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Crivello P, Arrieta-Bolaños E, He M, Wang T, Fingerson S, Gadalla SM, Paczesny S, Marsh SG, Lee SJ, Spellman SR, Bolon YT, Fleischhauer K. Impact of the HLA Immunopeptidome on Survival of Leukemia Patients After Unrelated Donor Transplantation. J Clin Oncol 2023; 41:2416-2427. [PMID: 36669145 PMCID: PMC10150892 DOI: 10.1200/jco.22.01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/10/2022] [Accepted: 11/15/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Immunopeptidome divergence between mismatched HLA-DP is a determinant of T-cell alloreactivity and clinical tolerability after fully HLA-A, -B, -C, -DRB1, -DQB1 matched unrelated donor hematopoietic cell transplantation (UD-HCT). Here, we tested this concept in HLA-A, -B, and -C disparities after single class I HLA-mismatched UD-HCT. PATIENTS AND METHODS We studied 2,391 single class I HLA-mismatched and 14,426 fully HLA-matched UD-HCT performed between 2008 and 2018 for acute leukemia or myelodysplastic syndromes. Hierarchical clustering of experimentally determined peptide-binding motifs (PBM) was used as a proxy for immunopeptidome divergence of HLA-A, -B, or -C disparities, allowing us to classify 1,629/2,391 (68.1%) of the HLA-mismatched UD-HCT as PBM-matched or PBM-mismatched. Risks associated with PBM-matching status were assessed by Cox proportional hazards models, with overall survival (OS) as the primary end point. RESULTS Relative to full matches, bidirectional or unidirectional PBM mismatches in graft-versus-host (GVH) direction (PBM-GVH mismatches, 60.7%) were associated with significantly lower OS (hazard ratio [HR], 1.48; P < .0001), while unidirectional PBM mismatches in host-versus-graft direction or PBM matches (PBM-GVH matches, 39.3%) were not (HR, 1.13; P = .1017). PBM-GVH mismatches also had significantly lower OS than PBM-GVH matches in direct comparison (HR, 1.32; P = .0036). The hazards for transplant-related mortality and acute and chronic graft-versus-host disease but not relapse increased stepwise from full HLA matches to single PBM-GVH matches, and single PBM-GVH mismatches. A webtool for PBM-matching of single class I HLA-mismatched donor-recipient pairs was developed. CONCLUSION PBM-GVH mismatches inform mortality risks after single class I HLA-mismatched UD-HCT, suggesting that prospective consideration of directional PBM-matching status might improve outcome. These findings highlight immunopeptidome divergence between mismatched HLA as a driver of clinical tolerability in UD-HCT.
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Affiliation(s)
- Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium, partner site Essen/Düsseldorf (DKTK), Heidelberg, Germany
| | - Meilun He
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Tao Wang
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI
- Department of Medicine, Medical College of Wisconsin, CIBMTR (Center for International Blood and Marrow Transplant Research), Milwaukee, WI
| | - Stephanie Fingerson
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Shahinaz M. Gadalla
- Division of Cancer Epidemiology and Genetics, NIH-NCI Clinical Genetics Branch, Rockville, MD
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Steven G.E. Marsh
- Anthony Nolan Research Institute and University College London Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Stephanie J. Lee
- Department of Medicine, Medical College of Wisconsin, CIBMTR (Center for International Blood and Marrow Transplant Research), Milwaukee, WI
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Stephen R. Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Yung-Tsi Bolon
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium, partner site Essen/Düsseldorf (DKTK), Heidelberg, Germany
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Leserer S, Graf T, Franke M, Bogdanov R, Arrieta-Bolaños E, Buttkereit U, Leimkühler N, Fleischhauer K, Reinhardt HC, Beelen DW, Turki AT. Time series clustering of T cell subsets dissects heterogeneity in immune reconstitution and clinical outcomes among MUD-HCT patients receiving ATG or PTCy. Front Immunol 2023; 14:1082727. [PMID: 37020562 PMCID: PMC10067907 DOI: 10.3389/fimmu.2023.1082727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/02/2023] [Indexed: 03/22/2023] Open
Abstract
IntroductionAnti-T-lymphocyte globulin (ATG) or post-transplant cyclophosphamide (PTCy) prevent graft-versus-host disease (GVHD) after hematopoietic cell transplantation (HCT), yet individual patients benefit differentially.MethodsGiven the sparse comparative data on the impact of cellular immune reconstitution in this setting, we studied flow cytometry and clinical outcomes in 339 recipients of 10/10 matched-unrelated donor (MUD) HCT using either ATG (n=304) or PTCy (n=35) for in vivo T cell manipulation along with a haploidentical PTCy control cohort (n=45). Longitudinal cellular immune reconstitution data were analyzed conventionally and with a data science approach using clustering with dynamic time warping to determine the similarity between time-series of T cell subsets.ResultsConsistent with published studies, no significant differences in clinical outcomes were observed at the cohort level between MUD-ATG and MUD-PTCy. However, cellular reconstitution revealed preferences for distinct T cell subpopulations associating with GVHD protection in each setting. Starting early after HCT, MUD-PTCy patients had higher regulatory T cell levels after HCT (p <0.0001), while MUD-ATG patients presented with higher levels of γδ T- or NKT cells (both p <0.0001). Time-series clustering further dissected the patient population’s heterogeneity revealing distinct immune reconstitution clusters. Importantly, it identified phenotypes that reproducibly associated with impaired clinical outcomes within the same in vivo T cell manipulation platform. Exemplarily, patients with lower activated- and αβ T cell counts had significantly higher NRM (p=0.032) and relapse rates (p =0.01).DiscussionThe improved understanding of the heterogeneity of cellular reconstitution in MUD patients with T cell manipulation both at the cohort and individual level may support clinicians in managing HCT complications.
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Affiliation(s)
- Saskia Leserer
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Computational Hematology Lab, Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Institute for Experimental Cellular Therapy, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Theresa Graf
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Computational Hematology Lab, Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Martina Franke
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Rashit Bogdanov
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Computational Hematology Lab, Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, West-German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner site Essen/Düsseldorf, Essen, Germany
| | - Ulrike Buttkereit
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Nils Leimkühler
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, West-German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partner site Essen/Düsseldorf, Essen, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Cancer Research Center Cologne Essen (CCCE), Essen, Germany
| | - Dietrich W. Beelen
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
| | - Amin T. Turki
- Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Computational Hematology Lab, Department of Hematology and Stem Cell Transplantation, West-German Cancer Center, University Hospital Essen, Essen, Germany
- Institute for Experimental Cellular Therapy, West-German Cancer Center, University Hospital Essen, Essen, Germany
- *Correspondence: Amin T. Turki,
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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Arrieta-Bolaños E, Crivello P, He M, Wang T, Gadalla SM, Paczesny S, Marsh SGE, Lee SJ, Spellman SR, Bolon YT, Fleischhauer K. A core group of structurally similar HLA-DPB1 alleles drives permissiveness after hematopoietic cell transplantation. Blood 2022; 140:659-663. [PMID: 35609150 PMCID: PMC9373015 DOI: 10.1182/blood.2022015708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/12/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Essen, Germany
| | - Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Meilun He
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Tao Wang
- Division of Biostatistics, Institute for Health and Equity, Medical College of Wisconsin, Milwaukee, WI
- CIBMTR (Center for International Blood and Marrow Transplant Research), Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, National Institutes of Health-National Cancer Institute Clinical Genetics Branch, Rockville, MD
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, United Kingdom
- UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Stephanie J Lee
- CIBMTR (Center for International Blood and Marrow Transplant Research), Medical College of Wisconsin, Milwaukee, WI; and
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Yung-Tsi Bolon
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Essen, Germany
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Arrieta-Bolaños E, Crivello P, Wang T, Gadalla SM, Paczesny S, Marsh SGE, Lee SJ, Bolon YT, Fleischhauer K. A refined model of HLA-DP permissiveness improves stratification of acute graft-versus-host disease risks after unrelated hematopoietic cell transplantation: a retrospective study from the CIBMTR. Transplant Cell Ther 2022. [DOI: 10.1016/s2666-6367(22)00191-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Barquera R, Lara-Riegos J, Ponnandai-Shanmugavel KS, Immel A, Arrieta-Bolaños E, Clayton S, Solís-Martínez R, Bravo-Acevedo A, Vázquez-Castillo TV, Hernández-Zaragoza DI, Vega-Martínez MDR, Salgado-Galicia N, Medina-Escobedo CE, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Campeche, Mexico: Campeche city and rural Campeche. Hum Immunol 2020; 81:566-568. [DOI: 10.1016/j.humimm.2019.07.281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
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Uribe-Duarte MG, Aguilar-Campos JA, Barquera R, Bravo-Acevedo A, Clayton S, Arrieta-Bolaños E, Ruíz-Corral MDJ, Hernández-Zaragoza DI, Serrano-Osuna R, Yunis EJ, Zúñiga J, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in three populations from Sonora, Mexico: Ciudad Obregón, Hermosillo and rural Sonora. Hum Immunol 2020; 81:478-481. [DOI: 10.1016/j.humimm.2019.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 11/17/2022]
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González-Medina L, Barquera R, Delgado-Aguirre H, Clayton S, Adalid-Sáinz C, Arrieta-Bolaños E, Pacheco-Ubaldo H, Hernández-Zaragoza DI, Escareño-Montiel N, Morán-Martínez J, Bravo-Acevedo A, Lona-Sánchez A, González-Martínez MDR, Jaramillo-Rodríguez Y, Salgado-Adame A, la Cruz FJD, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Durango, Mexico: Durango city and rural Durango. Hum Immunol 2020; 81:489-491. [DOI: 10.1016/j.humimm.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 01/04/2023]
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Barquera R, Bravo-Acevedo A, Clayton S, Munguía TJR, Hernández-Zaragoza DI, Adalid-Sáinz C, Arrieta-Bolaños E, Aquino-Rubio G, González-Martínez MDR, Lona-Sánchez A, Martínez-Álvarez JC, Arrazola-García MA, Delgado-Aguirre H, González-Medina L, Pacheco-Ubaldo H, Juárez-Barreto V, Benítez-Arvizu G, Escareño-Montiel N, Juárez-de la Cruz F, Jaramillo-Rodríguez Y, Salgado-Adame A, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Nuevo León, Mexico: Monterrey and rural Nuevo León. Hum Immunol 2020; 81:516-518. [DOI: 10.1016/j.humimm.2019.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022]
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Barquera R, Juárez-Nicolás F, Martínez-Álvarez JC, Ponnandai-Shanmugavel KS, Hernández-Zaragoza DI, Vázquez-Castillo TV, Arrieta-Bolaños E, Clayton S, Solís-Martínez R, Ortega-Yáñez A, Arrazola-García MA, Immel A, Bravo-Acevedo A, Vega-Martínez MDR, Benítez-Arvizu G, García-Álvarez R, Martínez-Bezies V, Escutia-González A, Juárez-Barreto V, Salgado-Galicia N, Novelo-Garza B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Chiapas, Mexico: Tuxtla Gutiérrez and rural Chiapas. Hum Immunol 2020; 81:563-565. [DOI: 10.1016/j.humimm.2019.07.285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 12/24/2022]
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Ballesteros-Romero M, Barquera R, Rodríguez-López ME, Hernández-Zaragoza DI, Goné-Vázquez I, Clayton S, Arrieta-Bolaños E, Escobedo-Ruíz A, Pantoja-Torres JA, García-Arias VE, Arellano-Prado FP, Bravo-Acevedo A, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Gómez-Navarro B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J, Acuña-Alonzo V. Genetic diversity of HLA system in two populations from Michoacán, Mexico: Morelia and rural Michoacán. Hum Immunol 2020; 81:506-509. [DOI: 10.1016/j.humimm.2019.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 11/28/2022]
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Barquera R, Hernández-Zaragoza DI, Arellano-Prado FP, Goné-Vázquez I, Clayton S, Arrieta-Bolaños E, Escobedo-Ruíz A, García-Arias VE, Bravo-Acevedo A, Rodríguez-López ME, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Gómez-Navarro B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Colima, Mexico: Colima city and rural Colima. Hum Immunol 2020; 81:513-515. [DOI: 10.1016/j.humimm.2019.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 12/30/2022]
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López Gil C, Barquera R, Pavón-Vargas MDLÁ, Ramos-de la Cruz FDR, Méndez-Mani P, Arrieta-Bolaños E, Clayton S, Hernández-Zaragoza DI, Bravo-Acevedo A, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Puebla, Mexico: Puebla city and rural Puebla. Hum Immunol 2020; 81:547-549. [DOI: 10.1016/j.humimm.2019.07.290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/14/2019] [Indexed: 11/29/2022]
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Barquera R, Martínez-Álvarez JC, Hernández-Zaragoza DI, Bravo-Acevedo A, Juárez-Nicolás F, Arriaga-Perea AJ, Vega-Martínez MDR, Ortega-Yáñez A, Benítez-Arvizu G, Arrieta-Bolaños E, Clayton S, Juárez-Cortés ED, López-Gil C, García-Álvarez R, Arrazola-García MA, Martínez-Bezies V, Juárez-Barreto V, Ramos-de la Cruz FDR, Macías-Medrano RM, Méndez-Mani P, Escutia-González A, Montiel-Hernández GD, Immel A, Pavón-Vargas MDLÁ, Salgado-Galicia N, Novelo-Garza B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in six populations from Mexico City Metropolitan Area, Mexico: Mexico City North, Mexico City South, Mexico City East, Mexico City West, Mexico City Center and rural Mexico City. Hum Immunol 2020; 81:539-543. [DOI: 10.1016/j.humimm.2019.07.297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 11/25/2022]
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Juárez-Nicolás F, Barquera R, Martínez-Álvarez JC, Hernández-Zaragoza DI, Ortega-Yáñez A, Arrieta-Bolaños E, Clayton S, Bravo-Acevedo A, Arrazola-García MA, Immel A, Juárez-Barreto V, Benítez-Arvizu G, Vega-Martínez MDR, García-Álvarez R, Martínez-Bezies V, Escutia-González AB, Díaz-López R, Guizar-López GU, Salgado-Galicia N, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in a population from Guerrero, Mexico. Hum Immunol 2020; 81:550-552. [DOI: 10.1016/j.humimm.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
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Clayton S, Barquera R, Uribe-Duarte MG, Goné Vázquez I, Zúñiga J, Arrieta-Bolaños E, Hernández-Zaragoza DI, Ruíz-Corral MDJ, Escobedo-Ruíz A, Arellano-Prado FP, García-Arias VE, Rodríguez-López ME, Bravo-Acevedo A, Sánchez-Fernández MGDJ, Aguilar-Campos JA, Serrano-Osuna R, Gómez-Navarro B, Sandoval-Sandoval MJ, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Sinaloa, Mexico: Culiacán and rural Sinaloa. Hum Immunol 2020; 81:482-484. [DOI: 10.1016/j.humimm.2019.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 01/04/2023]
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Pantoja-Torres JA, Barquera R, Ballesteros-Romero M, Bravo-Acevedo A, Arrieta-Bolaños E, Montiel-Hernández GD, Clayton S, Rodríguez-Rodríguez LI, Hernández-Zaragoza DI, Goné-Vázquez I, Escobedo-Ruíz A, García-Arias VE, Arellano-Prado FP, Rodríguez-López ME, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Gómez-Navarro B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in three populations from Guanajuato, Mexico: Guanajuato City, León and rural Guanajuato. Hum Immunol 2020; 81:510-512. [DOI: 10.1016/j.humimm.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
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Barquera R, Martínez-Álvarez JC, Trejo-Ordoz AV, Pavón-Vargas MDLÁ, Vega-Martínez MDR, Arrieta-Bolaños E, Clayton S, Ortega-Yáñez A, Juárez-Cortés ED, Juárez-Nicolás F, López-Gil C, Immel A, Arrazola-García MA, Juárez-Barreto V, Benítez-Arvizu G, Arriaga-Perea AJ, Martínez-Bezies V, Macías-Medrano RM, Ramos-de la Cruz FDR, Hernández-Zaragoza DI, Bravo-Acevedo A, Méndez-Mani P, Escutia-González AB, Montiel-Hernández GD, García-Álvarez R, Salgado-Galicia N, Novelo-Garza B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Hidalgo, Mexico: Pachuca and rural Hidalgo. Hum Immunol 2020; 81:535-538. [DOI: 10.1016/j.humimm.2019.07.293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
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Pavón-Vargas MDLÁ, Crawford MH, Barquera R, López-Gil C, Arrieta-Bolaños E, Clayton S, Hernández-Zaragoza DI, Bravo-Acevedo A, Ramos-de la Cruz FDR, Méndez-Mani P, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Tlaxcala, Mexico: Tlaxcala city and rural Tlaxcala. Hum Immunol 2020; 81:544-546. [DOI: 10.1016/j.humimm.2019.07.282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 11/30/2022]
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Medina-Escobedo CE, Barquera R, Ponnandai-Shanmugavel KS, Lara-Riegos J, Bravo-Acevedo A, Arrieta-Bolaños E, Clayton S, Hernández-Zaragoza DI, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Quintana Roo, Mexico: Cancún and rural Quintana Roo. Hum Immunol 2020; 81:573-575. [DOI: 10.1016/j.humimm.2019.07.279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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Bravo-Acevedo A, Barquera R, Arrieta-Bolaños E, Hernández-Zaragoza DI, Clayton S, Goné-Vázquez I, Escobedo-Ruíz A, Pantoja-Torres JA, Adalid-Sáinz C, Pacheco-Ubaldo H, Martínez-Álvarez JC, González-Martínez MDR, Lona-Sánchez A, González-Medina L, Escareño-Montiel N, Arrazola-García MA, Juárez-Barreto V, Benítez-Arvizu G, Delgado-Aguirre H, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Jaramillo-Rodríguez Y, Gómez-Navarro B, Salgado-Adame A, Juárez-de la Cruz F, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in a population sample from Aguascalientes, Mexico. Hum Immunol 2020; 81:519-521. [DOI: 10.1016/j.humimm.2019.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 02/08/2023]
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Goné-Vázquez I, Barquera R, Arellano-Prado FP, Hernández-Zaragoza DI, Escobedo-Ruíz A, Clayton S, Arrieta-Bolaños E, García-Arias VE, Rodríguez-López ME, Bravo-Acevedo A, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Gómez-Navarro B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Nayarit, Mexico: Tepic and rural Nayarit. Hum Immunol 2020; 81:499-501. [DOI: 10.1016/j.humimm.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
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Bravo-Acevedo A, Escobedo-Ruíz A, Barquera R, Clayton S, García-Arias VE, Arrieta-Bolaños E, Goné-Vázquez I, Hernández-Zaragoza DI, Arellano-Prado FP, Rodríguez-López ME, Sánchez-Fernández MGDJ, Sandoval-Sandoval MJ, Gómez-Navarro B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in six populations from Jalisco, Mexico: Guadalajara city, Tlajomulco, Tlaquepaque, Tonalá, Zapopan and rural Jalisco. Hum Immunol 2020; 81:502-505. [DOI: 10.1016/j.humimm.2019.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/26/2022]
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Pacheco-Ubaldo H, Adalid-Sáinz C, Barquera R, Clayton S, Arrieta-Bolaños E, Delgado-Aguirre H, González-Medina L, Hernández-Zaragoza DI, Escareño-Montiel N, Morán-Martínez J, Bravo-Acevedo A, Lona-Sánchez A, González-Martínez MDR, Jaramillo-Rodríguez Y, Salgado-Adame A, Juárez-de la Cruz F, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in three populations from Chihuahua, Mexico: Chihuahua City, Ciudad Juárez and rural Chihuahua. Hum Immunol 2020; 81:485-488. [DOI: 10.1016/j.humimm.2019.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
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Rodríguez-Munguía TJ, Barquera R, Adalid-Sáinz C, Hernández-Zaragoza DI, Arrieta-Bolaños E, Clayton S, Aquino-Rubio G, González-Martínez MDR, Pacheco-Ubaldo H, González-Medina L, Lona-Sánchez A, Bravo-Acevedo A, Delgado-Aguirre H, Escareño-Montiel N, Jaramillo-Rodríguez Y, Salgado-Adame A, Juárez-de la Cruz F, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Tamaulipas, Mexico: Ciudad Victoria and rural Tamaulipas. Hum Immunol 2020; 81:525-527. [DOI: 10.1016/j.humimm.2019.07.288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 12/16/2022]
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Lara-Riegos J, Barquera R, Castillo-Chávez OD, Medina-Escobedo CE, Hernández-Zaragoza DI, Arrieta-Bolaños E, Clayton S, Ponnandai-Shanmugavel KS, Bravo-Acevedo A, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in two populations from Yucatán, Mexico: Mérida and rural Yucatán. Hum Immunol 2020; 81:569-572. [DOI: 10.1016/j.humimm.2019.07.280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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van Balen P, Kester MGD, de Klerk W, Crivello P, Arrieta-Bolaños E, de Ru AH, Jedema I, Mohammed Y, Heemskerk MHM, Fleischhauer K, van Veelen PA, Falkenburg JHF. Immunopeptidome Analysis of HLA-DPB1 Allelic Variants Reveals New Functional Hierarchies. J I 2020; 204:3273-3282. [DOI: 10.4049/jimmunol.2000192] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/22/2023]
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29
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Arrieta-Bolaños E, Fleischhauer K. Learning the next-generation sequencing alphabet of immune reconstitution: factors determining CD8 + T-cell receptor α-chain repertoire dynamics after hematopoietic stem cell transplantation. Haematologica 2019; 104:422-425. [PMID: 30819834 DOI: 10.3324/haematol.2018.209130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen.,German Cancer Consortium, Heidelberg, Germany
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30
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Órlich-Pérez P, Moreira-Espinoza MJ, Paredes-Carias E, Vanegas-Padilla Y, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. High-resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries. HLA 2019; 91:514-529. [PMID: 29687625 DOI: 10.1111/tan.13280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 04/13/2018] [Accepted: 04/18/2018] [Indexed: 02/03/2023]
Abstract
The HLA system shows the most extensive polymorphism in the human genome. Allelic and haplotypic frequencies of HLA genes vary dramatically across human populations. Due to a complex history of migration, populations in Latin America show a broad variety of admixture proportions, usually varying not only between countries, but also within countries. Knowledge of HLA allele and haplotype frequencies is essential for medical fields such as transplantation, but also serves as a means to assess genetic diversity and ancestry in human populations. Here, we have determined high-resolution HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a sample of 713 healthy subjects from three Mestizo populations, one population of African descent, and Amerindians of five different groups from Costa Rica and Nicaragua and compared their profiles to a large set of indigenous populations from Iberia, Sub-Saharan Africa, and the Americas. Our results show a great degree of allelic and haplotypic diversity within and across these populations, with most extended haplotypes being private. Mestizo populations show alleles and haplotypes of putative European, Amerindian, and Sub-Saharan African origin, albeit with differential proportions. Despite some degree of gene flow, Amerindians and Afro-descendants show great similarity to other Amerindian and West African populations, respectively. This is the first comprehensive study reporting high-resolution HLA diversity in Central America, and its results will shed light into the genetic history of this region while also supporting the development of medical programs for organ and stem cell transplantation.
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Affiliation(s)
- E Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany.,Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica
| | | | - J E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - P Órlich-Pérez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.,División de Banco de Células Madre, Laboratorio Clínico, Hospital San Juan de Dios, San José, Costa Rica
| | - M J Moreira-Espinoza
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - E Paredes-Carias
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - Y Vanegas-Padilla
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - L Salazar-Sánchez
- Escuela de Medicina, Universidad de Costa Rica, San José, Costa Rica
| | - J A Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - S G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Cancer Institute, University College London, London, UK
| | - B E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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31
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. 4-Locus high-resolution HLA allele and haplotype frequencies in Amerindians from Costa Rica. Hum Immunol 2019; 80:409-410. [PMID: 31128907 DOI: 10.1016/j.humimm.2019.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/29/2022]
Abstract
A total of 125 Costa Ricans of Amerindian descent were genotyped at high-resolution for the human leukocyte antigen loci HLA-A, -B, -C, and -DRB1 using sequence-based typing methods. The respective allele and extended haplotype frequencies, as well as Hardy-Weinberg proportions were calculated. The most frequent extended haplotype identified was A*24:02:01-B*40:02:01-C*03:05-DRB1*04:07:01G, with an estimated frequency of 8.26%. A deviation from Hardy-Weinberg Equilibrium was detected at the DRB1 locus (p = 0.099). The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database under the population name "Costa Rica Amerindians" and the identifier AFN3608.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany; Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Jeremy E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | | | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Bronwen E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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32
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Órlich-Pérez P, Arrieta-Molina G, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. 5-Locus high-resolution HLA allele and haplotype frequencies in Costa Ricans from the Central Valley. Hum Immunol 2019; 80:413-414. [PMID: 31128906 DOI: 10.1016/j.humimm.2019.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/18/2022]
Abstract
A total of 221 Costa Rican Mestizos from the Central Valley were genotyped at high-resolution for the human leukocyte antigen loci HLA-A, -B, -C, -DRB1, and -DQB1 using sequence-based typing methods. The respective allele and extended haplotype frequencies, as well as Hardy-Weinberg proportions were calculated. The most frequent extended haplotype identified was A*24:02:01-B*40:02:01-C*03:05-DRB1*08:02:01-DQB1*04:02:01, with an estimated frequency of 2.04%. No deviation from Hardy-Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database under the population name "Costa Rica Central Valley Mestizo" and the identifier AFN3606.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany; Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Jeremy E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Priscilla Órlich-Pérez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica; División de Banco de Células Madre, Laboratorio Clínico, Hospital San Juan de Dios, San José, Costa Rica
| | | | | | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Bronwen E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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33
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Arrieta-Molina G, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. 4-Locus high-resolution HLA allele and haplotype frequencies in Costa Ricans from Guanacaste. Hum Immunol 2019; 80:415-416. [PMID: 31126638 DOI: 10.1016/j.humimm.2019.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 10/26/2022]
Abstract
A total of 110 Costa Rican Mestizos from the province of Guanacaste were genotyped at high-resolution for the human leukocyte antigen loci HLA-A, -B, -C, and -DRB1 using sequence-based typing methods. The respective allele and extended haplotype frequencies, as well as Hardy-Weinberg proportions were calculated. The most frequent extended haplotype identified was A*24:02:01-B*35:12:01-C*04:01:01-DRB1*04:07:01G, with an estimated frequency of 2.73%. No deviation from Hardy-Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database under the population name "Costa Rica Guanacaste Mestizo" and the identifier AFN3609.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany; Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Jeremy E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | | | | | - J Alejandro Madrigal
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Bronwen E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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Arrieta-Bolaños E, Madrigal-Sánchez JJ, Stein JE, Moreira-Espinoza MJ, Paredes-Carias E, Vanegas-Padilla Y, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. 4-Locus high-resolution HLA allele and haplotype frequencies in admixed population from Nicaragua. Hum Immunol 2019; 80:417-418. [PMID: 31122740 DOI: 10.1016/j.humimm.2019.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
A total of 155 Nicaraguan Mestizos from across the country were genotyped at high-resolution for the human leukocyte antigen loci HLA-A, -B, -C, and -DRB1 using sequence-based typing methods. The respective allele and extended haplotype frequencies, as well as Hardy-Weinberg proportions were calculated. The most frequent extended haplotype identified was A*24:02:01-B*40:02:01-C*03:05-DRB1*04:07:01G, with an estimated frequency of 2.26%. No deviation from Hardy-Weinberg Equilibrium was detected at any of the loci studied. The HLA genotypic data of the population sample reported here are available publicly in the Allele Frequencies Net Database under the population name "Nicaragua Mestizo" and the identifier AFN3610.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital, Essen, Germany; Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica.
| | | | - Jeremy E Stein
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | | | - Edel Paredes-Carias
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | - Yondra Vanegas-Padilla
- Departamento de Ciencias Morfológicas, Universidad Nacional Autónoma de Nicaragua, León, Nicaragua
| | | | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Bronwen E Shaw
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Center for International Blood and Marrow Transplant Research, Department of Medicine, Medical College of Wisconsin, Milwaukee, USA
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35
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Crivello P, Ahci M, Maaßen F, Wossidlo N, Arrieta-Bolaños E, Heinold A, Lange V, Falkenburg JHF, Horn PA, Fleischhauer K, Heinrichs S. Multiple Knockout of Classical HLA Class II β-Chains by CRISPR/Cas9 Genome Editing Driven by a Single Guide RNA. J Immunol 2019; 202:1895-1903. [PMID: 30700588 DOI: 10.4049/jimmunol.1800257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 12/11/2018] [Indexed: 12/22/2022]
Abstract
Comprehensive knockout of HLA class II (HLA-II) β-chain genes is complicated by their high polymorphism. In this study, we developed CRISPR/Cas9 genome editing to simultaneously target HLA-DRB, -DQB1, and -DPB1 through a single guide RNA recognizing a conserved region in exon 2. Abrogation of HLA-II surface expression was achieved in five different HLA-typed, human EBV-transformed B lymphoblastoid cell lines (BLCLs). Next-generation sequencing-based detection confirmed specific genomic insertion/deletion mutations with 99.5% penetrance in sorted cells for all three loci. No alterations were observed in HLA-I genes, the HLA-II peptide editor HLA-DMB, or its antagonist HLA-DOB, showing high on-target specificity. Transfection of full-length HLA-DPB1 mRNA into knockout BLCLs fully restored HLA-DP surface expression and recognition by alloreactive human CD4 T cells. The possibility to generate single HLA-II-expressing BLCLs by one-shot genome editing opens unprecedented opportunities for mechanistically dissecting the interaction of individual HLA variants with the immune system.
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Affiliation(s)
- Pietro Crivello
- Institute of Experimental Cellular Therapy, University Hospital Essen, 45147 Essen, Germany
| | - Müberra Ahci
- Institute of Experimental Cellular Therapy, University Hospital Essen, 45147 Essen, Germany
| | - Fabienne Maaßen
- Institute of Experimental Cellular Therapy, University Hospital Essen, 45147 Essen, Germany
| | - Natalie Wossidlo
- Institute for Transfusion Medicine, University Hospital Essen, 45147 Essen, Germany
| | | | - Andreas Heinold
- Institute for Transfusion Medicine, University Hospital Essen, 45147 Essen, Germany
| | | | | | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, 45147 Essen, Germany
| | - Katharina Fleischhauer
- Institute of Experimental Cellular Therapy, University Hospital Essen, 45147 Essen, Germany;
| | - Stefan Heinrichs
- Institute for Transfusion Medicine, University Hospital Essen, 45147 Essen, Germany;
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36
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Meurer T, Arrieta-Bolaños E, Metzing M, Langer MM, van Balen P, Falkenburg JHF, Beelen DW, Horn PA, Fleischhauer K, Crivello P. Dissecting Genetic Control of HLA-DPB1 Expression and Its Relation to Structural Mismatch Models in Hematopoietic Stem Cell Transplantation. Front Immunol 2018; 9:2236. [PMID: 30344521 PMCID: PMC6183238 DOI: 10.3389/fimmu.2018.02236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/10/2018] [Indexed: 11/22/2022] Open
Abstract
HLA expression levels have been suggested to be genetically controlled by single nucleotide polymorphisms (SNP) in the untranslated regions (UTR), and expression variants have been associated with the outcome of chronic viral infection and hematopoietic stem cell transplantation (HSCT). In particular, the 3′UTR rs9277534-G/A SNP in HLA-DPB1 has been associated with graft-versus-host-disease after HSCT (Expression model); however its relevance in different immune cells and its mode of action have not been systematically addressed. In addition, there is a strong though not complete overlap between the rs9277534-G/A SNP and structural HLA-DPB1 T cell epitope (TCE) groups which have also been associated with HSCT outcome (TCE Structural model). Here we confirm and extend previous findings of significantly higher HLA-DPB1 expression in B cell lines, unstimulated primary B cells, and monocytes homozygous for rs9277534-G compared to those homozygous for rs9277534-A. However, these differences were abrogated by interferon-γ stimulation or differentiation into dendritic cells. We identify at least seven 3′UTR rs9277534-G/A haplotypes differing by a total of 37 SNP, also characterized by linkage to length variants of a short tandem repeat (STR) in intron 2 and TCE group assignment. 3′UTR mapping did not show any significant differences in post-transcriptional regulation assessed by luciferase assays between two representative rs9277534-G/A haplotypes for any of eight overlapping fragments. Moreover, no evidence for alternative splicing associated with the intron 2 STR was obtained by RT-PCR. In an exemplary cohort of 379 HLA-DPB1 mismatched donor-recipient pairs, risk prediction by the Expression model and the Structural TCE model was 36.7% concordant, with the majority of discordances due to non-applicability of the Expression model. HLA-DPB1 from different TCE groups expressed in the absence of the 3′UTR at similar levels by transfected HeLa cells elicited significantly different mean alloreactive CD4+ T-cell responses, as assessed by CD137 upregulation assays in 178 independent cultures. Taken together, our data provide new insights into the cell type-specific and mechanistic basis of the association between the rs9277534-G/A SNP and HLA-DPB1 expression, and show that, despite partial overlap between both models in HSCT risk-prediction, differential alloreactivity determined by the TCE structural model occurs independently from HLA-DPB1 differential expression.
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Affiliation(s)
- Thuja Meurer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | | | - Maximilian Metzing
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Mona-May Langer
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Dietrich W Beelen
- Department of Bone Marrow Transplantation, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,Deusches Konsortium für Translationale Krebsforschung (DKTK), Heidelberg, Germany
| | - Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
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Arrieta-Bolaños E, Crivello P, Metzing M, Meurer T, Ahci M, Rytlewski J, Vignali M, Yusko E, van Balen P, Horn PA, Falkenburg JHF, Fleischhauer K. Alloreactive T Cell Receptor Diversity against Structurally Similar or Dissimilar HLA-DP Antigens Assessed by Deep Sequencing. Front Immunol 2018. [PMID: 29520276 PMCID: PMC5827552 DOI: 10.3389/fimmu.2018.00280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
T cell alloreactivity is mediated by a self-human leukocyte antigen (HLA)-restricted T cell receptor (TCR) repertoire able to recognize both structurally similar and dissimilar allogeneic HLA molecules (i.e., differing by a single or several amino acids in their peptide-binding groove). We hypothesized that thymic selection on self-HLA molecules could have an indirect impact on the size and diversity of the alloreactive response. To test this possibility, we used TCR Vβ immunophenotyping and immunosequencing technology in a model of alloreactivity between self-HLA selected T cells and allogeneic HLA-DPB1 (DPB1) differing from self-DPB1*04:02 by a single (DPB1*02:01) or several (DPB1*09:01) amino acids in the peptide-binding groove. CD4+ T cells from three different self-DPB1*04:01,*04:02 individuals were stimulated with HeLa cells stably transduced with the relevant peptide processing machinery, co-stimulatory molecules, and HLA-DP. Flow cytometric quantification of the DPB1-specific T cell response measured as upregulation of the activation marker CD137 revealed significantly lower levels of alloreactivity against DPB1*02:01 compared with DPB1*09:01 (mean CD4+CD137+ frequency 35.2 ± 9.9 vs. 61.5 ± 7.7%, respectively, p < 0.0001). These quantitative differences were, however, not reflected by differences in the breadth of the alloreactive response at the Vβ level, with both alloantigens eliciting specific responses from all TCR-Vβ specificities tested by flow cytometry, albeit with higher levels of reactivity from most Vβ specificities against DPB1*09:01. In line with these observations, TCRB-CDR3 immunosequencing showed no significant differences in mean clonality of sorted CD137+CD4+ cells alloreactive against DPB1*02:01 or DPB1*09:01 [0.39 (0.36–0.45) and 0.39 (0.30–0.46), respectively], or in the cumulative frequencies of the 10 most frequent responding clones (55–67 and 58–62%, respectively). Most of the clones alloreactive against DPB1*02:01 (68.3%) or DPB1*09:01 (75.3%) were characterized by low-abundance (i.e., they were not appreciable among the pre-culture T cells). Interestingly, however, their cumulative frequency was lower against DPB1*02:01 compared with DPB1*09:01 (mean cumulative frequency 35.3 vs. 50.6%, respectively). Our data show that, despite lower levels of alloreactivity, a similar clonal diversity can be elicited by structurally similar compared with structurally dissimilar HLA-DPB1 alloantigens and demonstrate the power of TCRB immunosequencing in unraveling subtle qualitative changes not appreciable by conventional methods.
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Affiliation(s)
| | - Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Maximilian Metzing
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Thuja Meurer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Müberra Ahci
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | | | | | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A Horn
- Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | | | - Katharina Fleischhauer
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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Arroyo J, Salazar-Sánchez L, Jiménez-Cruz G, Chaverri P, Arrieta-Bolaños E, Morera B. Prevalence and geographic distribution of haemophilia in Costa Rica. Hamostaseologie 2017. [DOI: 10.1055/s-0037-1619065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
SummaryHaemophilia is the most frequent hereditary haemorrhagic illness and it is due to the deficiency of coagulation factors VIII (haemophilia A, HA) or IX (haemophilia B, HB).The prevalence of this disease varies according to the country, those having better survival rates having also higher prevalences. Specifically in Costa Rica, there are around 130 HA and 30 HB families. This study reports the prevalence and a spatial distribution analysis of both types of the disease in this country. The prevalence of haemophilia in this country is 7 cases per 100 000 men, for HA it is 6 cases per 100 000 and for HB it is 1 case per 100 000 male inhabitants. The prevalence of this disease is low when compared with other populations. This low prevalence could be due to the many patients that have died because of infection with human immunodeficiency virus during the 1980s. The prevalence of haemophilia in Costa Rica is almost one half of that present in developed countries. Nevertheless, the ratio between HA and HB follows world tendency: 5 : 1. In this study, nationwide geographical distribution maps were drawn in order to visualize the origin of severe cases and how this influences the pattern of distribution for both types of haemophilia. By means of these maps, it was possible to state that there is no association between the sites of maximum prevalence of mutated alleles and ethnicity. With this study, haemophilia prevalence distribution maps can be used to improve efforts for the establishment of hemophilia clinics or specialized health centers in those areas which hold the highest prevalences in this country. Also, this knowledge can be applied to improve treatment skills and offer the possibility of developing focused genetic counseling for these populations.
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39
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Arrieta-Bolaños E, Mayor NP, Marsh SGE, Madrigal JA, Apperley JF, Kirkland K, Mackinnon S, Marks DI, McQuaker G, Perry J, Potter MN, Russell NH, Thomson K, Shaw BE. Polymorphism in TGFB1 is associated with worse non-relapse mortality and overall survival after stem cell transplantation with unrelated donors. Haematologica 2015; 101:382-90. [PMID: 26611472 DOI: 10.3324/haematol.2015.134999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/20/2015] [Indexed: 12/12/2022] Open
Abstract
Transforming growth factor β-1, encoded by the TGFB1 gene, is a cytokine that plays a central role in many physiological and pathogenic processes. We have sequenced TGFB1 regulatory region and assigned allelic genotypes in a large cohort of hematopoietic stem cell transplantation patients and donors. In this study, we analyzed 522 unrelated donor-patient pairs and examined the combined effect of all the common polymorphisms in this genomic region. In univariate analysis, we found that patients carrying a specific allele, 'p001', showed significantly reduced overall survival (5-year overall survival 30.7% for p001/p001 patients vs. 41.6% others; P=0.032) and increased non-relapse mortality (1-year non-relapse mortality: 39.0% vs. 25.4%; P=0.039) after transplantation. In multivariate analysis, the presence of a p001/p001 genotype in patients was confirmed as an independent factor for reduced overall survival [hazard ratio=1.53 (1.04-2.24); P=0.031], and increased non-relapse mortality [hazard ratio=1.73 (1.06-2.83); P=0.030]. In functional experiments we found a trend towards a higher percentage of surface transforming growth factor β-1-positive regulatory T cells after activation when the cells had a p001 allele (P=0.07). Higher or lower production of transforming growth factor β-1 in the inflammatory context of hematopoietic stem cell transplantation may influence the development of complications in these patients. Findings indicate that TGFB1 genotype could potentially be of use as a prognostic factor in hematopoietic stem cell transplantation risk assessment algorithms.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Anthony Nolan Research Institute, London, UK Cancer Institute, University College London, UK Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica
| | - Neema P Mayor
- Anthony Nolan Research Institute, London, UK Cancer Institute, University College London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK Cancer Institute, University College London, UK
| | - J Alejandro Madrigal
- Anthony Nolan Research Institute, London, UK Cancer Institute, University College London, UK
| | | | | | - Stephen Mackinnon
- Department of Haematology, University College London, Royal Free Campus, UK
| | - David I Marks
- Adult BMT Unit, University Hospitals Bristol NHS Trust, Bristol, UK
| | - Grant McQuaker
- Bone Marrow Transplant Unit, Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - Julia Perry
- BSBMT Data Registry, Guy's Hospital, London, UK
| | | | - Nigel H Russell
- Centre for Clinical Haematology, Nottingham University Hospital, and Academic Haematology, Nottingham University Hospitals, UK
| | - Kirsty Thomson
- Department of Haematology, University College Hospital, London, UK
| | - Bronwen E Shaw
- Anthony Nolan Research Institute, London, UK Cancer Institute, University College London, UK
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Arrieta-Bolaños E, Madrigal JA, Shaw BE. Novel alleles of the transforming growth factor β-1 regulatory region and exon 1. ACTA ACUST UNITED AC 2015; 85:484-91. [PMID: 25808355 DOI: 10.1111/tan.12555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/30/2015] [Accepted: 02/25/2015] [Indexed: 11/26/2022]
Abstract
Transforming growth factor β-1, encoded by the TGFB1 gene, is a cytokine that plays a central role in many physiologic and pathogenic processes with pleiotropic effects. Regulatory activity for this gene has been shown for 3.0 kb between positions -2665 and +423 from its translational start site. At least 17 TGFB1 regulatory region and exon 1 alleles have been defined on the basis of 18 polymorphic sites. Polymorphisms in TGFB1's regulatory region have been associated with differential levels of expression of this cytokine and to genetic risk in cancer and transplantation. In this report, we present 19 novel TGFB1 regulatory region and exon 1 alleles: p018-p036. Amplification of TGFB1's regulatory region was performed with an in-house protocol, and novel alleles were defined by either allele-specific amplification and/or molecular cloning of the amplicons, followed by sequencing in isolation. Three of these novel alleles (p018, p019, and p020) are shown to be formed by novel combinations of the aforementioned known polymorphic positions. Another 16 novel alleles are shown to carry additional known and unknown single-nucleotide polymorphisms. Polymorphism in TGFB1's regulatory region could have an impact on important processes, including embryogenesis, hematopoiesis, carcinogenesis, angiogenesis, fibrosis, immune responses, and transplantation, making its characterization necessary.
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Affiliation(s)
- E Arrieta-Bolaños
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; Cancer Institute, University College London, Royal Free Campus, London, UK; Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José, Costa Rica
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Arrieta-Bolaños E, McWhinnie AJ, Madrigal-Sánchez JJ, Calvo L, Salazar-Sánchez L, Madrigal JA, Marsh SGE, Shaw BE. A novel HLA-A allele,A*74:23, identified in an individual from Costa Rica. ACTA ACUST UNITED AC 2014; 84:583-4. [DOI: 10.1111/tan.12470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/01/2014] [Indexed: 11/29/2022]
Affiliation(s)
- E. Arrieta-Bolaños
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
- Royal Free Campus, Cancer Institute; University College London; London UK
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA); Universidad de Costa Rica; San José Costa Rica
| | - A. J. McWhinnie
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
| | - J. J. Madrigal-Sánchez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA); Universidad de Costa Rica; San José Costa Rica
| | - L. Calvo
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA); Universidad de Costa Rica; San José Costa Rica
| | - L. Salazar-Sánchez
- Centro de Investigaciones en Hematología y Trastornos Afines (CIHATA); Universidad de Costa Rica; San José Costa Rica
| | - J. A. Madrigal
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
- Royal Free Campus, Cancer Institute; University College London; London UK
| | - S. G. E. Marsh
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
- Royal Free Campus, Cancer Institute; University College London; London UK
| | - B. E. Shaw
- Anthony Nolan Research Institute; Royal Free Hospital; London UK
- Haemato-Oncology Research Unit, Division of Molecular Pathology; The Institute of Cancer Research; London UK
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Arrieta-Bolaños E, Alejandro Madrigal J, Shaw BE. Transforming growth factor-β1 polymorphisms and the outcome of hematopoietic stem cell transplantation. Int J Immunogenet 2012; 39:192-202. [DOI: 10.1111/j.1744-313x.2012.01089.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Arrieta-Bolaños E, Maldonado-Torres H, Dimitriu O, Hoddinott MA, Fowles F, Shah A, Órlich-Pérez P, McWhinnie AJ, Alfaro-Bourrouet W, Buján-Boza W, Little AM, Salazar-Sánchez L, Madrigal JA. HLA-A, -B, -C, -DQB1, and -DRB1,3,4,5 allele and haplotype frequencies in the Costa Rica Central Valley Population and its relationship to worldwide populations. Hum Immunol 2011; 72:80-6. [DOI: 10.1016/j.humimm.2010.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 09/27/2010] [Accepted: 10/04/2010] [Indexed: 10/19/2022]
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Arroyo J, Salazar-Sánchez L, Jiménez-Cruz G, Chaverri P, Arrieta-Bolaños E, Morera B. Prevalence and geographic distribution of haemophilia in Costa Rica. Hamostaseologie 2010; 30 Suppl 1:S28-S31. [PMID: 21042672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
Haemophilia is the most frequent hereditary haemorrhagic illness and it is due to the deficiency of coagulation factors VIII (haemophilia A, HA) or IX (haemophilia B, HB). The prevalence of this disease varies according to the country, those having better survival rates having also higher prevalences. Specifically in Costa Rica, there are around 130 HA and 30 HB families. This study reports the prevalence and a spatial distribution analysis of both types of the disease in this country. The prevalence of haemophilia in this country is 7 cases per 100000 men, for HA it is 6 cases per 100000 and for HB it is 1 case per 100000 male inhabitants. The prevalence of this disease is low when compared with other populations. This low prevalence could be due to the many patients that have died because of infection with human immunodeficiency virus during the 1980s. The prevalence of haemophilia in Costa Rica is almost one half of that present in developed countries. Nevertheless, the ratio between HA and HB follows world tendency: 5:1. In this study, nationwide geographical distribution maps were drawn in order to visualize the origin of severe cases and how this influences the pattern of distribution for both types of haemophilia. By means of these maps, it was possible to state that there is no association between the sites of maximum prevalence of mutated alleles and ethnicity. With this study, haemophilia prevalence distribution maps can be used to improve efforts for the establishment of hemophilia clinics or specialized health centers in those areas which hold the highest prevalences in this country. Also, this knowledge can be applied to improve treatment skills and offer the possibility of developing focused genetic counseling for these populations.
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Affiliation(s)
- J Arroyo
- University of Costa Rica, Centre for Research in Haematology and Related Disorders (CIHATA).
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