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Brown AJ, White J, Shaw L, Gross J, Slabodkin A, Kushner E, Greiff V, Matsuda J, Gapin L, Scott-Browne J, Kappler J, Marrack P. MHC heterozygosity limits T cell receptor variability in CD4 T cells. Sci Immunol 2024; 9:eado5295. [PMID: 38996008 DOI: 10.1126/sciimmunol.ado5295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
αβ T cell receptor (TCR) V(D)J genes code for billions of TCR combinations. However, only some appear on peripheral T cells in any individual because, to mature, thymocytes must react with low affinity but not high affinity with thymus expressed major histocompatibility (MHC)/peptides. MHC proteins are very polymorphic. Different alleles bind different peptides. Therefore, any individual might express many different MHC alleles to ensure that some peptides from an invader are bound to MHC and activate T cells. However, most individuals express limited numbers of MHC alleles. To explore this, we compared the TCR repertoires of naïve CD4 T cells in mice expressing one or two MHC alleles. Unexpectedly, the TCRs in heterozygotes were less diverse that those in the sum of their MHC homozygous relatives. Our results suggest that thymus negative selection cancels out the advantages of increased thymic positive selection in the MHC heterozygotes.
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MESH Headings
- Animals
- Mice
- CD4-Positive T-Lymphocytes/immunology
- Heterozygote
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Major Histocompatibility Complex/immunology
- Major Histocompatibility Complex/genetics
- Mice, Inbred C57BL
- Thymus Gland/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Mice, Transgenic
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Affiliation(s)
- Alexander J Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA
| | - Janice White
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Laura Shaw
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Jimmy Gross
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Andrei Slabodkin
- Department of Immunology, University of Oslo and Oslo University Hospital, Postboks 4950 Nydalen OUS HF Rikshospitalet, 0424 Oslo, Norway
| | - Ella Kushner
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Postboks 4950 Nydalen OUS HF Rikshospitalet, 0424 Oslo, Norway
| | - Jennifer Matsuda
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
| | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA
| | - James Scott-Browne
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA
| | - John Kappler
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Philippa Marrack
- Department of Immunology and Genomic Medicine, National Jewish Health, 1400 Jackson St, Denver, CO 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, USA
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Veríssimo A, Castro LFC, Muñoz-Mérida A, Almeida T, Gaigher A, Neves F, Flajnik MF, Ohta Y. An Ancestral Major Histocompatibility Complex Organization in Cartilaginous Fish: Reconstructing MHC Origin and Evolution. Mol Biol Evol 2023; 40:msad262. [PMID: 38059517 PMCID: PMC10751288 DOI: 10.1093/molbev/msad262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Cartilaginous fish (sharks, rays, and chimeras) comprise the oldest living jawed vertebrates with a mammalian-like adaptive immune system based on immunoglobulins (Ig), T-cell receptors (TCRs), and the major histocompatibility complex (MHC). Here, we show that the cartilaginous fish "adaptive MHC" is highly regimented and compact, containing (i) a classical MHC class Ia (MHC-Ia) region containing antigen processing (antigen peptide transporters and immunoproteasome) and presenting (MHC-Ia) genes, (ii) an MHC class II (MHC-II) region (with alpha and beta genes) with linkage to beta-2-microglobulin (β2m) and bromodomain-containing 2, (iii) nonclassical MHC class Ib (MHC-Ib) regions with 450 million-year-old lineages, and (iv) a complement C4 associated with the MHC-Ia region. No MHC-Ib genes were found outside of the elasmobranch MHC. Our data suggest that both MHC-I and MHC-II genes arose after the second round of whole-genome duplication (2R) on a human chromosome (huchr) 6 precursor. Further analysis of MHC paralogous regions across early branching taxa from all jawed vertebrate lineages revealed that Ig/TCR genes likely arose on a precursor of the huchr9/12/14 MHC paralog. The β2m gene is linked to the Ig/TCR genes in some vertebrates suggesting that it was present at 1R, perhaps as the donor of C1 domain to the primordial MHC gene. In sum, extant cartilaginous fish exhibit a conserved and prototypical MHC genomic organization with features found in various vertebrates, reflecting the ancestral arrangement for the jawed vertebrates.
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Affiliation(s)
- Ana Veríssimo
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences, University of Porto, Porto 4169-007, Portugal
- CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Matosinhos, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Tereza Almeida
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Arnaud Gaigher
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Fabiana Neves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão 4485-661, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
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Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
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Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula). Sci Rep 2023; 13:3837. [PMID: 36882519 PMCID: PMC9992475 DOI: 10.1038/s41598-023-30876-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
The major histocompatibility complex (MHC) is a multigene family responsible for pathogen detection, and initiation of adaptive immune responses. Duplication, natural selection, recombination, and their resulting high functional genetic diversity spread across several duplicated loci are the main hallmarks of the MHC. Although these features were described in several jawed vertebrate lineages, a detailed MHC IIβ characterization at the population level is still lacking for chondrichthyans (chimaeras, rays and sharks), i.e. the most basal lineage to possess an MHC-based adaptive immune system. We used the small-spotted catshark (Scyliorhinus canicula, Carcharhiniformes) as a case-study species to characterize MHC IIβ diversity using complementary molecular tools, including publicly available genome and transcriptome datasets, and a newly developed high-throughput Illumina sequencing protocol. We identified three MHC IIβ loci within the same genomic region, all of which are expressed in different tissues. Genetic screening of the exon 2 in 41 individuals of S. canicula from a single population revealed high levels of sequence diversity, evidence for positive selection, and footprints of recombination. Moreover, the results also suggest the presence of copy number variation in MHC IIβ genes. Thus, the small-spotted catshark exhibits characteristics of functional MHC IIβ genes typically observed in other jawed vertebrates.
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Some thoughts about what non-mammalian jawed vertebrates are telling us about antigen processing and peptide loading of MHC molecules. Curr Opin Immunol 2022; 77:102218. [PMID: 35687979 PMCID: PMC9586880 DOI: 10.1016/j.coi.2022.102218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/19/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex (MHC) of mammals encodes highly polymorphic classical class I and class II molecules with crucial roles in immune responses, as well as various nonclassical molecules encoded by the MHC and elsewhere in the genome that have a variety of functions. These MHC molecules are supported by antigen processing and peptide loading pathways which are well-understood in mammals. This review considers what has been learned about the MHC, MHC molecules and the supporting pathways in non-mammalian jawed vertebrates. From the initial understanding from work with the chicken MHC, a great deal of diversity in the structure and function has been found. Are there underlying principles? The genomic organisation of the MHC varies enormously across jawed vertebrates. Total numbers of MHC genes vary among vertebrates, with only a few classical MHC genes. Some nonclassical MHC and classical pathway genes appear earlier than others. Obvious co-evolution within MHC pathways occurs in some species, but not others. The promiscuity of interactions may correlate with differences in genomic organisation.
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Kataoka C, Kashiwada S. Ecological Risks Due to Immunotoxicological Effects on Aquatic Organisms. Int J Mol Sci 2021; 22:8305. [PMID: 34361068 PMCID: PMC8347160 DOI: 10.3390/ijms22158305] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022] Open
Abstract
The immunotoxic effects of some anthropogenic pollutants on aquatic organisms are among the causes of concern over the presence of these pollutants in the marine environment. The immune system is part of an organism's biological defense necessarily for homeostasis. Thus, the immunotoxicological impacts on aquatic organisms are important to understand the effects of pollutant chemicals in the aquatic ecosystem. When aquatic organisms are exposed to pollutant chemicals with immunotoxicity, it results in poor health. In addition, aquatic organisms are exposed to pathogenic bacteria, viruses, parasites, and fungi. Exposure to pollutant chemicals has reportedly caused aquatic organisms to show various immunotoxic symptoms such as histological changes of lymphoid tissue, changes of immune functionality and the distribution of immune cells, and changes in the resistance of organisms to infection by pathogens. Alterations of immune systems by contaminants can therefore lead to the deaths of individual organisms, increase the general risk of infections by pathogens, and probably decrease the populations of some species. This review introduced the immunotoxicological impact of pollutant chemicals in aquatic organisms, including invertebrates, fish, amphibians, and marine mammals; described typical biomarkers used in aquatic immunotoxicological studies; and then, discussed the current issues on ecological risk assessment and how to address ecological risk assessment through immunotoxicology. Moreover, the usefulness of the population growth rate to estimate the immunotoxicological impact of pollution chemicals was proposed.
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Affiliation(s)
- Chisato Kataoka
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan
| | - Shosaku Kashiwada
- Department of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan;
- Research Centre for Life and Environmental Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan
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Almeida T, Ohta Y, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Machado AM, Esteves PJ, Veríssimo A, Flajnik MF. A Highly Complex, MHC-Linked, 350 Million-Year-Old Shark Nonclassical Class I Lineage. THE JOURNAL OF IMMUNOLOGY 2021; 207:824-836. [PMID: 34301841 DOI: 10.4049/jimmunol.2000851] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 05/09/2021] [Indexed: 11/19/2022]
Abstract
Cartilaginous fish, or Chondrichthyes, are the oldest extant vertebrates to possess the MHC and the Ig superfamily-based Ag receptors, the defining genes of the gnathostome adaptive immune system. In this work, we have identified a novel MHC lineage, UEA, a complex multigene nonclassical class I family found in sharks (division Selachii) but not detected in chimaeras (subclass Holocephali) or rays (division Batoidea). This new lineage is distantly related to the previously reported nonclassical class I lineage UCA, which appears to be present only in dogfish sharks (order Squaliformes). UEA lacks conservation of the nine invariant residues in the peptide (ligand)-binding regions (PBR) that bind to the N and C termini of bound peptide in most vertebrate classical class I proteins, which are replaced by relatively hydrophobic residues compared with the classical UAA. In fact, UEA and UCA proteins have the most hydrophobic-predicted PBR of all identified chondrichthyan class I molecules. UEA genes detected in the whale shark and bamboo shark genome projects are MHC linked. Consistent with UEA comprising a very large gene family, we detected weak expression in different tissues of the nurse shark via Northern blotting and RNA sequencing. UEA genes fall into three sublineages with unique characteristics in the PBR. UEA shares structural and genetic features with certain nonclassical class I genes in other vertebrates, such as the highly complex XNC nonclassical class I genes in Xenopus, and we anticipate that each shark gene, or at least each sublineage, will have a unique function, perhaps in bacterial defense.
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Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - L Filipe C Castro
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - André M Machado
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Porto, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, MD; and
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