = 0.013), providing the first evidence that HLA-A3 and A11 may interact with KIR3DL2 in vivo. The nonsynonymous single nucleotide polymorphism 1190T (rs3745902) was associated with protection (OR = 0.52, p = 0.018). This SNP results in a threonine-to-methionine substitution. Individuals who have methionine in this position exhibit a lower percentage of KIR3DL2-positive natural killer (NK) cells and also lower intensity of KIR3DL2 on expressing natural killer cells; additionally, we show that the expression of KIR3DL2 is independent of other killer cell immunoglobulin-like receptors. Pemphigus foliaceus is a very unique complex disease strongly associated with immune-related genes. It is the only autoimmune disease known to be endemic, showing a strong correlation with environmental factors. Our data demonstrate that this relatively unknown autoimmune disease may facilitate understanding of the molecular mechanisms of KIR3DL2 ligand recognition.
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Affiliation(s)
- Danillo G. Augusto
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, 02139, USA
- Leidos Biomedical Research, Cancer and Inflammation Program, Laboratory for Experimental Immunology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Geraldine M. O’Connor
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Sara C. Lobo-Alves
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, 81531-980, Brazil
| | - Sara Bass
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Maureen P. Martin
- Leidos Biomedical Research, Cancer and Inflammation Program, Laboratory for Experimental Immunology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, 02139, USA
- Leidos Biomedical Research, Cancer and Inflammation Program, Laboratory for Experimental Immunology, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Daniel W. McVicar
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
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18
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Augusto DG, Petzl-Erler ML. KIR and HLA under pressure: evidences of coevolution across worldwide populations. Hum Genet 2015; 134:929-40. [PMID: 26099314 DOI: 10.1007/s00439-015-1579-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/15/2015] [Indexed: 01/13/2023]
Abstract
KIR (killer cell immunoglobulin-like receptors) and HLA (human leukocyte antigens) are two distinct gene families with remarkable importance for human immune responses. The recognition of HLA molecules by activating and inhibitory KIR promotes a balance of signals that regulates NK cell function and is especially important for the innate defense against pathogens and early placentation. There is no documented gametic association between these two gene families and no evidence of common regulation. However, due to the critical role of KIR recognition for immunity and reproduction, the possibility of KIR-HLA combinations being under selective pressure is not surprising. In this manuscript, we first summarize the HLA-KIR system, the HLA molecules that are the putative ligands for KIR, and then we review the evidences that suggest these two gene families are coevolving as an integrated system.
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Affiliation(s)
- Danillo G Augusto
- Departamento de Genética, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR, 81531-980, Brazil,
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19
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A deep look at KIR–HLA in Amerindians: Comprehensive meta-analysis reveals limited diversity of KIR haplotypes. Hum Immunol 2015; 76:272-80. [DOI: 10.1016/j.humimm.2015.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/05/2014] [Accepted: 01/15/2015] [Indexed: 11/17/2022]
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20
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Perce-da-Silva DS, Silva LA, Lima-Junior JC, Cardoso-Oliveira J, Ribeiro-Alves M, Santos F, Porto LCMS, Oliveira-Ferreira J, Banic DM. Killer cell immunoglobulin-like receptor (KIR) gene diversity in a population naturally exposed to malaria in Porto Velho, Northern Brazil. ACTA ACUST UNITED AC 2015; 85:190-9. [PMID: 25656387 DOI: 10.1111/tan.12523] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 11/10/2014] [Accepted: 01/13/2015] [Indexed: 11/28/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIR) are expressed mainly in natural killer cells and specifically recognize human leukocyte antigen (HLA) class I molecules. The repertoire of KIR genes and KIR-HLA pairs is known to play a key role in the susceptibilities to and the outcomes of several diseases, including malaria. The aim of this study was to investigate the distribution of KIR genes, KIR genotypes and KIR-HLA pair combinations in a population naturally exposed to malaria from Brazilian Amazon. All 16 KIR genes investigated were present in the studied population. Overall, 46 KIR genotypes were defined. The two most common genotypes in the Porto Velho communities, genotypes 1 and 2, were present at similar frequencies as in the Americas. Principal component analysis based on the frequencies of the KIR genes placed the Porto Velho population closer to the Venezuela Mestizos, USA California hispanic and Brazil Paraná Mixed in terms of KIR gene frequencies. This analysis highlights the multi-ethnic profile of the Porto Velho population. Most of the individuals were found to have at least one inhibitory KIR-HLA pair. Seventy-five KIR-HLA pair combinations were identified. The KIR-2DL2/3_HLA-C1, KIR3DL1_HLA-Bw4 and KIR2DL1_HLA-C2 pairs were the most common. There was no association between KIR genes, KIR genotypes or KIR-HLA pair combinations and malaria susceptibility in the studied population. This is the first report on the distribution of KIR and known HLA ligands in the Porto Velho population. Taken together, these results should provide baseline information that will be relevant to population evolutionary history, malaria and other diseases studies in populations of the Brazilian Amazon.
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Affiliation(s)
- D S Perce-da-Silva
- Laboratory of Simulids and Onchocerciasis "Malaria and Onchocerciasis Research", Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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Vojvodić SI, Ademović-Sazdanić DS, Popović SL, Konstantinidis NV. Distribution of killer cell immunoglobulin-like receptor genes in population of Vojvodina, Serbia. Ann Hum Biol 2014; 42:476-84. [PMID: 25359715 DOI: 10.3109/03014460.2014.966756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Killer cell immunoglobulin-like receptors (KIRs) are glycoproteins regulating the response of natural killer (NK) cells and a few sub-sets of T-cells. The KIR gene frequencies and genotype content vary considerably among different ethnic groups. AIM The aim of this study was to analyse KIR gene polymorphism in the population of Vojvodina and to compare it with selected worldwide populations. SUBJECTS AND METHODS The studied sample consists of 134 healthy unrelated individuals, residents of different geographical regions of Vojvodina. DNA samples isolated from peripheral blood leukocytes by the silica-based extraction method were used in reverse PCR-SSO and PCR-SSP technique to detect the presence and absence of KIR genes. RESULTS All 16 KIR genes, a total of 37 different KIR genotypes, were observed in the Vojvodina population with the presence of framework and pseudogenes in all individuals. The neighbour-joining phylogenetic tree shows that the Vojvodina population is in the same cluster with Croatians, Turkish, Russians, Czechs, Irish, Italians, French, Macedonians and Polish. The Vojvodina population shows polymorphism of the KIR gene family present in other European and European-derived populations studied previously. CONCLUSION The present study may serve as a reference for comparisons in further anthropological and disease association studies and also provide more informative data valuable for donor search strategy in haematopoietic stem cell transplantation.
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Affiliation(s)
- Svetlana I Vojvodić
- a Department for Laboratory Diagnostics , Institute for Blood Transfusion of Vojvodina , Hajduk Veljkova 9a , Novi Sad , Serbia
| | - Dušica S Ademović-Sazdanić
- a Department for Laboratory Diagnostics , Institute for Blood Transfusion of Vojvodina , Hajduk Veljkova 9a , Novi Sad , Serbia
| | - Stevan L Popović
- b Deprtment of Hematology , Institute for Internal Medicine , Novi Sad , Serbia , and
| | - Nada V Konstantinidis
- c Department of Oncology and Hematology , Institute for Child and Youth Health Care of Vojvodina , Novi Sad , Serbia
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Killer cell immunoglobulin-like receptors in Thai patients with leukemia and diffuse large B-cell lymphoma. Hum Immunol 2014; 75:673-6. [DOI: 10.1016/j.humimm.2014.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/06/2014] [Accepted: 04/06/2014] [Indexed: 02/02/2023]
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Augusto DG, Piovezan BZ, Tsuneto LT, Callegari-Jacques SM, Petzl-Erler ML. KIR gene content in amerindians indicates influence of demographic factors. PLoS One 2013; 8:e56755. [PMID: 23451080 PMCID: PMC3581531 DOI: 10.1371/journal.pone.0056755] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 01/14/2013] [Indexed: 11/18/2022] Open
Abstract
Although the KIR gene content polymorphism has been studied worldwide, only a few isolated or Amerindian populations have been analyzed. This extremely diverse gene family codifies receptors that are expressed mainly in NK cells and bind HLA class I molecules. KIR-HLA combinations have been associated to several diseases and population studies are important to comprehend their evolution and their role in immunity. Here we analyzed, by PCR-SSP (specific sequencing priming), 327 individuals from four isolated groups of two of the most important Brazilian Amerindian populations: Kaingang and Guarani. The pattern of KIR diversity among these and other ten Amerindian populations disclosed a wide range of variation for both KIR haplotypes and gene frequencies, indicating that demographic factors, such as bottleneck and founder effects, were the most important evolutionary factors in shaping the KIR polymorphism in these populations.
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Affiliation(s)
| | - Bruno Zagonel Piovezan
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luiza Tamie Tsuneto
- Laboratório de Imunogenética, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
- * E-mail:
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Hollenbach JA, Augusto DG, Alaez C, Bubnova L, Fae I, Fischer G, Gonzalez-Galarza FF, Gorodezky C, Karabon L, Kusnierczyk P, Noble J, Rickards O, Roberts C, Schaffer M, Shi L, Tavoularis S, Trachtenberg E, Yao Y, Middleton D. 16(th) IHIW: population global distribution of killer immunoglobulin-like receptor (KIR) and ligands. Int J Immunogenet 2012; 40:39-45. [PMID: 23280119 DOI: 10.1111/iji.12028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/06/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
Abstract
In the last fifteen years, published reports have described KIR gene-content frequency distributions in more than 120 populations worldwide. However, there have been limited studies examining these data in aggregate to detect overall patterns of variation at regional and global levels. Here, we present a summary of the collection of KIR gene-content data for 105 worldwide populations collected as part of the 15th and 16th International Histocompatibility and Immunogenetics Workshops, and preliminary results for data analysis.
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Affiliation(s)
- J A Hollenbach
- Children's Hospital Oakland Research Institute, Oakland, CA, USA.
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Augusto DG, Lobo-Alves SC, Melo MF, Pereira NF, Petzl-Erler ML. Activating KIR and HLA Bw4 ligands are associated to decreased susceptibility to pemphigus foliaceus, an autoimmune blistering skin disease. PLoS One 2012; 7:e39991. [PMID: 22768326 PMCID: PMC3388041 DOI: 10.1371/journal.pone.0039991] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 05/30/2012] [Indexed: 01/30/2023] Open
Abstract
The KIR genes and their HLA class I ligands have thus far not been investigated in pemphigus foliaceus (PF) and related autoimmune diseases, such as pemphigus vulgaris. We genotyped 233 patients and 204 controls for KIR by PCR-SSP. HLA typing was performed by LABType SSO reagent kits. We estimated the odds ratio, 95% confidence interval and performed logistic regression analyses to test the hypothesis that KIR genes and their known ligands influence susceptibility to PF. We found significant negative association between activating genes and PF. The activating KIR genes may have an overlapping effect in the PF susceptibility and the presence of more than three activating genes was protective (OR = 0.49, p = 0.003). A strong protective association was found for higher ratios activating/inhibitory KIR (OR = 0.44, p = 0.001). KIR3DS1 and HLA-Bw4 were negatively associated to PF either isolated or combined, but higher significance was found for the presence of both together (OR = 0.34, p<10−3) suggesting that the activating function is the major factor to interfere in the PF pathogenesis. HLA-Bw4 (80I and 80T) was decreased in patients. There is evidence that HLA-Bw4(80T) may also be important as KIR3DS1 ligand, being the association of this pair (OR = 0.07, p = 0.001) stronger than KIR3DS1-Bw4(80I) (OR = 0.31, p = 0.002). Higher levels of activating KIR signals appeared protective to PF. The activating KIR genes have been commonly reported to increase the risk for autoimmunity, but particularities of endemic PF, like the well documented influence the environmental exposure in the pathogenesis of this disease, may be the reason why activated NK cells probably protect against pemphigus foliaceus.
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Affiliation(s)
- Danillo G. Augusto
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Sara C. Lobo-Alves
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Marcia F. Melo
- Laboratório de Imunogenética, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Noemi F. Pereira
- Laboratório de Imunogenética, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
- * E-mail:
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