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Al Hadra B, Lukanov T, Mihaylova A, Naumova E. High-resolution characterization of KIR genes polymorphism in healthy subjects from the Bulgarian population-A pilot study. HLA 2024; 103:e15341. [PMID: 38180282 DOI: 10.1111/tan.15341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/06/2024]
Abstract
Although killer-cell immunoglobulin-like receptor (KIR) gene content has been widely studied in health and disease, with the advancement of next-generation sequencing (NGS) technology the high-resolution characterization of this complex gene region has become achievable. KIR allele-level diversity has lately been described across human populations. The present study aimed to analyze for the first time the allele-level polymorphism of nine KIR genes in 155 healthy, unrelated individuals from the Bulgarian population by applying NGS. The highest degree of polymorphism was detected for the KIR3DL3 gene with 40 observed alleles at five-digit resolution in total, 22 of which were common. On the other hand, the KIR3DS1 gene was found to have the lowest degree of polymorphism among the studied KIR genes with one common allele: KIR3DS1*01301 (31.6%). To better understand KIR allelic associations and patterns in Bulgarians, we have estimated the pairwise linkage disequilibrium (LD) for the 10 KIR loci, where KIR2DL3*00501 allele was found in strong LD with KIR2DL1*00101 (D' = 1.00, R2 = 0.742). This is the first study investigating KIR polymorphism at the allele level in a population from the South-East European region. Considering the effect of the populationally shaped KIR allelic polymorphism on NK cell function, this data could lead to a better understanding of the genetic heterogeneity of this region and can be carried into clinical practice by improvement of the strategies taken for NK-mediated diseases.
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Affiliation(s)
- Bushra Al Hadra
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria
| | - Tsvetelin Lukanov
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
- Department of Clinical Immunology, Medical University, Sofia, Bulgaria
| | - Anastasiya Mihaylova
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
| | - Elissaveta Naumova
- Clinic of Clinical Immunology and Stem Cell Bank, Alexandrovska University Hospital, Sofia, Bulgaria
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2
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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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3
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Schellin-Becker CM, Calonga-Solís V, Malaghini M, Sabbag LR, Petzl-Erler ML, Augusto DG, Malheiros D. Population structure and forensic genetic analyses in Guarani and Kaingang Amerindian populations from Brazil. Forensic Sci Int Genet 2022; 58:102678. [DOI: 10.1016/j.fsigen.2022.102678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 11/04/2022]
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4
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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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5
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Bolarín JM, Pérez-Cárceles M, Luna A, Minguela A, Muro M, Legaz I. Killer cell immunoglobulin-like receptors (KIR) genes can be an adequate tool in forensic anthropological studies: evaluation in a wide Caucasian Spanish population. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.1930156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- J. M. Bolarín
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - M.D. Pérez-Cárceles
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Luna
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
| | - A. Minguela
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - M. Muro
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), Murcia, Spain
| | - I. Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, Murcia, Spain
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Amorim LM, Augusto DG, Nemat-Gorgani N, Montero-Martin G, Marin WM, Shams H, Dandekar R, Caillier S, Parham P, Fernández-Viña MA, Oksenberg JR, Norman PJ, Hollenbach JA. High-Resolution Characterization of KIR Genes in a Large North American Cohort Reveals Novel Details of Structural and Sequence Diversity. Front Immunol 2021; 12:674778. [PMID: 34025673 PMCID: PMC8137979 DOI: 10.3389/fimmu.2021.674778] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
The KIR (killer-cell immunoglobulin-like receptor) region is characterized by structural variation and high sequence similarity among genes, imposing technical difficulties for analysis. We undertook the most comprehensive study to date of KIR genetic diversity in a large population sample, applying next-generation sequencing in 2,130 United States European-descendant individuals. Data were analyzed using our custom bioinformatics pipeline specifically designed to address technical obstacles in determining KIR genotypes. Precise gene copy number determination allowed us to identify a set of uncommon gene-content KIR haplotypes accounting for 5.2% of structural variation. In this cohort, KIR2DL4 is the framework gene that most varies in copy number (6.5% of all individuals). We identified phased high-resolution alleles in large multi-locus insertions and also likely founder haplotypes from which they were deleted. Additionally, we observed 250 alleles at 5-digit resolution, of which 90 have frequencies ≥1%. We found sequence patterns that were consistent with the presence of novel alleles in 398 (18.7%) individuals and contextualized multiple orphan dbSNPs within the KIR complex. We also identified a novel KIR2DL1 variant, Pro151Arg, and demonstrated by molecular dynamics that this substitution is predicted to affect interaction with HLA-C. No previous studies have fully explored the full range of structural and sequence variation of KIR as we present here. We demonstrate that pairing high-throughput sequencing with state-of-art computational tools in a large cohort permits exploration of all aspects of KIR variation including determination of population-level haplotype diversity, improving understanding of the KIR system, and providing an important reference for future studies.
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Affiliation(s)
- Leonardo M. Amorim
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danillo G. Augusto
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | - Gonzalo Montero-Martin
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Wesley M. Marin
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Stacy Caillier
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Peter Parham
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
| | | | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Structural Biology, Stanford University, Palo Alto, CA, United States
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, CA, United States
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7
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Hanis Zainal Abidin NW, Mohd Nor N, Sundararajulu P, Zafarina Z. Understanding the genetic history of Malay populations in Peninsular Malaysia via KIR genes diversity. Am J Hum Biol 2020; 33:e23545. [PMID: 33289243 DOI: 10.1002/ajhb.23545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 11/06/2020] [Accepted: 11/18/2020] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES Killer cell immunoglobulin-like receptor (KIR) genes with high polymorphism at genotypic levels are important in providing immune defense and have been expanded towards human population genetics. The aim of this study is to provide supporting information from this new biomarker to strengthen the comprehension of genetic history of the complex Malay population. METHODS KIR genotyping for 213 unadmixed Malay individuals from six subethnic groups (Acheh, Bugis, Champa, Mandailing, Minang and Kedah) was carried out using PCR-SSP (sequence specific primers) method in 16 independent reactions. RESULTS The most frequent KIR genotype observed is AA1, followed by AB4 and AB5. Five genotypes; AA1, AB4, AB5, AB7 and AB8 were shared among all Malay subethnic groups. The highest frequency of KIR haplotype A was observed in Minang Malays, whereas Acheh and Kedah Malays carry a balanced distribution of A and B KIR haplotypes. PCA for the KIR genes clearly illustrated six ethnogeographical population clusters; Africans, Amerindian, Northeast Asian, South Asian, Oceania and Southeast Asian populations. All six Malay subethnic groups fell within the Southeast Asian cluster. CONCLUSIONS The complex array of KIR genotypes observed in the Malays indicates their historical interactions with various populations, especially with the Chinese, Indians and Orang Asli. This study has demonstrated the potential of KIR genes as a genetic marker for deducing population structure and genetic relationship between populations.
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Affiliation(s)
| | - Norazmi Mohd Nor
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Panneerchelvam Sundararajulu
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Zainuddin Zafarina
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
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8
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Vargas LDB, Dourado RM, Amorim LM, Ho B, Calonga-Solís V, Issler HC, Marin WM, Beltrame MH, Petzl-Erler ML, Hollenbach JA, Augusto DG. Single Nucleotide Polymorphism in KIR2DL1 Is Associated With HLA-C Expression in Global Populations. Front Immunol 2020; 11:1881. [PMID: 32983108 PMCID: PMC7478174 DOI: 10.3389/fimmu.2020.01881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Regulation of NK cell activity is mediated through killer-cell immunoglobulin-like receptors (KIR) ability to recognize human leukocyte antigen (HLA) class I molecules as ligands. Interaction of KIR and HLA is implicated in viral infections, autoimmunity, and reproduction and there is growing evidence of the coevolution of these two independently segregating gene families. By leveraging KIR and HLA-C data from 1000 Genomes consortium we observed that the KIR2DL1 variant rs2304224 * T is associated with lower expression of HLA-C in individuals carrying the ligand HLA-C2 (p = 0.0059). Using flow cytometry, we demonstrated that this variant is also associated with higher expression of KIR2DL1 on the NK cell surface (p = 0.0002). Next, we applied next generation sequencing to analyze KIR2DL1 sequence variation in 109 Euro and 75 Japanese descendants. Analyzing the extended haplotype homozygosity, we show signals of positive selection for rs4806553 * G and rs687000 * G, which are in linkage disequilibrium with rs2304224 * T. Our results suggest that lower expression of HLA-C2 ligands might be compensated for higher expression of the receptor KIR2DL1 and bring new insights into the coevolution of KIR and HLA.
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Affiliation(s)
- Luciana de Brito Vargas
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Renata M Dourado
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Leonardo M Amorim
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Brenda Ho
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen C Issler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Wesley M Marin
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Marcia H Beltrame
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Danillo G Augusto
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
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9
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Calonga-Solís V, Malheiros D, Beltrame MH, Vargas LDB, Dourado RM, Issler HC, Wassem R, Petzl-Erler ML, Augusto DG. Unveiling the Diversity of Immunoglobulin Heavy Constant Gamma ( IGHG) Gene Segments in Brazilian Populations Reveals 28 Novel Alleles and Evidence of Gene Conversion and Natural Selection. Front Immunol 2019; 10:1161. [PMID: 31214166 PMCID: PMC6558194 DOI: 10.3389/fimmu.2019.01161] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Even though immunoglobulins are critical for immune responses and human survival, the diversity of the immunoglobulin heavy chain gene (IGH) is poorly known and mostly characterized only by serological methods. Moreover, this genomic region is not well-covered in genomic databases and genome-wide association studies due to particularities that impose technical difficulties for its analysis. Therefore, the IGH gene has never been systematically sequenced across populations. Here, we deliver an unprecedented and comprehensive characterization of the diversity of the IGHG1, IGHG2, and IGHG3 gene segments, which encode the constant region of the most abundant circulating immunoglobulins: IgG1, IgG2, and IgG3, respectively. We used Sanger sequencing to analyze 357 individuals from seven different Brazilian populations, including five Amerindian, one Japanese-descendant and one Euro-descendant population samples. We discovered 28 novel IGHG alleles and provided evidence that some of them may have been originated by gene conversion between common alleles of different gene segments. The rate of synonymous substitutions was significantly higher than the rate of the non-synonymous substitutions for IGHG1 and IGHG2 (p = 0.01 and 0.03, respectively), consistent with purifying selection. Fay and Wu's test showed significant negative values for most populations (p < 0.001), which indicates that positive selection in an adjacent position may be shaping IGHG variation by hitchhiking of variants in the vicinity, possibly the regions that encode the Ig variable regions. This study shows that the variation in the IGH gene is largely underestimated. Therefore, exploring its nucleotide diversity in populations may provide valuable information for comprehension of its evolution, its impact on diseases and vaccine research.
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Affiliation(s)
- Verónica Calonga-Solís
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Danielle Malheiros
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Marcia Holsbach Beltrame
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Luciana de Brito Vargas
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Renata Montoro Dourado
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Hellen Caroline Issler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Roseli Wassem
- Laboratório de Interação Planta-Bactéria, 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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10
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Augusto DG, Norman PJ, Dandekar R, Hollenbach JA. Fluctuating and Geographically Specific Selection Characterize Rapid Evolution of the Human KIR Region. Front Immunol 2019; 10:989. [PMID: 31156615 PMCID: PMC6533848 DOI: 10.3389/fimmu.2019.00989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/16/2019] [Indexed: 01/04/2023] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) region comprises a fast-evolving family of genes that encode receptors for natural killer (NK) cells and have crucial role in host defense. Evolution of KIR was examined in the context of the human genome. Gene-content diversity and single nucleotide polymorphisms (SNP) in the KIR genes and flanking regions were compared to >660,000 genome-wide SNPs in over 800 individuals from 52 populations of the human genome diversity panel (HGDP). KIR allelic diversity was further examined using next generation sequencing in a subset of 56 individuals. We identified the SNP rs587560 located in KIR3DL3 as a marker of KIR2DL2 and KIR2DL3 and, consequently, Cen A and Cen B haplotypes. We also show that combinations of two KIR2DL4 SNPs (rs35656676 and rs592645) distinguish KIR3DL1 from KIR3DS1 and also define the major KIR3DL1 high- and low-expressing alleles lineages. Comparing the diversity of the SNPs within the KIR region to remainder of the genome, we observed a high diversity for the centromeric KIR region consistent with balancing selection (p < 0.01); in contrast, centromeric KIR diversity is significantly reduced in East Asian populations (p < 0.01), indicating purifying selection. By analyzing SNP haplotypes in a region spanning ~500 kb that includes the KIR cluster, we observed evidence of strong positive selection in Africa for high-expressing KIR3DL1 alleles, favored over the low-expressing alleles (p < 0.01). In sharp contrast, the strong positive selection (p < 0.01) that we also observed in the telomeric KIR region in Oceanic populations tracked with a high frequency of KIR3DS1. In addition, we demonstrated that worldwide frequency of high-expression KIR3DL1 alleles was correlated with virus with virus (r = 0.64, p < 10−6) and protozoa (r = 0.69, p < 10−6) loads, which points to selection globally on KIR3DL1 high-expressing alleles attributable to pathogen exposure.
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Affiliation(s)
- Danillo G Augusto
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, Department of Immunology, University of Colorado, Denver, CO, United States
| | - Ravi Dandekar
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
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11
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Amorim LM, Santos THS, Hollenbach JA, Norman PJ, Marin WM, Dandekar R, Ribeiro EMDSF, Petzl-Erler ML, Augusto DG. Cost-effective and fast KIR gene-content genotyping by multiplex melting curve analysis. HLA 2018; 92:384-391. [PMID: 30468002 PMCID: PMC6433384 DOI: 10.1111/tan.13430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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)
| | | | - Jill A. Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado, Denver, USA
| | - Wesley M. Marin
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Ravi Dandekar
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Danillo G. Augusto
- Laboratório de Genética Molecular Humana, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Setor de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
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12
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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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13
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Issler HC, Amorim LM, Petzl-Erler ML, Carvalho LDD, Bezerra HD, Fagundes Júnior J, Gadelha SR, Augusto DG. Southern Bahia, Brazil: KIR gene-content distribution in the highly admixed population from Ilhéus. Hum Immunol 2018; 79:823-824. [PMID: 30253195 DOI: 10.1016/j.humimm.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/12/2018] [Accepted: 09/21/2018] [Indexed: 11/30/2022]
Abstract
We here describe the KIR gene-content genotypes in the highly admixed population from Ilhéus, a city located in Bahia State, Northeast Brazil. Bahia is the State with the largest contribution of African ethnicity in comparison to other Brazilian areas and this is the first report of a population from this region. A total of 32 KIR gene-content genotypes have been found, from which 18 were observed in single individuals. The distinct KIR gene-content distribution observed in Ilhéus, along with the elevated diversity of genotypes point to importance of describing KIR polymorphism in unique populations from Brazil.
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Affiliation(s)
| | | | | | | | - Hadany Dorea Bezerra
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Jomar Fagundes Júnior
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Sandra Rocha Gadelha
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil.
| | - Danillo G Augusto
- Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil; Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil.
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14
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Fagundes NJR, Tagliani-Ribeiro A, Rubicz R, Tarskaia L, Crawford MH, Salzano FM, Bonatto SL. How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data. Genet Mol Biol 2018; 41:206-214. [PMID: 29668018 PMCID: PMC5913727 DOI: 10.1590/1678-4685-gmb-2017-0087] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/23/2017] [Indexed: 12/31/2022] Open
Abstract
In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.
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Affiliation(s)
- Nelson J R Fagundes
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Alice Tagliani-Ribeiro
- Fertilitat Centro de Medicina Reprodutiva, Centro Clínico da Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Larissa Tarskaia
- Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS, USA
| | - Michael H Crawford
- Laboratory of Biological Anthropology, University of Kansas, Lawrence, KS, USA
| | - Francisco M Salzano
- Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Sandro L Bonatto
- Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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15
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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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16
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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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17
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Distribution of KIR genes and KIR2DS4 gene variants in two Mexican Mestizo populations. Hum Immunol 2017; 78:614-620. [PMID: 28734803 DOI: 10.1016/j.humimm.2017.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 07/15/2017] [Accepted: 07/16/2017] [Indexed: 12/24/2022]
Abstract
Killer immunoglobulin-like receptors (KIR) are transmembrane proteins that regulate NK and T cell subsets by recognizing HLA-I molecules as ligands. The KIR gene family consists of 16 genes, located at chromosome 19q13.4. KIR gene frequencies vary among populations. In Mexico, HLA and genetic ancestry studies show that Mestizo populations have different genetic backgrounds based on admixture with European, African, and Asian ancestry. This study aimed to evaluate the frequencies of KIR genes and genotypes in Guerrero and Jalisco, two Mexican Mestizo populations located in the south and the west of the country, respectively, and to compare these frequencies with those of other populations. KIR genotyping was performed by SSP-PCR. We observed that KIR gene frequencies were similar in both populations. There were 24 genotypes observed in Guerrero, 38 genotypes observed in Jalisco, 15 genotypes shared in both populations and 32 genotypes unique to one population or the other. In 10 individuals, nine novel genotypes were identified. KIR2DS4 gene variants showed significant differences: The KIR2DS4full gene was more common in Guerrero (p<0.0001), and the KIR2DS4del variant was more common in Jalisco (p<0.05). Differences in KIR2DS4 gene variants and genotypic profiles could be influenced by the genetic admixture in both regions.
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18
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Portela P, Merzoni J, Lindenau JD, Damin DC, Wilson TJ, Roesler R, Schwartsmann G, Jobim LF, Jobim M. KIR genes and HLA class I ligands in a Caucasian Brazilian population with colorectal cancer. Hum Immunol 2017; 78:263-268. [PMID: 28088355 DOI: 10.1016/j.humimm.2017.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 12/31/2016] [Accepted: 01/08/2017] [Indexed: 12/22/2022]
Abstract
Colorectal cancer (CRC) can occur anywhere in the colon or rectum and represents the third most common cancer in the world in both sexes. Natural killer cells (NK) are part of the innate immune system recognizing class I HLA molecules on target cells through their membrane receptors, called killer cell immunoglobulin-like receptors (KIR). The aim of our study was to evaluate the association between the KIR genes and HLA ligands in patients with colorectal cancer and healthy controls. We examined the polymorphism of 16 KIR genes and their HLA ligands in 154 caucasoid CRC patients and 216 controls. When both groups were compared, no significant differences were found for HLA ligands and KIR genes after Bonferroni correction. However, the Bx haplotypes (heterozygous and homozygous for the haplotype B) were more frequent in controls, when compared with patients. These findings suggest that individuals with Bx haplotypes could have some protection to colorectal cancer. The hypothesis is not related with the presence of a special KIR gene and HLA ligand related to the disease, but to the presence of several activating genes in the individuals with no better action of one in relation to other. Further studies to confirm this observation are warranted.
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Affiliation(s)
- Pâmela Portela
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Joice Merzoni
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Juliana D Lindenau
- Department of Genetic, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daniel C Damin
- Division of Coloproctology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Timothy John Wilson
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Rafael Roesler
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gilberto Schwartsmann
- Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE-HCPA), Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; Department of Internal Medicine, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luiz Fernando Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil; Department of Internal Medicine, School of Medicine, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mariana Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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19
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Vierra-Green C, Roe D, Jayaraman J, Trowsdale J, Traherne J, Kuang R, Spellman S, Maiers M. Estimating KIR Haplotype Frequencies on a Cohort of 10,000 Individuals: A Comprehensive Study on Population Variations, Typing Resolutions, and Reference Haplotypes. PLoS One 2016; 11:e0163973. [PMID: 27723813 PMCID: PMC5056762 DOI: 10.1371/journal.pone.0163973] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/16/2016] [Indexed: 12/04/2022] Open
Abstract
The killer cell immunoglobulin-like receptors (KIR) mediate human natural killer (NK) cell cytotoxicity via activating or inhibiting signals. Although informative and functional haplotype patterns have been reported, most genotyping has been performed at resolutions that are structurally ambiguous. In order to leverage structural information given low-resolution genotypes, we performed experiments to quantify the effects of population variations, reference haplotypes, and genotyping resolutions on population-level haplotype frequency estimations as well as predictions of individual haplotypes. We genotyped 10,157 unrelated individuals in 5 populations (518 African American[AFA], 258 Asian or Pacific Islander[API], 8,245 European[EUR], 1,073 Hispanic[HIS], and 63 Native American[NAM]) for KIR gene presence/absence (PA), and additionally half of the AFA samples for KIR gene copy number variation (CNV). A custom EM algorithm was used to estimate haplotype frequencies for each population by interpretation in the context of three sets of reference haplotypes. The algorithm also assigns each individual the haplotype pairs of maximum likelihood. Generally, our haplotype frequency estimates agree with similar previous publications to within <5% difference for all haplotypes. The exception is that estimates for NAM from the U.S. showed higher frequency association of cB02 with tA01 (+14%) instead of tB01 (-8.5%) compared to a previous study of NAM from south of the U.S. The higher-resolution CNV genotyping on the AFA samples allowed unambiguous haplotype-pair assignments for the majority of individuals, resulting in a 22% higher median typing resolution score (TRS), which measures likelihood of self-match in the context of population-specific haplo- and geno-types. The use of TRS to quantify reduced ambiguity with CNV data clearly revealed the few individuals with ambiguous genotypes as outliers. It is observed that typing resolution and reference haplotype set influence haplotype frequency estimates. For example, PA resolution may be used with reference haplotype sets up to the point where certain haplotypes are gene-content subsets of others. At that point, CNV must be used for all genes.
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Affiliation(s)
- Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - David Roe
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jyothi Jayaraman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - James Traherne
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Rui Kuang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, United States of America
| | - Martin Maiers
- Bioinformatics Research, National Marrow Donor Program, Minneapolis, Minnesota, United States of America
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20
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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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Lindenau JD, Salzano FM, Hurtado AM, Hill KR, Hutz MH. The role of variants from the innate immune system genes in tuberculosis and skin test response in a Native American population. Hum Immunol 2016; 77:981-984. [PMID: 27346696 DOI: 10.1016/j.humimm.2016.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/08/2016] [Accepted: 06/22/2016] [Indexed: 11/28/2022]
Abstract
Native American populations show higher tuberculosis (TB) mortality and infectivity rates than non-Native populations. Variants in the innate immune system seem to have an important role on TB susceptibility. The role of some innate immune system variants in TB susceptibility and/or skin test response (PPD) were investigated in the Aché, a Native American population. Complement receptor 1 and toll like receptor 9 variants were associated with anergy to PPD and protection to TB, respectively. These findings demonstrate an important role of the innate immune system variants in TB susceptibility.
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Affiliation(s)
- Juliana D Lindenau
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ana M Hurtado
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Kim R Hill
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Mara H Hutz
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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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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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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Lindenau JDR, Salzano FM, Hurtado AM, Hill KR, Petzl-Erler ML, Tsuneto LT, Hutz MH. Variability of innate immune system genes in Native American populations-relationship with history and epidemiology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:722-8. [PMID: 26667372 DOI: 10.1002/ajpa.22917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/27/2015] [Accepted: 11/23/2015] [Indexed: 01/04/2023]
Abstract
OBJECTIVES The immune system of a host, defending him/her against invading pathogens, has two main subsystems: innate immunity and acquired immunity. There are several evidences showing that Native American populations are immunologically different from non-Native populations. Our aim was to describe the variability of innate immune system genes in Native American populations. MATERIALS AND METHODS We investigated heterozygozities and patterns of population differentiation (FST ) of 14 polymorphisms related to the innate immune response in five Native American populations (Aché, Guarani-Kaiowá, Guarani-Ñandeva, Kaingang, and Xavante) and the results were compared with the three major world population data (YRI, CEU, and CHB) available at the 1,000 genomes database. RESULTS Mean heterozygosities ranged between 0.241 ± 0.057 (Aché) and 0.343 ± 0.033 (Kaingang), but no significant differences were observed (Friedman test, P = 0.197). Mean heterozygosities were also not significantly different when Amerindians were pooled and compared with the 1000 genomes populations (Friedman test, P = 0.506). When the Native American populations were grouped as Amerindians, a significantly higher FST value (0.194) was observed between the Amerindian and African populations. The Ewens-Watterson neutrality test showed that these markers are not under strong selective pressure. DISCUSSION Native American populations present similar levels of heterozygosity as those of other continents, but are different from Africans in the frequency of polymorphisms of innate immune genes. This higher differentiation is probably due to demographic processes that occurred during the out-of-Africa event.
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Affiliation(s)
- Juliana Dal-Ri Lindenau
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Francisco Mauro Salzano
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Ana Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402
| | | | - Luiza Tamie Tsuneto
- Departamento De Análises Clínicas, Universidade Estadual De Maringá, Maringá, PR, Brazil
| | - Mara Helena Hutz
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
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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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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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Villanea FA, Safi KN, Busch JW. A General Model of Negative Frequency Dependent Selection Explains Global Patterns of Human ABO Polymorphism. PLoS One 2015; 10:e0125003. [PMID: 25946124 PMCID: PMC4422588 DOI: 10.1371/journal.pone.0125003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 03/19/2015] [Indexed: 11/18/2022] Open
Abstract
The ABO locus in humans is characterized by elevated heterozygosity and very similar allele frequencies among populations scattered across the globe. Using knowledge of ABO protein function, we generated a simple model of asymmetric negative frequency dependent selection and genetic drift to explain the maintenance of ABO polymorphism and its loss in human populations. In our models, regardless of the strength of selection, models with large effective population sizes result in ABO allele frequencies that closely match those observed in most continental populations. Populations must be moderately small to fall out of equilibrium and lose either the A or B allele (N(e) ≤ 50) and much smaller (N(e) ≤ 25) for the complete loss of diversity, which nearly always involved the fixation of the O allele. A pattern of low heterozygosity at the ABO locus where loss of polymorphism occurs in our model is consistent with small populations, such as Native American populations. This study provides a general evolutionary model to explain the observed global patterns of polymorphism at the ABO locus and the pattern of allele loss in small populations. Moreover, these results inform the range of population sizes associated with the recent human colonization of the Americas.
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Affiliation(s)
- Fernando A. Villanea
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
| | - Kristin N. Safi
- Department of Anthropology, Washington State University, PO Box 644910, Pullman, Washington, 99164, United States of America
| | - Jeremiah W. Busch
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, Washington, 99164, United States of America
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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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Differing evolutionary histories of the ACTN3*R577X polymorphism among the major human geographic groups. PLoS One 2015; 10:e0115449. [PMID: 25706920 PMCID: PMC4338210 DOI: 10.1371/journal.pone.0115449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/24/2014] [Indexed: 01/23/2023] Open
Abstract
It has been proposed that the functional ACTN3*R577X polymorphism might have evolved due to selection in Eurasian human populations. To test this possibility we surveyed all available population-based data for this polymorphism and performed a comprehensive evolutionary analysis of its genetic diversity, in order to assess the action of adaptive and random mechanisms on its variation across human geographical distribution. The derived 577X allele increases in frequency with distance from Africa, reaching the highest frequencies on the American continent. Positive selection, detected by an extended haplotype homozygosisty test, was consistent only with the Eurasian data, but simulations with neutral models could not fully explain the results found in the American continent. It is possible that particularities of Native American population structure could be responsible for the observed allele frequencies, which would have resulted from a complex interaction between selective and random factors.
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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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Osman AE, Mubasher M, ElSheikh NE, AlHarthi H, Al Yami AS, Rajalingam R, Al-Dehaimi A, Middleton D, ElGhazali G. Characterization of human killer immunoglobulin-like receptors (KIRs) among healthy Saudis. Hum Immunol 2014; 75:536-40. [DOI: 10.1016/j.humimm.2014.02.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
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