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Gomes MB, Rodrigues V, Santos DC, Bôas PRV, Silva DA, de Sousa Azulay RS, Dib SA, Pavin EJ, Fernandes VO, Montenegro Junior RM, Felicio JS, Réa R, Negrato CA, Porto LC. Association between HLA Class II Alleles/Haplotypes and Genomic Ancestry in Brazilian Patients with Type 1 Diabetes: A Nationwide Exploratory Study. Genes (Basel) 2023; 14:genes14050991. [PMID: 37239351 DOI: 10.3390/genes14050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p < 0.05) accuracy for identifying HLA risk alleles related to European GA: for DRB1*03:01, the area under the curve was (AUC) 0.533; for DRB1*04:01 AUC = 0.558, for DRB1*04:02 AUC = 0.545. A better accuracy for identifying African GA was observed for the risk allele DRB1*09:01AUC = 0.679 and for the protective alleles DRB1*03:02 AUC = 0.649, DRB1*11:02 AUC = 0.636, and DRB1*15:03 AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p < 0.05). African GA percentage was higher in patients with protective haplotypes (p < 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil.
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Affiliation(s)
- Marília Brito Gomes
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
| | - Deborah Conte Santos
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Paulo Ricardo Villas Bôas
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Dayse A Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro 20550-900, Brazil
| | - Rossana Santiago de Sousa Azulay
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), São Luís 65020-070, Brazil
| | - Sergio Atala Dib
- Endocrinology Division, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Elizabeth João Pavin
- Endocrinology Division, School of Medical Sciences, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil
| | - Virgínia Oliveira Fernandes
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - Renan Magalhães Montenegro Junior
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - João Soares Felicio
- Endocrinology Division, João de Barros Barreto University Hospital, Federal University of Pará (UFPA), Belém 66073-000, Brazil
| | - Rosangela Réa
- Endocrinology Unit, Federal University of Paraná (UFPR), Curitiba 80060-900, Brazil
| | - Carlos Antonio Negrato
- Medical Doctor Program, School of Dentistry, University of São Paulo (USP), Bauru 17012-901, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
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2
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Lea AJ, Garcia A, Arevalo J, Ayroles JF, Buetow K, Cole SW, Eid Rodriguez D, Gutierrez M, Highland HM, Hooper PL, Justice A, Kraft T, North KE, Stieglitz J, Kaplan H, Trumble BC, Gurven MD. Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations. Proc Natl Acad Sci U S A 2023; 120:e2207544120. [PMID: 36574663 PMCID: PMC9910614 DOI: 10.1073/pnas.2207544120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/21/2022] [Indexed: 12/28/2022] Open
Abstract
A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | - Angela Garcia
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
| | - Jesusa Arevalo
- Department of Medicine, University of California, Los Angeles, CA90095
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ08544
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Kenneth Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Life Sciences, Arizona State University, Tempe, AZ85287
| | - Steve W. Cole
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA90095
- Department of Medicine, University of California, Los Angeles, CA90095
| | | | | | - Heather M. Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | - Paul L. Hooper
- Economic Science Institute, Chapman University, Orange, CA92866
| | | | - Thomas Kraft
- Department of Anthropology, University of Utah, Salt Lake City, UT84112
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | | | - Hillard Kaplan
- Institute for Economics and Society, Chapman University, Orange, CA92866
| | - Benjamin C. Trumble
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ85287
| | - Michael D. Gurven
- Department of Anthropology, University of California, Santa Barbara, CA93106
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3
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Fernandes VC, Pretti MAM, Tsuneto LT, Petzl-Erler ML, Suarez-Kurtz G. Distribution of a novel CYP2C haplotype in Native American populations. Front Genet 2023; 14:1114742. [PMID: 37025454 PMCID: PMC10071019 DOI: 10.3389/fgene.2023.1114742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/28/2023] [Indexed: 04/08/2023] Open
Abstract
The CYP2C19 gene, located in the CYP2C cluster, encodes the major drug metabolism enzyme CYP2C19. This gene is highly polymorphic and no-function (CYP2C19*2 and CYP2C19*3), reduced function (CYP2C19*9) and increased function (CYP2C19*17) star alleles (haplotypes) are commonly used to predict CYP2C19 metabolic phenotypes. CYP2C19*17 and the genotype-predicted rapid (RM) and ultrarapid (UM) CYP2C19 metabolic phenotypes are absent or rare in several Native American populations. However, discordance between genotype-predicted and pharmacokinetically determined CYP2C19 phenotypes in Native American cohorts have been reported. Recently, a haplotype defined by rs2860840T and rs11188059G alleles in the CYP2C cluster has been shown to encode increased rate of metabolism of the CYP2C19 substrate escitalopram, to a similar extent as CYP2C19*17. We investigated the distribution of the CYP2C:TG haplotype and explored its potential impact on CYP2C19 metabolic activity in Native American populations. The study cohorts included individuals from the One Thousand Genomes Project AMR superpopulation (1 KG_AMR), the Human Genome Diversity Project (HGDP), and from indigenous populations living in Brazil (Kaingang and Guarani). The frequency range of the CYP2C:TG haplotype in the study cohorts, 0.469 to 0.598, is considerably higher than in all 1 KG superpopulations (range: 0.014-to 0.340). We suggest that the high frequency of the CYP2C:TG haplotype might contribute to the reported discordance between CYP2C19-predicted and pharmacokinetically verified CYP2C19 metabolic phenotypes in Native American cohorts. However, functional studies involving genotypic correlations with pharmacokinetic parameters are warranted to ascertain the importance of the CYP2C:TG haplotype.
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Affiliation(s)
| | - Marco Antônio M. Pretti
- Laboratório de Bioinformática e Biologia Computacional, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Luiza Tamie Tsuneto
- Departamento de Análises Clínicas, Universidade Estadual de Maringá, Maringá, Brazil
| | - Maria Luiza Petzl-Erler
- Programa de Pós-Graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Guilherme Suarez-Kurtz
- Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- *Correspondence: Guilherme Suarez-Kurtz,
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4
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Roldan-Marin R, Rangel-Gamboa L, Vega-Memije ME, Hernández-Doño S, Ruiz-Gómez D, Granados J. Human leukocyte antigen Class II alleles associated with acral lentiginous melanoma in Mexican Mestizo patients: A case-control study. Indian J Dermatol Venereol Leprol 2022; 88:608-614. [PMID: 35138055 DOI: 10.25259/ijdvl_627_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/01/2021] [Indexed: 12/24/2022]
Abstract
Background Melanoma is an aggressive cutaneous cancer. Acral lentiginous melanoma is a melanoma subtype arising on palms, soles, and nail-units. The incidence, prevalence and prognosis differ among populations. The link between expression of major histocompatibility complex Class II alleles and melanoma progression is known. However, available studies report variable results regarding the association of melanoma with specific HLA Class II loci. Aims The aim of the study was to determine HLA Class II allele frequencies in acral lentiginous melanoma patients and healthy Mexican Mestizo individuals. Methods Eighteen patients with acral lentiginous melanoma and 99 healthy controls were recruited. HLA Class II typing was performed based on the sequence-specific oligonucleotide method. Results Three alleles were associated with increased susceptibility to develop acral lentiginous melanoma, namely: HLA-DRB1*13:01; pC = 0.02, odds ratio = 6.1, IC95% = 1.4-25.5, HLA-DQA1*01:03; pC = 0.001, odds ratio = 9.3, IC95% = 2.7-31.3 and HLA-DQB1*02:02; pC = 0.01, odds ratio = 3.7, IC95% = 1.4-10.3. Limitations The small sample size was a major limitation, although it included all acral lentiginous melanoma patients seen at the dermatology department of Dr. Manuel Gea González General Hospital during the study period. Conclusion HLA-DRB1*13:01, HLA-DQB1*02:02 and HLA-DQA*01:03 alleles are associated with increased susceptibility to develop acral lentiginous melanoma in Mexican Mestizo patients.
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Affiliation(s)
- Rodrigo Roldan-Marin
- OncoDermatology Clinic, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico
| | - Lucia Rangel-Gamboa
- Ecology of Pathogenic Agents, Division of Research, General Hospital Dr. Manuel Gea González, Mexico
| | | | - Susana Hernández-Doño
- Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Daniela Ruiz-Gómez
- Department of Internal Medicine, Fundación Clínica Médica Sur A.C, Mexico
| | - Julio Granados
- Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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5
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Joerin-Luque IA, Augusto DG, Calonga-Solís V, de Almeida RC, Lopes CVG, Petzl-Erler ML, Beltrame MH. Uniparental markers reveal new insights on subcontinental ancestry and sex-biased admixture in Brazil. Mol Genet Genomics 2022; 297:419-435. [DOI: 10.1007/s00438-022-01857-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
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6
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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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7
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Leal DFDVB, Santana da Silva MN, Fernandes DCRDO, Rodrigues JCG, Barros MCDC, Pinto PDDC, Pastana LF, da Silva CA, Fernandes MR, de Assumpção PP, dos Santos SEB, dos Santos NPC. Amerindian genetic ancestry as a risk factor for tuberculosis in an amazonian population. PLoS One 2020; 15:e0236033. [PMID: 32673332 PMCID: PMC7365596 DOI: 10.1371/journal.pone.0236033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023] Open
Abstract
In recent years, the incidence of tuberculosis (TB) has declined worldwide, although this disease still occurs at relatively high rates in Amerindian populations. This suggests that the genetic ancestry of Amerindians may be an important factor in the development of infections, and may account for at least some of the variation in infection rates in the different populations. The present study investigated the potential influence of Amerindian genetic ancestry on susceptibility to tuberculosis in an Amazon population. The study included 280 patients diagnosed with tuberculosis and 138 asymptomatic hospital employees with no history of TB, but who were in contact with bacterially active TB patients. Ancestry analysis was run on a set of 61 Ancestry-Informative Markers to estimate European, African, and Amerindian genetic ancestry using STRUCTURE v2.2. The TB group had significantly higher Amerindian ancestry in comparison with the control group, and significantly lower European ancestry. Amerindian ancestry in the 20–60% range was found to be the principal risk factor for increased susceptibility to TB. The results of the study indicate that Amerindian ancestry is an important risk factor for susceptibility to TB in the admixed population of the Brazilian Amazon region.
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Affiliation(s)
| | | | | | | | | | - Pablo Diego do Carmo Pinto
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | | | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
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Barquera R, Hernández-Zaragoza DI, Bravo-Acevedo A, Arrieta-Bolaños E, Clayton S, Acuña-Alonzo V, Martínez-Álvarez JC, López-Gil C, Adalid-Sáinz C, Vega-Martínez MDR, Escobedo-Ruíz A, Juárez-Cortés ED, Immel A, Pacheco-Ubaldo H, González-Medina L, Lona-Sánchez A, Lara-Riegos J, Sánchez-Fernández MGDJ, Díaz-López R, Guizar-López GU, Medina-Escobedo CE, Arrazola-García MA, Montiel-Hernández GD, Hernández-Hernández O, Ramos-de la Cruz FDR, Juárez-Nicolás F, Pantoja-Torres JA, Rodríguez-Munguía TJ, Juárez-Barreto V, Delgado-Aguirre H, Escutia-González AB, Goné-Vázquez I, Benítez-Arvizu G, Arellano-Prado FP, García-Arias VE, Rodríguez-López ME, Méndez-Mani P, García-Álvarez R, González-Martínez MDR, Aquino-Rubio G, Escareño-Montiel N, Vázquez-Castillo TV, Uribe-Duarte MG, Ruíz-Corral MDJ, Ortega-Yáñez A, Bernal-Felipe N, Gómez-Navarro B, Arriaga-Perea AJ, Martínez-Bezies V, Macías-Medrano RM, Aguilar-Campos JA, Solís-Martínez R, Serrano-Osuna R, Sandoval-Sandoval MJ, Jaramillo-Rodríguez Y, Salgado-Adame A, Juárez-de la Cruz F, Novelo-Garza B, Pavón-Vargas MDLÁ, Salgado-Galicia N, Bortolini MC, Gallo C, Bedoya G, Rothhammer F, González-José R, Ruiz-Linares A, Canizales-Quinteros S, Romero-Hidalgo S, Krause J, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure. Hum Immunol 2020; 81:461-474. [PMID: 32651014 DOI: 10.1016/j.humimm.2020.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.
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Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Diana Iraíz Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico; Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Alicia Bravo-Acevedo
- Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio César Martínez-Álvarez
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Concepción López-Gil
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Carmen Adalid-Sáinz
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - María Del Rosario Vega-Martínez
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Araceli Escobedo-Ruíz
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Eva Dolores Juárez-Cortés
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Alexander Immel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Institute of Clinical Molecular Biology (IKMB), Kiel University, University Hospital, Schleswig-Holstein, Germany
| | - Hanna Pacheco-Ubaldo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Liliana González-Medina
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Abraham Lona-Sánchez
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio Lara-Riegos
- Chemistry Faculty, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, Mexico
| | - María Guadalupe de Jesús Sánchez-Fernández
- Department of Nephrology and Transplantation Unit, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Rosario Díaz-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Gregorio Ulises Guizar-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Carolina Elizabeth Medina-Escobedo
- Unit of Research and Education in Health, Unidad Médica de Alta Especialidad (UMAE) # 10, Instituto Mexicano del Seguro Social (IMSS), Mérida, Yucatán, Mexico
| | - María Araceli Arrazola-García
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | | | - Flor Del Rocío Ramos-de la Cruz
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | | | - Jorge Arturo Pantoja-Torres
- Immunology Division, Unidad Médica de Alta Especialidad (UMAE) # 1, Instituto Mexicano del Seguro Social (IMSS), León, Guanajuato, Mexico
| | - Tirzo Jesús Rodríguez-Munguía
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | | | - Héctor Delgado-Aguirre
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - Isis Goné-Vázquez
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Gamaliel Benítez-Arvizu
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Francia Paulina Arellano-Prado
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Víctor Eduardo García-Arias
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Marla Estefanía Rodríguez-López
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Patricia Méndez-Mani
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Raquel García-Álvarez
- Pharmacology Laboratory, Research Unit, Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | | | - Guadalupe Aquino-Rubio
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | - Néstor Escareño-Montiel
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - María Guadalupe Uribe-Duarte
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - María de Jesús Ruíz-Corral
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Andrea Ortega-Yáñez
- Department of Development Genetics and Molecular Physiology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Benjamín Gómez-Navarro
- Central Office of Nephrology, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Agustín Jericó Arriaga-Perea
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Rosa María Macías-Medrano
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jesús Abraham Aguilar-Campos
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Raúl Solís-Martínez
- Department of Molecular Biology, Laboratorios Diagnóstica, Villahermosa, Tabasco, Mexico
| | - Ricardo Serrano-Osuna
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Mario J Sandoval-Sandoval
- Central Office of Transplantation, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico; Health Research Division, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Yolanda Jaramillo-Rodríguez
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Antonio Salgado-Adame
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Federico Juárez-de la Cruz
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Bárbara Novelo-Garza
- Medical Infrastructure Planning Committee, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María de Los Ángeles Pavón-Vargas
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Norma Salgado-Galicia
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Rothhammer
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sandra Romero-Hidalgo
- Department of Computational Genomics, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Edmond J Yunis
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carolina Bekker-Méndez
- Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Mexico City, Mexico.
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9
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Petzl-Erler ML. Beyond the HLA polymorphism: A complex pattern of genetic susceptibility to pemphigus. Genet Mol Biol 2020; 43:e20190369. [PMID: 32639508 PMCID: PMC7341728 DOI: 10.1590/1678-4685-gmb-2019-0369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Pemphigus is a group of autoimmune bullous skin diseases that result in
significant morbidity. As for other multifactorial autoimmune disorders,
environmental factors may trigger the disease in genetically susceptible
individuals. The goals of this review are to summarize the state of knowledge
about the genetic variation that may affect the susceptibility and pathogenesis
of pemphigus vulgaris and pemphigus foliaceus – both the endemic and the
sporadic forms –, to compare and discuss the possible meaning of the
associations reported, and to propose recommendations for new research
initiatives. Understanding how genetic variants translate into pathogenic
mechanisms and phenotypes remains a mystery for most of the polymorphisms that
contribute to disease susceptibility. However, genetic studies provide a strong
foundation for further developments in this field by generating testable
hypotheses. Currently, results still have limited influence on disease
prevention and prognosis, drug development, and clinical practice, although the
perspectives for future applications for the benefit of patients are
encouraging. Recommendations for the continued advancement of our understanding
as to the impact of genetic variation on pemphigus include these partially
overlapping goals: (1) Querying the functional effect of genetic variants on the
regulation of gene expression through their impact on the nucleotide sequence of
cis regulatory DNA elements such as promoters and enhancers, the splicing of
RNA, the structure of regulatory RNAs and proteins, binding of these regulatory
molecules to regulatory DNA elements, and alteration of epigenetic marks; (2)
identifying key cell types and cell states that are implicated in pemphigus
pathogenesis and explore their functional genomes; (3) integrating structural
and functional genomics data; (4) performing disease-progression longitudinal
studies to disclose the causal relationships between genetic and epigenetic
variation and intermediate disease phenotypes; (5) understanding the influence
of genetic and epigenetic variation in the response to treatment and the
severity of the disease; (6) exploring gene-gene and genotype-environment
interactions; (7) developing improved pemphigus-prone and non-prone animal
models that are appropriate for research about the mechanisms that link
genotypes to pemphigus. Achieving these goals will demand larger samples of
patients and controls and multisite collaborations.
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Affiliation(s)
- Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
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10
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Teles SF, Silva EA, Souza RMD, Tomimori J, Florian MC, Souza RO, Marcos EVC, Souza-Santana FCD, Gamba MA. Association between NDO-LID and PGL-1 for leprosy and class I and II human leukocyte antigen alleles in an indigenous community in Southwest Amazon. Braz J Infect Dis 2020; 24:296-303. [PMID: 32589879 PMCID: PMC9392080 DOI: 10.1016/j.bjid.2020.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/11/2020] [Accepted: 05/31/2020] [Indexed: 11/25/2022] Open
Abstract
The frequencies of the Human leukocyte antigen (HLA) alleles in the Puyanawa indigenous reserve population and their association with the NDO-LID and ELISA PGL-1 rapid serological test was assessed. This was a cross-sectional study with an epidemiological clinical design conducted in two indigenous communities in the state of Acre, Brazil. Blood was collected in a tube with EDTA to identify HLA alleles and perform serological tests. DNA was obtained using the salting out procedure. The LabType™ technique (One-Lambda-USA) was used for HLA class I (loci A*, B* and C*) and II (loci DRB1*, DQA1* and DQB1*) typing. Allele frequency was obtained by direct count, and the chi-square test was used to assess the association with the NDO-LID and PGL-1 tests. The most frequent alleles in the two communities were: HLA-A*02:01, HLA-B*40:02, HLA-DRB1*16:02, HLA-DQA1*05:05 and HLA-DQB1*03:01. The allele HLA-C*04:01 was the most common in the Barão community, and the allele HLA-C*07:01 in Ipiranga. Among individuals who presented seropositivity to the NDO-LID test, the association with alleles HLA-A*02 (43.18% vs 24.8%, p = 0.03, OR = 2.35) and HLA-B*53 (6.83% vs 0.0%, p = 0.03, OR = 8.95) was observed in the Barão community. HLA-B*15 was associated with non-seroconversion to the NDO-LID test in Ipiranga. In both communities, HLA-B*40 and HLA-C*03 were associated with positive serological response to ELISA PGL-1. The HLA class I and II alleles most frequently found in this study have already been described among Terena indigenous groups, and HLA class I contributes to seroconversion to NDO-LID and PGL-1 tests in inhabitants of the Barão and Ipiranga communities.
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11
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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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12
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Boquett JA, Bisso-Machado R, Zagonel-Oliveira M, Schüler-Faccini L, Fagundes NJR. HLA diversity in Brazil. HLA 2019; 95:3-14. [PMID: 31596032 DOI: 10.1111/tan.13723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/11/2019] [Accepted: 10/04/2019] [Indexed: 01/18/2023]
Abstract
Brazil is the fifth largest country in the world in area and the fifth most populous. The Brazilian voluntary Bone Marrow Donor Registry is the third largest in terms of number of donors in the world, being a valuable source of HLA genetics to characterize the donor population of Brazil as well. The genetic background of the Brazilian population is quite heterogeneous, resulting from 5 centuries of admixture among Native Americans, Europeans and Africans, making the Brazilian population unique in terms of genetic ancestry. The unique characteristics of populations in different Brazilian regions make them an exciting focus for genetic diversity studies. Studies on HLA genetic diversity of Brazilian populations have been conducted since the late 1980s and, in this review, we highlight the main findings from studies carried out in Brazil based on classical HLA. In addition, we calculated the genetic distance from the molecular data of the studies included in this review in order to have a broader view of the HLA diversity in Brazilian populations. We emphasize that characterization of HLA diversity is not only important for transplantation programs, but can shed a light on ancestry, history and other demographic patterns with or without association with autoimmune disease.
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Affiliation(s)
- Juliano A Boquett
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafael Bisso-Machado
- Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcelo Zagonel-Oliveira
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Applied Computing Graduate Program, Advanced Visualization & Geoinformatics Laboratory (VIZLab), Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
| | - Lavínia Schüler-Faccini
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Nelson J R Fagundes
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Porto Alegre, Brazil.,Post-graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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13
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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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14
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Measuring the impact of European colonization on Native American populations in Southern Brazil and Uruguay: Evidence from mtDNA. Am J Hum Biol 2019; 31:e23243. [DOI: 10.1002/ajhb.23243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/05/2019] [Accepted: 03/10/2019] [Indexed: 01/26/2023] Open
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15
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Galarza JM, Barquera R, Álvarez AMT, Hernández Zaragoza DI, Sevilla GP, Tamayo A, Pérez M, Dávila D, Birnberg L, Alonzo VA, Krause J, Grijalva M. Genetic diversity of the HLA system in human populations from the Sierra (Andean), Oriente (Amazonian) and Costa (Coastal) regions of Ecuador. Hum Immunol 2018; 79:639-650. [DOI: 10.1016/j.humimm.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/23/2018] [Accepted: 06/07/2018] [Indexed: 12/13/2022]
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16
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Hurley CK, Hou L, Lazaro A, Gerfen J, Enriquez E, Galarza P, Rodriguez Cardozo MB, Halagan M, Maiers M, Behm D, Ng J. Next generation sequencing characterizes the extent of HLA diversity in an Argentinian registry population. HLA 2018; 91:175-186. [DOI: 10.1111/tan.13210] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/22/2017] [Accepted: 01/09/2018] [Indexed: 01/11/2023]
Affiliation(s)
- C. K. Hurley
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - L. Hou
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - A. Lazaro
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - J. Gerfen
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - E. Enriquez
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - P. Galarza
- Directora Del Registro Nacional De Donantes De Celulas Progenitoras Hematopoyeticas Instituto Nacional Central Único Coordinador de Ablación e Implante (INCUCAI) Buenos Aires Argentina
| | - M. B. Rodriguez Cardozo
- Directora Del Registro Nacional De Donantes De Celulas Progenitoras Hematopoyeticas Instituto Nacional Central Único Coordinador de Ablación e Implante (INCUCAI) Buenos Aires Argentina
| | - M. Halagan
- Bioinformatics Research National Marrow Donor Program Minneapolis Minnesota
| | - M. Maiers
- Bioinformatics Research National Marrow Donor Program Minneapolis Minnesota
| | - D. Behm
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
| | - J. Ng
- CW Bill Young Marrow Donor Recruitment and Research Program, Departments of Oncology and Pediatrics Georgetown University Washington District of Columbia
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Distribution of HLA-A, -B and -DRB1 antigenic groups and haplotypes from the Brazilian bone marrow donor registry (REDOME). Hum Immunol 2017; 78:602-609. [DOI: 10.1016/j.humimm.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 07/08/2017] [Accepted: 08/08/2017] [Indexed: 11/19/2022]
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18
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Oriol-Tordera B, Llano A, Ganoza C, Cate S, Hildebrand W, Sanchez J, Calle ML, Brander C, Olvera A. Impact of HLA-DRB1 allele polymorphisms on control of HIV infection in a Peruvian MSM cohort. HLA 2017; 90:234-237. [PMID: 28677168 DOI: 10.1111/tan.13085] [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: 02/10/2017] [Revised: 04/06/2017] [Accepted: 06/15/2017] [Indexed: 11/27/2022]
Abstract
Associations between HLA class II polymorphisms and HIV control were assessed in a Peruvian MSM cohort. Among 233 treatment naïve HIV+ individuals, DRB1*13:02 was linked to elevated viral loads (P = .044) while DRB1*12:01 showed significantly lower viral set points (P = .015) and restricted a dominant T cell response to HIV Gag p24 (P = .038). The present work contributes to a better knowledge of the Peruvian immunogenetics and supports the important role of HLA class II restricted T cells in HIV control.
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Affiliation(s)
- B Oriol-Tordera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - A Llano
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - C Ganoza
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru
| | - S Cate
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, Oklahoma
| | - W Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma, Oklahoma
| | - J Sanchez
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru.,Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Lima, Peru.,Department of Global Health, University of Washington, Seattle, Washington
| | - M L Calle
- Faculty of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - C Brander
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - A Olvera
- IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
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19
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HLA-A, B, DRB1, DQA1, DQB1 alleles and haplotype frequencies in Dene and Cree cohorts in Manitoba, Canada. Hum Immunol 2017; 78:401-411. [PMID: 28359736 DOI: 10.1016/j.humimm.2017.03.009] [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: 12/12/2013] [Revised: 02/01/2017] [Accepted: 03/18/2017] [Indexed: 01/22/2023]
Abstract
BACKGROUND First Nations in the Canadian province of Manitoba have disproportionately high rates of epidemic and endemic TB. Gene polymorphisms that modulate HLA Class I and II antigens are among the risk markers for TB, along with other biologic, and social determinants of health. HLA-A, B, DRB1, DQA1, DQB1 were typed in two Manitoba First Nation indigenous groups to identify and compare the frequency of gene polymorphisms that may influence susceptibility or resistance to TB. METHODS Participants who self-identified as either Dene or Cree enrolled into the study from two First Nation communities in Manitoba, Canada. Genomic DNA was extracted from blood samples collected with informed consent from Dene (N=63) and Cree (N=42) First Nation study participants. Participants self-reported having treated active TB, treated latent TB or no TB. HLA Class I and II molecules were typed using sequence-specific oligonucleotide (SSO) probes from commercially available kits. RESULTS The rates of treated active and latent TB were marginally higher among the Dene than the Cree participants (p=0.112). Class I and II HLA loci were in Hardy-Weinberg equilibrium in both the Dene and Cree groups. In this exploratory analysis of TB and HLA allele frequencies in Dene and Cree cohorts HLA-A*03 and HLA-DQB1*05:03 were significantly associated with TB. CONCLUSIONS The high incidence of TB in both Dene and Cree populations in Canada requires both biomedical and socioeconomic prevention and control measures. Among the former, an understanding of HLA diversity among First Nations groups may aid the development of new effective vaccine and therapeutic modalities that depend on the interaction between small molecules and specific HLA epitopes.
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20
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da Costa Lima Caniatti MC, Borelli SD, Guilherme ALF, Tsuneto LT. Association between HLA genes and dust mite sensitivity in a Brazilian population. Hum Immunol 2016; 78:88-94. [PMID: 27780790 DOI: 10.1016/j.humimm.2016.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Type I hypersensitivity, also known as IgE-mediated allergy, is a complex, multifactorial condition whose onset and severity are influenced by both genetic and environmental factors. Mite allergens stimulate the production of humoral response (IgE), especially in children, which is closely involved in atopic asthma and rhinitis. OBJECTIVE This study aimed to investigate the association between HLA class I (-A, -B, and -C), and HLA class II (-DRB1) genes in individuals sensitive to dust mites (Dermatophagoides farinae, Dermatophagoides pteronyssinus, or Blomia tropicalis) and mite-insensitive controls. METHODS 396 participants were grouped as mite-sensitive and mite-insensitive according to immediate hypersensitivity as determined by skin-prick tests, and to HLA genotyping by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO). RESULTS After chi-square heterogeneity testing no significant differences were observed in HLA-A, B, and C genes, except for the HLA-DRB1 locus, which, showed a negative association for DRB1∗04, between mite-sensitive and mite-insensitive individuals. In high resolution, DRB1∗04:11 allele was significantly different from all other results (P=0.0042, OR=0.26, and 95%CI=0.09-0.70). The analysis stratified by etiologic agent confirmed these associations. CONCLUSION Our results suggest a possible association between HLA-DRB1 genes and hypersensitivity to dust mites.
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21
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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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22
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Abstract
Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.
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Affiliation(s)
- Raphael Carapito
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France
| | - Seiamak Bahram
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France.,Laboratoire Central d'Immunologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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23
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Souza de Lima D, Morishi Ogusku M, Porto dos Santos M, de Melo Silva CM, Alves de Almeida V, Assumpção Antunes I, Boechat AL, Ramasawmy R, Sadahiro A. Alleles of HLA-DRB1*04 Associated with Pulmonary Tuberculosis in Amazon Brazilian Population. PLoS One 2016; 11:e0147543. [PMID: 26901036 PMCID: PMC4764689 DOI: 10.1371/journal.pone.0147543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/04/2016] [Indexed: 12/16/2022] Open
Abstract
Immunogenetic host factors are associated with susceptibility or protection to tuberculosis (TB). Strong associations of HLA class II genes with TB are reported. We analyzed the HLA-DRB1*04 alleles to identify subtypes associated with pulmonary TB and their interaction with risk factors such as alcohol, smoking, and gender in 316 pulmonary TB patients and 306 healthy individuals from the Brazilian Amazon. The HLA-DRB1*04 was prevalent in patients with pulmonary TB (p<0.0001; OR = 2.94; 95% CI = 2.12 to 4.08). Direct nucleotide sequencing of DRB1 exon 2 identified nine subtypes of HLA-DRB1*04. The subtype HLA-DRB1*04:11:01 (p = 0.0019; OR = 2.23; 95% CI = 1.34 to 3.70) was associated with susceptibility to pulmonary TB while DRB1*04:07:01 (p<0.0001; OR = 0.02; 95% CI = 0.001 to 0.33) to protection. Notably, the interaction between alcohol and HLA-DRB1*04:11:01 increased the risk for developing pulmonary TB (p = 0.0001; OR = 51.3; 95% CI = 6.81 to 386). Multibacillary pulmonary TB, the clinical presentation of disease transmission, was strongly associated with interaction to alcohol (p = 0.0026; OR = 11.1; 95% CI = 3.99 to 30.9), HLA-DRB1*04:11:01 (p = 0.0442; OR = 2.01; 95% CI = 1.03 to 3.93) and DRB1*04:92 (p = 0.0112; OR = 8.62; 95% CI = 1.63 to 45.5). These results show that HLA-DRB1*04 are associated with pulmonary TB. Interestingly, three subtypes, DRB1*04:07:01, DRB1*04:11:01 and DRB1*04:92 of the HLA-DRB1*04 could be potential immunogenetic markers that may help to explain mechanisms involved in disease development.
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Affiliation(s)
- Dhêmerson Souza de Lima
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- * E-mail:
| | - Mauricio Morishi Ogusku
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Maisa Porto dos Santos
- Laboratório de Micobacteriologia, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brasil
| | - Cláudia Maria de Melo Silva
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas (FCF), Manaus, Amazonas, Brasil
| | - Vanessa Alves de Almeida
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | | | - Antonio Luiz Boechat
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
| | - Rajendranath Ramasawmy
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
- Fundação de Medicina Tropical Doutor Heitor Vieira Dourado (FMT/HVD), Manaus, Amazonas, Brasil
- Universidade Nilton Lins, Manaus, Amazonas, Brasil
| | - Aya Sadahiro
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brasil
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24
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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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25
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Jacovas VC, Rovaris DL, Peréz O, de Azevedo S, Macedo GS, Sandoval JR, Salazar-Granara A, Villena M, Dugoujon JM, Bisso-Machado R, Petzl-Erler ML, Salzano FM, Ashton-Prolla P, Ramallo V, Bortolini MC. Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes. PLoS One 2015; 10:e0137823. [PMID: 26382048 PMCID: PMC4575214 DOI: 10.1371/journal.pone.0137823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/24/2015] [Indexed: 02/05/2023] Open
Abstract
The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.
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Affiliation(s)
- Vanessa Cristina Jacovas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Diego Luiz Rovaris
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Orlando Peréz
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Soledad de Azevedo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Gabriel Souza Macedo
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - José Raul Sandoval
- Facultad de Medicina Humana, Universidad de San Martin de Porres (USMP), Lima, Peru
| | | | - Mercedes Villena
- Instituto Boliviano de Biología de Altura (IBBA), Universidad Mayor de San Andres, La Paz, Bolivia
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier Toulouse III, Toulouse, 31000, France
| | - Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Francisco Mauro Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
| | - Patricia Ashton-Prolla
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- Serviço de Genética Medica, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Virginia Ramallo
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Puerto Madryn, Argentina
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brasil
- * E-mail:
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26
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Juárez-Martín AI, González-Sobrino BZ, Olvera ÁEC, Falfán-Valencia R. HLA class II alleles in the Otomi population of the Mezquital Valley: a genetic approach to the history of interethnic migrations in the Mexican Central Plateau. Hum Biol 2015; 86:167-84. [PMID: 25836745 DOI: 10.13110/humanbiology.86.3.0167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
From a historical and genetic point of view, the Otomi of the Mezquital Valley are a frontier people that have played an important role in the population dynamics of the Mexican Central Plateau. Due to the antiquity of their presence in the area, the Otomi may be bearers of ancient genetic variability, shared mainly today with other groups belonging to the Otomanguean linguistic family and with the Nahua. In this study we analyzed the HLA class II allele frequencies reported in Mexican indigenous populations, in order to provide an intraregional-level historical perspective of the genetic relationships between the Otomi of the Mezquital Valley and indigenous populations from other regions of Mexico. We examined genetic variation in HLA-DRB1 and -DQB1 loci in 66 nonrelated individuals belonging to seven indigenous communities from the Ixmiquilpan municipality in the Mezquital Valley, in the State of Hidalgo, Mexico. The variability of the HLA-DRB1 gene among the Otomi of the Mezquital Valley was mainly concentrated in five alleles: -DRB1*08:02 (31.06%), -DRB1*04:07 (25.77%), -DRB1*14:06 (7.55%), -DRB1*14:02 (6.06%), and -DRB1*16:02 (4.55%); these alleles have been previously described in other indigenous populations. The most frequent alleles at the HLA-DQB1 locus were -DQB1*03:02 (34.09%), -DQB1*04:02 (31.03%), and -DQB1*03:01 (19.7%). Furthermore, the HLA-DQB1*02:02 allele was found in the Otomi group with a frequency of 2.27%; this allele has not been reported in Mexican indigenous populations. In conclusion, the genetic constitution of the Otomi population is intermediate to the northern groups and the genetic variability shared by the peoples of the central regions of Mexico. Furthermore, HLA-DRB1 and -DQB1 allelic variability among the Otomi provides insight into the historical processes implied in the biological admixture with European, Asian, and African populations as well as in the admixture with the population of Mexico City associated with long-standing migratory processes.
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Affiliation(s)
- Ana Itzel Juárez-Martín
- 1 Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
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27
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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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28
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Kuranov AB, Vavilov MN, Abildinova GZ, Akilzhanova AR, Iskakova AN, Zholdybayeva EV, Boldyreva MN, Müller CA, Momynaliev KT. Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan. PLoS One 2014; 9:e115265. [PMID: 25531278 PMCID: PMC4274022 DOI: 10.1371/journal.pone.0115265] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/20/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations. METHODOLOGY/PRINCIPAL FINDINGS A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians. CONCLUSIONS/SIGNIFICANCE The HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.
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Ayo CM, da Silveira Camargo AV, Xavier DH, Batista MF, Carneiro OA, Brandão de Mattos CC, Ricci O, de Mattos LC. Frequencies of allele groups HLA-A, HLA-B and HLA-DRB1 in a population from the northwestern region of São Paulo State, Brazil. Int J Immunogenet 2014; 42:19-25. [PMID: 25418108 DOI: 10.1111/iji.12159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 11/28/2022]
Abstract
The aim of this study was to estimate the HLA-A, HLA-B and HLA-DRB1 allele groups frequencies in a population of 1559 volunteer bone marrow donors from the northwestern region of São Paulo State grouped according to ethnicity. An additional objective was to compare the allele frequencies of the current study with data published for other Brazilian populations. The allele groups were characterized by the PCR-rSSO method using Luminex(®) technology. Twenty HLA-A, 32 HLA-B and 13 HLA-DRB1 allele groups were identified. The most common allele groups in European descent and mixed African and European descent samples were HLA-A*02, HLA-B*35 and HLA-DRB1*13, while HLA-A*02, HLA-B*35 and HLA-DRB1*11 were more common in African descent samples. The HLA-A*23, HLA-A*36, HLA-B*58 and HLA-B*81 allele groups were more common in sample from African descent than European descent, and the HLA-DRB1*08 was more common in mixed African and European descent than in European descent. Allele group frequencies were compared with samples from other Brazilian regions. The HLA-A*30 and HLA-A*23 were more common in this study than in the populations of Rio Grande do Sul and Paraná; and the HLA-A*01, HLA-B*18, HLA-B*57 and HLA-DRB1*11 were more common in this study than in the population of Piauí. The least frequent allele groups were HLA-A*31, HLA-B*15, HLA-B*40 and HLA-DRB1*08 for the population of Piauí, HLA-A*01 and HLA-A*11 for Parana, HLA-A*02 and -A*03 for Rio Grande do Sul and HLA-DRB1*04 for Paraná, Rio Grande do Sul and Piauí. These data provide an overview on the knowledge on HLA diversity in the population of the northwestern region of São Paulo State and show that the genes of this system are useful to distinguish different ethnic groups.
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Affiliation(s)
- C M Ayo
- Laboratório de Imunogenética, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, SP, Brazil
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Lindenau JD, Guimarães LSP, Hurtado AM, Hill KR, Tsuneto LT, Salzano FM, Petzl-Erler ML, Hutz MH. Association between HLA-DR4 haplotypes and tuberculin skin test response in the Aché population. ACTA ACUST UNITED AC 2014; 84:479-83. [DOI: 10.1111/tan.12451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 11/30/2022]
Affiliation(s)
- J. D. Lindenau
- Departamento de Genética, Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - L. S. P. Guimarães
- Unidade de Epidemiologia e Estatística; Hospital de Clínicas de Porto Alegre; Porto Alegre RS Brazil
| | - A. M. Hurtado
- School of Human Evolution and Social Change; Arizona State University; Tempe AZ USA
| | - K. R. Hill
- School of Human Evolution and Social Change; Arizona State University; Tempe AZ USA
| | - L. T. Tsuneto
- Departamento de Análises Clínicas; Universidade Estadual de Maringá; Maringá PR Brazil
| | - F. M. Salzano
- Departamento de Genética, Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
| | - M. L. Petzl-Erler
- Departamento de Genética; Universidade Federal do Paraná; Curitiba PR Brazil
| | - M. H. Hutz
- Departamento de Genética, Instituto de Biociências; Universidade Federal do Rio Grande do Sul; Porto Alegre RS Brazil
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Iorio A, De Angelis F, Garzoli A, Battistini A, De Stefano GF. HLA-DQA1 and HLA-DQB1 genes in Tsachilas Indians from Ecuador: new insights in population analysis by Human Leukocyte Antigens. Int J Immunogenet 2014; 41:222-30. [DOI: 10.1111/iji.12116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/11/2014] [Accepted: 02/23/2014] [Indexed: 11/29/2022]
Affiliation(s)
- A. Iorio
- Department of Biology; University of Rome Tor Vergata; Rome Italy
- Clinical Pathophysiology Center; AFaR, “San Giovanni Calibita” Fatebenefratelli Hospital; Rome Italy
| | - F. De Angelis
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - A. Garzoli
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - A. Battistini
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - G. F. De Stefano
- Department of Biology; University of Rome Tor Vergata; Rome Italy
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Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection. Genes Immun 2013; 14:518-26. [PMID: 24089150 DOI: 10.1038/gene.2013.47] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 11/08/2022]
Abstract
HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3'UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.
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Zúñiga J, Yu N, Barquera R, Alosco S, Ohashi M, Lebedeva T, Acuña-Alonzo V, Yunis M, Granados-Montiel J, Cruz-Lagunas A, Vargas-Alarcón G, Rodríguez-Reyna TS, Fernandez-Viña M, Granados J, Yunis EJ. HLA class I and class II conserved extended haplotypes and their fragments or blocks in Mexicans: implications for the study of genetic diversity in admixed populations. PLoS One 2013; 8:e74442. [PMID: 24086347 PMCID: PMC3781075 DOI: 10.1371/journal.pone.0074442] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/03/2023] Open
Abstract
Major histocompatibility complex (MHC) genes are highly polymorphic and informative in disease association, transplantation, and population genetics studies with particular importance in the understanding of human population diversity and evolution. The aim of this study was to describe the HLA diversity in Mexican admixed individuals. We studied the polymorphism of MHC class I (HLA-A, -B, -C), and class II (HLA-DRB1, -DQB1) genes using high-resolution sequence based typing (SBT) method and we structured the blocks and conserved extended haplotypes (CEHs) in 234 non-related admixed Mexican individuals (468 haplotypes) by a maximum likelihood method. We found that HLA blocks and CEHs are primarily from Amerindian and Caucasian origin, with smaller participation of African and recent Asian ancestry, demonstrating a great diversity of HLA blocks and CEHs in Mexicans from the central area of Mexico. We also analyzed the degree of admixture in this group using short tandem repeats (STRs) and HLA-B that correlated with the frequency of most probable ancestral HLA-C/−B and -DRB1/−DQB1 blocks and CEHs. Our results contribute to the analysis of the diversity and ancestral contribution of HLA class I and HLA class II alleles and haplotypes of Mexican admixed individuals from Mexico City. This work will help as a reference to improve future studies in Mexicans regarding allotransplantation, immune responses and disease associations.
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Affiliation(s)
- Joaquín Zúñiga
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Neng Yu
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - Sharon Alosco
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Marina Ohashi
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Tatiana Lebedeva
- HLA Laboratory, The American Red Cross Northeast Division, Dedham, Massachusetts, United States of America
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City, Mexico
| | - María Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Julio Granados-Montiel
- Tissue Engineering, Cell Therapy and Regenerative Medicine Research Unit, Instituto Nacional de Rehabilitación, Mexico City, Mexico
| | - Alfredo Cruz-Lagunas
- Department of Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Gilberto Vargas-Alarcón
- Laboratory of Genomics, Instituto Nacional de Cardiología Ignacio Chavez, Mexico City, Mexico
| | - Tatiana S. Rodríguez-Reyna
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- * E-mail: (EJY); (JG)
| | - Edmond J. Yunis
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (EJY); (JG)
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Fabreti-Oliveira RA, Nascimento E, Oliveira CKF, Vale EMG, Vilela B, Santos MA. Four novel HLA alleles, DRB1*04:11:03, DRB1*10:05, DRB1*15:94 and DRB1*16:22, identified in Brazilian individuals. Int J Immunogenet 2013; 41:151-3. [DOI: 10.1111/iji.12091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/09/2013] [Accepted: 08/25/2013] [Indexed: 11/29/2022]
Affiliation(s)
- R A Fabreti-Oliveira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Departamento da Ciência da Computação, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; IMUNOLAB - Laboratório de, Imunologia de Transplantes, Belo Horizonte, MG, Brazil
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Lindenau JD, Salzano FM, Guimarães LSP, Callegari-Jacques SM, Hurtado AM, Hill KR, Petzl-Erler ML, Tsuneto LT, Hutz MH. Distribution patterns of variability for 18 immune system genes in Amerindians - relationship with history and epidemiology. ACTA ACUST UNITED AC 2013; 82:177-85. [DOI: 10.1111/tan.12183] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 06/25/2013] [Accepted: 07/17/2013] [Indexed: 12/22/2022]
Affiliation(s)
- J. D. Lindenau
- Departamento de Genética; Universidade Federal do Rio Grande do Sul; Porto Alegre; Brazil
| | - F. M. Salzano
- Departamento de Genética; Universidade Federal do Rio Grande do Sul; Porto Alegre; Brazil
| | - L. S. P. Guimarães
- Unidade de Epidemiologia e Estatística; Hospital de Clínicas de Porto Alegre; Porto Alegre; Brazil
| | | | - A. M. Hurtado
- School of Human Evolution & Social Change; Arizona State University; Tempe; AZ; USA
| | - K. R. Hill
- School of Human Evolution & Social Change; Arizona State University; Tempe; AZ; USA
| | - M. L. Petzl-Erler
- Departamento de Genética; Universidade Federal do Paraná; Curitiba; Brazil
| | - L. T. Tsuneto
- Departamento de Análises Clínicas; Universidade Estadual de Maringá; Maringá; Brazil
| | - M. H. Hutz
- Departamento de Genética; Universidade Federal do Rio Grande do Sul; Porto Alegre; Brazil
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Yunis JJ, Yunis EJ, Yunis E. MHC Class II haplotypes of Colombian Amerindian tribes. Genet Mol Biol 2013; 36:158-66. [PMID: 23885196 PMCID: PMC3715280 DOI: 10.1590/s1415-47572013005000014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 01/29/2013] [Indexed: 11/21/2022] Open
Abstract
We analyzed 1041 individuals belonging to 17 Amerindian tribes of Colombia, Chimila, Bari and Tunebo (Chibcha linguistic family), Embera, Waunana (Choco linguistic family), Puinave and Nukak (Maku-Puinave linguistic families), Cubeo, Guanano, Tucano, Desano and Piratapuyo (Tukano linguistic family), Guahibo and Guayabero (Guayabero Linguistic Family), Curripaco and Piapoco (Arawak linguistic family) and Yucpa (Karib linguistic family). for MHC class II haplotypes (HLA-DRB1, DQA1, DQB1). Approximately 90% of the MHC class II haplotypes found among these tribes are haplotypes frequently encountered in other Amerindian tribes. Nonetheless, striking differences were observed among Chibcha and non-Chibcha speaking tribes. The DRB1*04:04, DRB1*04:11, DRB1*09:01 carrying haplotypes were frequently found among non-Chibcha speaking tribes, while the DRB1*04:07 haplotype showed significant frequencies among Chibcha speaking tribes, and only marginal frequencies among non-Chibcha speaking tribes. Our results suggest that the differences in MHC class II haplotype frequency found among Chibcha and non-Chibcha speaking tribes could be due to genetic differentiation in Mesoamerica of the ancestral Amerindian population into Chibcha and non-Chibcha speaking populations before they entered into South America.
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Affiliation(s)
- Juan J Yunis
- Departamento de Patología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia . ; Grupo de Identificación Humana e Inmunogenética, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia . ; Instituto de Genética, Servicios Médicos Yunis Turbay y Cia, Bogotá, Colombia
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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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Bardi MS, Jarduli LR, Jorge AJ, Camargo RBOG, Carneiro FP, Gelinski JR, Silva RAF, Lavado EL. HLA-A, B and DRB1 allele and haplotype frequencies in volunteer bone marrow donors from the north of Parana State. Rev Bras Hematol Hemoter 2012; 34:25-30. [PMID: 23049380 PMCID: PMC3459602 DOI: 10.5581/1516-8484.20120010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 11/29/2011] [Indexed: 11/27/2022] Open
Abstract
Background Knowledge of allele and haplotype frequencies of the human leukocyte antigen (HLA) system is important in the search for unrelated bone marrow donors. The Brazilian population is very heterogeneous and the HLA system is highly informative of populations because of the high level of polymorphisms. Aim The aim of this study was to characterize the immunogenetic profile of ethnic groups (Caucasians, Afro-Brazilians and Asians) in the north of Parana State. Methods A study was carried out of 3978 voluntary bone marrow donors registered in the Brazilian National Bone Marrow Donor Registry and typed for the HLA-A, B and DRB1 (low resolution) loci. The alleles were characterized by the polymerase chain reaction sequence-specific oligonucleotides method using the LabType SSO kit (One Lambda, CA, USA). The ARLEQUIN v.3.11 computer program was used to calculate allele and haplotype frequencies Results The most common alleles found in Caucasians were HLA-A*02, 24, 01; HLA-B*35, 44, 51; DRB1*11, 13, 07; for Afro-Brazilians they were HLA-A*02, 03, 30; HLA-B*35, 15, 44; DRB1*13, 11, 03; and for Asians they were: HLA-A*24, 02, 26; HLA-B*40, 51, 52; DRB1*04, 15, 09. The most common haplotype combinations were: HLA-A*01, B*08, DRB1*03 and HLA-A*29, B*44, DRB1*07 for Caucasians; HLA-A*29, B*44, DRB1*07 and HLA-A*01, B*08 and DRB1*03 for Afro-Brazilians; and HLA-A*24, B*52, DRB1*15 and HLA-A*24, B*40 and DRB1*09 for Asians. Conclusion There is a need to target and expand bone marrow donor campaigns in the north of Parana State. The data of this study may be used as a reference by the Instituto Nacional de Cancer/Brazilian National Bone Marrow Donor Registry to evaluate the immunogenetic profile of populations in specific regions and in the selection of bone marrow donors
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Affiliation(s)
- Marlene Silva Bardi
- Laboratory of Histocompatibility, Hospital Universitário, Universidade Estadual de Londrina - UEL, Londrina, PR, Brazil
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Utiyama SRDR, Ribas JLC, Nisihara RM, Kotze LMDS, de Messias-Reason IJ. Celiac disease in native Indians from Brazil: A clinical and epidemiological survey. NORTH AMERICAN JOURNAL OF MEDICAL SCIENCES 2012; 2:138-42. [PMID: 22624128 PMCID: PMC3354426 DOI: 10.4297/najms.2010.3138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: Celiac disease has been described in populations from around the world, with recent data emphasizing the occurrence of the disease in ethnic minorities. There are only a few studies evaluating celiac disease in native Indians. Aims: This study aimed to screen the anti-endomysial antibody (IgA-EmA) in Kaingang and Guarani Indians from southern Brazil, in order to establish a clinical serological evaluation of celiac disease in these individuals. Material and Methods: Serum samples from 321 individuals (125 male and 196 female; 4-86 years old) from Mangueirinha Indigenous Reserve, State of Parana, Brazil, and 180 non-Indigenous healthy individuals (62 male and 118 female; 2-81 years old) were analysed to the presence of anti-endomysial antibody class IgA by indirect immunofluorescence assay. Amongst the Indians, 158 were Kaingang, 98 Guarani and 65 of mixed race. Indians presenting complaints of diarrhea (N=12) were also evaluated to the IgG class of anti-endomisyal antibody. Results: None of the individuals showed positive results either to IgA or IgG anti-endomysial antibodies. Conclusions: Although the results indicate an absence of celiac disease in Kaingang and Guarani Indians, the authors call attention to the importance of following up indigenous children or adults presenting gastrointestinal complaints or other symptoms related to the disease. Consideration should be given to the genetic background of these individuals, allied to the inter ethnic marriages and the changing habits or occupational activities, that have gradually introduced diseases previously not described in indigenous populations.
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Impact of population diversity on the prediction of 7-SNP NAT2 phenotypes using the tagSNP rs1495741 or paired SNPs. Pharmacogenet Genomics 2012; 22:305-9. [PMID: 22336957 DOI: 10.1097/fpc.0b013e3283519c7c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel NAT2 tagSNP (rs1495741) and a 2-SNP genotype (rs1041983 and rs1801280) have been recently shown to accurately predict the NAT2 acetylator phenotypes in populations of exclusive or predominant European/White ancestry. We confirmed the accuracy of the tagSNP approach in White Brazilians, but not in Brown or Black Brazilians, sub-Saharan Mozambicans, and Guarani Amerindians. The combined rs1041983 and rs1801280 genotypes provided considerably better prediction of the NAT2 phenotype in Guarani, but no consistent improvement in Brown or Black Brazilians and Mozambicans. Best predictions of the NAT2 phenotype in Mozambicans using NAT2 SNP pairs were obtained with rs1801280 and rs1799930, but the accuracy of the estimates remained inadequate for clinical use or for investigations in this sub-Saharan group or in Brazilians with considerable African ancestry. In conclusion, the rs1495741 tagSNP cannot be applied to predict the NAT2 acetylation phenotype in Guarani and African-derived populations, whereas 2-SNP genotypes may accurately predict NAT2 phenotypes in Guarani, but not in Africans.
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41
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Beltrame MH, Pincerati MR, Dalla-Costa R, Wassem R, Köhler KF, Chautard-Freire-Maia EA, Tsuneto LT, Petzl-Erler ML. CD80 and CD86 polymorphisms in populations of various ancestries: 5 new CD80 promoter alleles. Hum Immunol 2012; 73:111-7. [DOI: 10.1016/j.humimm.2011.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/29/2011] [Accepted: 10/07/2011] [Indexed: 12/30/2022]
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Benitez O, Busson M, Charron D, Loiseau P. HLA polymorphism in a Guarani-Indian population from Paraguay and its usefulness for the Hispano-Indian admixture study in Paraguay. Int J Immunogenet 2011; 38:7-11. [PMID: 20670332 DOI: 10.1111/j.1744-313x.2010.00959.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study we investigated the human leucocyte antigen-A (HLA-A), -B and DRB1 polymorphism of Native American population of Paraguay, the Guarani Indians. We found that the HLA variability consisted of 5 HLA-A, 7 HLA-B and 6 HLA-DRB1 groups of alleles and of several specific alleles (B*1504, B*3505, B*3912, B*4004, B*5104, DRB1*0411, DRB1*1413) common in other Native American populations. The comparison of the HLA polymorphism of the Guaranis from Paraguay with the «Mestizos» of Paraguay and the Spaniards showed that the «Mestizos» of Paraguay are genetically very distant from the Guarani Indians of Paraguay but much more close to the Spaniards. This can be explained, at least in part, by the history of the country. Our results are of importance in transplantation, in particular in the search for an unrelated donor for a Paraguayan patient requiring hematopoietic stem cell transplantation.
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Affiliation(s)
- O Benitez
- Laboratoire d'Histocompatibilité et d'immunologie Inserm UMRS 940, Hôpital Saint Louis, AP-HP, Paris, France
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Vargens DD, Damasceno A, Petzl-Erler ML, Suarez-Kurtz G. Combined CYP2C9, VKORC1 and CYP4F2 frequencies among Amerindians, Mozambicans and Brazilians. Pharmacogenomics 2011; 12:769-72. [PMID: 21692610 DOI: 10.2217/pgs.11.35] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Vargens DD, Petzl-Erler ML, Suarez-Kurtz G. Distribution of CYP2C Polymorphisms in an Amerindian Population of Brazil. Basic Clin Pharmacol Toxicol 2011; 110:396-400. [DOI: 10.1111/j.1742-7843.2011.00807.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Silva-Alves H, Petzl-Erler ML, Chautard-Freire-Maia EA, Souza RLR. Variability of the BCHE gene in Amerindians from Paraná, Brazil. Am J Hum Biol 2011; 23:556-9. [PMID: 21547979 DOI: 10.1002/ajhb.21168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 01/14/2011] [Accepted: 02/06/2011] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE This study aims to better understand the variability of the BCHE gene, and regions adjacent to it, in different populations. More specifically, it also aims to analyze the diversity of this DNA segment among two Amerindian populations, whose distinct characteristics provide us an extremely interesting material for genetic, evolutionary and anthropological studies, since they diverge genetically and culturally in spite of a very close living relationship in space and time. METHODS The two Amerindian populations analysed were from Guarani-Mbyá and Kaingang ethnic groups, both from the Rio das Cobras indian reservation area (Paraná, Brazil). The other populations data were obtained from the HapMap Project data, NCBI data and previously studies. The variability of seven SNPs was analyzed: two downstream, three within and two upstream of the BCHE gene. RESULTS The number of different BCHE variants in Amerindians is lower than in other populations. The present data are in accordance with the genetic distance between Guarani and Kaingang, and from them to other populations. Some SNPs (rs3495, rs7624915 and rs4387996) presented an interesting frequency pattern, with a higher frequency of the ancestral allele in the region of the modern human origin and its frequency decreasing gradually, from Africa toward the Americas. CONCLUSIONS Despite the geographical coexistence throughout their dispersion, each of these two Amerindian groups retains a high degree of genetic identity, probably maintained by cultural and social isolation.
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Affiliation(s)
- Hugo Silva-Alves
- Department of Genetics, Federal University of Paraná, Curitiba, Brazil
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Shi L, Shi L, Yao YF, Matsushita M, Yu L, Huang XQ, Yi W, Oka T, Tokunaga K, Chu JY. Genetic link among Hani, Bulang and other Southeast Asian populations: evidence from HLA -A, -B, -C, -DRB1 genes and haplotypes distribution. Int J Immunogenet 2011; 37:467-75. [PMID: 20637045 DOI: 10.1111/j.1744-313x.2010.00949.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Human leucocyte antigen (HLA) genetic characteristic of different ethnic minorities would be useful for tracing the origin of modern human HLA matching in transplantation and disease associations. In this study, we reported HLA-A, -B, -C and -DRB1 alleles and haplotypes in the Bulang and Hani populations of southwestern China using a high-resolution polymerase chain reaction-Luminex (PCR-Luminex) typing method. A total of nine HLA-A, 22 HLA-B, 13 HLA-C and 18 HLA-DRB1 alleles were identified in the Bulang population, and 11 HLA-A, 25 HLA-B, 14 HLA-C and 19 HLA-DRB1 alleles were in the Hani population. Compared with other populations, the predominant A*1101-B*1502-DRB1*1202 haplotype in the Bulang and Hani populations was also common in Jinuo, Wa, Dai, Maonan and Vietnamese populations. The distribution of HLA genes indicate that Bulang and Hani populations belong to the Southeast Asia group and they have maintained their original genetic characteristics and kept a long genetic distance from other populations owing to founder effects and subsequent geographic isolation. In addition, the close relationship among ethnic groups in Yunnan province and the Thai and Vietnamese populations were confirmed, whereas the Mon-Kmer-speaking populations shared other common HLA alleles and haplotypes compared with other linguistic groups.
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Affiliation(s)
- L Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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Tovo-Rodrigues L, Callegari-Jacques SM, Petzl-Erler ML, Tsuneto L, Salzano FM, Hutz MH. Dopamine receptor D4 allele distribution in Amerindians: a reflection of past behavior differences? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 143:458-64. [PMID: 20623607 DOI: 10.1002/ajpa.21358] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The DRD4 variable number of tandem repeats (VNTR) allele distribution of 172 Guarani (Kaiowá and Ñandeva subgroups) and Kaingang Brazilian Amerindians is reported. These results are integrated with those previously obtained for this ethnic group. Allele frequencies for the three populations are within the interval observed for 15 other Native American populations and show intermediate values between those observed in Amazonia and Patagonia. Significant differences in allele distribution between recent past hunter-gatherer and agriculturalist populations are observed, with an increase of the 7R allele among hunter-gatherers (P < 0.001). Analysis of molecular variance (AMOVA) and pairwise F(ST) data suggest three distinct sectors for the genetic landscape of Native South America: Andes, Center/Southeast region, and Amazonia. Common traits among hunter-gatherers such as novelty-seeking temperament, hyperactivity, and impulsivity could have been important and advantageous in new environments during America's prehistoric colonization.
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Affiliation(s)
- Luciana Tovo-Rodrigues
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, RS, Brazil
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Martinez-Laso J, Montoya F, Areces C, Moscoso J, Silvera C, Rey D, Parga-Lozano C, Gomez-Prieto P, Enriquez de Salamanca M, Arnaiz-Villena A. HLA in Jaidukama: an Amerindian secluded Colombian population with new haplotypes and Asian and Pacific-shared alleles. Mol Biol Rep 2010; 38:3689-701. [DOI: 10.1007/s11033-010-0483-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 11/09/2010] [Indexed: 12/01/2022]
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Souza VAUF, Salzano FM, Petzl-Erler ML, Nascimento MC, Mayaud P, Borges JD, Pannuti CS. Variations in human herpesvirus type 8 seroprevalence in Native Americans, South America. Emerg Infect Dis 2010; 16:1003-6. [PMID: 20507758 PMCID: PMC3086216 DOI: 10.3201/eid1606.090961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To determine the epidemiology of human herpesvirus type 8 (HHV-8) among non-Amazonian native populations, we conducted a cross-sectional study in Brazil, Bolivia, and Paraquay. Our data show striking ethnic and geographic variations in the distribution of HHV-8 seroprevalences in Amazonian (77%) and non-Amazonian native populations (range 0%–83%).
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Zhang HB, Wei SG, Zheng HB, Yu B, Lai JH. Distribution of human leukocyte antigen alleles and haplotypes in Oroqen and Ewenki nationality minority in Inner Mongolia Autonomous Region of China. Int J Immunogenet 2010; 37:337-44. [PMID: 20518845 DOI: 10.1111/j.1744-313x.2010.00930.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The frequencies of the human leukocyte antigen alleles HLA-A,-B, DRB1 and the A-B, A-DRB1, B-DRB1, A-B-DRB1 haplotypes were investigated through means of PCR-based reverse line-strip sequence specific oligonucleotide hybridization on 108 Oroqen and 104 Ewenki nationality unrelated healthy individuals from the Inner Mongolia Autonomous Region of China. A total of thirteen different HLA-A alleles, 21 different HLA-B alleles and 13 different HLA-DRB1 alleles were detected in the Oroqen ethnic group and the most frequent HLA alleles found were A*24(35.65%), B*15(17.92%), and DRB1*09(17.59%), respectively. The common HLA-A-B-DRB1 haplotypes were A*24-B*40-DRB1*09(5.09%), A*24-B*48-DRB1*12(2.78%) and A*24-B*51-DRB1*04(2.78%); and the HLA-A*33-B*58, A*30-B*13, A*01-B*37, A*33-DRB1*03, A*01-DRB1*10, A*30-DRB1*07, B*37-DRB1*10, B*58-DRB1*03, B*38-DRB1*08, B*13-DRB1*07 were significant positive linkage disequilibrium in the Oroqen nationality group. In total, 14 different HLA-A alleles, 27 B alleles and 12 DRB1 alleles were found in Ewenki nationality group, and the most frequent HLA alleles found were A*24(24.49%), B*40(17.35%), and DRB1*04(14.80%), respectively. The common HLA-A-B-DRB1 haplotypes were A*33-B*58-DRB1*03(6.25%), A*01-B*51-DRB1*11(2.88%) and A*24-B*40-DRB1*09(2.88%); the HLA-A*33-B*58, A*29-B*44, A*03-B*52, A*33-DRB1*03, A*29-DRB1*07, A*24-DRB1*09, B*58-DRB1*03, B*08-DRB1*03, B*46-DRB1*09 were significant positive linkage disequilibrium in Ewenki nationality group. The distribution of HLA A,-B, DRB1, alleles haplotypes frequencies and phylogenetic tree indicated that the Oroqen and Ewenki population groups belongs to northern group of China, together as a group cluster.
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Affiliation(s)
- H B Zhang
- Key Laboratory of Ministry of Health for Forensic Sciences, School of Medicine, Xi'an Jiaotong University
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