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Peterson P. Novel Insights into the Autoimmunity from the Genetic Approach of the Human Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:3-18. [PMID: 38467969 DOI: 10.1007/978-981-99-9781-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a monogenic inborn error of autoimmunity that is caused by damaging germline variants in the AIRE gene and clinically manifests with multiple autoimmune diseases in patients. Studies on the function of the AIRE gene, discovered in 1997, have contributed to fundamental aspects of human immunology as they have been important in understanding the basic mechanism of immune balance between self and non-self. This chapter looks back to the discovery of the AIRE gene, reviews its main properties, and discusses the key findings of its function in the thymus. However, more recent autoantibody profilings in APECED patients have highlighted a gap in our knowledge of the disease pathology and point to the need to revisit the current paradigm of AIRE function. The chapter reviews these new findings in APECED patients, which potentially trigger new thoughts on the mechanism of immune tolerance.
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Affiliation(s)
- Pärt Peterson
- Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia.
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2
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Peel E, Silver L, Brandies P, Zhu Y, Cheng Y, Hogg CJ, Belov K. Best genome sequencing strategies for annotation of complex immune gene families in wildlife. Gigascience 2022; 11:6780307. [PMID: 36310247 PMCID: PMC9618407 DOI: 10.1093/gigascience/giac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation. RESULTS Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. CONCLUSIONS Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Luke Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610000, China
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Katherine Belov
- Correspondence address. Katherine Belov, School of Life and Environmental Sciences, Rm 206, RMC Gunn Building (B19), The University of Sydney, Sydney, NSW 2006, Australia. E-mail:
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Sirupurapu V, Safonova Y, Pevzner P. Gene prediction in the immunoglobulin loci. Genome Res 2022; 32:1152-1169. [PMID: 35545447 DOI: 10.1101/gr.276676.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
The V(D)J recombination process rearranges the variable (V), diversity (D), and joining (J) genes in the immunoglobulin loci to generate antibody repertoires. Annotation of these loci across various species and predicting the V, D, and J genes (IG genes) is critical for studies of the adaptive immune system. However, since the standard gene finding algorithms are not suitable for predicting IG genes, they have been semi-manually annotated in very few species. We developed the IGDetective algorithm for predicting IG genes and applied it to species with the assembled IG loci. IGDetective generated the first large collection of IG genes across many species and enabled their evolutionary analysis, including the analysis of the "bat IG diversity" hypothesis. This analysis revealed extremely conserved V genes in evolutionary distant species indicating that these genes may be subjected to the same selective pressure, e.g., pressure driven by common pathogens. IGDetective also revealed extremely diverged V genes and a new family of evolutionary conserved V genes in bats with unusual noncanonical cysteines. Moreover, in difference from all other previously reported antibodies, these cysteines are located within complementarity-determining regions. Since cysteines form disulfide bonds, we hypothesize that these cysteine-rich V genes might generate antibodies with noncanonical conformations and could potentially form a unique part of the immune repertoire in bats. We also analyzed the diversity landscape of the recombination signal sequences and revealed their features that trigger the high/low usage of the IG genes.
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Schraven AL, Hansen VL, Morrissey KA, Stannard HJ, Ong OT, Douek DC, Miller RD, Old JM. Developmental and comparative immunology single-cell transcriptome analysis of the B-cell repertoire reveals the usage of immunoglobulins in the gray short-tailed opossum (Monodelphis domestica). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104141. [PMID: 34038789 DOI: 10.1016/j.dci.2021.104141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
B-cells are key to humoral immunity, are found in multiple lymphoid organs, and have the unique ability to mediate the production of antigen-specific antibodies in the presence of pathogens. The marsupial immunoglobulin (Ig) heavy (H) chain locus encodes four constant region isotypes, IgA, IgG, IgM and IgE, but no IgD, and there are two light (L) chain isotypes, lambda (Igλ) and kappa (Igκ). To gain an understanding of the marsupial humoral immune system, B-cell transcriptomes generated by single-cell RNA sequencing from gray short-tailed opossum (Monodelphis domestica) splenocytes, and peripheral blood mononuclear cells were analysed. The cells used were from a single unimmunized animal and the majority of B-cells were transcribing IgM heavy chains. The ratio of Ig light chain use was roughly 2:1, Igλ:Igκ in this individual. This was not predicted due to Igκ being the more complex of the two L chain loci. The variable (V) gene segment pairs used in individual B-cells confirm greater diversity provided by the L chain V. This study is the first to report on using single cell analysis to investigate Ig repertoires in a marsupial and confirms a number of prior hypothesis, as well as revealing some surprises.
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Affiliation(s)
- Andrea L Schraven
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Victoria L Hansen
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Kimberly A Morrissey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Hayley J Stannard
- Charles Sturt University, School of Animal and Veterinary Sciences, Wagga Wagga, NSW, 2678, Australia
| | - Oselyne Tw Ong
- Children's Medical Research Institute, Westmead, NSW, 2145, Australia
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Julie M Old
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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Huttener R, Thorrez L, Veld TI, Potter B, Baele G, Granvik M, Van Lommel L, Schuit F. Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes. BMC Ecol Evol 2021; 21:153. [PMID: 34348656 PMCID: PMC8336415 DOI: 10.1186/s12862-021-01882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. RESULTS We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. CONCLUSIONS A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.
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Affiliation(s)
- Raf Huttener
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Lieven Thorrez
- Tissue Engineering Laboratory, Department of Development and Regeneration, KU Leuven, Kortrijk, Belgium
| | - Thomas In't Veld
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mikaela Granvik
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Leentje Van Lommel
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Frans Schuit
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium.
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7
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Peel E, Frankenberg S, Hogg CJ, Pask A, Belov K. Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus). Immunogenetics 2021; 73:263-275. [PMID: 33544183 DOI: 10.1007/s00251-020-01197-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/24/2020] [Indexed: 11/28/2022]
Abstract
Advances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these genome assemblies, it is not clear whether it is possible to comprehensively annotate highly variable and repetitive genes such as those involved in immunity. As such, immune genes have only been investigated in a handful of extinct genomes, mainly in human lineages. In 2018 the genome of the thylacine (Thylacinus cynocephalus), a carnivorous marsupial from Tasmania that went extinct in 1936, was sequenced. Here we attempt to characterise the immune repertoire of the thylacine and determine similarity to its closest relative with a genome available, the Tasmanian devil (Sarcophilus harrisii), as well as other marsupials. Members from all major immune gene families were identified. However, variable regions could not be characterised, and complex families such as the major histocompatibility complex (MHC) were highly fragmented and located across multiple small scaffolds. As such, at a gene level we were unable to reconstruct full-length coding sequences for the majority of thylacine immune genes. Despite this, we identified genes encoding functionally important receptors and immune effector molecules, which suggests the functional capacity of the thylacine immune system was similar to other mammals. However, the high number of partial immune gene sequences identified limits our ability to reconstruct an accurate picture of the thylacine immune repertoire.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | | | - Carolyn J Hogg
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Vic, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia.
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8
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Ott JA, Castro CD, Deiss TC, Ohta Y, Flajnik MF, Criscitiello MF. Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus. eLife 2018; 7:28477. [PMID: 29664399 PMCID: PMC5931798 DOI: 10.7554/elife.28477] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 04/16/2018] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Caitlin D Castro
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Texas, United States
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Transcriptome sequencing of the long-nosed bandicoot (Perameles nasuta) reveals conservation and innovation of immune genes in the marsupial order Peramelemorphia. Immunogenetics 2017; 70:327-336. [PMID: 29159447 DOI: 10.1007/s00251-017-1043-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]
Abstract
Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species. We find that the immune gene complement in bandicoot is often conserved with respect to other marsupials; however, the diversity of expressed transcripts in several key families, such as major histocompatibility complex, T cell receptor μ and natural killer cell receptors, appears greater in the bandicoot than other Australian marsupials, including devil and koala. This transcriptome is an important first step for future studies of bandicoots and the bilby, allowing for population level analysis and construction of bandicoot-specific immunological reagents and assays. Such studies will be critical to understanding the immunology and physiology of Peramelemorphia and to inform the conservation of these unique marsupials.
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10
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Morris KM, Cheng Y, Warren W, Papenfuss AT, Belov K. Identification and analysis of divergent immune gene families within the Tasmanian devil genome. BMC Genomics 2015; 16:1017. [PMID: 26611146 PMCID: PMC4662006 DOI: 10.1186/s12864-015-2206-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/12/2015] [Indexed: 02/01/2023] Open
Abstract
Background The Tasmanian devil (Sarcophilus harrisii) is being threatened with extinction in the wild by a disease known as devil facial tumour disease (DFTD). In order to prevent the spread of this disease a thorough understanding of the Tasmanian devil immune system and its response to the disease is required. In 2011 and 2012 two genome sequencing projects of the Tasmania devil were released. This has provided us with the raw data required to begin to investigate the Tasmanian devil immunome in depth. In this study we characterise immune gene families of the Tasmanian devil. We focus on immunoglobulins, T cell receptors and cytokine families. Results We identify and describe 119 cytokines including 40 interleukins, 39 chemokines, 8 interferons, 18 tumour necrosis family cytokines and 14 additional cytokines. Constant regions for immunoglobulins and T cell receptors were also identified. The repertoire of genes in these families was similar to the opossum, however devil specific duplications were seen and orthologs to eutherian genes not previously identified in any marsupial were also identified. Conclusions By using multiple data sources as well as targeted search methods, highly divergent genes across the Tasmanian devil immune system were identified and characterised. This understanding will allow for the development of devil specific assays and reagents and allow for future studies into the immune response of the Tasmanian devil immune system to DFTD. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2206-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katrina M Morris
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
| | - Yuanyuan Cheng
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
| | - Wesley Warren
- Washington University School of Medicine, 4444 Forest Park Ave, St Louis, MO, 63108, USA.
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, Australia. .,Bioinformatics and Cancer Genomics, Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, Camperdown, NSW, Australia.
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Vaz PK, Hartley CA, Browning GF, Devlin JM. Marsupial and monotreme serum immunoglobulin binding by proteins A, G and L and anti-kangaroo antibody. J Immunol Methods 2015; 427:94-9. [PMID: 26523413 DOI: 10.1016/j.jim.2015.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 12/20/2022]
Abstract
Serological studies are often conducted to examine exposure to infectious agents in wildlife populations. However, specific immunological reagents for wildlife species are seldom available and can limit the study of infectious diseases in these animals. This study examined the ability of four commercially available immunoglobulin-binding reagents to bind serum immunoglobulins from 17 species within the Marsupialia and Monotremata. Serum samples were assessed for binding, using immunoblots and ELISAs (Enzyme-linked immunosorbent assays), to three microbially-derived proteins - staphylococcal protein A, streptococcal protein G and peptostreptococcal protein L. Additionally, an anti-kangaroo antibody was included for comparison. The inter- and intra-familial binding patterns of the reagents to serum immunoglobulins varied and evolutionary distance between animal species was not an accurate predictor of the ability of reagents to bind immunoglobulins. Results from this study can be used to inform the selection of appropriate immunological reagents in future serological studies in these clades.
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Affiliation(s)
- Paola K Vaz
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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12
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Characterization of antibody V segment diversity in the Tasmanian devil (Sarcophilus harrisii). Vet Immunol Immunopathol 2015; 167:156-65. [DOI: 10.1016/j.vetimm.2015.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/25/2015] [Accepted: 08/06/2015] [Indexed: 10/23/2022]
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13
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Suthers AN, Young LJ. Isoforms of the CD79 signal transduction component of the macropod B-cell receptor. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 47:185-190. [PMID: 25064685 DOI: 10.1016/j.dci.2014.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 06/03/2023]
Abstract
B cell responses and their concomitant signal transduction pathways are not well understood in marsupial mammals, despite the availability of gene expression data for key immunoglobulin genes and for elements of the CD79a/CD79b heterodimer signalling complex for two model marsupials. Broader studies of factors that influence B cell responses are still hampered by a lack of species-specific reagents and there are few reports of other factors that influence gene expression such as the potential for splice variants in BCR components, which may influence immune signalling pathways. In this study, we characterise CD79a and CD79b genes in the endangered macropod marsupial, Onychogalea fraenata (the bridled nailtail wallaby) and show that domains and residues important for the structural and functional integrity of both monomers are conserved in this species, consistent with results previously reported for the closely-related macropod, Macropus eugenii (the tammar wallaby). We extend this work to report the detection of splice variants for CD79a and CD79b in wallaby species; three CD79a isoforms and one CD79b isoform. Of these, two CD79a isoforms and the CD79b isoform have not been reported in any other mammalian species.
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Affiliation(s)
- Amy N Suthers
- School of Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland 4702, Australia
| | - Lauren J Young
- School of Medical and Applied Sciences, Central Queensland University, Rockhampton, Queensland 4702, Australia; School of Science and Health, University of Western Sydney, Penrith, NSW 2751, Australia.
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14
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Saunders NR, Noor NM, Dziegielewska KM, Wheaton BJ, Liddelow SA, Steer DL, Ek CJ, Habgood MD, Wakefield MJ, Lindsay H, Truettner J, Miller RD, Smith AI, Dietrich WD. Age-dependent transcriptome and proteome following transection of neonatal spinal cord of Monodelphis domestica (South American grey short-tailed opossum). PLoS One 2014; 9:e99080. [PMID: 24914927 PMCID: PMC4051688 DOI: 10.1371/journal.pone.0099080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 05/09/2014] [Indexed: 01/08/2023] Open
Abstract
This study describes a combined transcriptome and proteome analysis of Monodelphis domestica response to spinal cord injury at two different postnatal ages. Previously we showed that complete transection at postnatal day 7 (P7) is followed by profuse axon growth across the lesion with near-normal locomotion and swimming when adult. In contrast, at P28 there is no axon growth across the lesion, the animals exhibit weight-bearing locomotion, but cannot use hind limbs when swimming. Here we examined changes in gene and protein expression in the segment of spinal cord rostral to the lesion at 24 h after transection at P7 and at P28. Following injury at P7 only forty genes changed (all increased expression); most were immune/inflammatory genes. Following injury at P28 many more genes changed their expression and the magnitude of change for some genes was strikingly greater. Again many were associated with the immune/inflammation response. In functional groups known to be inhibitory to regeneration in adult cords the expression changes were generally muted, in some cases opposite to that required to account for neurite inhibition. For example myelin basic protein expression was reduced following injury at P28 both at the gene and protein levels. Only four genes from families with extracellular matrix functions thought to influence neurite outgrowth in adult injured cords showed substantial changes in expression following injury at P28: Olfactomedin 4 (Olfm4, 480 fold compared to controls), matrix metallopeptidase (Mmp1, 104 fold), papilin (Papln, 152 fold) and integrin α4 (Itga4, 57 fold). These data provide a resource for investigation of a priori hypotheses in future studies of mechanisms of spinal cord regeneration in immature animals compared to lack of regeneration at more mature stages.
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Affiliation(s)
- Norman R. Saunders
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
- * E-mail:
| | - Natassya M. Noor
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | | | - Benjamin J. Wheaton
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | - Shane A. Liddelow
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
- Department of Neurobiology, Stanford University, Stanford, California, United States of America
| | - David L. Steer
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - C. Joakim Ek
- Department of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Mark D. Habgood
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | - Matthew J. Wakefield
- Walter & Eliza Hall Institute of Medical Research, Victoria, Australia
- Department of Genetics, The University of Melbourne, Victoria, Australia
| | - Helen Lindsay
- Walter & Eliza Hall Institute of Medical Research, Victoria, Australia
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Jessie Truettner
- The Miami Project to Cure Paralysis, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Robert D. Miller
- Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - A. Ian Smith
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - W. Dalton Dietrich
- The Miami Project to Cure Paralysis, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
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15
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Borthwick CR, Young LJ, Old JM. The development of the immune tissues in marsupial pouch young. J Morphol 2014; 275:822-39. [DOI: 10.1002/jmor.20250] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 12/05/2013] [Accepted: 01/02/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Casey R. Borthwick
- Native and Pest Animal Unit, School of Science and Health, Hawkesbury; University of Western Sydney; Locked bag 1797 Penrith New South Wales 2751 Australia
| | - Lauren J. Young
- Native and Pest Animal Unit, School of Science and Health, Hawkesbury; University of Western Sydney; Locked bag 1797 Penrith New South Wales 2751 Australia
| | - Julie M. Old
- Native and Pest Animal Unit, School of Science and Health, Hawkesbury; University of Western Sydney; Locked bag 1797 Penrith New South Wales 2751 Australia
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16
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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
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17
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Das S, Hirano M, McCallister C, Tako R, Nikolaidis N. Comparative genomics and evolution of immunoglobulin-encoding loci in tetrapods. Adv Immunol 2011; 111:143-78. [PMID: 21970954 DOI: 10.1016/b978-0-12-385991-4.00004-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The immunoglobulins (Igs or antibodies) as an integral part of the tetrapod adaptive immune response system have evolved toward producing highly diversified molecules that recognize a remarkably large number of different antigens. Antibodies and their respective encoding loci have been shaped by different and often contrasting evolutionary forces, some of which aim to conserve an established pattern or mechanism and others to generate alternative and diversified structural and functional configurations. The genomic organization, gene content, ratio between functional genes and pseudogenes, number and position of recombining genetic elements, and the different levels of divergence present at the germline of the Ig-encoding loci have been evolutionarily shaped and optimized in a lineage- and, in some cases, species-specific mode aiming to increase organismal fitness. Further, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, such as V(D)J recombination, class switch recombination, isotype exclusion, somatic hypermutation, and gene conversion. Diverse tetrapod species, based on their specific germline configurations, use these mechanisms in several different combinations to effectively generate a vast array of distinct antibody types and structures. This chapter summarizes our current knowledge on the Ig-encoding loci in tetrapods and discusses the different evolutionary mechanisms that shaped their diversification.
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Affiliation(s)
- Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, School of Medicine, Emory University, Atlanta, Georgia, USA
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18
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The phylogenetic origins of natural killer receptors and recognition: relationships, possibilities, and realities. Immunogenetics 2010; 63:123-41. [PMID: 21191578 DOI: 10.1007/s00251-010-0506-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 12/16/2010] [Indexed: 12/20/2022]
Abstract
Natural killer (NK) cells affect a form of innate immunity that recognizes and eliminates cells that are infected with certain viruses or have undergone malignant transformation. In mammals, this recognition can be mediated through immunoglobulin- (Ig) and/or lectin-type NK receptors (NKRs). NKR genes in mammals range from minimally polymorphic single-copy genes to complex multigene families that exhibit high levels of haplotypic complexity and exhibit significant interspecific variation. Certain single-copy NKR genes that are present in one mammal are present as expanded multigene families in other mammals. These observations highlight NKRs as one of the most rapidly evolving eukaryotic gene families and likely reflect the influence of pathogens, especially viruses, on their evolution. Although well characterized in human and mice, cytotoxic cells that are functionally similar to NK cells have been identified in species ranging from birds to reptiles, amphibians and fish. Although numerous receptors have been identified in non-mammalian vertebrates that share structural relationships with mammalian NKRs, functionally defining these lower vertebrate molecules as NKRs is confounded by methodological and interpretive complexities. Nevertheless, several lines of evidence suggest that NK-type function or its equivalent has sustained a long evolutionary history throughout vertebrate species.
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Abstract
Adaptive immunity is mediated through numerous genetic and cellular processes that generate favourable somatic variants of antigen-binding receptors under evolutionary selection pressure by pathogens and other factors. Advances in our understanding of immunity in mammals and other model organisms are revealing the underlying basis and complexity of this remarkable system. Although the evolution of adaptive immunity has been thought to occur by the acquisition of novel molecular capabilities, an increasing amount of information from new model systems suggest that co-option and redirection of pre-existing systems are the main source of innovation. We combine evidence from a wide range of organisms to obtain an integrated view of the origins and patterns of divergence in adaptive immunity.
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Affiliation(s)
- Gary W Litman
- Department of Molecular Genetics, All Children's Hospital, St. Petersburg, Florida 33701, USA.
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20
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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.
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Affiliation(s)
- Michael F Criscitiello
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, MD 21201, USA.
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