1
|
Jolly A, Fernández B, Mundo SL, Elguezabal N. Modeling Paratuberculosis in Laboratory Animals, Cells, or Tissues: A Focus on Their Applications for Pathogenesis, Diagnosis, Vaccines, and Therapy Studies. Animals (Basel) 2023; 13:3553. [PMID: 38003170 PMCID: PMC10668694 DOI: 10.3390/ani13223553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Paratuberculosis is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. Paratuberculosis that affects a wide variety of domestic and wild animals. It is considered one of the diseases with the highest economic impact on the ruminant industry. Despite many efforts and intensive research, paratuberculosis control still remains controversial, and the existing diagnostic and immunoprophylactic tools have great limitations. Thus, models play a crucial role in understanding the pathogenesis of infection and disease, and in testing novel vaccine candidates. Ruminant animal models can be restricted by several reasons, related to space requirements, the cost of the animals, and the maintenance of the facilities. Therefore, we review the potential and limitations of the different experimental approaches currently used in paratuberculosis research, focusing on laboratory animals and cell-based models. The aim of this review is to offer a vision of the models that have been used, and what has been achieved or discovered with each one, so that the reader can choose the best model to answer their scientific questions and prove their hypotheses. Also, we bring forward new approaches that we consider worth exploring in the near future.
Collapse
Affiliation(s)
- Ana Jolly
- Cátedra de Inmunología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina; (B.F.); (S.L.M.)
| | - Bárbara Fernández
- Cátedra de Inmunología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina; (B.F.); (S.L.M.)
- Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina
- Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina
| | - Silvia Leonor Mundo
- Cátedra de Inmunología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina; (B.F.); (S.L.M.)
- Instituto de Investigaciones en Producción Animal (INPA), CONICET-Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina
- Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Av. Chorroarín 280, Buenos Aires C1427CWO, Argentina
| | - Natalia Elguezabal
- Departamento de Sanidad Animal, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario-Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| |
Collapse
|
2
|
Dixon R, Preston SG, Dascalu S, Flammer PG, Fiddaman SR, McLoughlin K, Boyd A, Volf J, Rychlik I, Bonsall MB, Kaspers B, Smith AL. Repertoire analysis of γδ T cells in the chicken enables functional annotation of the genomic region revealing highly variable pan-tissue TCR gamma V gene usage as well as identifying public and private repertoires. BMC Genomics 2021; 22:719. [PMID: 34610803 PMCID: PMC8493715 DOI: 10.1186/s12864-021-08036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/17/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Despite increasing interest in γδ T cells and their non-classical behaviour, most studies focus on animals with low numbers of circulating γδ T cells, such as mice and humans. Arguably, γδ T cell functions might be more prominent in chickens where these cells form a higher proportion of the circulatory T cell compartment. The TCR repertoire defines different subsets of γδ T cells, and such analysis is facilitated by well-annotated TCR loci. γδ T cells are considered at the cusp of innate and adaptive immunity but most functions have been identified in γδ low species. A deeper understanding of TCR repertoire biology in γδ high and γδ low animals is critical for defining the evolution of the function of γδ T cells. Repertoire dynamics will reveal populations that can be classified as innate-like or adaptive-like as well as those that straddle this definition. RESULTS Here, a recent discrepancy in the structure of the chicken TCR gamma locus is resolved, demonstrating that tandem duplication events have shaped the evolution of this locus. Importantly, repertoire sequencing revealed large differences in the usage of individual TRGV genes, a pattern conserved across multiple tissues, including thymus, spleen and the gut. A single TRGV gene, TRGV3.3, with a highly diverse private CDR3 repertoire dominated every tissue in all birds. TRGV usage patterns were partly explained by the TRGV-associated recombination signal sequences. Public CDR3 clonotypes represented varying proportions of the repertoire of TCRs utilising different TRGVs, with one TRGV dominated by super-public clones present in all birds. CONCLUSIONS The application of repertoire analysis enabled functional annotation of the TCRG locus in a species with a high circulating γδ phenotype. This revealed variable usage of TCRGV genes across multiple tissues, a pattern quite different to that found in γδ low species (human and mouse). Defining the repertoire biology of avian γδ T cells will be key to understanding the evolution and functional diversity of these enigmatic lymphocytes in an animal that is numerically more reliant on them. Practically, this will reveal novel ways in which these cells can be exploited to improve health in medical and veterinary contexts.
Collapse
Affiliation(s)
- Robert Dixon
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Stefan Dascalu
- Department of Zoology, University of Oxford, Oxford, UK
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, United Kingdom
| | | | | | | | - Amy Boyd
- Department of Zoology, University of Oxford, Oxford, UK
| | - Jiri Volf
- Veterinary Research Institute, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Bernd Kaspers
- Veterinary Faculty, Ludwig Maximillians University, Planegg, Germany
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, UK.
| |
Collapse
|
3
|
Guriec N, Bussy F, Gouin C, Mathiaud O, Le Goff M, Delarue J, Collén PN. Activation of chicken gamma-delta T lymphocytes by a purified ulvan extract. Vet Immunol Immunopathol 2021; 237:110255. [PMID: 33965691 DOI: 10.1016/j.vetimm.2021.110255] [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: 12/04/2020] [Revised: 03/19/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Chicken γδ T lymphocytes are present in a variety of tissues such as blood, spleen and intestine. They constitute a major cytotoxic population. In chicken, Salmonella immunization as well as vaccination against Newcastle disease virus are accompanied by an increase of γδ T lymphocytes in peripheral blood, which may be activated, and thus represent a protective immune response. It has been published that activation of avian γδ T cells can occur in a MHC non-restricted manner. Ulvans are complex sulfated polysaccharides composed of disaccharide repetitions found in the cell walls of green algae belonging to the genus Ulva. We recently demonstrated that a purified ulvan extract activates chicken heterophils and monocytes in vivo through TLR2 and TLR4 receptors when given in drinking water. We demonstrate here, that the same extract given once in drinking water at 25 and 50 mg/l, results in increased membrane expression of Major Histocompatibility Complex class 2 as soon as day 2, as detected using flow cytometry. We conclude chicken γδ T lymphocytes to be activated, or at least primed, in vivo, with the extract. Further experiments are required to fully understand whether their activation or priming is the result of direct and/or indirect mechanisms.
Collapse
Affiliation(s)
- Nathalie Guriec
- Department of Nutritional Sciences, University Hospital, Faculty of Medicine, University of Brest, France.
| | | | | | | | | | - Jacques Delarue
- Department of Nutritional Sciences, University Hospital, Faculty of Medicine, University of Brest, France.
| | - Pi Nyvall Collén
- Amadeite SAS, 56580, Bréhan, France; R&D Breizh, 56500 Moustoir Ac, France.
| |
Collapse
|
4
|
Imbert C, Olive D. γδ T Cells in Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1273:91-104. [PMID: 33119877 DOI: 10.1007/978-3-030-49270-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Gamma delta (γδ) T cells which combine both innate and adaptive potential have extraordinary properties. Indeed, their strong cytotoxic and pro-inflammatory activity allows them to kill a broad range of tumor cells. Several studies have demonstrated that γδ T cells are an important component of tumor-infiltrated lymphocytes in patients affected by different types of cancer. Tumor-infiltrating γδ T cells are also considered as a good prognostic marker in many studies, though the presence of these cells is associated with poor prognosis in breast and colon cancers. The tumor microenvironment seems to drive γδ T-cell differentiation toward a tumor-promoting or a tumor-controlling phenotype, which suggests that some tumor microenvironments can limit the effectiveness of γδ T cells.The major γδ T-cell subsets in human are the Vγ9Vδ2 T cells that are specifically activated by phosphoantigens. This unique antigenic activation process operates in a framework that requires the expression of butyrophilin 3A (BTN3A) molecules. Interestingly, there is some evidence that BTN3A expression may be regulated by the tumor microenvironment. Given their strong antitumoral potential, Vγ9Vδ2 T cells are used in therapeutic approaches either by ex vivo culture and amplification, and then adoptive transfer to patients or by direct stimulation to propagate in vivo. These strategies have demonstrated promising initial results, but greater potency is needed. Combining Vγ9Vδ2 T-cell immunotherapy with systemic approaches to restore antitumor immune response in tumor microenvironment may improve efficacy.In this chapter, we first review the basic features of γδ T cells and their roles in the tumor microenvironment and then analyze the advances about the understanding of these cells' activation in tumors and why this represent unique challenges for therapeutics, and finally we discuss γδ T-cell-based therapeutic strategies and future perspectives of their development.
Collapse
Affiliation(s)
- Caroline Imbert
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille (CRCM), Immunity and Cancer, Institut Paoli Calmettes, Aix Marseille Université, Marseille, France.,Immunomonitoring Platform, Institut Paoli Calmettes, Marseille, France
| | - Daniel Olive
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille (CRCM), Immunity and Cancer, Institut Paoli Calmettes, Aix Marseille Université, Marseille, France. .,Immunomonitoring Platform, Institut Paoli Calmettes, Marseille, France.
| |
Collapse
|
5
|
Tan HM, Low WY. Rapid birth-death evolution and positive selection in detoxification-type glutathione S-transferases in mammals. PLoS One 2018; 13:e0209336. [PMID: 30586459 PMCID: PMC6306238 DOI: 10.1371/journal.pone.0209336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/04/2018] [Indexed: 01/04/2023] Open
Abstract
Glutathione S-Transferases (GSTs) are phase II detoxification enzymes that may have evolved in response to changes of environmental substrates. GST genes formed a multigene family and in mammals, there are six classes known as Alpha, Mu, Omega, Pi, Theta, and Zeta. Recent studies in phase I detoxification system specifically the cytochrome P450s provided a general explanation on why genes from a common origin such as those in a multigene family have both phylogenetically stable and unstable genes. Genes that participate in core functions of organisms such as development and physiology are stable whereas genes that play a role in detoxification are unstable and evolve in a process known as birth-death evolution, which is characterised by frequent gene gains and losses. The generality of the birth-death model at explaining the evolution of detoxification enzymes beyond the phase I enzyme has not been comprehensively explored. This work utilized 383 Gst genes and 300 pseudogenes across 22 mammalian species to study gene gains and losses. GSTs vary greatly in their phylogenetic stability despite their overall sequence similarity. Stable Gst genes from Omega and Zeta classes do not show fluctuation in gene numbers from human to opossum. These genes play a role in biosynthesis related functions. Unstable genes that include Alpha, Mu, Pi and Theta undergo frequent gene gain and loss in a process known as birth-death evolution. Gene members of these four classes are well known for their roles in detoxification. Our positive selection screen identified five positively selected sites in mouse GSTA3. Previous studies showed two of these sites (108H and 208E) were biochemically tested as important residues that conferred catalytic activity against the toxic aflatoxin B1-8,9-epoxide. The functional significance against aflatoxin of the remaining three positively selected sites warrant further investigation.
Collapse
Affiliation(s)
- Hui Ming Tan
- Center for Bioinformatics, Perdana University School of Data Science, Serdang, Selangor, Malaysia
| | - Wai Yee Low
- Center for Bioinformatics, Perdana University School of Data Science, Serdang, Selangor, Malaysia
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- * E-mail:
| |
Collapse
|
6
|
Breaux B, Hunter ME, Cruz-Schneider MP, Sena L, Bonde RK, Criscitiello MF. The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 85:71-85. [PMID: 29649552 DOI: 10.1016/j.dci.2018.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/06/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.
Collapse
Affiliation(s)
- Breanna Breaux
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Margaret E Hunter
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | | | - Leonardo Sena
- Laboratory of Medical and Human Genetics, Federal University of Pará, Belém, Pará, Brazil.
| | - Robert K Bonde
- Sirenia Project, Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
7
|
Curran DM, Gilleard JS, Wasmuth JD. MIPhy: identify and quantify rapidly evolving members of large gene families. PeerJ 2018; 6:e4873. [PMID: 29868279 PMCID: PMC5983006 DOI: 10.7717/peerj.4873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/10/2018] [Indexed: 11/20/2022] Open
Abstract
After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions. These can be identified by analyzing the gene family across several species and identifying patterns of gene duplication and loss that do not correlate with the known relationships between those species. This signature, termed phylogenetic instability, has been previously linked to adaptations that change the way an organism samples and responds to its environment; conversely, low phylogenetic instability has been previously linked to proteins with endogenous functions. With the increase in genome-level data, there is a need to identify and quantify phylogenetic instability. Here, we present Minimizing Instability in Phylogenetics (MIPhy), a tool that solves this problem by quantifying the incongruence of a gene's evolutionary history. The motivation behind MIPhy was to produce a tool to aid in interpreting phylogenetic trees. It can predict which members of a gene family are under adaptive evolution, working only from a gene tree and the relationship between the species under consideration. While it does not conduct any estimation of positive selection-which is the typical indication of adaptive evolution-the results tend to agree. We demonstrate the usefulness of MIPhy by accurately predicting which members of the mammalian cytochrome P450 gene superfamily metabolize xenobiotics and which metabolize endogenous compounds. Our predictions correlate very well with known substrate specificities of the human enzymes. We also analyze the Caenorhabditis collagen gene family and use MIPhy to predict genes that produce an observable phenotype when knocked down in C. elegans, and show that our predictions correlate well with existing knowledge. The software can be downloaded and installed from https://github.com/dave-the-scientist/miphy and is also available as an online web tool at http://www.miphy.wasmuthlab.org.
Collapse
Affiliation(s)
- David M. Curran
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - James D. Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
8
|
Scherer S, Göbel TW. Characterisation of chicken OX40 and OX40L. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 82:128-138. [PMID: 29407480 DOI: 10.1016/j.dci.2018.01.014] [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: 12/08/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
The Tumour Necrosis Factor superfamilies of receptors and ligands play a crucial role in the regulation of effective immune responses against pathogens and malignant cells. In chickens, only few members have been identified. Here, we characterise the chicken homologues for mammalian costimulatory molecules OX40 and OX40L, which are involved in sustaining T cell responses. Both genes were identified by virtue of their genomic localisation close to highly conserved genes and their structural relationship to their mammalian homologues. Following cloning and expression of soluble and cell-associated chicken OX40 and OX40L, we confirmed their mutual interaction via ELISA and flow cytometric analyses. In addition, we showed the application of soluble OX40-Fc in staining of chicken cells. Whereas non-activated cells did not express OX40L, activation by IL-2 and IL-12 resulted in upregulation of OX40L on αβ and γδ T cell populations. Our results demonstrate the existence of the costimulatory OX40-OX40L system in the chicken and provide the basis for further investigations of chicken T cell responses.
Collapse
Affiliation(s)
- Stephanie Scherer
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Thomas W Göbel
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany.
| |
Collapse
|
9
|
Hoeres T, Smetak M, Pretscher D, Wilhelm M. Improving the Efficiency of Vγ9Vδ2 T-Cell Immunotherapy in Cancer. Front Immunol 2018; 9:800. [PMID: 29725332 PMCID: PMC5916964 DOI: 10.3389/fimmu.2018.00800] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/03/2018] [Indexed: 12/28/2022] Open
Abstract
Increasing immunological knowledge and advances in techniques lay the ground for more efficient and broader application of immunotherapies. gamma delta (γδ) T-cells possess multiple favorable anti-tumor characteristics, making them promising candidates to be used in cellular and combination therapies of cancer. They recognize malignant cells, infiltrate tumors, and depict strong cytotoxic and pro-inflammatory activity. Here, we focus on human Vγ9Vδ2 T-cells, the most abundant γδ T-cell subpopulation in the blood, which are able to inhibit cancer progression in various models in vitro and in vivo. For therapeutic use they can be cultured and manipulated ex vivo and in the following adoptively transferred to patients, as well as directly stimulated to propagate in vivo. In clinical studies, Vγ9Vδ2 T-cells repeatedly demonstrated a low toxicity profile but hitherto only the modest therapeutic efficacy. This review provides a comprehensive summary of established and newer strategies for the enhancement of Vγ9Vδ2 T-cell anti-tumor functions. We discuss data of studies exploring methods for the sensitization of malignant cells, the improvement of recognition mechanisms and cytotoxic activity of Vγ9Vδ2 T-cells. Main aspects are the tumor cell metabolism, antibody-dependent cell-mediated cytotoxicity, antibody constructs, as well as activating and inhibitory receptors like NKG2D and immune checkpoint molecules. Several concepts show promising results in vitro, now awaiting translation to in vivo models and clinical studies. Given the array of research and encouraging findings in this area, this review aims at optimizing future investigations, specifically targeting the unanswered questions.
Collapse
Affiliation(s)
- Timm Hoeres
- Department of Hematology and Medical Oncology, Paracelsus Medical University, Nuremberg, Germany
| | - Manfred Smetak
- Department of Hematology and Medical Oncology, Paracelsus Medical University, Nuremberg, Germany
| | - Dominik Pretscher
- Department of Hematology and Medical Oncology, Paracelsus Medical University, Nuremberg, Germany
| | - Martin Wilhelm
- Department of Hematology and Medical Oncology, Paracelsus Medical University, Nuremberg, Germany
| |
Collapse
|
10
|
Huhle D, Hirmer S, Göbel TW. Splenic γδ T cell subsets can be separated by a novel mab specific for two CD45 isoforms. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:229-240. [PMID: 28842181 DOI: 10.1016/j.dci.2017.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
CD45 isoforms have been identified in a variety of different species and mab against various isoforms have been instrumental to define cellular subsets. In the process of generating novel mab against chicken γδ T cells two mab with specificity for CD45 were identified and characterized. The analysis of the chicken CD45 genomic structure suggested three exons being involved in alternative splicing. We cloned and expressed the full length CD45 isoform and three shorter isoforms. While the 7D12 mab reacted with all of these isoforms, the 8B1 mab selectively reacted with two short isoforms lacking either exons 3 and 5 or exons 3, 5 and 6. As expected, the reactivity of 7D12 included all leukocyte subsets, also including thrombocytes. In contrast, the 8B1 mab only reacted with lymphocytes and monocytes. 8B1 expression was found on almost all blood αβ T cells, while a γδ T cell subset and virtually all B cells lacked 8B1 reactivity. The fraction of 8B1- αβ and γδ cells was larger in splenocytes as compared to PBL and there was also a population of 8B1+ splenic B cells. CD3 stimulation of splenic T cells resulted in upregulation of the 8B1 antigen on all T cells. Three-color immunofluorescence revealed differences in CD28 expression between the 8B1⁺ and 8B1¯ γδ T cell subsets with a higher CD28 expression level on 8B1¯ cells. The CD28 antigen was upregulated upon stimulation of the cells with IL-2 and IL-12. This novel mab will be a useful tool to further analyze chicken γδ T cells in more detail.
Collapse
Affiliation(s)
- Daniela Huhle
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Sieglinde Hirmer
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Thomas W Göbel
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany.
| |
Collapse
|
11
|
Fenzl L, Göbel TW, Neulen ML. γδ T cells represent a major spontaneously cytotoxic cell population in the chicken. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 73:175-183. [PMID: 28377199 DOI: 10.1016/j.dci.2017.03.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 03/31/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
Natural killer cells in the chicken are mainly confined to the intestine, while only small frequencies are detectable in spleen, lung and blood. Here, we compared the spontaneous cytotoxicity of lymphocytes isolated from blood, spleen and intestine using a flow cytometric based cytotoxicity assay. There was no spontaneous cytotoxicity detected in chicken blood preparations. In contrast, freshly prepared splenocytes exhibited a spontaneous cytotoxicity of up to 50% and intestinal epithelial lymphocytes of up to 85%. This cytotoxicity was observed against the RP9 but not against the chicken CU24 target cell line. The observed cytotoxicity was MHC unrestricted since B2B2 derived effector cells killed RP9 target cells (B2B15) equally well compared to MHC mismatched 2D8 targets (B19B19). The cytotoxicity of splenocytes was enhanced by preincubation with IL-2 or strongly increased with IL-2 plus IL-12. By cell sorting, we identified the CD8+γδ T cell subset as the major effectors, whereas both CD8-γδ T cells and CD8+αβ T cells had only low cytolytic potential. Within intestinal lymphocyte CD45+cells displayed cytotoxicity as well as sorted γδ T cells and NK cell. In conclusion, the chicken γδ T cells represent a major cytotoxic lymphocyte subset that can lyse target cells in a MHC unrestricted manner.
Collapse
Affiliation(s)
- Lisa Fenzl
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany
| | - Thomas W Göbel
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany.
| | - Marie-Luise Neulen
- Institute for Animal Physiology, Department of Veterinary Sciences, University of Munich, Veterinärstrasse 13, 80539 Munich, Germany
| |
Collapse
|
12
|
Das S, Li J, Hirano M, Sutoh Y, Herrin BR, Cooper MD. Evolution of two prototypic T cell lineages. Cell Immunol 2015; 296:87-94. [PMID: 25958271 DOI: 10.1016/j.cellimm.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/14/2015] [Accepted: 04/24/2015] [Indexed: 01/06/2023]
Abstract
Jawless vertebrates, which occupy a unique position in chordate phylogeny, employ leucine-rich repeat (LRR)-based variable lymphocyte receptors (VLR) for antigen recognition. During the assembly of the VLR genes (VLRA, VLRB and VLRC), donor LRR-encoding sequences are copied in a step-wise manner into the incomplete germ-line genes. The assembled VLR genes are differentially expressed by discrete lymphocyte lineages: VLRA- and VLRC-producing cells are T-cell like, whereas VLRB-producing cells are B-cell like. VLRA(+) and VLRC(+) lymphocytes resemble the two principal T-cell lineages of jawed vertebrates that express the αβ or γδ T-cell receptors (TCR). Reminiscent of the interspersed nature of the TCRα/TCRδ locus in jawed vertebrates, the close proximity of the VLRA and VLRC loci facilitates sharing of donor LRR sequences during VLRA and VLRC assembly. Here we discuss the insight these findings provide into vertebrate T- and B-cell evolution, and the alternative types of anticipatory receptors they use for adaptive immunity.
Collapse
Affiliation(s)
- Sabyasachi Das
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Jianxu Li
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Masayuki Hirano
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Yoichi Sutoh
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, United States.
| |
Collapse
|
13
|
van Schaik B, Klarenbeek P, Doorenspleet M, van Kampen A, Moody DB, de Vries N, Van Rhijn I. Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire. THE JOURNAL OF IMMUNOLOGY 2014; 193:5338-44. [PMID: 25339678 DOI: 10.4049/jimmunol.1401380] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During infection and autoimmune disease, activation and expansion of T cells take place. Consequently, the TCR repertoire contains information about ongoing and past diseases. Analysis and interpretation of the human TCR repertoire are hampered by its size and stochastic variation and by the diversity of Ags and Ag-presenting molecules encoded by the MHC, but are highly desirable and would greatly impact fundamental and clinical immunology. A subset of the TCR repertoire is formed by invariant T cells. Invariant T cells express interdonor-conserved TCRs and recognize a limited set of Ags, presented by nonpolymorphic Ag-presenting molecules. Discovery of the three known invariant T cell populations has been a tedious and slow process, identifying them one by one. Because conservation of the TCR α-chain of invariant T cells is much higher than the β-chain, and because the TCR α-chain V gene segment TRAV1-2 is used by two of the three known invariant TCRs, we employed next-generation sequencing of TCR α-chains that contain the TRAV1-2 gene segment to identify 16 invariant TCRs shared among many blood donors. Frequency analysis of individual clones indicates these T cells are expanded in many donors, implying an important role in human immunity. This approach extends the number of known interdonor-conserved TCRs and suggests that many more exist and that these TCR patterns can be used to systematically evaluate human Ag exposure.
Collapse
Affiliation(s)
- Barbera van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Paul Klarenbeek
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Marieke Doorenspleet
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Antoine van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Ildiko Van Rhijn
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands
| |
Collapse
|
14
|
Moulana M, Taylor EB, Edholm ES, Quiniou SMA, Wilson M, Bengtén E. Identification and characterization of TCRγ and TCRδ chains in channel catfish, Ictalurus punctatus. Immunogenetics 2014; 66:545-61. [PMID: 25129471 DOI: 10.1007/s00251-014-0793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 07/31/2014] [Indexed: 11/28/2022]
Abstract
Channel catfish, Ictalurus punctatus, T cell receptors (TCR) γ and δ were identified by mining of expressed sequence tag databases, and full-length sequences were obtained by 5'-RACE and RT-PCR protocols. cDNAs for each of these TCR chains encode typical variable (V), diversity (D), joining (J), and constant (C) regions. Three TCRγ V families, seven TCRγ J sequences, and three TCRγ C sequences were identified from sequencing of cDNA. Primer walking on bacterial artificial chromosomes (BACs) confirmed that the TRG locus contained seven TRGJ segments and indicated that the locus consists of (Vγ3-Jγ6-Cγ2)-(Vγ1n-Jγ7-Cγ3)-(Vγ2-Jγ5-Jγ4-Jγ3-Jγ2-Jγ1-Cγ1). In comparison for TCRδ, two V families, four TCRδ D sequences, one TCRδ J sequence, and one TCRδ C sequence were identified by cDNA sequencing. Importantly, the finding that some catfish TCRδ cDNAs contain TCR Vα-D-Jδ rearrangements and some TCRα cDNAs contain Vδ-Jα rearrangements strongly implies that the catfish TRA and TRD loci are linked. Finally, primer walking on BACs and Southern blotting suggest that catfish have four TRDD gene segments and a single TRDJ and TRDC gene. As in most vertebrates, all three reading frames of each of the catfish TRDD segments can be used in functional rearrangements, and more than one TRDD segment can be used in a single rearrangement. As expected, catfish TCRδ CDR3 regions are longer and more diverse than TCRγ CDR3 regions, and as a group they utilize more nucleotide additions and contain more nucleotide deletions than catfish TCRγ rearrangements.
Collapse
Affiliation(s)
- Mohadetheh Moulana
- Department of Microbiology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS, 39216-4505, USA
| | | | | | | | | | | |
Collapse
|
15
|
Holderness J, Hedges JF, Ramstead A, Jutila MA. Comparative biology of γδ T cell function in humans, mice, and domestic animals. Annu Rev Anim Biosci 2013; 1:99-124. [PMID: 25387013 DOI: 10.1146/annurev-animal-031412-103639] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
γδ T cells are a functionally heterogeneous population and contribute to many early immune responses. The majority of their activity is described in humans and mice, but the immune systems of all jawed vertebrates include the γδ T cell lineage. Although some aspects of γδ T cells vary between species, critical roles in early immune responses are often conserved. Common features of γδ T cells include innate receptor expression, antigen presentation, cytotoxicity, and cytokine production. Herein we compare studies describing these conserved γδ T cell functions and other, potentially unique, functions. γδ T cells are well documented for their potential immunotherapeutic properties; however, these proposed therapies are often focused on human diseases and the mouse models thereof. This review consolidates some of these studies with those in other animals to provide a consensus for the current understanding of γδ T cell function across species.
Collapse
Affiliation(s)
- Jeff Holderness
- Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana 59717; , , ,
| | | | | | | |
Collapse
|
16
|
Vaccarelli G, Antonacci R, Tasco G, Yang F, Giordano L, El Ashmaoui HM, Hassanane MS, Massari S, Casadio R, Ciccarese S. Generation of diversity by somatic mutation in theCamelus dromedariusT-cell receptor gamma variable domains. Eur J Immunol 2012; 42:3416-28. [DOI: 10.1002/eji.201142176] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 08/20/2012] [Accepted: 09/03/2012] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Gianluca Tasco
- Biocomputing Group; CIRI-Health Science and Technologies/Department of Biology; University of Bologna; Bologna Italy
| | - Fengtang Yang
- Cytogenetics Core Facility,; Wellcome Trust Sanger Institute; Hinxton Cambridge UK
| | - Luca Giordano
- Department of Biosciences,; Biotechnologies and Pharmacological Sciences; University of Bari; Bari Italy
| | - Hassan M. El Ashmaoui
- Cell Biology Department National Research Center; Dokki Giza Egypt
- King Abdulaziz University; Biological Sciences; Jeddah Saudi Arabia
| | | | - Serafina Massari
- Department of Biological and Environmental Science e Technologies; University of Salento; Lecce Italy
| | - Rita Casadio
- Biocomputing Group; CIRI-Health Science and Technologies/Department of Biology; University of Bologna; Bologna Italy
| | | |
Collapse
|
17
|
Defining the nature of human γδ T cells: a biographical sketch of the highly empathetic. Cell Mol Immunol 2012; 10:21-9. [PMID: 23085947 DOI: 10.1038/cmi.2012.44] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The elusive task of defining the character of γδ T cells has been an evolving process for immunologists since stumbling upon their existence during the molecular characterization of the α and β T cell receptor genes of their better understood brethren. Defying the categorical rules used to distinctly characterize lymphocytes as either innate or adaptive in nature, γδ T cells inhabit a hybrid world of their own. At opposing ends of the simplified spectrum of modes of antigen recognition used by lymphocytes, natural killer and αβ T cells are particularly well equipped to respond to the 'missing self' and the 'dangerous non-self', respectively. However, between these two reductive extremes, we are chronically faced with the challenge of making peace with the 'safe non-self' and dealing with the inevitable 'distressed self', and it is within this more complex realm γδ T cells excel thanks to their highly empathetic nature. This review gives an overview of the latest insights revealing the unfolding story of human γδ T cells, providing a biographical sketch of these unique lymphocytes in an attempt to capture the essence of their fundamental nature and events that influence their life trajectory. What hangs in their balance is their nuanced ability to differentiate the friends from the foe and the pathological from the benign to help us adapt swiftly and efficiently to life's many stresses.
Collapse
|
18
|
Criscitiello MF, Ohta Y, Saltis M, McKinney EC, Flajnik MF. Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark. THE JOURNAL OF IMMUNOLOGY 2010; 184:6950-60. [PMID: 20488795 DOI: 10.4049/jimmunol.0902774] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cartilaginous fish are the oldest animals that generate RAG-based Ag receptor diversity. We have analyzed the genes and expressed transcripts of the four TCR chains for the first time in a cartilaginous fish, the nurse shark (Ginglymostoma cirratum). Northern blotting found TCR mRNA expression predominantly in lymphoid and mucosal tissues. Southern blotting suggested translocon-type loci encoding all four chains. Based on diversity of V and J segments, the expressed combinatorial diversity for gamma is similar to that of human, alpha and beta may be slightly lower, and delta diversity is the highest of any organism studied to date. Nurse shark TCRdelta have long CDR3 loops compared with the other three chains, creating binding site topologies comparable to those of mammalian TCR in basic paratope structure; additionally, nurse shark TCRdelta CDR3 are more similar to IgH CDR3 in length and heterogeneity than to other TCR chains. Most interestingly, several cDNAs were isolated that contained IgM or IgW V segments rearranged to other gene segments of TCRdelta and alpha. Finally, in situ hybridization experiments demonstrate a conservation of both alpha/beta and gamma/delta T cell localization in the thymus across 450 million years of vertebrate evolution, with gamma/delta TCR expression especially high in the subcapsular region. Collectively, these data make the first cellular identification of TCR-expressing lymphocytes in a cartilaginous fish.
Collapse
Affiliation(s)
- Michael F Criscitiello
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD 21201, USA.
| | | | | | | | | |
Collapse
|
19
|
Reinink P, Van Rhijn I. The bovine T cell receptor alpha/delta locus contains over 400 V genes and encodes V genes without CDR2. Immunogenetics 2009; 61:541-9. [PMID: 19568741 PMCID: PMC2706379 DOI: 10.1007/s00251-009-0384-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2009] [Accepted: 06/17/2009] [Indexed: 01/02/2023]
Abstract
αβ T cells and γδ T cells perform nonoverlapping immune functions. In mammalian species with a high percentage of very diverse γδ T cells, like ruminants and pigs, it is often assumed that αβ T cells are less diverse than γδ T cells. Based on the bovine genome, we have created a map of the bovine TRA/TRD locus and show that, in cattle, in addition to the anticipated >100 TRDV genes, there are also >300 TRAV or TRAV/DV genes. Among the V genes in the TRA/TRD locus, there are several genes that lack a CDR2 and are functionally rearranged and transcribed and, in some cases, have an extended CDR1. The number of bovine V genes is a multiple of the number in mice and humans and may encode T cell receptors that use a novel way of interacting with antigen.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Cattle/genetics
- Cattle/immunology
- Chromosome Mapping
- Complementarity Determining Regions
- Databases, Genetic
- Gene Rearrangement, T-Lymphocyte
- Genes, T-Cell Receptor alpha
- Genes, T-Cell Receptor delta
- Humans
- Immunogenetic Phenomena
- Mice
- Molecular Sequence Data
- Phylogeny
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/chemistry
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Sequence Homology, Amino Acid
- Species Specificity
Collapse
Affiliation(s)
- Peter Reinink
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL Utrecht, The Netherlands
| | - Ildiko Van Rhijn
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL Utrecht, The Netherlands
| |
Collapse
|
20
|
Connelley T, Aerts J, Law A, Morrison WI. Genomic analysis reveals extensive gene duplication within the bovine TRB locus. BMC Genomics 2009; 10:192. [PMID: 19393068 PMCID: PMC2685407 DOI: 10.1186/1471-2164-10-192] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 04/24/2009] [Indexed: 12/18/2022] Open
Abstract
Background Diverse TR and IG repertoires are generated by V(D)J somatic recombination. Genomic studies have been pivotal in cataloguing the V, D, J and C genes present in the various TR/IG loci and describing how duplication events have expanded the number of these genes. Such studies have also provided insights into the evolution of these loci and the complex mechanisms that regulate TR/IG expression. In this study we analyze the sequence of the third bovine genome assembly to characterize the germline repertoire of bovine TRB genes and compare the organization, evolution and regulatory structure of the bovine TRB locus with that of humans and mice. Results The TRB locus in the third bovine genome assembly is distributed over 5 scaffolds, extending to ~730 Kb. The available sequence contains 134 TRBV genes, assigned to 24 subgroups, and 3 clusters of DJC genes, each comprising a single TRBD gene, 5–7 TRBJ genes and a single TRBC gene. Seventy-nine of the TRBV genes are predicted to be functional. Comparison with the human and murine TRB loci shows that the gene order, as well as the sequences of non-coding elements that regulate TRB expression, are highly conserved in the bovine. Dot-plot analyses demonstrate that expansion of the genomic TRBV repertoire has occurred via a complex and extensive series of duplications, predominantly involving DNA blocks containing multiple genes. These duplication events have resulted in massive expansion of several TRBV subgroups, most notably TRBV6, 9 and 21 which contain 40, 35 and 16 members respectively. Similarly, duplication has lead to the generation of a third DJC cluster. Analyses of cDNA data confirms the diversity of the TRBV genes and, in addition, identifies a substantial number of TRBV genes, predominantly from the larger subgroups, which are still absent from the genome assembly. The observed gene duplication within the bovine TRB locus has created a repertoire of phylogenetically diverse functional TRBV genes, which is substantially larger than that described for humans and mice. Conclusion The analyses completed in this study reveal that, although the gene content and organization of the bovine TRB locus are broadly similar to that of humans and mice, multiple duplication events have led to a marked expansion in the number of TRB genes. Similar expansions in other ruminant TR loci suggest strong evolutionary pressures in this lineage have selected for the development of enlarged sets of TR genes that can contribute to diverse TR repertoires.
Collapse
Affiliation(s)
- Timothy Connelley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK.
| | | | | | | |
Collapse
|
21
|
Heterogeneity of avian gammadelta T cells. Vet Immunol Immunopathol 2008; 124:241-52. [PMID: 18455805 DOI: 10.1016/j.vetimm.2008.03.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 03/07/2008] [Accepted: 03/25/2008] [Indexed: 12/30/2022]
Abstract
gammadelta T cells are distinct with respect to tissue localisation, phenotype and biological functions and similarities between species are not very apparent. To elucidate local and functional heterogeneity of non-stimulated avian gammadelta T cells, the CD8-characterised gammadelta T cell subsets [CD8alpha(+high) (CD8alphaalpha(+) and CD8alphabeta(+)); CD8alpha(+dim); CD8(-)] of blood, spleen and caecum were flow cytometrically quantified and analysed for proliferation state as well as sorted for determination of immune-relevant gene expression by quantitative real-time RT-PCR. The number of avian CD8-characterised gammadelta T cell subsets differed in dependence on tissue and age of bird. Compared to blood and spleen, caecum showed the highest percentage of gammadelta T cells as well as of the CD8alpha(+high) gammadelta T cell subset in 7-week-old birds. Generally, the CD8alphabeta(+) cells significantly outnumbered the CD8alphaalpha(+) lymphocytes within the CD8alpha(+high) gammadelta T cell population of all organs. Additionally, the splenic CD8alphabeta(+) subpopulation revealed the highest proliferation activity. By RT-PCR, mRNA expression of immune-relevant genes was proved in non-stimulated gammadelta T cell subsets, but on different levels. Generally, both CD8alpha(+high) cell subsets (CD8alphaalpha(+) and CD8alphabeta(+)) of blood and spleen showed elevated expression levels for Fas ligand (FasL), XCL1 (lymphotactin) and interferon-gamma (IFNgamma) compared to the CD8alpha(-) gammadelta T cell subset. In contrast, all caecal gammadelta T cell subsets showed similar high levels of these transcripts. Notably, the CD8alphaalpha(+) cells of all locations showed unique expression of TLR4 and interleukin (IL)-2. The results demonstrated that avian gammadelta T cells are not only heterogeneous concerning their CD8 antigen characteristics and tissue localisation, but also with regard to functional features such as proliferation and mRNA expression.
Collapse
|
22
|
Parra ZE, Baker ML, Hathaway J, Lopez AM, Trujillo J, Sharp A, Miller RD. Comparative genomic analysis and evolution of the T cell receptor loci in the opossum Monodelphis domestica. BMC Genomics 2008; 9:111. [PMID: 18312668 PMCID: PMC2275272 DOI: 10.1186/1471-2164-9-111] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 02/29/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND All jawed-vertebrates have four T cell receptor (TCR) chains: alpha (TRA), beta (TRB), gamma (TRG) and delta (TRD). Marsupials appear unique by having an additional TCR: mu (TRM). The evolutionary origin of TRM and its relationship to other TCR remain obscure, and is confounded by previous results that support TRM being a hybrid between a TCR and immunoglobulin locus. The availability of the first marsupial genome sequence allows investigation of these evolutionary relationships. RESULTS The organization of the conventional TCR loci, encoding the TRA, TRB, TRG and TRD chains, in the opossum Monodelphis domestica are highly conserved with and of similar complexity to that of eutherians (placental mammals). There is a high degree of conserved synteny in the genomic regions encoding the conventional TCR across mammals and birds. In contrast the chromosomal region containing TRM is not well conserved across mammals. None of the conventional TCR loci contain variable region gene segments with homology to those found in TRM; rather TRM variable genes are most similar to that of immunoglobulin heavy chain genes. CONCLUSION Complete genomic analyses of the opossum TCR loci continue to support an origin of TRM as a hybrid between a TCR and immunoglobulin locus. None of the conventional TCR loci contain evidence that such a recombination event occurred, rather they demonstrate a high degree of stability across distantly related mammals. TRM, therefore, appears to be derived from receptor genes no longer extant in placental mammals. These analyses provide the first genomic scale structural detail of marsupial TCR genes, a lineage of mammals used as models of early development and human disease.
Collapse
Affiliation(s)
- Zuly E Parra
- Center for Evolutionary and Theoretical Immunology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | | | | | | | | | | | | |
Collapse
|
23
|
Adaptive evolution of multiple-variable exons and structural diversity of drug-metabolizing enzymes. BMC Evol Biol 2007; 7:69. [PMID: 17475008 PMCID: PMC1885805 DOI: 10.1186/1471-2148-7-69] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 05/02/2007] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The human genome contains a large number of gene clusters with multiple-variable-first exons, including the drug-metabolizing UDP glucuronosyltransferase (UGT1) and I-branching beta-1,6-N-acetylglucosaminyltransferase (GCNT2, also known as IGNT) clusters, organized in a tandem array, similar to that of the protocadherin (PCDH), immunoglobulin (IG), and T-cell receptor (TCR) clusters. To gain insight into the evolutionary processes that may have shaped their diversity, we performed comprehensive comparative analyses for vertebrate multiple-variable-first-exon clusters. RESULTS We found that there are species-specific variable-exon duplications and mutations in the vertebrate Ugt1, Gcnt2, and Ugt2a clusters and that their variable and constant genomic organizations are conserved and vertebrate-specific. In addition, analyzing the complete repertoires of closely-related Ugt2 clusters in humans, mice, and rats revealed extensive lineage-specific duplications. In contrast to the Pcdh gene clusters, gene conversion does not play a predominant role in the evolution of the vertebrate Ugt1, Gcnt2 and Ugt2 gene clusters. Thus, their tremendous diversity is achieved through "birth-and-death" evolution. Comparative analyses and homologous modeling demonstrated that vertebrate UGT proteins have similar three-dimensional structures each with N-terminal and C-terminal Rossmann-fold domains binding acceptor and donor substrates, respectively. Molecular docking experiments identified key residues in donor and acceptor recognition and provided insight into the catalytic mechanism of UGT glucuronidation, suggesting the human UGT1A1 residue histidine 39 (H39) as a general base and the residue aspartic acid 151 (D151) as an important electron-transfer helper. In addition, we identified four hypervariable regions in the N-terminal Rossmann domain that form an acceptor-binding pocket. Finally, analyzing patterns of nonsynonymous and synonymous nucleotide substitutions identified codon sites that are subject to positive Darwinian selection at the molecular level. These diversified residues likely play an important role in recognition of myriad xenobiotics and endobiotics. CONCLUSION Our results suggest that enormous diversity of vertebrate multiple variable first exons is achieved through birth-and-death evolution and that adaptive evolution of specific codon sites enhances vertebrate UGT diversity for defense against environmental agents. Our results also have interesting implications regarding the staggering molecular diversity required for chemical detoxification and drug clearance.
Collapse
|
24
|
Thomas JH. Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet 2007; 3:e67. [PMID: 17500592 PMCID: PMC1866355 DOI: 10.1371/journal.pgen.0030067] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 03/14/2007] [Indexed: 12/15/2022] Open
Abstract
Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50-80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth-death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer.
Collapse
Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
| |
Collapse
|
25
|
Herzig CTA, Blumerman SL, Baldwin CL. Identification of three new bovine T-cell receptor delta variable gene subgroups expressed by peripheral blood T cells. Immunogenetics 2006; 58:746-57. [PMID: 16896832 DOI: 10.1007/s00251-006-0136-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2006] [Accepted: 05/31/2006] [Indexed: 01/23/2023]
Abstract
To understand the biology of gammadelta T cells in ruminants, it is necessary to have a comprehensive picture of gammadelta T-cell receptor gene diversity and expression. In this study, three new subgroups of bovine T-cell receptor delta (TRD) variable genes were identified by RT-PCR and sequencing and homology with TRDV genes from other mammals determined. Previously unidentified TRDV subgroup genes described in this study include the bovine homologues of ovine TRDV2, TRDV3, and TRDV4 which were named accordingly. TRDV2 subgroup has two genes (TRDV2-1 and TRDV2-2) while we found the previously identified TRDV1 has at least eight genes corresponding to separate genomic sequences. Nucleotide and amino acid sequences for particular gene subgroups between cattle and sheep were more than 87% identical but identities among TRDV subgroups within a species were much less, with bovine TRDV4 having <45% identity to the other three bovine TRDV gene subgroups. Analysis of circulating bovine gammadelta T cells revealed that genes from all four TRDV subgroups were expressed in combination with TRDJ1, TRDJ3, and TRDC, although TRDV4 was the least represented, and all displayed a variety of CDR3 junctional lengths. Finally, some genes within the TRDV1, TRDV2, and TRDV3 subgroups recombined with TRAV incorporating TRAJs, suggesting dual use.
Collapse
Affiliation(s)
- Carolyn T A Herzig
- Department of Veterinary and Animal Sciences, Paige Laboratory, University of Massachusetts, Amherst, MA 01003, USA
| | | | | |
Collapse
|
26
|
Herzig C, Blumerman S, Lefranc MP, Baldwin C. Bovine T cell receptor gamma variable and constant genes: combinatorial usage by circulating gammadelta T cells. Immunogenetics 2006; 58:138-51. [PMID: 16541255 DOI: 10.1007/s00251-006-0097-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 01/29/2006] [Indexed: 10/24/2022]
Abstract
Studies here describe expression and sequence of several new bovine T cell receptor gamma (TRG) genes to yield a total of 11 TRG variable (TRGV) genes (in eight subgroups) and six TRG constant (TRGC) genes. Publicly available genomic sequences were annotated to show their placement. Homologous TRG genes in cattle and sheep were assigned, using four accepted criteria. New genes described here include the bovine TRGC6, TRGV2, and TRGV4, homologues of ovine TRGC4, TRGV2, and TRGV4, respectively. The bovine Vgamma7 and BTGV1 clones (previously TRGV4 and TRGV2, respectively) were reassigned to new subgroups TRGV7 and TRGV8, respectively, with approval by the IMGT Nomenclature Committee. Three TRGV subgroups (TRGV5, TRGV6, and TRGV8) were further designated as TRGV5-1 and TRGV5-2, TRGV6-1 and TRGV6-2, and TRGV8-1 and TRGV8-2 because each subgroup is comprised of two mapped genes. The complete sequence of bovine TRGC5 is also reported, for which a limited number of nucleotides was previously available, and shown to be most closely related to ovine TRGC5. Analysis of circulating gammadelta T cells revealed that rearrangement of TRGV genes with TRGC genes is largely dictated by their proximity within one of the six genomic V-J-C cassettes, with all TRG genes expressed by bovine peripheral blood gammadelta T cells. Cattle are useful models for gammadelta T cell biology because they have gammadelta T cells that respond to isopentenylpyrophosphate (IPP) antigens, while mice do not, and some bovine TRGV genes cluster closely with human genes.
Collapse
Affiliation(s)
- Carolyn Herzig
- Paige Laboratory, Department of Veterinary and Animal Sciences and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA.
| | | | | | | |
Collapse
|
27
|
Cho S, Zhang J. Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals. Gene 2006; 373:116-25. [PMID: 16530354 DOI: 10.1016/j.gene.2006.01.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 01/17/2006] [Accepted: 01/18/2006] [Indexed: 12/13/2022]
Abstract
Members of the ribonuclease (RNase) A superfamily participate in a diverse array of biological processes, including digestion, angiogenesis, innate immunity, and possibly male reproduction. The superfamily is vertebrate-specific, with 13-20 highly divergent members in primates and rodents, but only a few members in chicken and fish. This has led to the proposal that the superfamily started off from a progenitor with structural similarities to angiogenin and that the superfamily underwent a dramatic expansion during mammalian evolution. To date this evolutionary expansion and understand the functional diversification of the superfamily, we here determine its entire repertoire in the sequenced genomes of dog, cow, and opossum. We identified 7, 20, and 21 putatively functional RNase genes from these three species, respectively. Many of the identified genes are highly divergent from all previously known RNase genes, thus representing new lineages within the superfamily. Phylogenetic analysis indicates that the superfamily expansion predated the separation of placental and marsupial mammals and that differential gene loss and duplication occurred in different species, generating a great variation in gene number and content among extant mammals.
Collapse
Affiliation(s)
- Soochin Cho
- Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Natural Science Building, 830 North University Avenue, Ann Arbor, MI 48109, USA
| | | |
Collapse
|
28
|
Abstract
Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.
Collapse
Affiliation(s)
- Masatoshi Nei
- Institute of Molecular Evolutionary Genetics and1 Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Alejandro P. Rooney
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois 61604;
| |
Collapse
|
29
|
Parra ZE, Arnold T, Nowak MA, Hellman L, Miller RD. TCR gamma chain diversity in the spleen of the duckbill platypus (Ornithorhynchus anatinus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:699-710. [PMID: 16303181 DOI: 10.1016/j.dci.2005.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 10/03/2005] [Accepted: 10/05/2005] [Indexed: 05/05/2023]
Abstract
TCR gamma (TRG) chain diversity in splenic gammadelta T cells was determined for an egg-laying mammal (or monotreme), the duckbill platypus. Three distinct V subgroups were found in the expressed TRG chains and these three subgroups are members of a clade not found so far in eutherian mammals or birds. Each subgroup contains approximately five V gene segments, and their overall divergence is much less than is found in eutherians and birds, consistent with their recent evolution from an ancestral V gene segment. The platypus TRG locus also contains three C region genes and many of the residues involved in TCR function, such as interactions with CD3, were conserved in the monotreme C regions. All non-eutherian mammals (monotremes and marsupials) lacked the second cysteine residue necessary to form the intradomain disulfide bond in the C region, a loss apparently due to independent mutations in marsupials and monotremes. Monotreme TRGC regions also had among the most variation in the length of the connecting peptide region described for any species due to repeated motifs.
Collapse
Affiliation(s)
- Zuly E Parra
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | | | | | | | | |
Collapse
|
30
|
Houston EF, Connelley T, Parsons K, MacHugh ND, Morrison WI. Analysis of T-cell receptor BV gene sequences in cattle reveals extensive duplication within the BV9 and BV20 subgroups. Immunogenetics 2005; 57:674-81. [PMID: 16187058 DOI: 10.1007/s00251-005-0040-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 08/08/2005] [Indexed: 10/25/2022]
Abstract
We investigated the repertoire of functional T-cell receptor beta-chain variable genes (TRBV genes) in cattle by analysing the nucleotide sequences and predicted amino acid sequences of a set of cDNA clones isolated from lymph node T cells. Thirty-nine distinct TRBV sequences were identified, bringing the total number of recognised bovine TRBV gene segments to more than 40. Sixteen TRBV subgroups were defined based on their sequence homology to each other and to human TRBV genes. All of the main phylogenetic lineages of BV gene subgroups described in humans and mice were represented. Eight of the subgroups were found to contain more than one member. The most striking feature of the results was the large number of sequences (more than half of the sequenced clones) in the BV9 and BV20 subgroups, which were found to contain 12 and 8 distinct sequences, respectively. In contrast, the corresponding human TRBV subfamilies contain a single member. The results indicate that, as in humans, there has been extensive gene duplication within the TRBV locus during evolution. However, duplication of different BV subgroups in cattle has resulted in a TRBV gene repertoire distinct from that found in other species.
Collapse
Affiliation(s)
- E F Houston
- Institute for Animal Health, Compton, Newbury, Berkshire, RG20 7NN, UK
| | | | | | | | | |
Collapse
|
31
|
Baker ML, Osterman AK, Brumburgh S. Divergent T-cell receptor delta chains from marsupials. Immunogenetics 2005; 57:665-73. [PMID: 16160827 DOI: 10.1007/s00251-005-0030-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 07/17/2005] [Indexed: 10/25/2022]
Abstract
Complementary DNAs (cDNAs) encoding T-cell receptor delta (TRD) chains from the northern brown bandicoot, Isoodon macrourus, were identified while sequencing expressed sequence tags (ESTs) from a thymus cDNA library. Surprisingly, the I. macrourus TRD sequences were not orthologous to previously published TRD sequences from another Australian marsupial, the tammar wallaby, Macropus eugenii. Identification of TRD genes in the recently completed whole genome sequence of the South American opossum, Monodelphis domestica, revealed the presence of two highly divergent TRD loci. To determine whether the presence of multiple TRD loci accounts for the lack of orthology between the I. macrourus and M. eugenii cDNAs, additional TRD sequences were obtained from both species of marsupials. The results of this analysis revealed that, unlike eutherian mammals, all three species of marsupials have multiple, highly divergent TRD loci. One group of marsupial TRD sequences was closely related to TR sequences from eutherian mammals. A second group of TRD sequences formed a unique marsupial-specific clade, separate from TR sequences from eutherians. An interesting expression pattern of TRD variable (TRDV) and constant (TRDC) segments was evident in cDNAs from I. macrourus and M. eugenii. TRDV and TRDC sequences that were closely related to TRD genes from eutherian mammals were only found in association with each other in cDNAs from both marsupial species. A similar pattern was seen between TRDV and TRDC sequences that were most closely related to other marsupial TRD genes.
Collapse
Affiliation(s)
- Michelle L Baker
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | | | | |
Collapse
|
32
|
Cho KS, Zhai SK, Esteves PJ, Knight KL. Characterization of the T-cell receptor gamma locus and analysis of the variable gene segment expression in rabbit. Immunogenetics 2005; 57:352-63. [PMID: 15868143 DOI: 10.1007/s00251-005-0795-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2004] [Revised: 03/07/2005] [Indexed: 11/24/2022]
Abstract
The genomic organization and expression of genes of the T-cell receptor gamma (TRG) locus are described for mice and humans, but not for species such as rabbits (Oryctolagus cuniculus), in which gammadelta T cells compose a sizeable proportion of T cells in the periphery. We cloned 200 kb of the rabbit TRG locus and determined the TRGV gene usage in adult and newborn rabbits by RT-PCR. We identified two TRGJ genes, one TRGC gene, and 22 TRGV genes, all of which encoded functional variable regions. One TRGV gene is the unique member of the TRGV2 subgroup, whereas the other genes belong to the TRGV1 subgroup. Evolutionary analyses of TRGV1 genes identified three distinct groups that can be explained by separate duplication events in the rabbit genome. Evidence of gene conversion between TRGV1.1 and TRGV1.6 was observed. Both TRGV1 and TRGV2 subgroup genes were expressed in the spleen, intestine, and appendix of adult rabbits, and the repertoire of TRGV genes expressed in these tissues was similar. In these tissues from newborns, and in skin from adults, only the genes from the TRGV1 subgroup were expressed. Greater TRGV-J junctional diversity was found in tissues from adult compared to newborn rabbits. Our analyses indicate rabbits have a larger germ line encoded TRG repertoire compared with that of mice and humans. In addition, we found TRGV gene usage is alike in most tissues of rabbits similar to that found in humans but in contrast to that found in mice.
Collapse
Affiliation(s)
- Kathy S Cho
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 5-153, USA
| | | | | | | |
Collapse
|
33
|
Belov K, Miller RD, Ilijeski A, Hellman L, Harrison GA. Isolation of monotreme T-cell receptor alpha and beta chains. Immunogenetics 2004; 56:164-9. [PMID: 15133646 DOI: 10.1007/s00251-004-0679-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Revised: 04/08/2004] [Indexed: 11/29/2022]
Abstract
Monotremes are an ancient mammalian lineage that last shared a common ancestor with the marsupial and eutherian (placental) mammals about 170 million years ago. Characterization of their immune genes is allowing us to gain insights into the evolutionary processes that lead to the 'mammalian' immune response. Here we describe the characterization of the first cDNA clones encoding T-cell receptors from a monotreme. Two TCR alpha-chain cDNAs ( TCRA) from the short-beaked echidna, Tachyglossus aculeatus, containing complete variable, joining and constant regions were isolated. The echidna TCRA constant region shares approximately 37% amino acid identity with other mammalian TCRA constant region sequences. The two variable regions belong to the TCRAV group C, which also contains V genes from humans, mice, cattle and chickens. One echidna TCR beta-chain cDNA ( TCRB) containing the entire constant region was isolated and sequenced. It shares about 63% identity with other mammalian TCRB constant region sequences. The echidna TCRBV belongs to TCRBV group A, which also contains V genes from various eutherian species. Southern blot analysis indicates that, like in other mammalian species, there is only one TCRA constant region copy in the echidna genome, but at least two TCRB constant regions.
Collapse
Affiliation(s)
- Katherine Belov
- Evolutionary Biology Unit, Australian Museum, 6 College St, 2010, Sydney, NSW, Australia.
| | | | | | | | | |
Collapse
|
34
|
Burgess SC. Proteomics in the chicken: tools for understanding immune responses to avian diseases. Poult Sci 2004; 83:552-73. [PMID: 15109053 DOI: 10.1093/ps/83.4.552] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The entire chicken genome sequence will be available by the time this review is in press. Chickens will be the first production animal species to enter the "postgenomic era." This fundamental structural genomics achievement allows, for the first time, complete functional genomics approaches for understanding the molecular basis of chicken normo- and pathophysiology. The functional genomics paradigm, which contrasts with classical functional genetic investigations of one gene (or few) in isolation, is the systematic holistic genetic analyses of biological systems in defined contexts. Context-dependent gene interactions are the fundamental mechanics of all life. Functional genomics uses high-throughput large-scale experimental methods combined with statistical and computational analyses. Projects with expressed sequence tags in chickens have already allowed the creation of cDNA microarrays for large-scale context-dependant mRNA analysis (transcriptomics). However, proteins are the functional units of almost all biological processes, and protein expression very often bears no correlation to mRNA expression. Proteomics, a discipline within functional genomics, is the context-defined analysis of complete complements of proteins. Proteomics bridges the "sequence-to-phenotype gap;" it complements structural and other functional genomics approaches. Proteomics requires high capital investment but has ubiquitous biological applications. Although currently the fastest-growing human biomedical discipline, new paradigms may need to be established for production animal proteomics research. The prospective promise and potential pitfalls of using proteomics approaches to improve poultry pathogen control will be specifically highlighted. The first stage of our recently established proteomics program is global protein profiling to identify differentially expressed proteins in the context of the commercially important pathogens. Our trials and tribulations in establishing our proteomics program, as well some of our initial data to understand chicken immune system function, will be discussed.
Collapse
Affiliation(s)
- S C Burgess
- Department of Basic Sciences, Mississippi State University, College of Veterinary Medicine, PO Box 6100, Mississippi State, Mississippi 39762-6100, USA.
| |
Collapse
|
35
|
Guerrero JE, Pacheco DP, Suárez CF, Martínez P, Aristizabal F, Moncada CA, Patarroyo ME, Patarroyo MA. Characterizing T-cell receptor gamma-variable gene in Aotus nancymaae owl monkey peripheral blood. ACTA ACUST UNITED AC 2003; 62:472-82. [PMID: 14617030 DOI: 10.1046/j.1399-0039.2003.00130.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Gammadelta T lymphocytes have a heterodimeric complex formed by the association of gamma and delta chains as receptor. Proliferation of this lymphocyte population has been observed, when infection by several pathogens such as Mycobacterium tuberculosis and Plasmodium spp. occurs. The New World Monkey Aotus nancymaae has become a very good experimental model for the immunological and physiopathological study of these infectious agents. The A. nancymaae gamma-variable region was characterized from peripheral blood samples by using cDNA and genomic DNA polymerase chain reaction amplification, DNA sequencing, and dot-blot hybridization techniques. Seventeen different T-cell receptor gamma-variable (TCRGV) sequences were obtained. These sequences were distributed among TCRGV subsets 1, 2, or 3, according to human subset classification. Although no subset 4 amplification was obtained, this subset was detected by dot-blot hybridization. The presence of these 4 subsets resembles the behavior displayed by 'gammadelta-low species' (humans and mice), where high diversity among these lymphocytes can be observed. Homologies greater than 70% were found with respect to humans. Sequence convergence between human and A. nancymaae subsets 1 and 3 highlights Aotus as a promising model for studying these lymphocyte functions.
Collapse
Affiliation(s)
- J E Guerrero
- Molecular Biology Department, Fundación Instituto de Inmunología de Colombia, Santa Fe de Bogotá, Colombia Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Elemento O, Lefranc MP. IMGT/PhyloGene: an on-line tool for comparative analysis of immunoglobulin and T cell receptor genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2003; 27:763-779. [PMID: 12818634 DOI: 10.1016/s0145-305x(03)00078-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ((R)). IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr.
Collapse
Affiliation(s)
- Olivier Elemento
- IMGT, the International ImMunoGeneTics Information System, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Université Montpellier II, UPR CNRS 1142, Institut de Génétique Humaine (IGH), 141 rue de la Cardonille, 34396 Cedex 5, Montpellier, France
| | | |
Collapse
|
37
|
Harrison GA, Taylor CL, Miller RD, Deane EM. Primary structure and variation of the T-cell receptor delta-chain from a marsupial, Macropus eugenii. Immunol Lett 2003; 88:117-25. [PMID: 12880681 DOI: 10.1016/s0165-2478(03)00072-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although gammadelta T-cells form only a small portion of circulating T-cells in mice and humans, they are more frequent in many other types of mammals and this has lead to speculation regarding their roles and the evolutionary significance of their relative abundance. Moreover, whilst clear homologues of four types of T-cell receptor (TCR) chains (alpha, beta, delta and gamma) have been identified in vertebrates as distantly related as eutherian mammals and cartilaginous fish, there are still many gaps in our knowledge of these TCR components from various taxa. Such knowledge would further illuminate the evolution and function of these receptors and of gammadelta T-cells. Here, we report the molecular cloning of a TCR-delta chain cDNA from the tammar wallaby (Macropus eugenii) which represents the first component of the gammadelta TCR to be characterised from a marsupial. A PCR-based survey of variable (V) segment usage in tammar wallaby mammary-associated lymph node indicated that, although gammadelta T-cells may be sparse in this type of tissue, this species has at least three subfamilies of V genes that have been broadly conserved across vertebrate evolution. Two V subfamilies found in the tammar wallaby were relatively similar and may have diverged more recently, an event that probably occurred at some point in the marsupial lineage.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- Conserved Sequence/genetics
- Evolution, Molecular
- Humans
- Marsupialia/genetics
- Marsupialia/immunology
- Mice
- Molecular Sequence Data
- Phylogeny
- Receptors, Antigen, T-Cell, gamma-delta/chemistry
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- Gavan A Harrison
- School of Science, Food and Horticulture, University of Western Sydney, BCRI Building, Locked Bag 1797, Penrith South DC, NSW 1797, Australia
| | | | | | | |
Collapse
|
38
|
Abstract
The study of immunoglobulin genes in non-mouse and non-human models has shown that different vertebrate groups have evolved distinct methods of generating antibody diversity. By contrast, the development of T cells in the thymus is quite similar in all of the species that have been examined. The three mechanisms by which B cells uniquely modify their immunoglobulin genes -- somatic hypermutation, gene conversion and class switching -- are increasingly believed to share some fundamental mechanisms, which studies in different vertebrate groups have helped (and will continue to help) to resolve. When these mechanisms are better understood, we should be able to look to the constitutive pathways from which they have evolved and perhaps determine whether the rearrangement of variable, diversity and joining antibody gene segments -- V(D)J recombination -- was superimposed on an existing adaptive immune system.
Collapse
Affiliation(s)
- Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, Maryland 21201, USA.
| |
Collapse
|
39
|
Daubenberger CA, Salomon M, Vecino W, Hübner B, Troll H, Rodriques R, Patarroyo ME, Pluschke G. Functional and structural similarity of V gamma 9V delta 2 T cells in humans and Aotus monkeys, a primate infection model for Plasmodium falciparum malaria. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:6421-30. [PMID: 11714808 DOI: 10.4049/jimmunol.167.11.6421] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gammadelta T cells are implicated to play crucial roles during early immune responses to pathogens. A subset of human gammadelta T cells carrying the Vgamma9Vdelta2 TCR recognize small, phosphorylated nonpeptidic Ags. However, the precise role of these cells and the ligands recognized in human immune responses against pathogens remains unclear because of the lack of suitable animal models. We have analyzed the reactivity of spleen cells of the New World monkey Aotus nancymaae against isopentenyl pyrophosphate (IPP), a phosphorylated microbial metabolite selectively activating Vgamma9Vdelta2 T cells. Spleen cells were stimulated by IPP and the expanding cell population expressed the Vgamma9 TCR. TRGV-J and TRDV-D-J rearrangements expressed by IPP-stimulated cells of Aotus were analyzed by RT-PCR and DNA sequencing. The TRGV-J and TRDV-D-J rearrangements expressed by IPP-stimulated Aotus and human gammadelta T cells were similar with respect to 1) TCR gene segment usage, 2) a high degree of germline sequence homology of the TCR gene segments used, and 3) the diversity of the CDR3 regions. Phylogenetic analysis of human, Pan troglodytes, and A. nancymaae TRGV gene segments showed that the interspecies differences are smaller than the intraspecies differences with TRGV9 gene segments located on a distinct clade of the phylogenetic tree. The structural and functional conservation of Vgamma9Vdelta2 T cells in A. nancymaae and humans implicates a functionally important and evolutionary conserved mechanism of recognition of phosphorylated microbial metabolites.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Aotidae
- Base Sequence
- Cells, Cultured
- Disease Models, Animal
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Gene Rearrangement, delta-Chain T-Cell Antigen Receptor/drug effects
- Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor/drug effects
- Hemiterpenes
- Humans
- Immunoglobulin Joining Region/genetics
- Immunoglobulin Variable Region/genetics
- Interferon-gamma/biosynthesis
- Interferon-gamma/genetics
- Lymphocyte Activation/drug effects
- Malaria, Falciparum/immunology
- Malaria, Falciparum/metabolism
- Molecular Sequence Data
- Organophosphorus Compounds/pharmacology
- Pan troglodytes
- Receptors, Antigen, T-Cell, gamma-delta/chemistry
- Receptors, Antigen, T-Cell, gamma-delta/drug effects
- Receptors, Antigen, T-Cell, gamma-delta/physiology
- Sequence Analysis, DNA
- T-Lymphocyte Subsets/drug effects
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
Collapse
Affiliation(s)
- C A Daubenberger
- Department of Molecular Immunology, Swiss Tropical Institute, Basel, Switzerland.
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Baker ML, Rosenberg GH, Zuccolotto P, Harrison GA, Deane EM, Miller RD. Further characterization of T cell receptor chains of marsupials. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2001; 25:495-507. [PMID: 11356229 DOI: 10.1016/s0145-305x(01)00016-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
cDNA clones encoding T cell receptor alpha (TCRalpha) and beta (TCRbeta) from the South American opossum, Monodelphis domestica were isolated and characterized. A single clone isolated encoding a TCRalpha chain was full length, containing the complete V (variable), J (joining) and C (constant) regions. Three partial cDNA clones were isolated for TCRbeta which contained complete C sequences. Phylogenetic analysis of the TCR Valpha revealed that the M. domestica sequence and a sequence from the Australian brushtail possum, Trichosurus vulpecula, belong to separate Valpha families and intersperse with sequences from eutherian mammals. Similar to results described for marsupial and eutherian light chains, diversity at the V region of the TCR is ancient and maintained. In contrast phylogenetic analysis of the TCR Calpha and Cbeta sequences from M. domestica, T. vulpecula, and other vertebrates revealed that the marsupial TCR C grouped together forming a sister group to eutherian mammals.
Collapse
Affiliation(s)
- M L Baker
- Department of Biology, University of New Mexico, 87131, Albuquerque, NM, USA
| | | | | | | | | | | |
Collapse
|
41
|
Su C, Nei M. Evolutionary dynamics of the T-cell receptor VB gene family as inferred from the human and mouse genomic sequences. Mol Biol Evol 2001; 18:503-13. [PMID: 11264401 DOI: 10.1093/oxfordjournals.molbev.a003829] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diversity of T-cell receptors is generated primarily by the variable-region gene families, each of which is composed of a large number of member genes. The entire genomic sequence of the variable region (VB) of the T- cell receptor beta chain from humans and mice has become available. To understand the evolutionary dynamics of the VB gene family, we conducted a phylogenetic analysis of all VB genes from humans and mice, as well as a detailed analysis of internal DNA duplications in the human genomic VB region. The phylogenetic tree obtained shows that human and mouse VB genes intermingle extensively rather than forming two separate clusters and that many gene duplications occurred both before and after the divergence between primates and rodents. Analyzing the genomic maps of transposable elements (e.g., LINEs and SINEs) and relic VB genes in the VB gene region, we present evidence that a 20-kb VB region duplicated tandemly four times in the human lineage during the last 32 Myr, and 6 out of the 15 VB genes in this region have become nonfunctional during this period. Our results show that the VB gene family is subject to evolution by a birth-and-death process rather than to concerted evolution.
Collapse
Affiliation(s)
- C Su
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, USA.
| | | |
Collapse
|
42
|
Zhang J, Dyer KD, Rosenberg HF. Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc Natl Acad Sci U S A 2000; 97:4701-6. [PMID: 10758160 PMCID: PMC18296 DOI: 10.1073/pnas.080071397] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mammalian RNase A superfamily comprises a diverse array of ribonucleolytic proteins that have a variety of biochemical activities and physiological functions. Two rapidly evolving RNases of higher primates are of particular interest as they are major secretory proteins of eosinophilic leukocytes and have been found to possess anti-pathogen activities in vitro. To understand how these RNases acquired this function during evolution and to develop animal models for the study of their functions in vivo, it is necessary to investigate these genes in many species. Here, we report the sequences of 38 functional genes and 23 pseudogenes of the eosinophil-associated RNase (EAR) family from 5 rodent species. Our phylogenetic analysis of these genes showed a clear pattern of evolution by a rapid birth-and-death process and gene sorting, a process characterized by rapid gene duplication and deactivation occurring differentially among lineages. This process ultimately generates distinct or only partially overlapping inventories of the genes, even in closely related species. Positive Darwinian selection also contributed to the diversification of these EAR genes. The striking similarity between the evolutionary patterns of the EAR genes and those of the major histocompatibility complex, immunoglobulin, and T cell receptor genes stands in strong support of the hypothesis that host-defense and generation of diversity are among the primary physiological function of the rodent EARs. The discovery of a large number of divergent EARs suggests the intriguing possibility that these proteins have been specifically tailored to fight against distinct rodent pathogens.
Collapse
Affiliation(s)
- J Zhang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | |
Collapse
|