1
|
Wojczulanis-Jakubas K, Hoover B, Jakubas D, Fort J, Grémillet D, Gavrilo M, Zielińska S, Zagalska-Neubauer M. Diversity of major histocompatibility complex of II B gene and mate choice in a monogamous and long-lived seabird, the Little Auk (Alle alle). PLoS One 2024; 19:e0304275. [PMID: 38865310 PMCID: PMC11168636 DOI: 10.1371/journal.pone.0304275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024] Open
Abstract
The major histocompatibility complex (MHC) plays a key role in the adaptive immune system of vertebrates, and is known to influence mate choice in many species. In birds, the MHC has been extensively examined but mainly in galliforms and passerines while other taxa that represent specific ecological and evolutionary life-histories, like seabirds, are underexamined. Here, we characterized diversity of MHC Class II B exon 2 in a colonial pelagic seabird, the Little Auk (or Dovekie Alle alle). We further examined whether MHC variation could be maintained through balancing selection and disassortative mating. We found high polymorphism at the genotyped MHC fragment, characterizing 99 distinct alleles across 140 individuals from three populations. The alleles frequencies exhibited a similar skewed distribution in both sexes, with the four most commonly occurring alleles representing approximately 35% of allelic variation. The results of a Bayesian site-by-site selection analysis suggest evidence of balancing selection and no direct evidence for MHC-dependent disassortative mating preferences in the Little Auk. The latter result might be attributed to the high overall polymorphism of the examined fragment, which itself may be maintained by the large population size of the species.
Collapse
Affiliation(s)
| | - Brian Hoover
- Farallon Institute, Petaluma, California, United States of America
| | - Dariusz Jakubas
- Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Jérôme Fort
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS – La Rochelle University, 17000 La Rochelle, France
| | - David Grémillet
- Excellence Chair Nouvelle Aquitaine - CEBC UMR 7372 CNRS, La Rochelle Université, Villiers-en-Bois, France & FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | | | - Sylwia Zielińska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | |
Collapse
|
2
|
Phillips SR. MHC-B Diversity and Signs of Respiratory Illness in Wild, East African Chimpanzees ( Pan troglodytes schweinfurthii ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551731. [PMID: 37577711 PMCID: PMC10418158 DOI: 10.1101/2023.08.02.551731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Many traits, intrinsic and extrinsic to an organism, contribute to interindividual variation in immunity in wild habitats. The vertebrate Major Histocompatibility Complex (MHC) includes genes encoding antigen-presenting molecules that are highly variable, and that variation often predicts susceptibility/resistance to and recovery from pathogen infection. I compare MHC-B variation at two long-term chimpanzee research sites, Kibale National Park in Uganda and Gombe National Park in Tanzania. Using decades of respiratory health data available for these chimpanzees, I test hypotheses associated with maintenance of diversity at MHC loci, including heterozygote, divergent allele, and rare allele advantage hypotheses, and predictions for unique function of MHC-B in great apes. I found, despite confirmation of recent shared ancestry between Kibale and Gombe chimpanzees, including an overlapping MHC-B allele repertoire and similar MHC-B phenotype compositions, chimpanzees from the two research sites experienced differences in the occurrence of respiratory signs and had different associations of MHC-B diversity with signs of respiratory illness. Kibale chimpanzees with heterozygous genotypes and different peptide-binding supertypes were observed less often with respiratory signs than those homozygous or possessing the same supertypes, but this same association was not observed among Gombe chimpanzees. Gombe chimpanzees with specific MHC-B phenotypes that enable engagement of Natural Killer (NK) cells were observed more often with respiratory signs than chimpanzees with other phenotypes, but this was not observed at Kanyawara. This study emphasizes local adaptation in shaping genetic and phenotypic traits in different infectious disease contexts, even among close genetic relatives of the same subspecies, and highlights utility for continued and simultaneous tracking of host immune genes and specific pathogens in wild species.
Collapse
|
3
|
Pudjihartono N, Ho D, Golovina E, Fadason T, Kempa-Liehr AW, O'Sullivan JM. Juvenile idiopathic arthritis-associated genetic loci exhibit spatially constrained gene regulatory effects across multiple tissues and immune cell types. J Autoimmun 2023; 138:103046. [PMID: 37229810 DOI: 10.1016/j.jaut.2023.103046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 05/27/2023]
Abstract
Juvenile idiopathic arthritis (JIA) is an autoimmune, inflammatory joint disease with complex genetic etiology. Previous GWAS have found many genetic loci associated with JIA. However, the biological mechanism behind JIA remains unknown mainly because most risk loci are located in non-coding genetic regions. Interestingly, increasing evidence has found that regulatory elements in the non-coding regions can regulate the expression of distant target genes through spatial (physical) interactions. Here, we used information on the 3D genome organization (Hi-C data) to identify target genes that physically interact with SNPs within JIA risk loci. Subsequent analysis of these SNP-gene pairs using data from tissue and immune cell type-specific expression quantitative trait loci (eQTL) databases allowed the identification of risk loci that regulate the expression of their target genes. In total, we identified 59 JIA-risk loci that regulate the expression of 210 target genes across diverse tissues and immune cell types. Functional annotation of spatial eQTLs within JIA risk loci identified significant overlap with gene regulatory elements (i.e., enhancers and transcription factor binding sites). We found target genes involved in immune-related pathways such as antigen processing and presentation (e.g., ERAP2, HLA class I and II), the release of pro-inflammatory cytokines (e.g., LTBR, TYK2), proliferation and differentiation of specific immune cell types (e.g., AURKA in Th17 cells), and genes involved in physiological mechanisms related to pathological joint inflammation (e.g., LRG1 in arteries). Notably, many of the tissues where JIA-risk loci act as spatial eQTLs are not classically considered central to JIA pathology. Overall, our findings highlight the potential tissue and immune cell type-specific regulatory changes contributing to JIA pathogenesis. Future integration of our data with clinical studies can contribute to the development of improved JIA therapy.
Collapse
Affiliation(s)
- N Pudjihartono
- The Liggins Institute, The University of Auckland, Auckland, New Zealand.
| | - D Ho
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - E Golovina
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - T Fadason
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - A W Kempa-Liehr
- Department of Engineering Science, The University of Auckland, Auckland, New Zealand
| | - J M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand; The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand; MRC Lifecourse Epidemiology Unit, University of Southampton, United Kingdom; Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, New South Wales, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia; A*STAR Singapore Institute for Clinical Sciences, Singapore, Singapore.
| |
Collapse
|
4
|
Czaja AJ. Incorporating the Molecular Mimicry of Environmental Antigens into the Causality of Autoimmune Hepatitis. Dig Dis Sci 2023:10.1007/s10620-023-07967-5. [PMID: 37160542 PMCID: PMC10169207 DOI: 10.1007/s10620-023-07967-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Molecular mimicry between foreign and self-antigens has been implicated as a cause of autoimmune hepatitis in experimental models and cross-reacting antibodies in patients. This review describes the experimental and clinical evidence for molecular mimicry as a cause of autoimmune hepatitis, indicates the limitations and uncertainties of this premise, and encourages investigations that assess diverse environmental antigens as sources of disease-relevant molecular mimics. Pertinent articles were identified in PubMed using multiple search phrases. Several pathogens have linear or conformational epitopes that mimic the self-antigens of autoimmune hepatitis. The occurrence of an acute immune-mediated hepatitis after vaccination for severe acute respiratory syndrome (SARS)-associated coronavirus 2 (SARS-CoV-2) has suggested that vaccine-induced peptides may mimic disease-relevant tissue antigens. The intestinal microbiome is an under-evaluated source of gut-derived antigens that could also engage in molecular mimicry. Chaperone molecules may enhance the pathogenicity of molecular mimics, and they warrant investigation. Molecular mimics of immune dominant epitopes within cytochrome P450 IID6, the autoantigen most closely associated with autoimmune hepatitis, should be sought in diverse environmental antigens and assessed for pathogenicity. Avoidance strategies, dietary adjustments, vaccine improvement, and targeted manipulation of the intestinal microbiota may emerge as therapeutic possibilities. In conclusion, molecular mimicry may be a missing causality of autoimmune hepatitis. Molecular mimics of key immune dominant epitopes of disease-specific antigens must be sought in diverse environmental antigens. The ubiquity of molecular mimicry compels rigorous assessments of peptide mimics for immunogenicity and pathogenicity in experimental models. Molecular mimicry may complement epigenetic modifications as causative mechanisms of autoimmune hepatitis.
Collapse
Affiliation(s)
- Albert J Czaja
- Professor Emeritus of Medicine, Mayo Clinic College of Medicine and Science, 200 First Street SW, Rochester, MN, 55905, USA.
| |
Collapse
|
5
|
Card DC, Van Camp AG, Santonastaso T, Jensen-Seaman MI, Anthony NM, Edwards SV. Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes. Front Genet 2022; 13:979746. [PMID: 36425073 PMCID: PMC9679377 DOI: 10.3389/fgene.2022.979746] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022] Open
Abstract
The major histocompatibility complex (MHC) is an important genomic region for adaptive immunity and has long been studied in ecological and evolutionary contexts, such as disease resistance and mate and kin selection. The MHC has been investigated extensively in mammals and birds but far less so in squamate reptiles, the third major radiation of amniotes. We localized the core MHC genomic region in two squamate species, the green anole (Anolis carolinensis) and brown anole (A. sagrei), and provide the first detailed characterization of the squamate MHC, including the presence and ordering of known MHC genes in these species and comparative assessments of genomic structure and composition in MHC regions. We find that the Anolis MHC, located on chromosome 2 in both species, contains homologs of many previously-identified mammalian MHC genes in a single core MHC region. The repetitive element composition in anole MHC regions was similar to those observed in mammals but had important distinctions, such as higher proportions of DNA transposons. Moreover, longer introns and intergenic regions result in a much larger squamate MHC region (11.7 Mb and 24.6 Mb in the green and brown anole, respectively). Evolutionary analyses of MHC homologs of anoles and other representative amniotes uncovered generally monophyletic relationships between species-specific homologs and a loss of the peptide-binding domain exon 2 in one of two mhc2β gene homologs of each anole species. Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. Altogether, our investigation fills a major gap in understanding of amniote MHC diversity and evolution and provides an important foundation for future squamate-specific or vertebrate-wide investigations of the MHC.
Collapse
Affiliation(s)
- Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
- *Correspondence: Daren C. Card,
| | - Andrew G. Van Camp
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
| | - Trenten Santonastaso
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | | | - Nicola M. Anthony
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, United States
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States
| |
Collapse
|
6
|
Petersen RM, Bergey CM, Roos C, Higham JP. Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate. Ecol Evol 2022; 12:e9346. [PMID: 36311412 PMCID: PMC9596323 DOI: 10.1002/ece3.9346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome-wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome-wide and locus-specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (i.e., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper-variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (Papio anubis), we conducted double digest restriction site-associated DNA sequencing to estimate genome-wide heterozygosity and kinship, and sequenced two class I and two class II MHC loci. We found that genome-wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome-wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC-associated mate choice.
Collapse
Affiliation(s)
- Rachel M. Petersen
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
| | - Christina M. Bergey
- Department of Genetics and the Human Genetics Institute of New JerseyRutgers UniversityPiscatawayNew JerseyUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics LaboratoryGerman Primate CenterLeibniz Institute for Primate ResearchGöttingenGermany
| | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
| |
Collapse
|
7
|
Using de novo genome assembly and high-throughput sequencing to characterize the MHC region in a non-model bird, the Eurasian coot. Sci Rep 2022; 12:7031. [PMID: 35488050 PMCID: PMC9054815 DOI: 10.1038/s41598-022-11018-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Genes of the Major Histocompatibility Complex (MHC) form a key component of vertebrate adaptive immunity, as they code for molecules which bind antigens of intra- and extracellular pathogens (MHC class I and II, respectively) and present them to T cell receptors. In general, MHC genes are hyper-polymorphic and high MHC diversity is often maintained within natural populations (via balancing selection) and within individuals (via gene duplications). Because of its complex architecture with tandems of duplicated genes, characterization of MHC region in non-model vertebrate species still poses a major challenge. Here, we combined de novo genome assembly and high-throughput sequencing to characterize MHC polymorphism in a rallid bird species, the Eurasian coot Fulica atra. An analysis of genome assembly indicated high duplication rate at MHC-I, which was also supported by targeted sequencing of peptide-binding exons (at least five MHC-I loci genotyped). We found high allelic richness at both MHC-I and MHC-II, although signature of diversifying selection and recombination (gene conversion) was much stronger at MHC-II. Our results indicate that Eurasian coot retains extraordinary polymorphism at both MHC classes (when compared to other non-passerine bird species), although they may be subject to different evolutionary mechanism.
Collapse
|
8
|
CDR3 binding chemistry controls TCR V-domain rotational probability and germline CDR2 scanning of polymorphic MHC. Mol Immunol 2022; 144:138-151. [DOI: 10.1016/j.molimm.2021.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/17/2021] [Accepted: 11/21/2021] [Indexed: 11/21/2022]
|
9
|
Buzan E, Potušek S, Duniš L, Pokorny B. Neutral and Selective Processes Shape MHC Diversity in Roe Deer in Slovenia. Animals (Basel) 2022; 12:ani12060723. [PMID: 35327121 PMCID: PMC8944837 DOI: 10.3390/ani12060723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 03/10/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Disease prevention and appropriate wildlife management are among the major challenges in wildlife conservation. In the present study, we made a first assessment of the variability of major histocompatibility complex (MHC) genes in roe deer in Slovenia and evaluated local population adaptation by comparing MHC variability with neutral microsatellites. We discovered three new MHC DRB exon 2 alleles in addition to seven previously described in the literature. Moreover, we found evidence of historical positive selection, as selection analysis indicated that approx. 10% of the encoded amino acids were subjected to episodic positive selection. This study provides the basis for further research on immunogenetic variation in roe deer and highlights opportunities to incorporate genetic data into science-based population management. Abstract Disease control and containment in free-ranging populations is one of the greatest challenges in wildlife management. Despite the importance of major histocompatibility complex (MHC) genes for immune response, an assessment of the diversity and occurrence of these genes is still rare in European roe deer, the most abundant and widespread large mammal in Europe. Therefore, we examined immunogenetic variation in roe deer in Slovenia to identify species adaptation by comparing the genetic diversity of the MHC genes with the data on neutral microsatellites. We found ten MHC DRB alleles, three of which are novel. Evidence for historical positive selection on the MHC was found using the maximum likelihood codon method. Patterns of MHC allelic distribution were not congruent with neutral population genetic findings. The lack of population genetic differentiation in MHC genes compared to existing structure in neutral markers suggests that MHC polymorphism was influenced primarily by balancing selection and, to a lesser extent, by neutral processes such as genetic drift, with no clear evidence of local adaptation. Selection analyses indicated that approx. 10% of amino acids encoded under episodic positive selection. This study represents one of the first steps towards establishing an immunogenetic map of roe deer populations across Europe, aiming to better support science-based management of this important game species.
Collapse
Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Correspondence: ; Tel.: +38-65-6117570; Fax: +38-65-61175
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Luka Duniš
- Faculty of Mathematics, Natural Sciences, and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (S.P.); (L.D.)
| | - Boštjan Pokorny
- Environmental Protection College, Trg Mladosti 7, 3320 Velenje, Slovenia;
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia
| |
Collapse
|
10
|
Discovery of an ancient MHC category with both class I and class II features. Proc Natl Acad Sci U S A 2021; 118:2108104118. [PMID: 34903649 PMCID: PMC8713811 DOI: 10.1073/pnas.2108104118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
Two classes of major histocompatibility complex (MHC) molecules, MHC class I and MHC class II, constitute the basis of our elaborate, adaptive immune system as antigen-presenting molecules. They perform distinct, critical functions: especially, MHC class I in case of antivirus and antitumor defenses, and MHC class II, in case of effective antibody responses. This important class diversification has long been enigmatic, as vestiges of the evolutionary molecular changes have not been found. The revealed ancient MHC category represents a plausible intermediate group between the two classes, and the data suggest that class II preceded class I in molecular evolution. Fundamental understanding of the molecular evolution of MHC molecules should contribute to understanding the basis of our complex biological defense system. Two classes of major histocompatibility complex (MHC) molecules, MHC class I and class II, play important roles in our immune system, presenting antigens to functionally distinct T lymphocyte populations. However, the origin of this essential MHC class divergence is poorly understood. Here, we discovered a category of MHC molecules (W-category) in the most primitive jawed vertebrates, cartilaginous fish, and also in bony fish and tetrapods. W-category, surprisingly, possesses class II–type α- and β-chain organization together with class I–specific sequence motifs for interdomain binding, and the W-category α2 domain shows unprecedented, phylogenetic similarity with β2-microglobulin of class I. Based on the results, we propose a model in which the ancestral MHC class I molecule evolved from class II–type W-category. The discovery of the ancient MHC group, W-category, sheds a light on the long-standing critical question of the MHC class divergence and suggests that class II type came first.
Collapse
|
11
|
Wu Y, Zhang N, Hashimoto K, Xia C, Dijkstra JM. Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First. Front Immunol 2021; 12:621153. [PMID: 34194421 PMCID: PMC8236899 DOI: 10.3389/fimmu.2021.621153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β2-microglobulin (β2-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β2-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β2-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred.
Collapse
Affiliation(s)
- Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Keiichiro Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| |
Collapse
|
12
|
Minias P, He K, Dunn PO. The strength of selection is consistent across both domains of the MHC class I peptide-binding groove in birds. BMC Ecol Evol 2021; 21:80. [PMID: 33964878 PMCID: PMC8106206 DOI: 10.1186/s12862-021-01812-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/28/2021] [Indexed: 02/26/2023] Open
Abstract
Background The Major Histocompatibility Complex (MHC) codes for the key vertebrate immune receptors responsible for pathogen recognition. Foreign antigens are recognized via their compatibility to hyper-variable region of the peptide-binding groove (PBR), which consists of two separate protein domains. Specifically, the PBR of the MHC class I receptors, which recognize intra-cellular pathogens, has two α domains encoded by exon 2 (α1) and exon 3 (α2) of the same gene. Most research on avian MHC class I polymorphism has traditionally focused exclusively on exon 3 and comparisons of selection between the two domains have been hampered by the scarcity of molecular data for exon 2. Thus, it is not clear whether the two domains vary in their specificity towards different antigens and whether they are subject to different selective pressure. Results Here, we took advantage of rapidly accumulating genomic resources to test for the differences in selection patterns between both MHC class I domains of the peptide-binding groove in birds. For this purpose, we compiled a dataset of MHC class I exon 2 and 3 sequences for 120 avian species from 46 families. Our phylogenetically-robust approach provided strong evidence for highly consistent levels of selection on the α1 and α2 domains. There were strong correlations in all selection measures (number of positively/negatively selected residues and dN/dS ratios) between both PBR exons. Similar positive associations were found for the level of amino acid polymorphism across the two domains. Conclusions We conclude that the strength of selection and the level of polymorphism are highly consistent between both peptide-binding domains (α1 and α2) of the avian MHC class I. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01812-x.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, USA
| |
Collapse
|
13
|
Liu C, Lei H, Ran X, Wang J. Genetic variation and selection in the major histocompatibility complex Class II gene in the Guizhou pony. PeerJ 2020; 8:e9889. [PMID: 32999762 PMCID: PMC7505079 DOI: 10.7717/peerj.9889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/17/2020] [Indexed: 11/20/2022] Open
Abstract
The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
Collapse
Affiliation(s)
- Chang Liu
- College of Animal Sciences, Guizhou University, Guiyang, China.,College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hongmei Lei
- College of Animal Sciences, Guizhou University, Guiyang, China
| | - Xueqin Ran
- College of Animal Sciences, Guizhou University, Guiyang, China
| | - Jiafu Wang
- College of Animal Sciences, Guizhou University, Guiyang, China.,Tongren University, Tongren, China
| |
Collapse
|
14
|
Cruz-López M, Fernández G, Hipperson H, Palacios E, Cavitt J, Galindo-Espinosa D, Gómez Del Angel S, Pruner R, Gonzalez O, Burke T, Küpper C. Allelic diversity and patterns of selection at the major histocompatibility complex class I and II loci in a threatened shorebird, the Snowy Plover (Charadrius nivosus). BMC Evol Biol 2020; 20:114. [PMID: 32912143 PMCID: PMC7488298 DOI: 10.1186/s12862-020-01676-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 08/20/2020] [Indexed: 12/02/2022] Open
Abstract
Background Understanding the structure and variability of adaptive loci such as the major histocompatibility complex (MHC) genes is a primary research goal for evolutionary and conservation genetics. Typically, classical MHC genes show high polymorphism and are under strong balancing selection, as their products trigger the adaptive immune response in vertebrates. Here, we assess the allelic diversity and patterns of selection for MHC class I and class II loci in a threatened shorebird with highly flexible mating and parental care behaviour, the Snowy Plover (Charadrius nivosus) across its broad geographic range. Results We determined the allelic and nucleotide diversity for MHC class I and class II genes using samples of 250 individuals from eight breeding population of Snowy Plovers. We found 40 alleles at MHC class I and six alleles at MHC class II, with individuals carrying two to seven different alleles (mean 3.70) at MHC class I and up to two alleles (mean 1.45) at MHC class II. Diversity was higher in the peptide-binding region, which suggests balancing selection. The MHC class I locus showed stronger signatures of both positive and negative selection than the MHC class II locus. Most alleles were present in more than one population. If present, private alleles generally occurred at very low frequencies in each population, except for the private alleles of MHC class I in one island population (Puerto Rico, lineage tenuirostris). Conclusion Snowy Plovers exhibited an intermediate level of diversity at the MHC, similar to that reported in other Charadriiformes. The differences found in the patterns of selection between the class I and II loci are consistent with the hypothesis that different mechanisms shape the sequence evolution of MHC class I and class II genes. The rarity of private alleles across populations is consistent with high natal and breeding dispersal and the low genetic structure previously observed at neutral genetic markers in this species.
Collapse
Affiliation(s)
- Medardo Cruz-López
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico.
| | - Guillermo Fernández
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apartado Postal 811, 82040, Mazatlán, Sinaloa, Mexico
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Eduardo Palacios
- Centro de Investigación Científica y de Educación Superior de Ensenada, Unidad La Paz, Miraflores 334, Col. Bellavista, 23050, La Paz, Baja California Sur, Mexico
| | - John Cavitt
- Avian Ecology Laboratory Department of Zoology, Weber State University, Ogden, UT, 84408, USA
| | - Daniel Galindo-Espinosa
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Carretera al Sur km 5.5, A.P. 19-B, 23080, La Paz, B.C.S., Mexico
| | - Salvador Gómez Del Angel
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, Mexico
| | - Raya Pruner
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Panama City, FL, USA
| | - Oscar Gonzalez
- Grupo Aves del Perú, Gómez del Carpio 135, Barrio Medico, 34, Lima, Peru.,Department of Natural Sciences, Emmanuel College, Franklin Springs, GA, 30369, USA
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Clemens Küpper
- Max Planck Institute for Ornithology, Eberhard-Gwinner-Strasse, 82319, Seewiesen, Germany.
| |
Collapse
|
15
|
Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
Collapse
Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
16
|
Demharter S, Knapp B, Deane C, Minary P. HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo. J Chem Inf Model 2019; 59:2894-2899. [PMID: 31070900 PMCID: PMC7007188 DOI: 10.1021/acs.jcim.9b00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Indexed: 11/28/2022]
Abstract
MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilizes the open conformation of the MHCII binding groove when no peptide is bound. While a structure of the MHCII/HLA-DM complex exists, the mechanism of stabilization is still largely unknown. Here, we applied customized Natural Move Monte Carlo to investigate this interaction. We found a possible long-range mechanism that implicates the configuration of the membrane-proximal globular domains in stabilizing the open state of the empty MHCII binding groove.
Collapse
Affiliation(s)
- Samuel Demharter
- Biotech
Research and Innovation Centre, University
of Copenhagen, Copenhagen 2200, Denmark
- Department
of Computer Science, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Bernhard Knapp
- Bioinformatics
and Immunoinformatics Research Group, Department of Basic Sciences, International University of Catalonia, 08195 Barcelona, Spain
| | - Charlotte Deane
- Protein
Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Peter Minary
- Department
of Computer Science, University of Oxford, Oxford OX1 3QD, United Kingdom
| |
Collapse
|
17
|
Gao C, Xin C, Wang X, Quan J, Li C, Wang J, Chen H. Molecular genetic characterization and haplotype diversity of swine leukocyte antigen in Chinese Rongshui miniature pigs. Mol Immunol 2019; 112:215-222. [PMID: 31177058 DOI: 10.1016/j.molimm.2019.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/30/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
The Rongshui miniature pig is an important model animal for studying livestock disease prevention and control in China. The highly polymorphic swine leukocyte antigen (SLA) has been the focus of considerable interest because of the strong, reproducible associations between particular SLA haplotypes and infectious diseases. In this study, we identified 42 alleles at eight polymorphic SLA loci (SLA-1, SLA-3, SLA-2, SLA-6, DRA, DRB1, DQA, and DQB1) representing seven class I and six class II haplotypes using reverse transcription-polymerase chain reaction (RT-PCR) sequence-based typing and PCR-sequence specific primers in Rongshui miniature pigs. The official names were designated by the SLA Nomenclature Committee of the International Society for Animal Genetics. Seven class I haplotypes, Hp-5b.0, 86.0, 87.0, 88.0, 89.0, 90.0 and 91.0, and four class II haplotypes, Hp-0.18b, 0.19c, 0.41 and 0.47, had not previously been reported in other pig breeds. We also comprehensively analyzed the molecular genetic characterization and phylogenies of the identified alleles and the SLA haplotype diversity in Rongshui miniature pigs. SLA-1 and SLA-6 genes were under positive selection, while SLA-2 was under neutral selection, and the other five genes were under purifying selection. The highly polymorphic new alleles may be derived by nucleotide mutations, insertions and deletions, and fragment recombination, and alleles segregated based on sequence differences and peptide-binding motifs, rather than on pig breed. SLA haplotype diversity was generated by allele/gene conversion and recombination. These results will be helpful for elucidating the molecular genetic mechanisms influencing differential disease resistance among pigs with different SLA haplotypes.
Collapse
Affiliation(s)
- Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China
| | - Chang Xin
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China
| | - Xiuying Wang
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China
| | - Jinqiang Quan
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China
| | - Changwen Li
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China
| | - Jingyu Wang
- Laboratory Animal Center, Dalian Medical University, Dalian, 116027, China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, China.
| |
Collapse
|
18
|
Shin DH, Baek IC, Kim HJ, Choi EJ, Ahn M, Jung MH, Suh BK, Cho WK, Kim TG. HLA alleles, especially amino-acid signatures of HLA-DPB1, might contribute to the molecular pathogenesis of early-onset autoimmune thyroid disease. PLoS One 2019; 14:e0216941. [PMID: 31091281 PMCID: PMC6519818 DOI: 10.1371/journal.pone.0216941] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/01/2019] [Indexed: 11/17/2022] Open
Abstract
The major histocompatibility complex region has been suggested to play an important role in the development of autoimmune thyroid disease (AITD). In this study, we investigated the associations of human leukocyte antigen (HLA) alleles and amino acid variants of HLA with early-onset AITD. HLA class I and class II genes were analyzed in 116 Korean children with AITDs (Graves’ disease [GD]: 71, Hashimoto’s disease [HD]: 45) and 142 healthy controls. HLA-B*46:01 (OR = 3.96, Pc = 0.008), -C*01:02 (OR = 2.51 Pc = 0.04), -DPB1*02:02 (OR = 3.99, Pc = 0.04), and -DPB1*05:01 (OR = 4.6, Pc = 0.003) were significantly associated with GD, and HLA-A*02:07 (OR = 4.68, Pc = 0.045) and -DPB1*02:02 (OR = 6.57, Pc = 0.0001) with HD. The frequency of HLA-DPB1*05:01 was significantly higher in GD patients than in HD patients (Pc = 0.0005). Furthermore, differences were found between patients with Thyroid associated ophthalmopathy (TAO) and those without TAO in the distribution of HLA-B*54:01 (8.6% vs. 30.6%, P = 0.04) and -C*03:03 (37.1% vs. 11.1%, P = 0.02). In the analysis of amino acid variants of HLA molecules, both Leu35 (OR = 23.38, P = 0.0002) and Glu55 (OR = 23.38, P = 0.0002) of HLA-DPB1 were strongly associated with GD and showed different distributions between GD and HD (P = 0.001). Our results suggest that HLA alleles, especially amino-acid signatures of the HLA-DP β chain, might contribute to the molecular pathogenesis of early-onset AITD.
Collapse
Affiliation(s)
- Dong-Hwan Shin
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In-Cheol Baek
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyung Jae Kim
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Moonbae Ahn
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Min Ho Jung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byung-Kyu Suh
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Won Kyoung Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
19
|
Rocha RG, Magalhães V, López-Bao JV, van der Loo W, Llaneza L, Alvares F, Esteves PJ, Godinho R. Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore. BMC Evol Biol 2019; 19:90. [PMID: 30975084 PMCID: PMC6460805 DOI: 10.1186/s12862-019-1420-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/04/2019] [Indexed: 01/26/2023] Open
Abstract
Background Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci. Results Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection. Conclusion Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity. Electronic supplementary material The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rita G Rocha
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Vanessa Magalhães
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - José V López-Bao
- Research Unit of Biodiversity (UO/CSIC/PA), University of Oviedo, 33600, Mieres, Spain
| | - Wessel van der Loo
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- A.RE.NA, S.L. Asesores en Recursos Naturales S.L., 27003, Lugo, Spain
| | - Francisco Alvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
| |
Collapse
|
20
|
Thibodeau J, Moulefera MA, Balthazard R. On the structure–function of MHC class II molecules and how single amino acid polymorphisms could alter intracellular trafficking. Hum Immunol 2019; 80:15-31. [DOI: 10.1016/j.humimm.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/01/2022]
|
21
|
Vereerstraeten P, Andrien M, Dupont E, Abramowicz D, de Pauw L, Goldman M, Kinnaert P. Detrimental role of donor-recipient HLA-DQ5
and -DQ6
disparities on cadaver kidney graft survival. Transpl Int 2018. [DOI: 10.1111/tri.1992.5.s1.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
22
|
Minias P, Pikus E, Whittingham LA, Dunn PO. A global analysis of selection at the avian MHC. Evolution 2018; 72:1278-1293. [PMID: 29665025 DOI: 10.1111/evo.13490] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/29/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Recent advancements in sequencing technology have resulted in rapid progress in the study of the major histocompatibility complex (MHC) in non-model avian species. Here, we analyze a global dataset of avian MHC class I and class II sequences (ca. 11,000 sequences from over 250 species) to gain insight into the processes that govern macroevolution of MHC genes in birds. Analysis of substitution rates revealed striking differences in the patterns of diversifying selection between passerine and non-passerine birds. Non-passerines showed stronger selection at MHC class II, which is primarily involved in recognition of extracellular pathogens, while passerines showed stronger selection at MHC class I, which is involved in recognition of intracellular pathogens. Positions of positively selected amino-acid residues showed marked discrepancies with peptide-binding residues (PBRs) of human MHC molecules, suggesting that using a human classification of PBRs to assess selection patterns at the avian MHC may be unjustified. Finally, our analysis provided evidence that indel mutations can make a substantial contribution to adaptive variation at the avian MHC.
Collapse
Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland
| | - Linda A Whittingham
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53211
| | - Peter O Dunn
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, 90-237, Poland.,Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53211
| |
Collapse
|
23
|
Saka T, Nishita Y, Masuda R. Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan. Immunogenetics 2017; 70:115-124. [PMID: 28689276 DOI: 10.1007/s00251-017-1020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/25/2017] [Indexed: 12/12/2022]
Abstract
Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.
Collapse
Affiliation(s)
- Toshinori Saka
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan. .,Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan.
| |
Collapse
|
24
|
Wroblewski EE, Guethlein LA, Norman PJ, Li Y, Shaw CM, Han AS, Ndjango JBN, Ahuka-Mundeke S, Georgiev AV, Peeters M, Hahn BH, Parham P. Bonobos Maintain Immune System Diversity with Three Functional Types of MHC-B. THE JOURNAL OF IMMUNOLOGY 2017; 198:3480-3493. [PMID: 28348269 PMCID: PMC5469624 DOI: 10.4049/jimmunol.1601955] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
Abstract
Fast-evolving MHC class I polymorphism serves to diversify NK cell and CD8 T cell responses in individuals, families, and populations. Because only chimpanzee and bonobo have strict orthologs of all HLA class I, their study gives unique perspectives on the human condition. We defined polymorphism of Papa-B, the bonobo ortholog of HLA-B, for six wild bonobo populations. Sequences for Papa-B exon 2 and 3 were determined from the genomic DNA in 255 fecal samples, minimally representing 110 individuals. Twenty-two Papa-B alleles were defined, each encoding a different Papa-B protein. No Papa-B is identical to any chimpanzee Patr-B, human HLA-B, or gorilla Gogo-B. Phylogenetic analysis identified a clade of MHC-B, defined by residues 45-74 of the α1 domain, which is broadly conserved among bonobo, chimpanzee, and gorilla. Bonobo populations have 3-14 Papa-B allotypes. Three Papa-B are in all populations, and they are each of a different functional type: allotypes having the Bw4 epitope recognized by killer cell Ig-like receptors of NK cells, allotypes having the C1 epitope also recognized by killer cell Ig-like receptors, and allotypes having neither epitope. For population Malebo, these three Papa-B are the only Papa-B allotypes. Although small in number, their sequence divergence is such that the nucleotide diversity (mean proportional distance) of Papa-B in Malebo is greater than in the other populations and is also greater than expected for random combinations of three Papa-B Overall, Papa-B has substantially less diversity than Patr-B in chimpanzee subspecies and HLA-B in indigenous human populations, consistent with bonobo having experienced narrower population bottlenecks.
Collapse
Affiliation(s)
- Emily E Wroblewski
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christiana M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alex S Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, 2012 Kisangani, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicales, 1197 Kinshasa, Democratic Republic of the Congo.,University of Kinshasa, 190 Kinshasa, Democratic Republic of the Congo.,Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Alexander V Georgiev
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Martine Peeters
- Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France; and
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| |
Collapse
|
25
|
Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations. Immunogenetics 2016; 68:429-437. [PMID: 27225422 DOI: 10.1007/s00251-016-0916-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022]
Abstract
Strong spatiotemporal variation in population size often leads to reduced genetic diversity limiting the adaptive potential of individual populations. Key genes of adaptive variation are encoded by the immune genes of the major histocompatibility complex (MHC) playing an essential role in parasite resistance. How MHC variation persists in rodent populations that regularly experience population bottlenecks remains an important topic in evolutionary genetics. We analysed the consequences of strong population fluctuations on MHC class II DRB exon 2 diversity in two distant common vole (Microtus arvalis) populations in three consecutive years using a high-throughput sequencing approach. In 143 individuals, we detected 25 nucleotide alleles translating into 14 unique amino acid MHC alleles belonging to at least three loci. Thus, the overall allelic diversity and amino acid distance among the remaining MHC alleles, used as a surrogate for the range of pathogenic antigens that can be presented to T-cells, are still remarkably high. Both study populations did not show significant population differentiation between years, but significant differences were found between sites. We concluded that selection processes seem to be strong enough to maintain moderate levels of MHC diversity in our study populations outcompeting genetic drift, as the same MHC alleles were conserved between years. Differences in allele frequencies between populations might be the outcome of different local parasite pressures and/or genetic drift. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in cyclic populations.
Collapse
|
26
|
Arbanasic H, Galov A, Salajpal K, Curik I. Diversity of equine major histocompatiblity complex class II DRA locus in Posavina and Croatian Coldblood horse: a new polymorphism detected. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s3.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Ana Galov
- University of ZagrebUniversity of Zagreb, Croatia
| | | | - Ino Curik
- Department of Animal ScienceUniversity of Zagreb, Croatia
| |
Collapse
|
27
|
Ruan R, Ruan J, Wan XL, Zheng Y, Chen MM, Zheng JS, Wang D. Organization and characteristics of the major histocompatibility complex class II region in the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). Sci Rep 2016; 6:22471. [PMID: 26932528 PMCID: PMC4773811 DOI: 10.1038/srep22471] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 02/16/2016] [Indexed: 11/30/2022] Open
Abstract
Little is known about the major histocompatibility complex (MHC) in the genome of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) (YFP) or other cetaceans. In this study, a high-quality YFP bacterial artificial chromosome (BAC) library was constructed. We then determined the organization and characterization of YFP MHC class II region by screening the BAC library, followed by sequencing and assembly of positive BAC clones. The YFP MHC class II region consists of two segregated contigs (218,725 bp and 328,435 bp respectively) that include only eight expressed MHC class II genes, three pseudo MHC genes and twelve non-MHC genes. The YFP has fewer MHC class II genes than ruminants, showing locus reduction in DRB, DQA, DQB, and loss of DY. In addition, phylogenic and evolutionary analyses indicated that the DRB, DQA and DQB genes might have undergone birth-and-death evolution, whereas the DQB gene might have evolved under positive selection in cetaceans. These findings provide an essential foundation for future work, such as estimating MHC genetic variation in the YFP or other cetaceans. This work is the first report on the MHC class II region in cetaceans and offers valuable information for understanding the evolution of MHC genome in cetaceans.
Collapse
Affiliation(s)
- Rui Ruan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jue Ruan
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Guangdong 518120, China
| | - Xiao-Ling Wan
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yang Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
| | - Min-Min Chen
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Jin-Song Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| |
Collapse
|
28
|
Bjorkman PJ. Not second class: the first class II MHC crystal structure. THE JOURNAL OF IMMUNOLOGY 2016; 194:3-4. [PMID: 25527790 DOI: 10.4049/jimmunol.1402828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| |
Collapse
|
29
|
Falconer J, Mahida R, Venkatesh D, Pearson J, Robinson JH. Unconventional T-cell recognition of an arthritogenic epitope of proteoglycan aggrecan released from degrading cartilage. Immunology 2015; 147:389-98. [PMID: 26581676 DOI: 10.1111/imm.12557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 11/29/2022] Open
Abstract
It has been proposed that peptide epitopes bind to MHC class II molecules to form distinct structural conformers of the same MHC II-peptide complex termed type A and type B, and that the two conformers of the same peptide-MHC II complex are recognized by distinct CD4 T cells, termed type A and type B T cells. Both types recognize short synthetic peptides but only type A recognize endosomally processed intact antigen. Type B T cells that recognize self peptides from exogenously degraded proteins have been shown to escape negative selection during thymic development and so have the potential to contribute to the pathogenesis of autoimmunity. We generated and characterized mouse CD4 T cells specific for an arthritogenic epitope of the candidate joint autoantigen proteoglycan aggrecan. Cloned T-cell hybridomas specific for a synthetic peptide containing the aggrecan epitope showed two distinct response patterns based on whether they could recognize processed intact aggrecan. Fine mapping demonstrated that both types of T-cell recognized the same core epitope. The results are consistent with the generation of aggrecan-specific type A and type B T cells. Type B T cells were activated by supernatants released from degrading cartilage, indicating the presence of antigenic extracellular peptides or fragments of aggrecan. Type B T cells could play a role in the pathogenesis of proteoglycan-induced arthritis in mice, a model for rheumatoid arthritis, by recognizing extracellular peptides or protein fragments of joint autoantigens released by inflamed cartilage.
Collapse
Affiliation(s)
- Jane Falconer
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rahul Mahida
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Divya Venkatesh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jeffrey Pearson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - John H Robinson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
30
|
Wroblewski EE, Norman PJ, Guethlein LA, Rudicell RS, Ramirez MA, Li Y, Hahn BH, Pusey AE, Parham P. Signature Patterns of MHC Diversity in Three Gombe Communities of Wild Chimpanzees Reflect Fitness in Reproduction and Immune Defense against SIVcpz. PLoS Biol 2015; 13:e1002144. [PMID: 26020813 PMCID: PMC4447270 DOI: 10.1371/journal.pbio.1002144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
Major histocompatibility complex (MHC) class I molecules determine immune responses to viral infections. These polymorphic cell-surface glycoproteins bind peptide antigens, forming ligands for cytotoxic T and natural killer cell receptors. Under pressure from rapidly evolving viruses, hominoid MHC class I molecules also evolve rapidly, becoming diverse and species-specific. Little is known of the impact of infectious disease epidemics on MHC class I variant distributions in human populations, a context in which the chimpanzee is the superior animal model. Population dynamics of the chimpanzees inhabiting Gombe National Park, Tanzania have been studied for over 50 years. This population is infected with SIVcpz, the precursor of human HIV-1. Because HLA-B is the most polymorphic human MHC class I molecule and correlates strongly with HIV-1 progression, we determined sequences for its ortholog, Patr-B, in 125 Gombe chimpanzees. Eleven Patr-B variants were defined, as were their frequencies in Gombe's three communities, changes in frequency with time, and effect of SIVcpz infection. The growing populations of the northern and central communities, where SIVcpz is less prevalent, have stable distributions comprising a majority of low-frequency Patr-B variants and a few high-frequency variants. Driving the latter to high frequency has been the fecundity of immigrants to the northern community, whereas in the central community, it has been the fecundity of socially dominant individuals. In the declining population of the southern community, where greater SIVcpz prevalence is associated with mortality and emigration, Patr-B variant distributions have been changing. Enriched in this community are Patr-B variants that engage with natural killer cell receptors. Elevated among SIVcpz-infected chimpanzees, the Patr-B*06:03 variant has striking structural and functional similarities to HLA-B*57, the human allotype most strongly associated with delayed HIV-1 progression. Like HLA-B*57, Patr-B*06:03 correlates with reduced viral load, as assessed by detection of SIVcpz RNA in feces.
Collapse
Affiliation(s)
- Emily E. Wroblewski
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| | - Paul J. Norman
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rebecca S. Rudicell
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Sanofi, Cambridge, Massachusetts, United States of America
| | - Miguel A. Ramirez
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (EEW); (PP)
| |
Collapse
|
31
|
Hall BM. T Cells: Soldiers and Spies--The Surveillance and Control of Effector T Cells by Regulatory T Cells. Clin J Am Soc Nephrol 2015; 10:2050-64. [PMID: 25876770 DOI: 10.2215/cjn.06620714] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Traditionally, T cells were CD4+ helper or CD8+ cytotoxic T cells, and with antibodies, they were the soldiers of immunity. Now, many functionally distinct subsets of activated CD4+ and CD8+ T cells have been described, each with distinct cytokine and transcription factor expression. For CD4+ T cells, these include Th1 cells expressing the transcription factor T-bet and cytokines IL-2, IFN-γ, and TNF-β; Th2 cells expressing GATA-3 and the cytokines IL-4, IL-5, and IL-13; and Th17 cells expressing RORγt and cytokines IL-17A, IL-17F, IL-21, and IL-22. The cytokines produced determine the immune inflammation that they mediate. T cells of the effector lineage can be naïve T cells, recently activated T cells, or memory T cells that can be distinguished by cell surface markers. T regulatory cells or spies were characterized as CD8+ T cells expressing I-J in the 1970s. In the 1980s, suppressor cells fell into disrepute when the gene for I-J was not present in the mouse MHC I region. At that time, a CD4+ T cell expressing CD25, the IL-2 receptor-α, was identified to transfer transplant tolerance. This was the same phenotype of activated CD4+ CD25+ T cells that mediated rejection. Thus, the cells that could induce tolerance and undermine rejection had similar badges and uniforms as the cells effecting rejection. Later, FOXP3, a transcription factor that confers suppressor function, was described and distinguishes T regulatory cells from effector T cells. Many subtypes of T regulatory cells can be characterized by different expressions of cytokines and receptors for cytokines or chemokines. In intense immune inflammation, T regulatory cells express cytokines characteristic of effector cells; for example, Th1-like T regulatory cells express T-bet, and IFN-γ-like Th1 cells and effector T cells can change sides by converting to T regulatory cells. Effector T cells and T regulatory cells use similar molecules to be activated and mediate their function, and thus, it can be very difficult to distinguish soldiers from spies.
Collapse
Affiliation(s)
- Bruce M Hall
- Immune Tolerance Laboratory, Department of Medicine, University of New South Wales, Sydney, Australia; and Renal Unit, Liverpool Hospital, Sydney, Australia
| |
Collapse
|
32
|
Sommer S, Rakotondranary SJ, Ganzhorn JU. Maintaining microendemic primate species along an environmental gradient - parasites as drivers for species differentiation. Ecol Evol 2014; 4:4751-65. [PMID: 25558366 PMCID: PMC4278824 DOI: 10.1002/ece3.1311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/10/2014] [Accepted: 10/10/2014] [Indexed: 11/07/2022] Open
Abstract
Understanding the drivers of species adaptations to changing environments on the one hand and the limits for hybridization on the other hand is among the hottest questions in evolutionary biology. Parasites represent one of the major selective forces driving host evolution and at least those with free-living stages are at the same time dependent on the ecological conditions of their host's habitat. Local immunological adaptations of host species to varying parasite pressure are therefore expected and might represent the genetic basis for ecological speciation and the maintenance of recently diverged species. Madagascar provides one of the rare examples where two partially sympatric primate species (Microcebus griseorufus, M. murinus) and their hybrids, as well as an allopatric species (M. cf rufus) live in close proximity along a very steep environmental gradient ranging from southern dry spiny bush to gallery forest to evergreen eastern humid rain forest, thus mimicking the situation encountered during extensions and retreats of vegetation formations under changing climatic conditions. This system was used to study parasite infection and immune gene (MHC) adaptations to varying parasite pressure that might provide selective advantages to pure species over hybrids. Parasite burdens increased with increasing humidity. M. griseorufus, M. murinus, and their hybrids but not M. rufus shared the same MHC alleles, indicating either retention of ancestral polymorphism or recent gene flow. The hybrids had much higher prevalence of intestinal parasites than either of the parent species living under identical environmental conditions. The different representation of parasites can indicate a handicap for hybrids that maintains species identities.
Collapse
Affiliation(s)
- Simone Sommer
- Evolutionary Genetics, Leibniz-Institute for Zoo- and Wildlife ResearchAlfred-Kowalke-Strasse 10, Berlin, 10315, Germany
- Institute for Experimental Ecology, University of UlmAlbert-Einstein Allee 11, Ulm, 89069, Germany
| | - Solofomalla Jacques Rakotondranary
- Department of Animal Ecology and Conservation, University of Hamburg, Biozentrum GrindelMartin-Luther-King Platz 3, Hamburg, 20146, Germany
| | - Jörg U Ganzhorn
- Department of Animal Ecology and Conservation, University of Hamburg, Biozentrum GrindelMartin-Luther-King Platz 3, Hamburg, 20146, Germany
| |
Collapse
|
33
|
Gao C, Jiang Q, Guo D, Liu J, Han L, Qu L. Characterization of swine leukocyte antigen (SLA) polymorphism by sequence-based and PCR-SSP methods in Chinese Bama miniature pigs. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 45:87-96. [PMID: 24560654 DOI: 10.1016/j.dci.2014.02.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
The highly polymorphic swine leukocyte antigen (SLA) genes have been repeatedly shown to influence swine immune traits, disease resistance, vaccine responsiveness and tumour penetrance. Analysis of the SLA diversity in as many pig breeds as possible is important to clarify the relationships between SLA genes and diseases or traits, and develop these pigs as valuable animal models for biomedical research. The Chinese Bama miniature pig breed is an economically significant breed that is available at several research institutions in China. In this study, we identified a total of 32 alleles at five polymorphic SLA loci (SLA-1, SLA-3, SLA-2, DRB1 and DQB1) representing nine class I and seven class II haplotypes using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. The possible functional sites of the SLA genes were predicted and analyzed by comparison with those of the human and mouse. Based on the sequence information, we subsequently developed a rapid PCR-based typing assay using sequence-specific primers (PCR-SSP) to efficiently follow the SLA types of the progeny. In the studied cohort (2n = 562), the most prevalent Haplotype Hp-35.6 (SLA-1(∗)1201, SLA-1(∗)1301-SLA-3(∗)0502-SLA-2(∗)1001-DRB1(∗)0501-DQB1(∗)0801) was identified in 182 Bama pigs with a frequency of 32.38%. The presence of the duplicated SLA-1 locus was confirmed in five of the class I haplotypes. Moreover, we identified two crossovers within the class I region and one between the class I and class II regions, which corresponded to recombination frequencies of 0.36% and 0.18%, respectively. The information of this study is essential for an understanding of the SLA allelic architecture and diversity, and it will be helpful for studying the adaptive immune response and further developing the more effective vaccines in the context of SLA specificities.
Collapse
Affiliation(s)
- Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Qian Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Jiasen Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China
| | - Liandong Qu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150001, China.
| |
Collapse
|
34
|
Morris KM, Kirby K, Beatty JA, Barrs VR, Cattley S, David V, O'Brien SJ, Menotti-Raymond M, Belov K. Development of MHC-Linked Microsatellite Markers in the Domestic Cat and Their Use to Evaluate MHC Diversity in Domestic Cats, Cheetahs, and Gir Lions. J Hered 2014; 105:493-505. [PMID: 24620003 PMCID: PMC4048552 DOI: 10.1093/jhered/esu017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 01/14/2014] [Indexed: 11/15/2022] Open
Abstract
Diversity within the major histocompatibility complex (MHC) reflects the immunological fitness of a population. MHC-linked microsatellite markers provide a simple and an inexpensive method for studying MHC diversity in large-scale studies. We have developed 6 MHC-linked microsatellite markers in the domestic cat and used these, in conjunction with 5 neutral microsatellites, to assess MHC diversity in domestic mixed breed (n = 129) and purebred Burmese (n = 61) cat populations in Australia. The MHC of outbred Australian cats is polymorphic (average allelic richness = 8.52), whereas the Burmese population has significantly lower MHC diversity (average allelic richness = 6.81; P < 0.01). The MHC-linked microsatellites along with MHC cloning and sequencing demonstrated moderate MHC diversity in cheetahs (n = 13) and extremely low diversity in Gir lions (n = 13). Our MHC-linked microsatellite markers have potential future use in diversity and disease studies in other populations and breeds of cats as well as in wild felid species.
Collapse
Affiliation(s)
- Katrina M Morris
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Katherine Kirby
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Julia A Beatty
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Vanessa R Barrs
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Sonia Cattley
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Victor David
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Stephen J O'Brien
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Marilyn Menotti-Raymond
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien)
| | - Katherine Belov
- From the Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia (Morris, Kirby, Beatty, Barrs, and Belov); the ANGIS, University of Sydney, Sydney, NSW 2006, Australia (Cattley); the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201 (David and Menotti-Raymond); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33314-7796 (O'Brien).
| |
Collapse
|
35
|
Autoantibody and human leukocyte antigen profiles in children with autoimmune liver disease and their first-degree relatives. J Pediatr Gastroenterol Nutr 2014; 58:457-62. [PMID: 24231645 DOI: 10.1097/mpg.0000000000000245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Familial clustering of juvenile autoimmune liver disease (AILD), including autoimmune hepatitis and autoimmune sclerosing cholangitis (ASC), is rare, despite a high prevalence of autoimmune disorders in AILD families. METHODS To investigate this discrepancy, we measured autoantibodies diagnostic for AILD, anti-nuclear, anti-smooth muscle, anti-liver kidney microsomal type 1, anti-liver cytosol type 1, and anti-soluble liver antigen antibodies, and human leukocyte antigen profiles in 31 patients and 65 of their first-degree relatives (FDR). The autoantibody profile was compared with that of 42 healthy subjects (HS). RESULTS Autoantibodies were detected in 71% (22/31) patients. Anti-nuclear antibody or anti-smooth muscle antibody were present in 4/65 FDR (6.2%). HS were negative for all autoantibodies. The frequencies of homozygous HLA DRB1*0301 (DR3) genes and haplotype A1-B8-DR3 were higher in the patients (25% and 43%) than in FDR (9% and 27%) and HS (0% and 16%). The frequencies of disease-protective genes DR4 and/or DR15 were lower in the patients (25%) than in FDR (42%) and HS (42%). Only 1 family contained 2 patients with AILD, 1 with ASC and 1 with primary sclerosing cholangitis. Both patients possessed A1-B8-DR3 genes, the ASC being homozygous and the primary sclerosing cholangitis heterozygous. Six FDR had nonhepatic autoimmune disorders, none being autoantibody positive. CONCLUSIONS Homozygosity for DR3 plays a major role in the predisposition to juvenile AILD. Diagnostic autoantibodies for AILD are rare among patients' FDR and not linked to clinical manifestation of AILD.
Collapse
|
36
|
Alcaide M, Muñoz J, Martínez-de la Puente J, Soriguer R, Figuerola J. Extraordinary MHC class II B diversity in a non-passerine, wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae). Ecol Evol 2014; 4:688-98. [PMID: 24683452 PMCID: PMC3967895 DOI: 10.1002/ece3.974] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/30/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022] Open
Abstract
The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next-generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide-binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high-frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non-passerine bird.
Collapse
Affiliation(s)
- Miguel Alcaide
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Joaquin Muñoz
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
- The University of Oklahoma Biological Station15389 Station Road, Kingston, Oklahoma, 73439
| | | | - Ramón Soriguer
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Jordi Figuerola
- Estación Biológica de Doñana – CSICAvda. Américo Vespucio s/n, 41092, Sevilla, Spain
| |
Collapse
|
37
|
Niskanen AK, Kennedy LJ, Ruokonen M, Kojola I, Lohi H, Isomursu M, Jansson E, Pyhäjärvi T, Aspi J. Balancing selection and heterozygote advantage in major histocompatibility complex loci of the bottlenecked Finnish wolf population. Mol Ecol 2014; 23:875-89. [DOI: 10.1111/mec.12647] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 02/03/2023]
Affiliation(s)
- A. K. Niskanen
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - L. J. Kennedy
- Centre for Integrated Genomic Medical Research; University of Manchester; Stopford Building Oxford Road Manchester M13 9PT UK
| | - M. Ruokonen
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - I. Kojola
- Finnish Game and Fisheries Research Institute; Paavo Havaksen tie 3 PO Box 413 FI-90014 Oulu Finland
| | - H. Lohi
- Department of Veterinary Biosciences; Research Programs Unit; Molecular Neurology; Folkhälsan Institute of Genetics; Biomedicum Helsinki; University of Helsinki; PO Box 63 FI-00014 Helsinki Finland
| | - M. Isomursu
- Fish and Wildlife Health Research Unit; Finnish Food Safety Authority Evira; PO Box 517 FI-90101 Oulu Finland
| | - E. Jansson
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - T. Pyhäjärvi
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| | - J. Aspi
- Department of Biology; University of Oulu; PO Box 3000 FI-90014 Oulu Finland
| |
Collapse
|
38
|
Abstract
The most important transplantation antigens in the discrimination between "self" and "nonself" are encoded by genes in the major histocompatibility complex (MHC) locus (H-2 in mice). It has been assumed that T lymphocytes are the effector cells for allograft rejection, as athymic nude rodents fail to reject allografts. In 1988, we i.p. transplanted Meth A (H-2D(d)K(d)) tumor cells into C57BL/6 (H-2D(b)K(b)) mice and found macrophages to be cytotoxic against the allografts. In 1996, several groups using CD4 or CD8 knockout mice reported that non-T cells were the effector cells for the rejection of skin or organ allografts. In 1998, we ascertained that macrophages were the effector cells of skin allograft rejection. Recently, we isolated cDNA clones encoding monocyte/macrophage MHC receptors (MMRs) for H-2D(d) and H-2K(d); established H-2D(d)- and/or H-2K(d)-transgenic mice and lymphoma cells; and found, using MMR-deficient mice, that MMR and T-cell receptor were essential for the rejection of transgenic skin and lymphoma, respectively.
Collapse
Affiliation(s)
- Ryotaro Yoshida
- Department of Research Laboratory, Osaka Medical College, Takatsuki, Japan.
| |
Collapse
|
39
|
Bannai HP, Nonaka M. Comprehensive analysis of medaka major histocompatibility complex (MHC) class II genes: implications for evolution in teleosts. Immunogenetics 2013; 65:883-95. [PMID: 23989892 DOI: 10.1007/s00251-013-0731-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/19/2013] [Indexed: 12/29/2022]
Abstract
The major histocompatibility complex (MHC) class II molecules play central roles in adaptive immunity by regulating immune response via the activation of CD4 T cells. The full complement of the MHC class II genes has been elucidated only in mammalian species to date. To understand the evolution of these genes, we performed their first comprehensive analysis in nonmammalian species using a teleost, medaka (Oryzias latipes). Based on a database search, cDNA cloning, and genomic PCR, medaka was shown to possess five pairs of expressed class II genes, comprising one IIA and one IIB gene. Each pair was located on a different chromosome and was not linked to the class I genes. Only one pair showed a high degree of polymorphism and was considered to be classical class II genes, whereas the other four pairs were nonclassical. Phylogenetic analysis of all medaka class II genes and most reported teleost class II genes revealed that the IIA and IIB genes formed separate clades, each containing three well-corresponding lineages. One lineage contained three medaka genes and all known classical class II genes of Ostariophysi and Euteleostei and was presumed to be an original lineage of the teleost MHC class II genes. The other two lineages contained one nonclassical medaka gene each and some Euteleostei genes. These results indicate that multiple lineages of the teleost MHC class II genes have been conserved for hundreds of millions of years and that the tightly linked IIA and IIB genes have undergone concerted evolution.
Collapse
Affiliation(s)
- Hidemi P Bannai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
| | | |
Collapse
|
40
|
Galaverni M, Caniglia R, Fabbri E, Lapalombella S, Randi E. MHC variability in an isolated wolf population in Italy. J Hered 2013; 104:601-12. [PMID: 23885092 DOI: 10.1093/jhered/est045] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Small, isolated populations may experience increased extinction risk due to reduced genetic variability at important functional genes, thus decreasing the population's adaptive potential. The major histocompatibility complex (MHC), a key immunological gene cluster, usually shows high variability maintained by positive or balancing selection in response to challenges by pathogens. Here we investigated for the first time, the variability of 3 MHC class II genes (DRB1, DQA1, and DQB1) in 94 samples collected from Italian wolves. The Italian wolf population has been long isolated south of the Alps and is presently recovering from a recent bottleneck that decreased the population to less than 100 individuals. Despite the bottleneck, Italian wolves show remarkable MHC variability with 6-9 alleles per locus, including 2 recently described alleles at DRB1. MHC sequences show signatures of historical selective pressures (high d N/d S ratio, ω > 1.74) but no evidence of ongoing selection. Variation at the MHC genes and 12 background microsatellite loci were not apparently affected by the recent bottleneck. Although MHC alleles of domestic dog origin were detected in 8 genetically admixed individuals, these alleles were rare or absent in nonadmixed wolves. Thus, despite known hybridization events between domestic dogs and Italian wolves, the Italian wolf population does not appear affected by deep introgression of domestic dog MHC alleles.
Collapse
Affiliation(s)
- Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale, Ozzano dell’Emilia, Bologna, Italy.
| | | | | | | | | |
Collapse
|
41
|
Xiang R, Zhang H, Deng Q, Yue R, Tang H, Zhang Y, Ling F, Zhuo M, Du H, Xu S, Xu Q, Wang X. Comprehensive identification of high-frequency and co-occurring Mafa-DPA1, Mafa-DQA1, Mafa-DRA, and Mafa-DOA alleles in Vietnamese cynomolgus macaques. Immunogenetics 2013; 65:667-74. [PMID: 23793105 DOI: 10.1007/s00251-013-0713-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/29/2013] [Indexed: 12/22/2022]
Abstract
High-frequency alleles and/or co-occurring human leukocyte antigen alleles across loci appear to be more important than individual alleles as markers of disease risk and have clinical value as biomarkers for targeted screening or the development of new disease therapies. To better elucidate the major histocompatibility complex (MHC) background and to facilitate the experimental use of cynomolgus macaques, Mafa-DPA1, Mafa-DQA1, Mafa-DRA, and Mafa-DOA alleles were characterized, and their combinations were investigated in 30 Vietnamese macaques by gene cloning and sequencing. A total of 26 Mafa-DPA1, 18 Mafa-DQA1, 9 Mafa-DRA, and 15 Mafa-DOA alleles, including 7 high-frequency alleles, were identified in this study, respectively. In addition, 15 Mafa-DQA1, 17 Mafa-DPA1, 15 Mafa-DOA, and 2 Mafa-DRA alleles represented novel sequences that had not been documented in earlier studies. Our results also showed that the Vietnamese macaques might be valuable because no less than 30% of the test animals possessed Mafa-DRA*01:02:01 (90%), -DQA1*26:01:03 (37%), -DOA*01:02:07 (34%), and -DQA1*01:03:03 (30%). We previously reported that the combinations of MHC class II alleles, including the combination of DOA*01:02:07-DPA1*02:09 and DOA*01:02:07-DQA1*01:03:03, were detected in 17 and 14% of the animals, respectively. Interestingly, more than two Mafa-DQA1 and Mafa-DPA1 alleles were detected in one animal in this study, which suggested that they might be caused by a chromosomal duplication. If our findings can be validated by other studies, it will further enrich the number of known Mafa-DPA1 and Mafa-DQA1 polymorphisms. Our results identified the co-occurring MHC alleles across loci in a cohort of Vietnamese cynomolgus macaques, which emphasized the value of this species as a model for biomedical research.
Collapse
Affiliation(s)
- Ruirui Xiang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Weber DS, Van Coeverden De Groot PJ, Peacock E, Schrenzel MD, Perez DA, Thomas S, Shelton JM, Else CK, Darby LL, Acosta L, Harris C, Youngblood J, Boag P, Desalle R. Low MHC variation in the polar bear: implications in the face of Arctic warming? Anim Conserv 2013. [DOI: 10.1111/acv.12045] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- D. S. Weber
- Division of Natural Sciences; New College of Florida; Sarasota FL USA
- American Museum of Natural History; New York NY USA
| | | | - E. Peacock
- Department of Environment; The Government of Nunavut; Igloolik NU Canada
| | - M. D. Schrenzel
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - D. A. Perez
- American Museum of Natural History; New York NY USA
- Stevens Institute of Technology; Hoboken NJ USA
| | - S. Thomas
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - J. M. Shelton
- American Museum of Natural History; New York NY USA
- Brooklyn College; City University of New York; New York NY USA
| | | | - L. L. Darby
- American Museum of Natural History; New York NY USA
- Columbia University; New York NY USA
| | - L. Acosta
- American Museum of Natural History; New York NY USA
- Villanova University; Villanova PA USA
| | - C. Harris
- Biology Department; Queen's University; Kingston ON Canada
| | - J. Youngblood
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - P. Boag
- Biology Department; Queen's University; Kingston ON Canada
| | - R. Desalle
- American Museum of Natural History; New York NY USA
| |
Collapse
|
43
|
Ferrante A. For many but not for all: how the conformational flexibility of the peptide/MHCII complex shapes epitope selection. Immunol Res 2013; 56:85-95. [PMID: 22753017 PMCID: PMC4197051 DOI: 10.1007/s12026-012-8342-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The adaptive immune response starts when CD4+ T cells recognize peptide antigens presented by class II molecules of the Major Histocompatibility Complex (MHCII). Two outstanding features of MHCII molecules are their polymorphism and the ability of each allele to bind a large panoply of peptides. The ability of each MHCII molecule to interact with a limited, though broad, range of amino acid sequences, or "permissive specificity" of binding, is the result of structural flexibility. This flexibility has been identified through biochemical and biophysical studies, and molecular dynamic simulations have modeled the conformational rearrangements that the peptide and the MHCII undergo during interaction. Moreover, there is evidence that the structural flexibility of the peptide/MHCII complex correlates with the activity of the "peptide-editing" molecule DM. In light of the impact that these recent findings have on our ability to predict MHCII epitopes, a review of the structural and thermodynamic determinants of peptide binding to MHCII is proposed.
Collapse
Affiliation(s)
- Andrea Ferrante
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775-7000, USA.
| |
Collapse
|
44
|
Arbanasić H, Galov A, Ambriović-Ristov A, Grizelj J, Arsenos G, Marković B, Dovenski T, Vince S, Curik I. Extensive polymorphism of the major histocompatibility complex DRA gene in Balkan donkeys: perspectives on selection and genealogy. Anim Genet 2013; 44:711-6. [PMID: 23621397 DOI: 10.1111/age.12054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2013] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) contains genes important for immune response in mammals, and these genes exhibit high polymorphism and diversity. The DRA gene, a member of the MHC class II family, is highly conserved across a large number of mammalian species, but it displays exceptionally rich sequence variations in Equidae members. We analyzed allelic polymorphism of the DRA locus in 248 donkeys sampled across the Balkan Peninsula (Albania, Bulgaria, Croatia, Macedonia, Greece and Montenegro). Five known alleles and two new alleles were identified. The new allele Eqas-DRA*0601 was found to carry a synonymous mutation, and new allele Eqas-DRA*0701, a non-synonymous mutation. We further analyzed the historical selection and allele genealogy at the DRA locus in equids. Signals of positive selection obtained by various tests were ambiguous. A conservative conclusion is that DRA polymorphism occurred relatively recently and that positive selection has been acting on the DRA locus for a relatively brief period.
Collapse
Affiliation(s)
- Haidi Arbanasić
- Division of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Kuduk K, Babik W, Bojarska K, Śliwińska EB, Kindberg J, Taberlet P, Swenson JE, Radwan J. Evolution of major histocompatibility complex class I and class II genes in the brown bear. BMC Evol Biol 2012; 12:197. [PMID: 23031405 PMCID: PMC3508869 DOI: 10.1186/1471-2148-12-197] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/18/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. RESULTS We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. CONCLUSIONS Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South-north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.
Collapse
Affiliation(s)
- Katarzyna Kuduk
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Wiesław Babik
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, Kraków, 31-016, Poland
| | - Katarzyna Bojarska
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Ewa B Śliwińska
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, Kraków, 31-120, Poland
| | - Jonas Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, SE, 901 83, Sweden
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine (LECA), Génomique des Populations et Biodiversité, CNRS UMR 5553, Université Joseph Fourier, BP 53, Grenoble Cedex 9, F-38041, France
| | - Jon E Swenson
- Department of Ecology and Natural Resources Management, Norwegian University of Life Sciences, Ãs, NO-1432, Norway
- Norwegian Institute for Nature Research, Trondheim, NO-7485, Norway
| | - Jacek Radwan
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| |
Collapse
|
46
|
Bexfield NH, Watson PJ, Aguirre-Hernandez J, Sargan DR, Tiley L, Heeney JL, Kennedy LJ. DLA class II alleles and haplotypes are associated with risk for and protection from chronic hepatitis in the English Springer spaniel. PLoS One 2012; 7:e42584. [PMID: 22870335 PMCID: PMC3411618 DOI: 10.1371/journal.pone.0042584] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 07/09/2012] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis (CH) is common in dogs in the United Kingdom. An increased prevalence of the disease is seen in the English Springer spaniel (ESS), and this breed suffer from a severe form with young to middle aged female dogs being predisposed. The disease shares histological features with those of human viral hepatitis, although the specific aetiological agent has not yet been identified. The aim of the current study was to investigate whether dog leucocyte antigen (DLA) class II alleles and haplotypes are associated with susceptibility/resistance to CH in the ESS. Sequence-based genotyping of the polymorphic exon 2 from DLA-DRB1, -DQA1 and -DQB1 class II loci were performed in 66 ESSs with CH and 84 healthy controls. There was a significant difference in the distribution of the protective alleles DRB1*00501 (3.0% vs. 12.0%, odds ratio [OR] = 0.23, 95% confidence interval [CI] = 0.06–0.74) and DQB1*00501 (3.8% vs. 12.0%, OR = 0.29, 95% CI = 0.09–0.85) between cases and controls. The haplotype DLA-DRB1*00501/DQA1*00301/DQB1*00501 was present in 11.9% of controls and 3.0% of cases and was significantly associated with protection against disease development (OR = 0.26, 95% CI = 0.08–0.80). There was a significant difference in the distribution of the risk alleles DRB1*00601 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) and DQB1*00701 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) between cases and controls. A risk haplotype (DLA-DRB1*00601/DQA1*005011/DQB1*00701) was present in 14.4% of cases and 6.5% of controls and conferred an elevated risk of developing CH with an OR of 3.13 (95% CI = 1.20–8.26). These results demonstrate that DLA class II is significantly associated with risk and protection from developing CH in ESSs.
Collapse
Affiliation(s)
- Nicholas H Bexfield
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
47
|
Naskar S, Deb SM, Niranjan SK, Kumar S, Sharma D, Sakaram D, Sharma A. Molecular characterization of MHC-DRB cDNA in water buffalo (Bubalus bubalis). Genet Mol Biol 2012; 35:95-8. [PMID: 22481880 PMCID: PMC3313522 DOI: 10.1590/s1415-47572012005000013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 10/26/2011] [Indexed: 11/22/2022] Open
Abstract
In the present study, water buffalo MHC (Bubu)-DRB cDNA was cloned and characterized. The 1022 base long-amplified cDNA product encompassed a single open reading frame of 801 bases that coded for 266 amino acids. The Bubu-DRB sequence showed maximum homology with the BoLA-DRB3*0101 allele of cattle. A total of seven amino acid residues were found to be unique for the Bubu-DRB sequence. The majority of amino acid substitutions was observed in the β1 domain. Residues associated with important functions were mostly conserved. Water buffalo DRB was phylogenetically closer to goat DRB*A.
Collapse
Affiliation(s)
- Soumen Naskar
- Animal Genetics Division, Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | | | | | | | | | | | | |
Collapse
|
48
|
Ploshnitsa AI, Goltsman ME, Macdonald DW, Kennedy LJ, Sommer S. Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus). Ecol Evol 2012; 2:165-80. [PMID: 22408734 PMCID: PMC3297186 DOI: 10.1002/ece3.42] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/24/2011] [Accepted: 08/26/2011] [Indexed: 11/11/2022] Open
Abstract
Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970-1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples.
Collapse
|
49
|
Evidence for evolutionary convergence at MHC in two broadly distributed mesocarnivores. Immunogenetics 2011; 64:289-301. [DOI: 10.1007/s00251-011-0588-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/31/2011] [Indexed: 12/21/2022]
|
50
|
Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0213-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|