101
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Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Natural selection is an important influence on human genetic variation. Because immune and inflammatory function genes are enriched for signals of positive selection, the prevalence of rheumatic disease-risk alleles seen in different populations is partially the result of differing selective pressures (eg, due to pathogens). This review summarizes the genetic regions associated with susceptibility to different rheumatic diseases and concomitant evidence for natural selection, including known agents of selection exerting selective pressure in these regions.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, 96 Jonathan Lucas Street, Suite 816, Charleston, SC 29425, USA; Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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102
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Lee H, Kingsford C. Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery. Genome Biol 2018; 19:16. [PMID: 29415772 PMCID: PMC5804087 DOI: 10.1186/s13059-018-1388-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/08/2018] [Indexed: 01/07/2023] Open
Abstract
Accurate typing of human leukocyte antigen (HLA) is important because HLA genes play important roles in immune responses and disease genesis. Previously available computational methods are database-matching approaches and their outputs are inherently limited by the completeness of already known types, making them unsuitable for discovery of novel alleles. We have developed a graph-guided assembly technique for classical HLA genes, which can construct allele sequences given high-coverage whole-genome sequencing data. Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art methods. Using various data, we also demonstrate that our method can type novel alleles.
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Affiliation(s)
- Heewook Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Carl Kingsford
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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103
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Parham P, Guethlein LA. Genetics of Natural Killer Cells in Human Health, Disease, and Survival. Annu Rev Immunol 2018; 36:519-548. [PMID: 29394121 DOI: 10.1146/annurev-immunol-042617-053149] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Natural killer (NK) cells have vital functions in human immunity and reproduction. In the innate and adaptive immune responses to infection, particularly by viruses, NK cells respond by secreting inflammatory cytokines and killing infected cells. In reproduction, NK cells are critical for genesis of the placenta, the organ that controls the supply of oxygen and nutrients to the growing fetus. Controlling NK cell functions are interactions of HLA class I with inhibitory NK cell receptors. First evolved was the conserved interaction of HLA-E with CD94:NKG2A; later established were diverse interactions of HLA-A, -B, and -C with killer cell immunoglobulin-like receptors. Characterizing the latter interactions is rapid evolution, which distinguishes human populations and all species of higher primate. Driving this evolution are the different and competing selections imposed by pathogens on NK cell-mediated immunity and by the constraints of human reproduction on NK cell-mediated placentation. Promoting rapid evolution is independent segregation of polymorphic receptors and ligands throughout human populations.
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Affiliation(s)
- Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
| | - Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
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104
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Sebastian A, Migalska M, Biedrzycka A. AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data. Methods Mol Biol 2018; 1802:249-273. [PMID: 29858815 DOI: 10.1007/978-1-4939-8546-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.
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Affiliation(s)
- Alvaro Sebastian
- Sixth Researcher, Poznan, Poland. .,Instituto Aragonés de Empleo (INAEM), Zaragoza, Spain. .,Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| | - Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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105
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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106
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Abstract
Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. From the dawn of humanity and throughout history, infectious diseases have shaped human evolution, demography, migrations and history.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute (UGI), Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Lucy van Dorp
- UCL Genetics Institute (UGI), Darwin Building, Gower Street, London, WC1E 6BT UK
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107
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Sanchez-Mazas A, Černý V, Di D, Buhler S, Podgorná E, Chevallier E, Brunet L, Weber S, Kervaire B, Testi M, Andreani M, Tiercy JM, Villard J, Nunes JM. The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection. Mol Ecol 2017; 26:6238-6252. [PMID: 28950417 DOI: 10.1111/mec.14366] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/11/2017] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) genes play a key role in the immune response to infectious diseases, some of which are highly prevalent in specific environments, like malaria in sub-Saharan Africa. Former case-control studies showed that one particular HLA-B allele, B*53, was associated with malaria protection in Gambia, but this hypothesis was not tested so far within a population genetics framework. In this study, our objective was to assess whether pathogen-driven selection associated with malaria contributed to shape the HLA-B genetic landscape of Africa. To that aim, we first typed the HLA-A and -B loci in 484 individuals from 11 populations living in different environments across the Sahel, and we analysed these data together with those available for 29 other populations using several approaches including linear modelling on various genetic, geographic and environmental parameters. In addition to relevant signatures of populations' demography and migrations history in the genetic differentiation patterns of both HLA-A and -B loci, we found that the frequencies of three HLA alleles, B*53, B*78 and A*74, were significantly associated with Plasmodium falciparum malaria prevalence, suggesting their increase through pathogen-driven selection in malaria-endemic environments. The two HLA-B alleles were further identified, by high-throughput sequencing, as B*53:01:01 (in putative linkage disequilibrium with one HLA-C allele, C*04:01:01:01) and B*78:01 in all but one individuals tested, making them appropriate candidates to malaria protection. These results highlight the role of environmental factors in the evolution of the HLA polymorphism and open key perspectives for functional studies focusing on HLA peptide-binding properties.
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Affiliation(s)
- Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
| | - Viktor Černý
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Stéphane Buhler
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Elodie Chevallier
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Lydie Brunet
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Stephan Weber
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland
| | - Barbara Kervaire
- Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Manuela Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Marco Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation, Policlinic of the University of Tor Vergata, Rome, Italy
| | - Jean-Marie Tiercy
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - Jean Villard
- Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland.,Department of Genetic and Laboratory Medicine, Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility (UIT/LNRH), Geneva University Hospitals, Geneva, Switzerland
| | - José Manuel Nunes
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History (AGP), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), Geneva, Switzerland
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108
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Hadadianpour A, Samiee Aref MH, Zeinali S. High-Resolution HLA-A Typing in Normal Iranian Population. IRANIAN BIOMEDICAL JOURNAL 2017; 22:134-7. [PMID: 28952291 PMCID: PMC5786660 DOI: 10.22034/ibj.22.2.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Background: Human leukocyte antigen (HLA) gene is a highly polymorphic region. HLA typing is required to match patients and donors for transplantation; therefore, development of HLA registries is necessary for finding HLA match donors. HLA system is highly informative, and numerous studies have been conducted on HLA allele distribution in different populations. Methods: In this study, 100 unrelated Iranian individuals were typed for HLA-A locus using sequence-based typing method. Samples were subjected to the PCR, followed by Sanger sequencing and software analysis. Results: A*02:01 (13%) and A*24:02 (12%) were the two most frequent alleles, while A*01:14, A*02:05, A*02:11, A*02:34, A*02:50, A*11:04, A*23:02, A*24:34, A*25:01, A*26:09, A*26:43, A*29:67, A*30:54, A*31:02, A*31:66, A*32:03, A*32:04, A*33:03, and A*66:15 alleles had the least frequencies (1%). Conclusion: This is the first report of HLA-A allele level typing in a randomized population of Iran and can be useful for development of national registries of HLA-typed volunteer marrow donors and local cord blood banks.
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Affiliation(s)
- Azadeh Hadadianpour
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.,Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mohammad Hasan Samiee Aref
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.,Kawsar Human Genetics Research Center, Tehran, Iran
| | - Sirous Zeinali
- Kawsar Human Genetics Research Center, Tehran, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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109
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Kaesler E, Kappeler PM, Brameier M, Demeler J, Kraus C, Rakotoniaina JH, Hämäläinen AM, Huchard E. Shared evolutionary origin of major histocompatibility complex polymorphism in sympatric lemurs. Mol Ecol 2017; 26:5629-5645. [PMID: 28833696 DOI: 10.1111/mec.14336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 07/12/2017] [Accepted: 08/05/2017] [Indexed: 12/11/2022]
Abstract
Genes of the major histocompatibility complex (MHC) play a central role in adaptive immune responses of vertebrates. They exhibit remarkable polymorphism, often crossing species boundaries with similar alleles or allelic motifs shared across species. This pattern may reflect parallel parasite-mediated selective pressures, either favouring the long maintenance of ancestral MHC allelic lineages across successive speciation events by balancing selection ("trans-species polymorphism"), or alternatively favouring the independent emergence of functionally similar alleles post-speciation via convergent evolution. Here, we investigate the origins of MHC similarity across several species of dwarf and mouse lemurs (Cheirogaleidae). We examined MHC class II variation in two highly polymorphic loci (DRB, DQB) and evaluated the overlap of gut-parasite communities in four sympatric lemurs. We tested for parasite-MHC associations across species to determine whether similar parasite pressures may select for similar MHC alleles in different species. Next, we integrated our MHC data with those previously obtained from other Cheirogaleidae to investigate the relative contribution of convergent evolution and co-ancestry to shared MHC polymorphism by contrasting patterns of codon usage at functional vs. neutral sites. Our results indicate that parasites shared across species may select for functionally similar MHC alleles, implying that the dynamics of MHC-parasite co-evolution should be envisaged at the community level. We further show that balancing selection maintaining trans-species polymorphism, rather than convergent evolution, is the primary mechanism explaining shared MHC sequence motifs between species that diverged up to 30 million years ago.
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Affiliation(s)
- Eva Kaesler
- Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung, Verhaltensökologie & Soziobiologie, Göttingen, Germany
| | - Peter M Kappeler
- Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung, Verhaltensökologie & Soziobiologie, Göttingen, Germany.,Johann Friedrich Blumenbach Institut für Zoologie & Anthropologie, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Markus Brameier
- Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung, Göttingen, Germany
| | - Janina Demeler
- Institut für Parasitologie und Tropenveterinärmedizin, Berlin, Germany
| | - Cornelia Kraus
- Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung, Verhaltensökologie & Soziobiologie, Göttingen, Germany.,Johann Friedrich Blumenbach Institut für Zoologie & Anthropologie, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Josué H Rakotoniaina
- Johann Friedrich Blumenbach Institut für Zoologie & Anthropologie, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Anni M Hämäläinen
- Johann Friedrich Blumenbach Institut für Zoologie & Anthropologie, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Elise Huchard
- Institute for Evolutionary Biology, Montpellier (ISEM, UMR 5554), CNRS, Université Montpellier, Montpellier Cedex 5, France
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110
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Detecting signatures of past pathogen selection on human HLA loci: are there needles in the haystack? Parasitology 2017; 145:731-739. [PMID: 28809135 DOI: 10.1017/s0031182017001159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human leucocyte antigens (HLAs) are responsible for the display of peptide fragments for recognition by T-cell receptors. The gene family encoding them is thus integral to human adaptive immunity, and likely to be under strong pathogen selection. Despite this, it has proved difficult to demonstrate specific examples of pathogen-HLA coevolution. Selection from multiple pathogens simultaneously could explain why the evolutionary signatures of particular pathogens on HLAs have proved elusive. Here, we present an individual-based model of HLA evolution in the presence of two mortality-causing pathogens. We demonstrate that it is likely that individual pathogen species causing high mortality have left recognizable signatures on the HLA genomic region, despite more than one pathogen being present. Such signatures are likely to exist at the whole-population level, and involve haplotypic combinations of HLA genes rather than single loci.
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111
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Razali H, O'Connor E, Drews A, Burke T, Westerdahl H. A quantitative and qualitative comparison of illumina MiSeq and 454 amplicon sequencing for genotyping the highly polymorphic major histocompatibility complex (MHC) in a non-model species. BMC Res Notes 2017; 10:346. [PMID: 28754172 PMCID: PMC5534077 DOI: 10.1186/s13104-017-2654-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 07/21/2017] [Indexed: 11/24/2022] Open
Abstract
Background High-throughput sequencing enables high-resolution genotyping of extremely duplicated genes. 454 amplicon sequencing (454) has become the standard technique for genotyping the major histocompatibility complex (MHC) genes in non-model organisms. However, illumina MiSeq amplicon sequencing (MiSeq), which offers a much higher read depth, is now superseding 454. The aim of this study was to quantitatively and qualitatively evaluate the performance of MiSeq in relation to 454 for genotyping MHC class I alleles using a house sparrow (Passer domesticus) dataset with pedigree information. House sparrows provide a good study system for this comparison as their MHC class I genes have been studied previously and, consequently, we had prior expectations concerning the number of alleles per individual. Results We found that 454 and MiSeq performed equally well in genotyping amplicons with low diversity, i.e. amplicons from individuals that had fewer than 6 alleles. Although there was a higher rate of failure in the 454 dataset in resolving amplicons with higher diversity (6–9 alleles), the same genotypes were identified by both 454 and MiSeq in 98% of cases. Conclusions We conclude that low diversity amplicons are equally well genotyped using either 454 or MiSeq, but the higher coverage afforded by MiSeq can lead to this approach outperforming 454 in amplicons with higher diversity. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2654-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haslina Razali
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Emily O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden.
| | - Anna Drews
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, 223 62, Lund, Sweden
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112
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Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC. Fast and accurate HLA typing from short-read next-generation sequence data with xHLA. Proc Natl Acad Sci U S A 2017; 114:8059-8064. [PMID: 28674023 PMCID: PMC5544337 DOI: 10.1073/pnas.1707945114] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer.
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Affiliation(s)
- Chao Xie
- Human Longevity Singapore Pte Ltd., Singapore 138543;
| | - Zhen Xuan Yeo
- Human Longevity Singapore Pte Ltd., Singapore 138543
| | - Marie Wong
- Human Longevity Singapore Pte Ltd., Singapore 138543
| | - Jason Piper
- Human Longevity Singapore Pte Ltd., Singapore 138543
| | - Tao Long
- Human Longevity, Inc., San Diego, CA 92121
| | | | | | - Ken Bloom
- Human Longevity, Inc., San Diego, CA 92121
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401
| | - Cynthia Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401
| | - Colleen Brady
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN 55401
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037
- Department of Pathology, University of California at San Diego, La Jolla, CA 92093
| | | | | | | | - Yaron Turpaz
- Human Longevity Singapore Pte Ltd., Singapore 138543
- Human Longevity, Inc., San Diego, CA 92121
| | - J Craig Venter
- Human Longevity, Inc., San Diego, CA 92121;
- J. Craig Venter Institute, La Jolla, CA 92037
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113
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Biedrzycka A, O'Connor E, Sebastian A, Migalska M, Radwan J, Zając T, Bielański W, Solarz W, Ćmiel A, Westerdahl H. Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions. BMC Evol Biol 2017; 17:159. [PMID: 28679358 PMCID: PMC5497381 DOI: 10.1186/s12862-017-0997-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/14/2017] [Indexed: 11/23/2022] Open
Abstract
Background Recent work suggests that gene duplications may play an important role in the evolution of immunity genes. Passerine birds, and in particular Sylvioidea warblers, have highly duplicated major histocompatibility complex (MHC) genes, which are key in immunity, compared to other vertebrates. However, reasons for this high MHC gene copy number are yet unclear. High-throughput sequencing (HTS) allows MHC genotyping even in individuals with extremely duplicated genes. This HTS data can reveal evidence of selection, which may help to unravel the putative functions of different gene copies, i.e. neofunctionalization. We performed exhaustive genotyping of MHC class I in a Sylvioidea warbler, the sedge warbler, Acrocephalus schoenobaenus, using the Illumina MiSeq technique on individuals from a wild study population. Results The MHC diversity in 863 genotyped individuals by far exceeds that of any other bird species described to date. A single individual could carry up to 65 different alleles, a large proportion of which are expressed (transcribed). The MHC alleles were of three different lengths differing in evidence of selection, diversity and divergence within our study population. Alleles without any deletions and alleles containing a 6 bp deletion showed characteristics of classical MHC genes, with evidence of multiple sites subject to positive selection and high sequence divergence. In contrast, alleles containing a 3 bp deletion had no sites subject to positive selection and had low divergence. Conclusions Our results suggest that sedge warbler MHC alleles that either have no deletion, or contain a 6 bp deletion, encode classical antigen presenting MHC molecules. In contrast, MHC alleles containing a 3 bp deletion may encode molecules with a different function. This study demonstrates that highly duplicated MHC genes can be characterised with HTS and that selection patterns can be useful for revealing neofunctionalization. Importantly, our results highlight the need to consider the putative function of different MHC genes in future studies of MHC in relation to disease resistance and fitness. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0997-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aleksandra Biedrzycka
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland.
| | - Emily O'Connor
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, 223 62, Lund, Sweden
| | - Alvaro Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University in Poznań, ul. Umultowska 89, 61-614, Poznań, Poland
| | - Tadeusz Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Wojciech Bielański
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Wojciech Solarz
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Adam Ćmiel
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Mickiewicza 33, 31-120, Kraków, Poland
| | - Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, 223 62, Lund, Sweden
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114
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017. [PMID: 28449694 DOI: 10.1186/s13059-017-1207-1.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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115
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017; 18:76. [PMID: 28449694 PMCID: PMC5406920 DOI: 10.1186/s13059-017-1207-1] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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116
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Deschamps M, Quintana-Murci L. Immunité innée et maladies chez l’homme. Med Sci (Paris) 2017; 32:1079-1086. [DOI: 10.1051/medsci/20163212011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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117
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Minias P, Whittingham LA, Dunn PO. Coloniality and migration are related to selection on MHC genes in birds. Evolution 2016; 71:432-441. [PMID: 27921293 DOI: 10.1111/evo.13142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
The major histocompatibility complex (MHC) plays a key role in pathogen recognition as a part of the vertebrate adaptive immune system. The great diversity of MHC genes in natural populations is maintained by different forms of balancing selection and its strength should correlate with the diversity of pathogens to which a population is exposed and the rate of exposure. Despite this prediction, little is known about how life-history characteristics affect selection at the MHC. Here, we examined whether the strength of balancing selection on MHC class II genes in birds (as measured with nonsynonymous nucleotide substitutions, dN) was related to their social or migratory behavior, two life-history characteristics correlated with pathogen exposure. Our comparative analysis indicated that the rate of nonsynonymous substitutions was higher in colonial and migratory species than solitary and resident species, suggesting that the strength of balancing selection increases with coloniality and migratory status. These patterns could be attributed to: (1) elevated transmission rates of pathogens in species that breed in dense aggregations, or (2) exposure to a more diverse fauna of pathogens and parasites in migratory species. Our study suggests that differences in social structure and basic ecological traits influence MHC diversity in natural vertebrate populations.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
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118
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Fischer A, Rausell A. Primary immunodeficiencies suggest redundancy within the human immune system. Sci Immunol 2016; 1:1/6/eaah5861. [PMID: 28783693 DOI: 10.1126/sciimmunol.aah5861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/03/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
Pathogen-driven evolution has shaped the complexity of the human immune system. Our genome contains at least 1854 gene products involved in immune responses. However, the redundancy and robustness of the immune system need further characterization. One way to examine this redundancy is through the study of monogenic primary immunodeficiencies (PIDs) associated with infections. Causal mutations affecting innate immunity genes are, in relative terms, close to seven times less frequent than those affecting adaptive immunity genes in PIDs. Loss-of-function mutations of innate immunity genes encoding pattern-recognition receptors (PRRs) and associated pathways rarely cause susceptibility to infections, which suggests that PRR pathways are partially redundant in the immune responses to infection. This dispensability has also been observed for constitutive products of the immune system, such as secretory immunoglobulin A, and for innate immune cells, such as natural killer and innate lymphoid cell subsets, which are not essential for viability. This Review discusses these findings in the context of their implications for the identification of previously unknown classes of PIDs and assessment of the susceptibility to infection associated with various targeted immunotherapies.
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Affiliation(s)
- Alain Fischer
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France. .,Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Paris, France.,Collège de France, Paris, France
| | - Antonio Rausell
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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119
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Winternitz J, Abbate JL, Huchard E, Havlíček J, Garamszegi LZ. Patterns of MHC-dependent mate selection in humans and nonhuman primates: a meta-analysis. Mol Ecol 2016; 26:668-688. [DOI: 10.1111/mec.13920] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Affiliation(s)
- J. Winternitz
- Department of Evolutionary Ecology; Max Planck Institute for Evolutionary Biology; August-Thienemann-Strasse 2 24306 Ploen Germany
- Institute of Vertebrate Biology; Czech Academy of Sciences; v.v.i. Květná 8 603 65 Brno Czech Republic
- Institute of Botany; Czech Academy of Sciences; v.v.i. Lidická 25/27 657 20 Brno Czech Republic
| | - J. L. Abbate
- Institute of Ecology and Evolution; University of Bern; Balterstrasse 6 3006 Bern Switzerland
- INRA - UMR 1062 CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); 755 Avenue du campus Agropolis 34988 Montferrier-sur-Lez France
| | - E. Huchard
- CEFE UMR5175; CNRS - Université de Montpellier - EPHE; 1919 Route de Mende 34295 Montpellier Cedex 5 France
| | - J. Havlíček
- Department of Zoology; Faculty of Science; Charles University; Viničná 7 128 44 Prague 2 Czech Republic
| | - L. Z. Garamszegi
- Department of Evolutionary Ecology; Estación Biológica de Doñana-CSIC; c/Americo Vespucio s/n 41092 Seville Spain
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120
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Abstract
The wealth of available genetic information is allowing the reconstruction of human demographic and adaptive history. Demography and purifying selection affect the purge of rare, deleterious mutations from the human population, whereas positive and balancing selection can increase the frequency of advantageous variants, improving survival and reproduction in specific environmental conditions. In this review, I discuss how theoretical and empirical population genetics studies, using both modern and ancient DNA data, are a powerful tool for obtaining new insight into the genetic basis of severe disorders and complex disease phenotypes, rare and common, focusing particularly on infectious disease risk.
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Affiliation(s)
- Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Department of Genomes & Genetics, Institut Pasteur, Paris, 75015, France.
- Centre National de la Recherche Scientifique, URA3012, Paris, 75015, France.
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, 75015, France.
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121
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Sarri CA, Markantoni M, Stamatis C, Papa A, Tsakris A, Pervanidou D, Baka A, Politis C, Billinis C, Hadjichristodoulou C, Mamuris Z. Genetic Contribution of MHC Class II Genes in Susceptibility to West Nile Virus Infection. PLoS One 2016; 11:e0165952. [PMID: 27812212 PMCID: PMC5094746 DOI: 10.1371/journal.pone.0165952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
WNV is a zoonotic neurotropic flavivirus that has recently emerged globally as a significant cause of viral encephalitis. The last five years, 624 incidents of WNV infection have been reported in Greece. The risk for severe WNV disease increases among immunosuppressed individuals implying thus the contribution of the MHC locus to the control of WNV infection. In order to investigate a possible association of MHC class II genes, especially HLA-DPA1, HLA-DQA1, HLA-DRB1, we examined 105 WNV patients, including 68 cases with neuroinvasive disease and 37 cases with mild clinical phenotype, collected during the period from 2010 to2013, and 100 control individuals selected form the Greek population. Typing was performed for exon 2 for all three genes. DQA1*01:01 was considered to be "protective" against WNV infection (25.4% vs 40.1%, P = 0.004) while DQA1*01:02 was associated with increased susceptibility (48.0% vs 32.1%, P = 0.003). Protection against neuroinvasion was associated with the presence of DRB1*11:02 (4.99% vs 0.0%, P = 0.018). DRB1*16:02 was also absent from the control cohort (P = 0.016). Three additional population control groups were used in order to validate our results. No statistically significant association with the disease was found for HLA-DPA alleles. The results of the present study provide some evidence that MHC class II is involved in the response to WNV infection, outlining infection "susceptibility" and "CNS-high-risk" candidates. Furthermore, three new alleles were identified while the frequency of all alleles in the study was compared with worldwide data. The characterization of the MHC locus could help to estimate the risk for severe WNV cases in a country.
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Affiliation(s)
- Constantina A. Sarri
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Maria Markantoni
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Costas Stamatis
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Anna Papa
- Arboviruses Reference Laboratory, 1st Microbiological Laboratory, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Tsakris
- Laboratory of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Danai Pervanidou
- Hellenic Centre for Disease Control and Prevention (HCDCP), Attika, Greece
| | - Agoritsa Baka
- Hellenic Centre for Disease Control and Prevention (HCDCP), Attika, Greece
| | | | - Charalambos Billinis
- Laboratory of Microbiology and Parasitology, Faculty of Veterinary Medicine, University of Thessaly, Karditsa, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
- * E-mail:
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122
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Salmier A, de Thoisy B, Crouau-Roy B, Lacoste V, Lavergne A. Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species. BMC Evol Biol 2016; 16:229. [PMID: 27782798 PMCID: PMC5080761 DOI: 10.1186/s12862-016-0802-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background Although bats are natural reservoirs of many pathogens, few studies have been conducted on the genetic variation and detection of selection in major histocompatibility complex (MHC) genes. These genes are critical for resistance and susceptibility to diseases, and host–pathogen interactions are major determinants of their extensive polymorphism. Here we examined spatial patterns of diversity of the expressed MHC class II DRB gene of three sympatric Neotropical bats, Carollia perspicillata and Desmodus rotundus (Phyllostomidae), and Molossus molossus (Molossidae), all of which use the same environments (e.g., forests, edge habitats, urban areas). Comparison with neutral marker (mtDNA D-loop) diversity was performed at the same time. Results Twenty-three DRB alleles were identified in 19 C. perspicillata, 30 alleles in 35 D. rotundus and 20 alleles in 28 M. molossus. The occurrence of multiple DRB loci was found for the two Phyllostomidae species. The DRB polymorphism was high in all sampling sites and different signatures of positive selection were detected depending on the environment. The patterns of DRB diversity were similar to those of neutral markers for C. perspicillata and M. molossus. In contrast, these patterns were different for D. rotundus for which a geographical structure was highlighted. A heterozygote advantage was also identified for this species. No recombination or gene conversion event was found and phylogenetic relationships showed a trans-species mode of evolution in the Phyllostomids. Conclusions This study of MHC diversity demonstrated the strength of the environment and contrasting pathogen pressures in shaping DRB diversity. Differences between positively selected sites identified in bat species highlighted the potential role of gut microbiota in shaping immune responses. Furthermore, multiple geographic origins and/or population admixtures observed in C. perspicillata and M. molossus populations acted as an additional force in shaping DRB diversity. In contrast, DRB diversity of D. rotundus was shaped by environment rather than demographic history. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0802-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arielle Salmier
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, 23 avenue Pasteur, BP 6010, 97306, Cayenne, Cedex, French Guiana
| | - Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, 23 avenue Pasteur, BP 6010, 97306, Cayenne, Cedex, French Guiana
| | - Brigitte Crouau-Roy
- CNRS, Université Toulouse 3 UPS, ENFA, UMR 5174 EDB (Laboratoire Évolution et Diversité Biologique), 118 Route de Narbonne, 31062, Toulouse, France
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, 23 avenue Pasteur, BP 6010, 97306, Cayenne, Cedex, French Guiana
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, 23 avenue Pasteur, BP 6010, 97306, Cayenne, Cedex, French Guiana.
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123
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MYD88 and functionally related genes are associated with multiple infections in a model population of Kenyan village dogs. Mol Biol Rep 2016; 43:1451-1463. [PMID: 27655108 DOI: 10.1007/s11033-016-4078-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 09/09/2016] [Indexed: 12/25/2022]
Abstract
The purpose of this study was to seek associations between immunity-related molecular markers and endemic infections in a model population of African village dogs from Northern Kenya with no veterinary care and no selective breeding. A population of village dogs from Northern Kenya composed of three sub-populations from three different areas (84, 50 and 55 dogs) was studied. Canine distemper virus (CDV), Hepatozoon canis, Microfilariae (Acantocheilonema dracunculoides, Acantocheilonema reconditum) and Neospora caninum were the pathogens studied. The presence of antibodies (CDV, Neospora), light microscopy (Hepatozoon) and diagnostic PCR (Microfilariae) were the methods used for diagnosing infection. Genes involved in innate immune mechanisms, NOS3, IL6, TLR1, TLR2, TLR4, TLR7, TLR9, LY96, MYD88, and three major histocompatibility genes class II genes were selected as candidates. Single nucleotide polymorphism (SNP) markers were detected by Sanger sequencing, next generation sequencing and PCR-RFLP. The Fisher´s exact test for additive and non-additive models was used for association analyses. Three SNPs within the MYD88 gene and one TLR4 SNP marker were associated with more than one infection. Combined genotypes and further markers identified by next generation sequencing confirmed associations observed for individual genes. The genes associated with infection and their combinations in specific genotypes match well our knowledge on their biological role and on the role of the relevant biological pathways, respectively. Associations with multiple infections observed between the MYD88 and TLR4 genes suggest their involvement in the mechanisms of anti-infectious defenses in dogs.
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124
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Willenbring RC, Jin F, Hinton DJ, Hansen M, Choi DS, Pavelko KD, Johnson AJ. Modulatory effects of perforin gene dosage on pathogen-associated blood-brain barrier (BBB) disruption. J Neuroinflammation 2016; 13:222. [PMID: 27576583 PMCID: PMC5006384 DOI: 10.1186/s12974-016-0673-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/17/2016] [Indexed: 11/12/2022] Open
Abstract
Background CD8 T cell-mediated blood-brain barrier (BBB) disruption is dependent on the effector molecule perforin. Human perforin has extensive single nucleotide variants (SNVs), the significance of which is not fully understood. These SNVs can result in reduced, but not ablated, perforin activity or expression. However, complete loss of perforin expression or activity results in the lethal disease familial hemophagocytic lymphohistiocytosis type 2 (FHL 2). In this study, we address the hypothesis that a single perforin allele can alter the severity of BBB disruption in vivo using a well-established model of CNS vascular permeability in C57Bl/6 mice. The results of this study provide insight into the significance of perforin SNVs in the human population. Methods We isolated the effect a single perforin allele has on CNS vascular permeability through the use of perforin-heterozygous (perforin+/−) C57BL/6 mice in the peptide-induced fatal syndrome (PIFS) model of immune-mediated BBB disruption. Seven days following Theiler’s murine encephalomyelitis virus (TMEV) CNS infection, neuroinflammation and TMEV viral control were assessed through flow cytometric analysis and quantitative real-time PCR of the viral genome, respectively. Following immune-mediated BBB disruption, gadolinium-enhanced T1-weighted MRI, with 3D volumetric analysis, and confocal microscopy were used to define CNS vascular permeability. Finally, the open field behavior test was used to assess locomotor activity of mice following immune-mediated BBB disruption. Results Perforin-null mice had negligible CNS vascular permeability. Perforin-WT mice have extensive CNS vascular permeability. Interestingly, perforin-heterozygous mice had an intermediate level of CNS vascular permeability as measured by both gadolinium-enhanced T1-weighted MRI and fibrinogen leakage in the brain parenchyma. Differences in BBB disruption were not a result of increased CNS immune infiltrate. Additionally, TMEV was controlled in a perforin dose-dependent manner. Furthermore, a single perforin allele is sufficient to induce locomotor deficit during immune-mediated BBB disruption. Conclusions Perforin modulates BBB disruption in a dose-dependent manner. This study demonstrates a potentially advantageous role for decreased perforin expression in reducing BBB disruption. This study also provides insight into the effect SNVs in a single perforin allele could have on functional deficit in neurological disease.
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Affiliation(s)
- Robin C Willenbring
- Mayo Graduate School, Mayo Clinic, Rochester, MN, USA.,Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Fang Jin
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - David J Hinton
- Mayo Graduate School, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Mike Hansen
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Doo-Sup Choi
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | | | - Aaron J Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN, USA. .,Department of Neurology, Mayo Clinic, Rochester, MN, USA.
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125
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Caljon G, De Muylder G, Durnez L, Jennes W, Vanaerschot M, Dujardin JC. Alice in microbes' land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts. FEMS Microbiol Rev 2016; 40:664-85. [PMID: 27400870 DOI: 10.1093/femsre/fuw018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/24/2022] Open
Abstract
In the present review, we aim to provide a general introduction to different facets of the arms race between pathogens and their hosts/environment, emphasizing its evolutionary aspects. We focus on vector-borne parasitic protozoa, which have to adapt to both invertebrate and vertebrate hosts. Using Leishmania, Trypanosoma and Plasmodium as main models, we review successively (i) the adaptations and counter-adaptations of parasites and their invertebrate host, (ii) the adaptations and counter-adaptations of parasites and their vertebrate host and (iii) the impact of human interventions (chemotherapy, vaccination, vector control and environmental changes) on these adaptations. We conclude by discussing the practical impact this knowledge can have on translational research and public health.
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Affiliation(s)
- Guy Caljon
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Géraldine De Muylder
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Lies Durnez
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Wim Jennes
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium Columbia University, College of Physicians and Surgeons, Department of Microbiology and Immunology, Fidock Lab, New York, NY 10032, USA
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
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126
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Lenz TL, Spirin V, Jordan DM, Sunyaev SR. Excess of Deleterious Mutations around HLA Genes Reveals Evolutionary Cost of Balancing Selection. Mol Biol Evol 2016; 33:2555-64. [PMID: 27436009 PMCID: PMC5026253 DOI: 10.1093/molbev/msw127] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Deleterious mutations are expected to evolve under negative selection and are usually purged from the population. However, deleterious alleles segregate in the human population and some disease-associated variants are maintained at considerable frequencies. Here, we test the hypothesis that balancing selection may counteract purifying selection in neighboring regions and thus maintain deleterious variants at higher frequency than expected from their detrimental fitness effect. We first show in realistic simulations that balancing selection reduces the density of polymorphic sites surrounding a locus under balancing selection, but at the same time markedly increases the population frequency of the remaining variants, including even substantially deleterious alleles. To test the predictions of our simulations empirically, we then use whole-exome sequencing data from 6,500 human individuals and focus on the most established example for balancing selection in the human genome, the major histocompatibility complex (MHC). Our analysis shows an elevated frequency of putatively deleterious coding variants in nonhuman leukocyte antigen (non-HLA) genes localized in the MHC region. The mean frequency of these variants declined with physical distance from the classical HLA genes, indicating dependency on genetic linkage. These results reveal an indirect cost of the genetic diversity maintained by balancing selection, which has hitherto been perceived as mostly advantageous, and have implications both for the evolution of recombination and also for the epidemiology of various MHC-associated diseases.
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Affiliation(s)
- Tobias L Lenz
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Evolutionary Immunogenomics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Victor Spirin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Daniel M Jordan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Shamil R Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA
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127
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Buhler S, Nunes JM, Sanchez-Mazas A. HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics 2016; 68:401-416. [PMID: 27233953 PMCID: PMC4911380 DOI: 10.1007/s00251-016-0918-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023]
Abstract
The main function of HLA class I molecules is to present pathogen-derived peptides to cytotoxic T lymphocytes. This function is assumed to drive the maintenance of an extraordinary amount of polymorphism at each HLA locus, providing an immune advantage to heterozygote individuals capable to present larger repertories of peptides than homozygotes. This seems contradictory, however, with a reduced diversity at individual HLA loci exhibited by some isolated populations. This study shows that the level of functional diversity predicted for the two HLA-A and HLA-B genes considered simultaneously is similar (almost invariant) between 46 human populations, even when a reduced diversity exists at each locus. We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential. The distinct pattern observed for HLA-C is explained by its functional evolution towards killer cell immunoglobulin-like receptor (KIR) activity regulation rather than peptide presentation.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Transplantation Immunology Unit & National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland.
| | - José Manuel 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 (iGE3), University of Geneva, Geneva, Switzerland
| | - Alicia 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 (iGE3), University of Geneva, Geneva, Switzerland
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128
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Zhou F, Cao H, Zuo X, Zhang T, Zhang X, Liu X, Xu R, Chen G, Zhang Y, Zheng X, Jin X, Gao J, Mei J, Sheng Y, Li Q, Liang B, Shen J, Shen C, Jiang H, Zhu C, Fan X, Xu F, Yue M, Yin X, Ye C, Zhang C, Liu X, Yu L, Wu J, Chen M, Zhuang X, Tang L, Shao H, Wu L, Li J, Xu Y, Zhang Y, Zhao S, Wang Y, Li G, Xu H, Zeng L, Wang J, Bai M, Chen Y, Chen W, Kang T, Wu Y, Xu X, Zhu Z, Cui Y, Wang Z, Yang C, Wang P, Xiang L, Chen X, Zhang A, Gao X, Zhang F, Xu J, Zheng M, Zheng J, Zhang J, Yu X, Li Y, Yang S, Yang H, Wang J, Liu J, Hammarström L, Sun L, Wang J, Zhang X. Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease. Nat Genet 2016; 48:740-6. [PMID: 27213287 DOI: 10.1038/ng.3576] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/29/2016] [Indexed: 12/13/2022]
Abstract
The human major histocompatibility complex (MHC) region has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint the causal variants for these associations because of the extreme complexity of the region. We thus sequenced the entire 5-Mb MHC region in 20,635 individuals of Han Chinese ancestry (10,689 controls and 9,946 patients with psoriasis) and constructed a Han-MHC database that includes both variants and HLA gene typing results of high accuracy. We further identified multiple independent new susceptibility loci in HLA-C, HLA-B, HLA-DPB1 and BTNL2 and an intergenic variant, rs118179173, associated with psoriasis and confirmed the well-established risk allele HLA-C*06:02. We anticipate that our Han-MHC reference panel built by deep sequencing of a large number of samples will serve as a useful tool for investigating the role of the MHC region in a variety of diseases and thus advance understanding of the pathogenesis of these disorders.
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Affiliation(s)
- Fusheng Zhou
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Hongzhi Cao
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xianbo Zuo
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Xiaoguang Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Ricong Xu
- Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China
| | - Gang Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yuanwei Zhang
- BGI-Shenzhen, Shenzhen, China.,School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiaodong Zheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Jinping Gao
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Yujun Sheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Bo Liang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Changbing Shen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Caihong Zhu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xing Fan
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Min Yue
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xianyong Yin
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, China
| | - Cuicui Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liang Yu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Mengyun Chen
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Lili Tang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Longmao Wu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Jian Li
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yu Xu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Suli Zhao
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yu Wang
- BGI-Shenzhen, Shenzhen, China
| | - Ge Li
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Lei Zeng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | | | | | | | | | - Yanyan Wu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | - Zhengwei Zhu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Zaixing Wang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Chunjun Yang
- Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China
| | - Peiguang Wang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Leihong Xiang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Anping Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xinghua Gao
- Department of Dermatology, No. 1 Hospital of China Medical University, Shenyang, China
| | - Furen Zhang
- Shandong Provincial Institute of Dermatology and Venereology, Shandong Academy of Medical Sciences, Jinan, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China
| | - Min Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Zheng
- Department of Dermatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Xueqing Yu
- Department of Nephrology, First Affiliated Hospital, Sun Yat-sen University, Key Laboratory of Nephrology, Ministry of Health, Guangzhou, China
| | - Yingrui Li
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sen Yang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jianjun Liu
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, China.,Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,iCarbonX, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Princess Al-Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.,Department of Medicine, University of Hong Kong, Hong Kong, China.,State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
| | - Xuejun Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.,Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, China.,Department of Dermatology, Huashan Hospital and Collaborative Innovation Center of Complex and Severe Skin Disease, Fudan University, Shanghai, China
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129
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Guethlein LA, Norman PJ, Hilton HG, Parham P. Co-evolution of MHC class I and variable NK cell receptors in placental mammals. Immunol Rev 2016; 267:259-82. [PMID: 26284483 DOI: 10.1111/imr.12326] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Shaping natural killer (NK) cell functions in human immunity and reproduction are diverse killer cell immunoglobulin-like receptors (KIRs) that recognize polymorphic MHC class I determinants. A survey of placental mammals suggests that KIRs serve as variable NK cell receptors only in certain primates and artiodactyls. Divergence of the functional and variable KIRs in primates and artiodactyls predates placental reproduction. Among artiodactyls, cattle but not pigs have diverse KIRs. Catarrhine (humans, apes, and Old World monkeys) and platyrrhine (New World monkeys) primates, but not prosimians, have diverse KIRs. Platyrrhine and catarrhine systems of KIR and MHC class I are highly diverged, but within the catarrhines, a stepwise co-evolution of MHC class I and KIR is discerned. In Old World monkeys, diversification focuses on MHC-A and MHC-B and their cognate lineage II KIR. With evolution of C1-bearing MHC-C from MHC-B, as informed by orangutan, the focus changes to MHC-C and its cognate lineage III KIR. Evolution of C2 from C1 and fixation of MHC-C drove further elaboration of MHC-C-specific KIR, as exemplified by chimpanzee. In humans, the evolutionary trajectory changes again. Emerging from reorganization of the KIR locus and selective attenuation of KIR avidity for MHC class I are the functionally distinctive KIR A and KIR B haplotypes.
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Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Norman
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Hugo G Hilton
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
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130
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Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
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131
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Ghirotto S, Tassi F, Barbujani G, Pattini L, Hayward C, Vollenweider P, Bochud M, Rampoldi L, Devuyst O. The Uromodulin Gene Locus Shows Evidence of Pathogen Adaptation through Human Evolution. J Am Soc Nephrol 2016; 27:2983-2996. [PMID: 26966016 DOI: 10.1681/asn.2015070830] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/30/2016] [Indexed: 12/15/2022] Open
Abstract
Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. To determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead UMOD variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. The T allele of rs4293393, associated with CKD risk, has high frequency in most modern populations and was the one detected in primate genomes. In contrast, we identified only the derived, C allele in Denisovan and Neanderthal genomes. The distribution of the UMOD ancestral allele did not follow the ancestral susceptibility model observed for variants associated with salt-sensitive hypertension. Instead, the global frequencies of the UMOD alleles significantly correlated with pathogen diversity (bacteria, helminths) and prevalence of antibiotic-resistant urinary tract infections (UTIs). The inverse correlation found between urinary levels of uromodulin and markers of UTIs in the general population substantiates the link between UMOD variants and protection against UTIs. These data strongly suggest that the UMOD ancestral allele, driving higher urinary excretion of uromodulin, has been kept at a high frequency because of its protective effect against UTIs.
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Affiliation(s)
- Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Vollenweider
- Department of Internal Medicine, Institute of Social and Preventive Medicine, Lausanne University Hospital Center, Lausanne, Switzerland
| | - Murielle Bochud
- Department of Internal Medicine, Institute of Social and Preventive Medicine, Lausanne University Hospital Center, Lausanne, Switzerland
| | - Luca Rampoldi
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy; and
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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132
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Hernández Rivera J, Ibarra Villanueva A, Espinoza Pérez R, Cancino López J, Silva Rueda I, Rodríguez Gómez R, García Covarrubias L, Reyes Díaz E, Pérez López M, Salazar Mendoza M. Specific Antigens by Federal Entity in Patients at the Transplant Unit of Specialities Hospital, National Medical Center Twenty-First Century, Mexico. Transplant Proc 2016; 48:575-7. [DOI: 10.1016/j.transproceed.2016.02.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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133
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Hernández Rivera J, González Ramos J, Pérez López M, Carmona Becerril A, Escárcega Vázquez A, Cruz Santiago J, Siordia Jiménez S, Bermúdez Aceves L, Salazar Mendoza M. The Most Common HLA Antigens Found in Patients With Renal Transplants at the Specialties Hospital of “La Raza” Medical Center, Mexico. Transplant Proc 2016; 48:572-4. [DOI: 10.1016/j.transproceed.2016.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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134
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Currat M, Gerbault P, Di D, Nunes JM, Sanchez-Mazas A. Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection. Evol Bioinform Online 2016; 11:27-39. [PMID: 26949332 PMCID: PMC4768942 DOI: 10.4137/ebo.s33488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 12/20/2022] Open
Abstract
SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.
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Affiliation(s)
- Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Pascale Gerbault
- Research Department of Genetics, Evolution and Environment, University College London, London, UK.; Department of Anthropology, University College London, London, UK
| | - Da Di
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - José M Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
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135
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Nunes JM. Using uniformat and gene[rate] to Analyze Data with Ambiguities in Population Genetics. Evol Bioinform Online 2016; 11:19-26. [PMID: 26917942 PMCID: PMC4762493 DOI: 10.4137/ebo.s32415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/13/2023] Open
Abstract
Some genetic systems frequently present ambiguous data that cannot be straightforwardly analyzed with common methods of population genetics. Two possibilities arise to analyze such data: one is the arbitrary simplification of the data and the other is the development of methods adapted to such ambiguous data. In this article, we present an attempt at such a development, the uniformat grammar and The gene[rate] tools, highlighting the specific aspects and the adaptations required to analyze ambiguous nominal data in population genetics.
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Affiliation(s)
- José Manuel Nunes
- Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
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136
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Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (Lagopus lagopus scotica). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0810-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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137
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Olsen LR, Simon C, Kudahl UJ, Bagger FO, Winther O, Reinherz EL, Zhang GL, Brusic V. A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding. BMC Med Genomics 2015; 8 Suppl 4:S1. [PMID: 26679766 PMCID: PMC4682376 DOI: 10.1186/1755-8794-8-s4-s1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte antigen molecules. However, experimental studies have shown that T cells often target diverse regions in highly variable viral pathogens and this diversity may need to be addressed through redefinition of suitable peptide targets. Methods We have developed a method for antigen assessment and target selection for polyvalent vaccines, with which we identified immune epitopes from variable regions, where all variants bind HLA. These regions, although variable, can thus be considered stable in terms of HLA binding and represent valuable vaccine targets. Results We applied this method to predict CD8+ T-cell targets in influenza A H7N9 hemagglutinin and significantly increased the number of potential vaccine targets compared to the number of targets discovered using the traditional approach where low-frequency peptides are excluded. Conclusions We developed a webserver with an intuitive visualization scheme for summarizing the T cell-based antigenic potential of any given protein or proteome using human leukocyte antigen binding predictions and made a web-accessible software implementation freely available at http://met-hilab.cbs.dtu.dk/blockcons/.
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138
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Lindenau JDR, Salzano FM, Hurtado AM, Hill KR, Petzl-Erler ML, Tsuneto LT, Hutz MH. Variability of innate immune system genes in Native American populations-relationship with history and epidemiology. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:722-8. [PMID: 26667372 DOI: 10.1002/ajpa.22917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/27/2015] [Accepted: 11/23/2015] [Indexed: 01/04/2023]
Abstract
OBJECTIVES The immune system of a host, defending him/her against invading pathogens, has two main subsystems: innate immunity and acquired immunity. There are several evidences showing that Native American populations are immunologically different from non-Native populations. Our aim was to describe the variability of innate immune system genes in Native American populations. MATERIALS AND METHODS We investigated heterozygozities and patterns of population differentiation (FST ) of 14 polymorphisms related to the innate immune response in five Native American populations (Aché, Guarani-Kaiowá, Guarani-Ñandeva, Kaingang, and Xavante) and the results were compared with the three major world population data (YRI, CEU, and CHB) available at the 1,000 genomes database. RESULTS Mean heterozygosities ranged between 0.241 ± 0.057 (Aché) and 0.343 ± 0.033 (Kaingang), but no significant differences were observed (Friedman test, P = 0.197). Mean heterozygosities were also not significantly different when Amerindians were pooled and compared with the 1000 genomes populations (Friedman test, P = 0.506). When the Native American populations were grouped as Amerindians, a significantly higher FST value (0.194) was observed between the Amerindian and African populations. The Ewens-Watterson neutrality test showed that these markers are not under strong selective pressure. DISCUSSION Native American populations present similar levels of heterozygosity as those of other continents, but are different from Africans in the frequency of polymorphisms of innate immune genes. This higher differentiation is probably due to demographic processes that occurred during the out-of-Africa event.
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Affiliation(s)
- Juliana Dal-Ri Lindenau
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Francisco Mauro Salzano
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Ana Magdalena Hurtado
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402
| | - Kim R Hill
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287-2402
| | | | - Luiza Tamie Tsuneto
- Departamento De Análises Clínicas, Universidade Estadual De Maringá, Maringá, PR, Brazil
| | - Mara Helena Hutz
- Departamento De Genética, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
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139
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Bateson ZW, Whittingham LA, Johnson JA, Dunn PO. Contrasting patterns of selection and drift between two categories of immune genes in prairie-chickens. Mol Ecol 2015; 24:6095-106. [PMID: 26547898 DOI: 10.1111/mec.13459] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/31/2015] [Accepted: 11/03/2015] [Indexed: 12/22/2022]
Abstract
Immune-receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid co-evolution between hosts and pathogens. In contrast, many 'mediating' genes of the immune system do not interact directly with specific pathogens and are involved in signalling (e.g. cytokines) or controlling immune cell growth. As a consequence, we might expect stronger selection at immune-receptor than mediating genes, but these two types of genes have not been compared directly in wild populations. Here, we tested the hypothesis that selection differs between MHC (class I and II) and mediating genes by comparing levels of population differentiation across the range of greater prairie-chickens (Tympanuchus cupido). As predicted, there was stronger population differentiation and isolation by distance at immune receptor (MHC) than at either mediating genes or neutral microsatellites, suggesting a stronger role of local adaptation at the MHC. In contrast, mediating genes displayed weaker differentiation between populations than neutral microsatellites, consistent with selection favouring similar alleles across populations for mediating genes. In addition to selection, drift also had a stronger effect on immune receptor (MHC) than mediating genes as indicated by the stronger decline of MHC variation in relation to population size. This is the first study in the wild to show that the effects of selection and drift on immune genes vary across populations depending on their functional role.
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Affiliation(s)
- Zachary W Bateson
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jeff A Johnson
- Department of Biological Sciences, Institute of Applied Sciences, University of North Texas, Denton, TX, USA
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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140
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Heterogeneity of dN/dS Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny. J Mol Evol 2015; 82:38-50. [PMID: 26573803 DOI: 10.1007/s00239-015-9713-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 10/30/2015] [Indexed: 10/22/2022]
Abstract
The classical class I HLA loci of humans show an excess of nonsynonymous with respect to synonymous substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. Additionally, high polymporphism, linkage disequilibrium, and disease associations suggest that one or more balancing selection regimes have acted upon these genes. However, several questions about these selective regimes remain open. First, it is unclear if stronger evidence for selection on deep timescales is due to changes in the intensity of selection over time or to a lack of power of most methods to detect selection on recent timescales. Another question concerns the functional entities which define the selected phenotype. While most analyses focus on selection acting on individual alleles, it is also plausible that phylogenetically defined groups of alleles ("lineages") are targets of selection. To address these questions, we analyzed how dN/dS (ω) varies with respect to divergence times between alleles and phylogenetic placement (position of branches). We find that ω for ARS codons of class I HLA genes increases with divergence time and is higher for inter-lineage branches. Throughout our analyses, we used non-selected codons to control for possible effects of inflation of ω associated to intra-specific analysis, and showed that our results are not artifactual. Our findings indicate the importance of considering the timescale effect when analysing ω over a wide spectrum of divergences. Finally, our results support the divergent allele advantage model, whereby heterozygotes with more divergent alleles have higher fitness than those carrying similar alleles.
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141
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Di D, Sanchez-Mazas A, Currat M. Computer simulation of human leukocyte antigen genes supports two main routes of colonization by human populations in East Asia. BMC Evol Biol 2015; 15:240. [PMID: 26530905 PMCID: PMC4632674 DOI: 10.1186/s12862-015-0512-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022] Open
Abstract
Background Recent genetic studies have suggested that the colonization of East Asia by modern humans was more complex than a single origin from the South, and that a genetic contribution via a Northern route was probably quite substantial. Results Here we use a spatially-explicit computer simulation approach to investigate the human migration hypotheses of this region based on one-route or two-route models. We test the likelihood of each scenario by using Human Leukocyte Antigen (HLA) − A, −B, and − DRB1 genetic data of East Asian populations, with both selective and demographic parameters considered. The posterior distribution of each parameter is estimated by an Approximate Bayesian Computation (ABC) approach. Conclusions Our results strongly support a model with two main routes of colonization of East Asia on both sides of the Himalayas, with distinct demographic histories in Northern and Southern populations, characterized by more isolation in the South. In East Asia, gene flow between populations originating from the two routes probably existed until a remote prehistoric period, explaining the continuous pattern of genetic variation currently observed along the latitude. A significant although dissimilar level of balancing selection acting on the three HLA loci is detected, but its effect on the local genetic patterns appears to be minor compared to those of past demographic events. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0512-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Da Di
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), 1 rue Michel-Servet, Geneva, CH-1211, Geneva 4, Switzerland.
| | - Mathias Currat
- Department of Genetics and Evolution - Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling history (AGP lab), University of Geneva, 12 rue Gustave-Revilliod, Geneva, CH-1211, Geneva 4, Switzerland.
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142
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Patarčić I, Gelemanović A, Kirin M, Kolčić I, Theodoratou E, Baillie KJ, de Jong MD, Rudan I, Campbell H, Polašek O. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis. Sci Rep 2015; 5:16119. [PMID: 26524966 PMCID: PMC4630784 DOI: 10.1038/srep16119] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022] Open
Abstract
Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.
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Affiliation(s)
- Inga Patarčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Andrea Gelemanović
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Mirna Kirin
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Midlothian, UK.,Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, Split, Croatia.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
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143
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Ramos PS, Shedlock AM, Langefeld CD. Genetics of autoimmune diseases: insights from population genetics. J Hum Genet 2015; 60:657-64. [PMID: 26223182 PMCID: PMC4660050 DOI: 10.1038/jhg.2015.94] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/12/2015] [Accepted: 06/19/2015] [Indexed: 12/14/2022]
Abstract
Human genetic diversity is the result of population genetic forces. This genetic variation influences disease risk and contributes to health disparities. Autoimmune diseases (ADs) are a family of complex heterogeneous disorders with similar underlying mechanisms characterized by immune responses against self. Collectively, ADs are common, exhibit gender and ethnic disparities, and increasing incidence. As natural selection is an important influence on human genetic variation, and immune function genes are enriched for signals of positive selection, it is thought that the prevalence of AD risk alleles seen in different population is partially the result of differing selective pressures (for example, due to pathogens). With the advent of high-throughput technologies, new analytical methodologies and large-scale projects, evidence for the role of natural selection in contributing to the heritable component of ADs keeps growing. This review summarizes the genetic regions associated with susceptibility to different ADs and concomitant evidence for selection, including known agents of selection exerting selective pressure in these regions. Examples of specific adaptive variants with phenotypic effects are included as an evidence of natural selection increasing AD susceptibility. Many of the complexities of gene effects in different ADs can be explained by population genetics phenomena. Integrating AD susceptibility studies with population genetics to investigate how natural selection has contributed to genetic variation that influences disease risk will help to identify functional variants and elucidate biological mechanisms. As such, the study of population genetics in human population holds untapped potential for elucidating the genetic causes of human disease and more rapidly focusing to personalized medicine.
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Affiliation(s)
- Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, and Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, SC, USA
- Hollings Marine Laboratory Center for Marine Biomedicine and College of Graduate Studies, Medical University of South Carolina, Charleston, SC, USA
| | - Carl D Langefeld
- Division of Public Health Sciences, Department of Biostatistical Sciences; and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
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144
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White KD, Chung WH, Hung SI, Mallal S, Phillips EJ. Evolving models of the immunopathogenesis of T cell-mediated drug allergy: The role of host, pathogens, and drug response. J Allergy Clin Immunol 2015; 136:219-34; quiz 235. [PMID: 26254049 DOI: 10.1016/j.jaci.2015.05.050] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/12/2022]
Abstract
Immune-mediated (IM) adverse drug reactions (ADRs) are an underrecognized source of preventable morbidity, mortality, and cost. Increasingly, genetic variation in the HLA loci is associated with risk of severe reactions, highlighting the importance of T-cell immune responses in the mechanisms of both B cell-mediated and primary T cell-mediated IM-ADRs. In this review we summarize the role of host genetics, microbes, and drugs in IM-ADR development; expand on the existing models of IM-ADR pathogenesis to address multiple unexplained observations; discuss the implications of this work in clinical practice today; and describe future applications for preclinical drug toxicity screening, drug design, and development.
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Affiliation(s)
- Katie D White
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Wen-Hung Chung
- Department of Dermatology, Chang Gung Memorial Hospital, Keelung, Taiwan; Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shuen-Iu Hung
- Program in Molecular Medicine, Institute of Pharmacology, School of Medicine, Infection and Immunity Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Simon Mallal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Elizabeth J Phillips
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia.
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145
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Clozato CL, Mazzoni CJ, Moraes-Barros N, Morgante JS, Sommer S. Spatial pattern of adaptive and neutral genetic diversity across different biomes in the lesser anteater (Tamandua tetradactyla). Ecol Evol 2015; 5:4932-48. [PMID: 26640672 PMCID: PMC4662318 DOI: 10.1002/ece3.1656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/08/2015] [Accepted: 07/13/2015] [Indexed: 01/03/2023] Open
Abstract
The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and activation of the adaptive immune response and are thought to be regulated by natural selection, especially due to pathogen‐driven selective pressure. In this study, we investigated the spatial distribution of MHC class IIDRB exon 2 gene diversity of the lesser anteater (Tamandua tetradactyla) across five Brazilian biomes using next‐generation sequencing and compared the MHC pattern with that of neutral markers (microsatellites). We found a noticeable high level of diversity in DRB (60 amino acid alleles in 65 individuals) and clear signatures of historical positive selection acting on this gene. Higher allelic richness and proportion of private alleles were found in rain forest biomes, especially Amazon forest, a megadiverse biome, possibly harboring greater pathogen richness as well. Neutral markers, however, showed a similar pattern to DRB, demonstrating the strength of demography as an additional force to pathogen‐driven selection in shaping MHC diversity and structure. This is the first characterization and description of diversity of a MHC gene for any member of the magna‐order Xenarthra, one of the basal lineages of placental mammals.
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Affiliation(s)
- Camila L Clozato
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo R. do Matão, 277 05508-090 São Paulo Brasil ; Leibniz-Institute for Zoo and Wildlife Research (IZW) Evolutionary Genetics Alfred- Kowalke-Straße 17 D-10315 Berlin Germany
| | - Camila J Mazzoni
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Evolutionary Genetics Alfred- Kowalke-Straße 17 D-10315 Berlin Germany ; Berlin Center for Genomics in Biodiversity Research (BeGenDiv) Koenigin-Luise-Straße. 6-8 D-14195 Berlin Germany
| | - Nadia Moraes-Barros
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo R. do Matão, 277 05508-090 São Paulo Brasil ; CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBio Laboratório Associado Universidade do Porto R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - João S Morgante
- Laboratório de Biologia Evolutiva e Conservação de Vertebrados Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo R. do Matão, 277 05508-090 São Paulo Brasil
| | - Simone Sommer
- Leibniz-Institute for Zoo and Wildlife Research (IZW) Evolutionary Genetics Alfred- Kowalke-Straße 17 D-10315 Berlin Germany ; Evolutionary Ecology and Conservation Genomics University of Ulm Albert-Einstein Strasse 11 D-89069 Ulm Germany
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146
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Dos Santos Francisco R, Buhler S, Nunes JM, Bitarello BD, França GS, Meyer D, Sanchez-Mazas A. HLA supertype variation across populations: new insights into the role of natural selection in the evolution of HLA-A and HLA-B polymorphisms. Immunogenetics 2015; 67:651-63. [PMID: 26459025 PMCID: PMC4636516 DOI: 10.1007/s00251-015-0875-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/29/2015] [Indexed: 01/03/2023]
Abstract
Supertypes are groups of human leukocyte antigen (HLA) alleles which bind overlapping sets of peptides due to sharing specific residues at the anchor positions-the B and F pockets-of the peptide-binding region (PBR). HLA alleles within the same supertype are expected to be functionally similar, while those from different supertypes are expected to be functionally distinct, presenting different sets of peptides. In this study, we applied the supertype classification to the HLA-A and HLA-B data of 55 worldwide populations in order to investigate the effect of natural selection on supertype rather than allelic variation at these loci. We compared the nucleotide diversity of the B and F pockets with that of the other PBR regions through a resampling procedure and compared the patterns of within-population heterozygosity (He) and between-population differentiation (G ST) observed when using the supertype definition to those estimated when using randomized groups of alleles. At HLA-A, low levels of variation are observed at B and F pockets and randomized He and G ST do not differ from the observed data. By contrast, HLA-B concentrates most of the differences between supertypes, the B pocket showing a particularly high level of variation. Moreover, at HLA-B, the reassignment of alleles into random groups does not reproduce the patterns of population differentiation observed with supertypes. We thus conclude that differently from HLA-A, for which supertype and allelic variation show similar patterns of nucleotide diversity within and between populations, HLA-B has likely evolved through specific adaptations of its B pocket to local pathogens.
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Affiliation(s)
- Rodrigo Dos Santos Francisco
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil. .,Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Hospital Israelita Albert Einstein, São Paulo, Brazil.
| | - Stéphane Buhler
- 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, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - José Manuel 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 (IGE3), Geneva, Switzerland
| | | | - Gustavo Starvaggi França
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, Brazil.,Molecular Oncology Center, Sírio-Libanês Hospital, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil.
| | - Alicia 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 (IGE3), Geneva, Switzerland.
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147
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Lau Q, Yasukochi Y, Satta Y. A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages. ACTA ACUST UNITED AC 2015; 86:343-52. [PMID: 26392055 PMCID: PMC5054888 DOI: 10.1111/tan.12667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 11/29/2022]
Abstract
Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co‐evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide‐binding and pathogen‐recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non‐peptide‐binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non‐exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.
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Affiliation(s)
- Q Lau
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kanagawa, Japan
| | - Y Yasukochi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Y Satta
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kanagawa, Japan
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148
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Human Leukocyte Antigen Diversity: A Southern African Perspective. J Immunol Res 2015; 2015:746151. [PMID: 26347896 PMCID: PMC4549606 DOI: 10.1155/2015/746151] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/26/2015] [Indexed: 12/30/2022] Open
Abstract
Despite the increasingly well-documented evidence of high genetic, ethnic, and linguistic diversity amongst African populations, there is limited data on human leukocyte antigen (HLA) diversity in these populations. HLA is part of the host defense mechanism mediated through antigen presentation to effector cells of the immune system. With the high disease burden in southern Africa, HLA diversity data is increasingly important in the design of population-specific vaccines and the improvement of transplantation therapeutic interventions. This review highlights the paucity of HLA diversity data amongst southern African populations and defines a need for information of this kind. This information will support disease association studies, provide guidance in vaccine design, and improve transplantation outcomes.
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149
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Stutz WE, Schmerer M, Coates JL, Bolnick DI. Among-lake reciprocal transplants induce convergent expression of immune genes in threespine stickleback. Mol Ecol 2015; 24:4629-46. [PMID: 26118468 DOI: 10.1111/mec.13295] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 12/25/2022]
Abstract
Geographic variation in parasite communities can drive evolutionary divergence in host immune genes. However, biotic and abiotic environmental variation can also induce plastic differences in immune function among populations. At present, there is little information concerning the relative magnitudes of heritable vs. induced immune divergence in natural populations. We examined immune gene expression profiles of threespine stickleback (Gasterosteus aculeatus) from six lakes on Vancouver Island, British Columbia. Parasite community composition differs between lake types (large or small, containing limnetic- or benthic-like stickleback) and between watersheds. We observed corresponding differences in immune gene expression profiles among wild-caught stickleback, using a set of seven immune genes representing distinct branches of the immune system. To evaluate the role of environmental effects on this differentiation, we experimentally transplanted wild-caught fish into cages in their native lake, or into a nearby foreign lake. Transplanted individuals' immune gene expression converged on patterns typical of their destination lake, deviating from their native expression profile. Transplant individuals' source population had a much smaller effect, suggesting relatively weak genetic underpinning of population differences in immunity, as viewed through gene expression. This strong environmental regulation of immune gene expression provides a counterpoint to the large emerging literature documenting microevolution and genetic diversification of immune function. Our findings illustrate the value of studying immunity in natural environmental settings where the immune system has evolved and actively functions.
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Affiliation(s)
- William E Stutz
- Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, TX, 78712, USA
| | - Matthew Schmerer
- Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, TX, 78712, USA
| | - Jessica L Coates
- Department of Biology, Spelman College, 350 Spelman Lane SW, Atlanta, GA, 30314, USA
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, TX, 78712, USA.,Howard Hughes Medical Institute, University of Texas at Austin, One University Station C0990, Austin, TX, 78712, USA
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Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture. J Hum Genet 2015. [PMID: 26202576 DOI: 10.1038/jhg.2015.90] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The human leukocyte antigen (HLA) region is the most polymorphic region in the human genome. The polymorphic nature of the HLA region is thought to have been shaped from balancing selection. The complex migration events during the Out-of-Africa expansion have influenced geographic patterns of HLA allele frequencies and diversities across present-day human populations. Differences in the HLA allele frequency may contribute geographic differences in the susceptibility to many diseases, such as infectious, autoimmune and metabolic diseases. Here we briefly reviewed characteristics of frequency distribution of HLA alleles and haplotypes in Japanese population. A large part of HLA alleles and haplotypes that are common in Japanese are shared with neighboring Asian populations. The differentiations in HLA alleles and haplotypes across Japanese regional populations may provide clues to model for peopling of Japanese Archipelago and for design of genetic association studies. Finally, we introduce recent topics that new HLA alleles derived from ancient admixtures with Neanderthals and Denisovans are thought to have played an important role in the adaptation of modern humans to local pathogens during Out-of-Africa expansion.
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