1
|
Tan MH, Tiedje KE, Feng Q, Zhan Q, Pascual M, Shim H, Chan YB, Day KP. A paradoxical population structure of var DBLα types in Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565723. [PMID: 37986738 PMCID: PMC10659346 DOI: 10.1101/2023.11.05.565723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The var multigene family encodes the P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology of P. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBLα-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBLα types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm, cUps, we performed an in silico exploration of DBLα conservation through time and space in Africa. In all three ups groups, the population structure of DBLα types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBLα types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBLα types within each isolate DBLα repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBLα types in Africa.
Collapse
Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Kathryn E Tiedje
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Qian Feng
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Qi Zhan
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Heejung Shim
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Yao-Ban Chan
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Karen P Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| |
Collapse
|
2
|
DeGiorgio M, Szpiech ZA. A spatially aware likelihood test to detect sweeps from haplotype distributions. PLoS Genet 2022; 18:e1010134. [PMID: 35404934 PMCID: PMC9022890 DOI: 10.1371/journal.pgen.1010134] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 04/21/2022] [Accepted: 03/04/2022] [Indexed: 01/13/2023] Open
Abstract
The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the “width” of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics, though strong signals in low-recombination regions merit extra scrutiny. As a positive control, we apply it to two well-studied human populations from the 1000 Genomes Project and examine haplotype frequency spectrum patterns at the LCT and MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software. Identifying regions of the genome that contain adaptive variation is of fundamental interest in evolutionary biology, providing insight into an organism’s history and biology. When positive selection is recent or ongoing, we expect to find genomic patterns such as high frequency haplotypes and low genetic diversity in the vicinity of the adaptive locus. Here we develop a statistic to identify these regions based on distortions of the haplotype frequency spectrum from a background distribution. We evaluate the performance of this statistic under numerous realistic settings of interest to empiricists and demonstrate its superior performance relative to other haplotype-based selection statistics. We also apply this statistic to real population-genetic data. As a positive control, we explore two well-studied loci, LCT and MHC, in a European and an African human population that show strong evidence for selection. We also apply this statistic to the genomes of an urban brown rat population, where we uncover evidence for adaptation in olfactory perception genes. We release user-friendly software implementing this statistic.
Collapse
Affiliation(s)
- Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida, United States of America
- * E-mail: (MD); (ZAS)
| | - Zachary A. Szpiech
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (MD); (ZAS)
| |
Collapse
|
3
|
Di D, Nunes JM, Jiang W, Sanchez-Mazas A. Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules. Mol Biol Evol 2021; 38:1580-1594. [PMID: 33320202 PMCID: PMC8355449 DOI: 10.1093/molbev/msaa325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.
Collapse
Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Jose Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
| |
Collapse
|
4
|
Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
Collapse
Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| |
Collapse
|
5
|
Langton DJ, Bourke SC, Lie BA, Reiff G, Natu S, Darlay R, Burn J, Echevarria C. The influence of HLA genotype on the severity of COVID-19 infection. HLA 2021; 98:14-22. [PMID: 33896121 PMCID: PMC8251294 DOI: 10.1111/tan.14284] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/19/2021] [Indexed: 12/17/2022]
Abstract
The impact of COVID‐19 varies markedly, not only between individual patients but also between different populations. We hypothesised that differences in HLA genes might influence this variation. Using next generation sequencing, we analysed the class I and class II classical HLA genes of 147 individuals of European descent experiencing variable clinical outcomes following COVID‐19 infection. Forty‐nine of these patients were admitted to hospital with severe respiratory disease. They had no significant pre‐existing comorbidities. We compared the results to those obtained from a group of 69 asymptomatic hospital workers who evidence of COVID exposure based on blood antibody testing. Allele frequencies in both the severe and asymptomatic groups were compared to local and national healthy controls with adjustments made for age and sex. With the inclusion of hospital staff who had reported localised symptoms only (limited to loss of smell/taste, n = 13) or systemic symptoms not requiring hospital treatment (n = 16), we carried out ordinal logistic regression modelling to determine the relative influence of age, BMI, sex and the presence of specific HLA genes on symptomatology. We found a significant difference in the allele frequency of HLA‐DRB1*04:01 in the severe patient compared to the asymptomatic staff group (5.1% vs. 16.7%, P = .003 after adjustment for age and sex). There was a significantly lower frequency of the haplotype DQA1*01:01‐DQB1*05:01‐DRB1*01:01 in the asymptomatic group compared to the background population (P = .007). Ordinal logistic regression modelling confirmed the significant influence of DRB1*04:01 on the clinical severity of COVID‐19 observed in the cohorts. These alleles are found in greater frequencies in the North Western European population. This regional study provides evidence that HLA genotype influences clinical outcome in COVID‐19 infection. Validation studies must take account of the complex genetic architecture of the immune system across different geographies and ethnicities.
Collapse
Affiliation(s)
- David J Langton
- ExplantLab, The Biosphere, Newcastle Helix, Newcastle-upon-Tyne, UK
| | - Stephen C Bourke
- Northumbria Healthcare NHS Trust, North Tyneside General Hospital, North Shields, Tyne and Wear, UK
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo, Oslo, Norway
| | | | | | - Rebecca Darlay
- Newcastle University Translational and Clinical Research Institute, International Centre for Life (for John Burn) and Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, for Rebecca Darlay, Newcastle-upon-Tyne, UK
| | - John Burn
- Newcastle University Translational and Clinical Research Institute, International Centre for Life (for John Burn) and Population & Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, for Rebecca Darlay, Newcastle-upon-Tyne, UK
| | - Carlos Echevarria
- Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| |
Collapse
|
6
|
Harris AM, DeGiorgio M. A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data. Mol Biol Evol 2021; 37:3023-3046. [PMID: 32392293 PMCID: PMC7530616 DOI: 10.1093/molbev/msaa115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
Collapse
Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, PA.,Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
| |
Collapse
|
7
|
Valley-Omar Z, Maart S, Seele K, Gray CM. Characterization of the novel HLA-DQB1*05:272 allele in a South African patient by next-generation sequencing. HLA 2020; 97:173-174. [PMID: 33219591 DOI: 10.1111/tan.14143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/09/2023]
Abstract
HLA-DQB1*05:272 has a single transversion compared to the most similar variant, HLA-DQB1*05:01:01 in IPD-IMGT/HLA database.
Collapse
Affiliation(s)
- Ziyaad Valley-Omar
- Laboratory of Tissue Immunology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Shireen Maart
- Laboratory of Tissue Immunology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Karen Seele
- Division of Cardio-Thoracic Surgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Clive M Gray
- Laboratory of Tissue Immunology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.,Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
8
|
Souza AS, Sonon P, Paz MA, Tokplonou L, Lima THA, Porto IOP, Andrade HS, Silva NDSB, Veiga-Castelli LC, Oliveira MLG, Sadissou IA, Massaro JD, Moutairou KA, Donadi EA, Massougbodji A, Garcia A, Ibikounlé M, Meyer D, Sabbagh A, Mendes-Junior CT, Courtin D, Castelli EC. Hla-C genetic diversity and evolutionary insights in two samples from Brazil and Benin. HLA 2020; 96:468-486. [PMID: 32662221 DOI: 10.1111/tan.13996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function because it also interacts with Killer-cell immunoglobulin-like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, are poorly addressed, and few population-based studies explored the HLA-C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA-C diversity, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA-C promoter and 3'UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3'UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in the HLA-C leader peptide, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA-C locus in both populations.
Collapse
Affiliation(s)
- Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paulin Sonon
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Léonidas Tokplonou
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France.,Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nayane Dos S B Silva
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ibrahim Abiodoun Sadissou
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin
| | - André Garcia
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo (USP), São Paulo, Brazil
| | - Audrey Sabbagh
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - David Courtin
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| |
Collapse
|
9
|
Barquera R, Collen E, Di D, Buhler S, Teixeira J, Llamas B, Nunes JM, Sanchez-Mazas A. Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide. HLA 2020; 96:277-298. [PMID: 32475052 PMCID: PMC7300650 DOI: 10.1111/tan.13956] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022]
Abstract
We report detailed peptide‐binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV‐1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide‐binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV‐1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA‐A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV‐1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.
Collapse
Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Evelyn Collen
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia
| | - Da Di
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - João Teixeira
- Australian Centre for Ancient DNA (ACAD), Department of Genetics and Evolution, The University of Adelaide, Adelaide, South Australia, Australia.,School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- School of Biological Sciences, Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia.,The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - José M Nunes
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| |
Collapse
|
10
|
Guerra SG, Hamilton-Jones S, Brown CJ, Navarrete CV, Chong W. Next generation sequencing of 11 HLA loci characterises a diverse UK cord blood bank. Hum Immunol 2020; 81:269-279. [PMID: 32305144 DOI: 10.1016/j.humimm.2020.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 12/16/2022]
Abstract
The introduction of next generation sequencing (NGS) for stem cell donor registry typing has contributed to faster identification of compatible stem cell donors. However, the successful search for a matched unrelated donor for some patient groups is still affected by their ethnicity. In this study, DNA samples from 714 National Health Service (NHS) Cord Blood Bank donors were typed for HLA-A, -B, -C, -DRB1, -DRB345, -DQA1, -DQB1, -DPA1 and -DPB1 by NGS. Analysis of the ethnic diversity showed a high level of diversity, with the cohort comprising of 62.3% European and 37.7% of either multi-ethnic or non-European donors, of which 12.3% were multi-ethnic. The HLA diversity was further confirmed using PyPop analysis, 405 distinct alleles were observed in the overall NHS-CBB cohort, of which 37 alleles are non-CWD, including A*31:14N, B*35:68:02, C*14:23 and DQA1*05:10. Furthermore, HLA-DQA1 and HLA-DPA1 analysis showed 12% and 10%, respectively, of the alleles currently submitted to IMGT, confirming further diversity of the NHS-CBB cohort. The application of 11 HLA loci resolution by NGS revealed a high level of diversity in the NHS-CBB cohort. The incorporation of this data coupled with ethnicity data could lead to improved donor selection, contributing to better clinical outcomes for patients.
Collapse
Affiliation(s)
- Sandra G Guerra
- National Histocompatibility & Immunogenetics Service Development Laboratory, National Health Service Blood and Transplant (NHSBT), Colindale, London, UK
| | - Siobhan Hamilton-Jones
- National Histocompatibility & Immunogenetics Service Development Laboratory, National Health Service Blood and Transplant (NHSBT), Colindale, London, UK
| | - Colin J Brown
- Histocompatibility & Immunogenetics Laboratory, National Health Service Blood and Transplant (NHSBT), Colindale, London, UK; Faculty of Life Sciences and Medicine, King College London, UK
| | - Cristina V Navarrete
- National Histocompatibility & Immunogenetics Service Development Laboratory, National Health Service Blood and Transplant (NHSBT), Colindale, London, UK; Division of Infection and Immunity, University College London, London, UK
| | - Winnie Chong
- National Histocompatibility & Immunogenetics Service Development Laboratory, National Health Service Blood and Transplant (NHSBT), Colindale, London, UK.
| |
Collapse
|
11
|
Assessment by Extended-Coverage Next-Generation Sequencing Typing of DPA1 and DPB1 Mismatches in Siblings Matching at HLA-A, -B, -C, -DRB1, and -DQ Loci. Biol Blood Marrow Transplant 2019; 25:2507-2509. [DOI: 10.1016/j.bbmt.2019.07.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 01/28/2023]
|
12
|
Goeury T, Creary LE, Fernandez-Vina MA, Tiercy JM, Nunes JM, Sanchez-Mazas A. Mandenka from Senegal: Next Generation Sequencing typings reveal very high frequencies of particular HLA class II alleles and haplotypes. HLA 2019; 91:148-150. [PMID: 29280562 DOI: 10.1111/tan.13197] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 12/19/2017] [Indexed: 01/10/2023]
Affiliation(s)
- T Goeury
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - L E Creary
- Stanford University, School of Medicine, Palo Alto, California
| | | | - J-M Tiercy
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Geneva University Hospital, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - J M Nunes
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - A Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, AGP Laboratory, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| |
Collapse
|
13
|
Goeury T, Creary LE, Brunet L, Galan M, Pasquier M, Kervaire B, Langaney A, Tiercy JM, Fernández-Viña MA, Nunes JM, Sanchez-Mazas A. Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well-documented population from sub-Saharan Africa. HLA 2019; 91:36-51. [PMID: 29160618 PMCID: PMC5767763 DOI: 10.1111/tan.13180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/01/2017] [Accepted: 11/15/2017] [Indexed: 01/06/2023]
Abstract
With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.
Collapse
Affiliation(s)
- T Goeury
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - L Brunet
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M Galan
- INRA, UMR 1062 CBGP, avenue du Campus Agropolis, Montferrier sur Lez, France
| | - M Pasquier
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - B Kervaire
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - A Langaney
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - J-M Tiercy
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland.,Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospital, Geneva, Switzerland
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - J M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - A Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| |
Collapse
|
14
|
González-Quezada BA, Creary LE, Munguia-Saldaña AJ, Flores-Aguilar H, Fernández-Viña MA, Gorodezky C. Exploring the ancestry and admixture of Mexican Oaxaca Mestizos from Southeast Mexico using next-generation sequencing of 11 HLA loci. Hum Immunol 2019; 80:157-162. [PMID: 30708029 DOI: 10.1016/j.humimm.2019.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/03/2018] [Accepted: 01/17/2019] [Indexed: 02/01/2023]
Abstract
The Mestizos of Oaxaca resulted from the admixture of Zapotecan Natives with Spaniards and Africans. We selected 112 donors from Oaxaca and applied next-generation sequencing to characterize exon and intron variants in complete or extended HLA genes. Some alleles found, are unique to Mexican Natives and most likely will be absent in most major ethnicities, namely: Caucasians, Africans or Asians. Among these are HLA-A*68:03:01, HLA-A*68:05:01, HLA-C*03:04:01:02, HLA-C*15:09, HLA-C*3:05, HLA-C*03:06:01, HLA-B*39:05:01, HLA-B*35:14:01, HLA-B*35:12:01, HLA-B*35:43:01, HLA-B*40:05, HLA-B:40:08, HLA-B*51:02:01, HLA-B*35:24:01 and HLA-B*39:08. HLA-DQA1*05:05:01:05 and some HLA-DRB1 alleles were only present in Amerindians/Mestizos. Three haplotypes are unique to Mexican Natives, five to Middle-Eastern and Sephardi-Jews. We detected a novel HLA-DQA1*04:01:01 exon 4 variant. Any novel allele may have been positively selected to enlarge the peptide-binding repertoire, and some, like HLA-B*39:02:02 and HLA-B*39:05:01 were found with unique haplotype associations, suggesting convergent evolution events and/or allele lineage diversification. The allele frequencies were fairly evenly distributed in most HLA loci with the exception of HLA-DPB1. The application of NGS in Oaxaca is novel and will lead to better use in the clinical setting. It offers deep knowledge on the population structure, origins, migration, and discovery of new alleles and haplotypes that other techniques did not achieve.
Collapse
Affiliation(s)
- B A González-Quezada
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
| | - L E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - A J Munguia-Saldaña
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico.
| | - H Flores-Aguilar
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
| | - M A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - C Gorodezky
- Dept. of Immunology & Immunogenetics, InDRE, Secretary of Health, Mexico City, Mexico; Fundación Comparte Vida, A.C., Mexico City, Mexico.
| |
Collapse
|
15
|
Sanchez-Mazas A, Nunes JM. Does NGS typing highlight our understanding of HLA population diversity? Hum Immunol 2019; 80:62-66. [DOI: 10.1016/j.humimm.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/08/2023]
|