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Shibasaki Y, Afanasyev S, Fernández-Montero A, Ding Y, Watanabe S, Takizawa F, Lamas J, Fontenla-Iglesias F, Leiro JM, Krasnov A, Boudinot P, Sunyer JO. Cold-blooded vertebrates evolved organized germinal center-like structures. Sci Immunol 2023; 8:eadf1627. [PMID: 37910630 PMCID: PMC11152321 DOI: 10.1126/sciimmunol.adf1627] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/31/2023] [Indexed: 11/03/2023]
Abstract
Germinal centers (GCs) or analogous secondary lymphoid microstructures (SLMs) are thought to have evolved in endothermic species. However, living representatives of their ectothermic ancestors can mount potent secondary antibody responses upon infection or immunization, despite the apparent lack of SLMs in these cold-blooded vertebrates. How and where adaptive immune responses are induced in ectothermic species in the absence of GCs or analogous SLMs remain poorly understood. Here, we infected a teleost fish (trout) with the parasite Ichthyophthirius multifiliis (Ich) and identified the formation of large aggregates of highly proliferating IgM+ B cells and CD4+ T cells, contiguous to splenic melanomacrophage centers (MMCs). Most of these MMC-associated lymphoid aggregates (M-LAs) contained numerous antigen (Ag)-specific B cells. Analysis of the IgM heavy chain CDR3 repertoire of microdissected splenic M-LAs and non-M-LA areas revealed that the most frequent B cell clones induced after Ich infection were highly shared only within the M-LAs of infected animals. These M-LAs represented highly polyclonal SLMs in which Ag-specific B cell clonal expansion occurred. M-LA-associated B cells expressed high levels of activation-induced cytidine deaminase and underwent significant apoptosis, and somatic hypermutation of Igμ genes occurred prevalently in these cells. Our findings demonstrate that ectotherms evolved organized SLMs with GC-like roles. Moreover, our results also point to primordially conserved mechanisms by which M-LAs and mammalian polyclonal GCs develop and function.
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Affiliation(s)
- Yasuhiro Shibasaki
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Sergei Afanasyev
- I.M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Laboratory of Neurophysiology and Behavioral Pathology, Torez 44, Saint-Petersburg 194223, Russia
| | - Alvaro Fernández-Montero
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yang Ding
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shota Watanabe
- College of Bioresource Sciences, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Fumio Takizawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui 917-0003, Japan
| | - Jesús Lamas
- Department of Functional Biology, Institute of Aquaculture, Campus Vida, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - Francisco Fontenla-Iglesias
- Department of Functional Biology, Campus Vida, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - José Manuel Leiro
- Laboratory of Parasitology, Department of Microbiology and Parasitology, Institute of Research on Chemical and Biological Analysis, Campus Vida, University of Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | | | - Pierre Boudinot
- Universite Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas 78350, France
| | - J. Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Boudinot P, Novas S, Jouneau L, Mondot S, Lefranc MP, Grimholt U, Magadán S. Evolution of T cell receptor beta loci in salmonids. Front Immunol 2023; 14:1238321. [PMID: 37649482 PMCID: PMC10464911 DOI: 10.3389/fimmu.2023.1238321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/17/2023] [Indexed: 09/01/2023] Open
Abstract
T-cell mediated immunity relies on a vast array of antigen specific T cell receptors (TR). Characterizing the structure of TR loci is essential to study the diversity and composition of T cell responses in vertebrate species. The lack of good-quality genome assemblies, and the difficulty to perform a reliably mapping of multiple highly similar TR sequences, have hindered the study of these loci in non-model organisms. High-quality genome assemblies are now available for the two main genera of Salmonids, Salmo and Oncorhynchus. We present here a full description and annotation of the TRB loci located on chromosomes 19 and 25 of rainbow trout (Oncorhynchus mykiss). To get insight about variations of the structure and composition of TRB locus across salmonids, we compared rainbow trout TRB loci with other salmonid species and confirmed that the basic structure of salmonid TRB locus is a double set of two TRBV-D-J-C loci in opposite orientation on two different chromosomes. Our data shed light on the evolution of TRB loci in Salmonids after their whole genome duplication (WGD). We established a coherent nomenclature of salmonid TRB loci based on comprehensive annotation. Our work provides a fundamental basis for monitoring salmonid T cell responses by TRB repertoire sequencing.
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Affiliation(s)
- Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Samuel Novas
- Immunology Laboratory, Research Center for Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Unni Grimholt
- Fish Health Research Section, Norwegian Veterinary Institute, Oslo, Norway
| | - Susana Magadán
- Immunology Laboratory, Research Center for Nanomaterials and Biomedicine (CINBIO), Universidade de Vigo, Vigo, Spain
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3
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Han L, Li J, Wang W, Luo K, Chai M, Xiang C, Luo Z, Ren L, Gu Q, Tao M, Zhang C, Wang J, Liu S. Immunoglobulin heavy-chain loci in ancient allotetraploid goldfish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 135:104476. [PMID: 35718131 DOI: 10.1016/j.dci.2022.104476] [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: 03/02/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
As an ancient allotetraploid species, goldfish (Carassius auratus) have two sets of subgenomes. In this study, immunoglobulin heavy-chain (IGH) genes were cloned from the red crucian carp (Carassius auratus red var.), and the corresponding loci were identified in the gynogenetic diploid red crucian carp (GRCC) genome as well as the genomes of three other goldfish strains (Wakin, G-12, and CaTCV-1). Examination showed that each goldfish strain possessed two sets of parallel IGH loci: a complete IGHA locus and a degenerated IGHB locus that was nearly 40 × smaller. In the IGHA locus, multiple τ chain loci were arranged in tandem between the μ&δ chain locus and the variable genes, but no τ-like genes were found in the IGHB locus.
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Affiliation(s)
- Linmei Han
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jihong Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Wen Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Mingli Chai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Caixia Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Ziye Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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4
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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5
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Castro R, Magadán S, Jouneau L, Mhana V, Pham HP, Mariotti-Ferrandiz E, Six A, Huetz F, Boudinot P. Clonotypic IgH Response against Systemic Viral infection in Pronephros and Spleen of a Teleost Fish. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2573-2582. [PMID: 35577368 DOI: 10.4049/jimmunol.2200088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Upon infection, B lymphocytes develop clonal responses. In teleost fish, which lack lymph nodes, the kinetics and location of B cell responses remain poorly characterized. Fish pronephros is the site of B cell differentiation and the main niche for persistence of plasma cells. In this study, we undertook the analysis of the rainbow trout IgHμ repertoire in this critical tissue for humoral adaptive immunity after primary immunization and boost with a rhabdovirus, the viral hemorrhagic septicemia virus (VHSV). We used a barcoded 5' RACE-cDNA sequencing approach to characterize modifications of the IgHμ repertoire, including VH usage in expressed V(D)J rearrangements, clonal diversity, and clonotype sharing between individual fish and treatments. In the pronephros, our approach quantified the clonotype frequency across the whole IgH repertoire (i.e., with all VH), measuring the frequency of Ag-responding clonotypes. Viral infection led to extensive modifications of the pronephros B cell repertoire, implicating several VH subgroups after primary infection. In contrast, only modest changes in repertoire persisted 5 mo later, including VHSV-specific public expansions. The IgM public response implicating IgHV1-18 and JH5, previously described in spleen, was confirmed in pronephros in all infected fish, strongly correlated to the response. However, the distribution of top clonotypes showed that pronephros and spleen B cells constitute distinct compartments with different IgH repertoires. Unexpectedly, after boost, the frequency of anti-VHSV clonotypes decreased both in pronephros and spleen, raising questions about B cell circulation. A better monitoring of B cell response kinetics in lymphoid tissues will be an essential step to understand B memory and plasmocyte formation mechanisms in fish.
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Affiliation(s)
- Rosario Castro
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadán
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Campus Lagoas Marcosende, Vigo, Pontevedra, Spain
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Vanessa Mhana
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | - Hang-Phuong Pham
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | | | - Adrien Six
- Sorbonne University, INSERM, UMR S959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France; and
| | - François Huetz
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR 1222 INSERM, Paris, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France;
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6
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Lefranc MP, Lefranc G. IMGT ®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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7
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Babrak L, Marquez S, Busse CE, Lees WD, Miho E, Ohlin M, Rosenfeld AM, Stervbo U, Watson CT, Schramm CA. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol 2022; 2453:279-296. [PMID: 35622332 PMCID: PMC9761530 DOI: 10.1007/978-1-0716-2115-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
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Affiliation(s)
- Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Christian E Busse
- Division of B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
- Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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8
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Manso T, Folch G, Giudicelli V, Jabado-Michaloud J, Kushwaha A, Nguefack Ngoune V, Georga M, Papadaki A, Debbagh C, Pégorier P, Bertignac M, Hadi-Saljoqi S, Chentli I, Cherouali K, Aouinti S, El Hamwi A, Albani A, Elazami Elhassani M, Viart B, Goret A, Tran A, Sanou G, Rollin M, Duroux P, Kossida S. IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res 2021; 50:D1262-D1272. [PMID: 34875068 PMCID: PMC8728119 DOI: 10.1093/nar/gkab1136] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 11/15/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org/, is at the forefront of the immunogenetics and immunoinformatics fields with more than 30 years of experience. IMGT® makes available databases and tools to the scientific community pertaining to the adaptive immune response, based on the IMGT-ONTOLOGY. We focus on the recent features of the IMGT® databases, tools, reference directories and web resources, within the three main axes of IMGT® research and development. Axis I consists in understanding the adaptive immune response, by deciphering the identification and characterization of the immunoglobulin (IG) and T cell receptor (TR) genes in jawed vertebrates. It is the starting point of the two other axes, namely the analysis and exploration of the expressed IG and TR repertoires based on comparison with IMGT reference directories in normal and pathological situations (Axis II) and the analysis of amino acid changes and functions of 2D and 3D structures of antibody and TR engineering (Axis III).
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Affiliation(s)
- Taciana Manso
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Géraldine Folch
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Joumana Jabado-Michaloud
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anjana Kushwaha
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Viviane Nguefack Ngoune
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maria Georga
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Ariadni Papadaki
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Chahrazed Debbagh
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Perrine Pégorier
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Morgane Bertignac
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Saida Hadi-Saljoqi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Imène Chentli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Karima Cherouali
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Safa Aouinti
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Amar El Hamwi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Alexandre Albani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Merouane Elazami Elhassani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Benjamin Viart
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Agathe Goret
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anna Tran
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Gaoussou Sanou
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maël Rollin
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
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9
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Long-term efficacy of nasal vaccination against enteric red mouth (ERM) disease and infectious hematopoietic necrosis (IHN) in juvenile rainbow trout (Oncorhynchus mykiss). Vaccine 2021; 40:229-238. [PMID: 34893343 DOI: 10.1016/j.vaccine.2021.11.077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 01/19/2023]
Abstract
Previous research demonstrated that bacterial and viral vaccines delivered via the nasal route in rainbow trout (Oncorhynchus mykiss) at 7 and 28 days post-vaccination are highly protective (>95% protection). Long-term protection following nasal vaccination in teleosts has not been evaluated. The goal of this study was to assess efficacy and immune responses at 6 months (mo) post-vaccination (mpv), and long-lasting immune responses at 12 mpv of two different vaccines: an inactivated enteric red mouth disease (ERM) Yersinia ruckeri bacterin and a live attenuated infectious hematopoietic necrosis virus (IHNV) vaccine. Juvenile rainbow trout were vaccinated for Y. ruckeri via intraperitoneal (I.P.) and intranasal (I.N.) routes, and for IHNV by intramuscular (I.M.) and I.N. routes, then challenged at 6 mpv. Immune responses were determined at 6 and 12 mpv. ERM vaccine I.P. delivery elicited significantly higher serum IgM-specific titers that remained elevated compared to mock-vaccinated fish at 6 mpv. By 12 mpv, antibody titers to Y. ruckeri were not significantly different across all treatments. Following Y. ruckeri challenge at 6 mpv, a significant difference in cumulative percent mortality (CPM) was found for I.P.-vaccinated fish but not I.N.-vaccinated fish. I.M. and I.N. vaccination with live attenuated IHNV did not result in significant specific serum IgM titers at 6 or 12 mpv. Yet, I.N.-vaccinated fish showed the lowest CPM 6 mpv indicating long-term protection that does not correlate with systemic IgM responses. Repertoire analyses confirmed unique expansions of VH-JH rearrangements in the spleen of rainbow trout 12 mpv that varied with the type of vaccine and route of vaccination. Combined, these data demonstrate that I.N. vaccination with a live attenuated viral vaccine confers long lasting protection, but I.N. ERM vaccination does not and booster before 6 mpv is recommended.
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10
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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11
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Salinas I, Fernández-Montero Á, Ding Y, Sunyer JO. Mucosal immunoglobulins of teleost fish: A decade of advances. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 121:104079. [PMID: 33785432 PMCID: PMC8177558 DOI: 10.1016/j.dci.2021.104079] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 05/03/2023]
Abstract
Immunoglobulins (Igs) are complex glycoproteins that play critical functions in innate and adaptive immunity of all jawed vertebrates. Given the unique characteristics of mucosal barriers, secretory Igs (sIgs) have specialized to maintain homeostasis and keep pathogens at bay at mucosal tissues from fish to mammals. In teleost fish, the three main IgH isotypes, IgM, IgD and IgT/Z can be found in different proportions at the mucosal secretions of the skin, gills, gut, nasal, buccal, and pharyngeal mucosae. Similar to the role of mammalian IgA, IgT plays a predominant role in fish mucosal immunity. Recent studies in IgT have illuminated the primordial role of sIgs in both microbiota homeostasis and pathogen control at mucosal sites. Ten years ago, IgT was discovered to be an immunoglobulin class specialized in mucosal immunity. Aiming at this 10-year anniversary, the goal of this review is to summarize the current status of the field of fish Igs since that discovery, while identifying knowledge gaps and future avenues that will move the field forward in both basic and applied science areas.
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Affiliation(s)
- Irene Salinas
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Álvaro Fernández-Montero
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yang Ding
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - J Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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12
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Gao G, Magadan S, Waldbieser GC, Youngblood RC, Wheeler PA, Scheffler BE, Thorgaard GH, Palti Y. A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout. G3-GENES GENOMES GENETICS 2021; 11:6146524. [PMID: 33616628 DOI: 10.1093/g3journal/jkab052] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is shown through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.
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Affiliation(s)
- Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
| | - Susana Magadan
- Centro de Investigaciones Biomédicas, Universidade de Vigo, Campus Universitario Lagoas Marcosende, 36310 Vigo, España
| | | | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, USA
| | - Paul A Wheeler
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA
| | - Brian E Scheffler
- USDA-ARS Genomics and Bioinformatics Research Unit, Stoneville, MS 38776, USA
| | - Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-4236, USA
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
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13
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Li A, Thwaite R, Kellie S, Barnes AC. Serum IgM heavy chain sub-isotypes and light chain variants revealed in giant grouper (Epinephelus lanceolatus) via protein A affinity purification, mass spectrometry and genome sequencing. FISH & SHELLFISH IMMUNOLOGY 2021; 113:42-50. [PMID: 33794338 DOI: 10.1016/j.fsi.2021.03.014] [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: 12/11/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Two IgM heavy (H) chain sub-isotypes (80 and 40 kDa) and two light (L) chain variants (25 and 30 kDa) were detected in the serum of giant grouper (Epinephelus lanceolatus), purified by ammonium sulphate precipitation followed by protein A affinity chromatography. This method yielded 5.6 mg/mL high purity IgM from grouper serum, with efficiency estimated at 39.5% recovery from crude serum. The H and L chains were identified by SDS-PAGE and mass spectrometry (MS). Nanopore long-read sequencing was used to generate a genomic contig (MW768935), containing Cμ, Cδ loci, VH regions, and a H chain Joining segment. cDNA sequencing of Cμ transcripts (MW768933 and MW768934) were used to polish the genomic contig and determine the exons and introns of the corresponding locus. MS peptide mapping revealed that the 80 kDa H chain consisted of CH1-4 domains while peptides from the 40 kDa H chain only mapped to CH1-2 domains. Our genomic contig showed the Cμ locus has a Cμ1-Cμ2-Cμ3-Cμ4 arrangement on the same strand as the other Ig loci identified in this genomic sequence. Our study corrects the NCBI annotations of the opposing Cμ loci (LOC117268697 and LOC117268550) in chromosome 16 (NC_047006). Further, we identified both κ and λ L chain isotypes in serum IgM. The molecular weight differences observed may result from different combinations of CL and VL genes. Putative IgM sub-isotypes have also been reported in Epinephelus itajara and Epinephelus coioides. The presence of IgM sub-isotypes may be a conserved trait among Epinephelus species.
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Affiliation(s)
- Angus Li
- The University of Queensland, School of Biological Sciences, Australia
| | - Rosemary Thwaite
- The University of Queensland, School of Biological Sciences, Australia
| | - Stuart Kellie
- School of Chemistry and Molecular Biosciences, Brisbane, QLD4072, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, Australia.
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14
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Magadan S, Mondot S, Palti Y, Gao G, Lefranc MP, Boudinot P. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 118:103998. [PMID: 33450314 DOI: 10.1016/j.dci.2021.103998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate annotation of Ig mRNA deep sequencing data. Complete genome sequences of Atlantic salmon and rainbow trout (Swanson line) recently allowed us to establish a comprehensive and coherent annotation of Salmonid IGH genes following IMGT standards. Here we analyzed the IGHV, D, and J genes from the newly released genome of a second rainbow trout line (Arlee). We confirmed the validity of salmonid IGHV subgroups, and extended the description of the rainbow trout IGH gene repertoire with novel sequences, while keeping nomenclature continuity. This work provides an important resource for annotation of high-throughput Ab repertoire sequencing data.
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Affiliation(s)
- Susana Magadan
- Centro de Investigaciones Biomédicas, Universidade de Vigo, Campus Universitario Lagoas Marcosende, 36310, Vigo, Spain.
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Marie Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR9002 CNRS, Université de Montpellier, Montpellier, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
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15
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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16
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Entrican G, Lunney JK, Wattegedera SR, Mwangi W, Hope JC, Hammond JA. The Veterinary Immunological Toolbox: Past, Present, and Future. Front Immunol 2020; 11:1651. [PMID: 32849568 PMCID: PMC7399100 DOI: 10.3389/fimmu.2020.01651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/22/2020] [Indexed: 12/02/2022] Open
Abstract
It is well-recognized that research capability in veterinary species is restricted by a lack of immunological reagents relative to the extensive toolboxes for small rodent biomedical model species and humans. This creates a barrier to the strategic development of disease control solutions for livestock, companion animals and wildlife that not only affects animal health but can affect human health by increasing the risk of transmission of zoonotic pathogens. There have been a number of projects aimed at reducing the capability gaps in the veterinary immunological toolbox, the majority of these focusing on livestock species. Various approaches have been taken to veterinary immunological reagent development across the globe and technological advances in molecular biology and protein biochemistry have accelerated toolbox development. While short-term funding initiatives can address specific gaps in capability, they do not account for long-term sustainability of reagents and databases that requires a different funding model. We review the past, present and future of the veterinary immunological toolbox with specific reference to recent developments discussed at the International Union of Immunological Societies (IUIS) Veterinary Immunology Committee (VIC) Immune Toolkit Workshop at the 12th International Veterinary Immunology Symposium (IVIS) in Seattle, USA, 16–19 August 2019. The future availability of these reagents is critical to research for improving animal health, responses to infectious pathogens and vaccine design as well as for important analyses of zoonotic pathogens and the animal /human interface for One Health initiatives.
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Affiliation(s)
- Gary Entrican
- The Roslin Institute at The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD, United States
| | - Sean R Wattegedera
- Moredun Research Institute, Pentlands Science Park, Edinburgh, United Kingdom
| | | | - Jayne C Hope
- The Roslin Institute at The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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17
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Criscitiello MF, Kraev I, Petersen LH, Lange S. Deimination Protein Profiles in Alligator mississippiensis Reveal Plasma and Extracellular Vesicle-Specific Signatures Relating to Immunity, Metabolic Function, and Gene Regulation. Front Immunol 2020; 11:651. [PMID: 32411128 PMCID: PMC7198796 DOI: 10.3389/fimmu.2020.00651] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Alligators are crocodilians and among few species that endured the Cretaceous-Paleogene extinction event. With long life spans, low metabolic rates, unusual immunological characteristics, including strong antibacterial and antiviral ability, and cancer resistance, crocodilians may hold information for molecular pathways underlying such physiological traits. Peptidylarginine deiminases (PADs) are a group of calcium-activated enzymes that cause posttranslational protein deimination/citrullination in a range of target proteins contributing to protein moonlighting functions in health and disease. PADs are phylogenetically conserved and are also a key regulator of extracellular vesicle (EV) release, a critical part of cellular communication. As little is known about PAD-mediated mechanisms in reptile immunology, this study was aimed at profiling EVs and protein deimination in Alligator mississippiensis. Alligator plasma EVs were found to be polydispersed in a 50-400-nm size range. Key immune, metabolic, and gene regulatory proteins were identified to be posttranslationally deiminated in plasma and plasma EVs, with some overlapping hits, while some were unique to either plasma or plasma EVs. In whole plasma, 112 target proteins were identified to be deiminated, while 77 proteins were found as deiminated protein hits in plasma EVs, whereof 31 were specific for EVs only, including proteins specific for gene regulatory functions (e.g., histones). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed KEGG pathways specific to deiminated proteins in whole plasma related to adipocytokine signaling, while KEGG pathways of deiminated proteins specific to EVs included ribosome, biosynthesis of amino acids, and glycolysis/gluconeogenesis pathways as well as core histones. This highlights roles for EV-mediated export of deiminated protein cargo with roles in metabolism and gene regulation, also related to cancer. The identification of posttranslational deimination and EV-mediated communication in alligator plasma revealed here contributes to current understanding of protein moonlighting functions and EV-mediated communication in these ancient reptiles, providing novel insight into their unusual immune systems and physiological traits. In addition, our findings may shed light on pathways underlying cancer resistance, antibacterial and antiviral resistance, with translatable value to human pathologies.
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Affiliation(s)
- Michael F. Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, United States
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, United Kingdom
| | - Lene H. Petersen
- Department of Marine Biology, Texas A&M University at Galvestone, Galveston, TX, United States
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, United Kingdom
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18
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Criscitiello MF, Kraev I, Lange S. Post-Translational Protein Deimination Signatures in Serum and Serum-Extracellular Vesicles of Bos taurus Reveal Immune, Anti-Pathogenic, Anti-Viral, Metabolic and Cancer-Related Pathways for Deimination. Int J Mol Sci 2020; 21:E2861. [PMID: 32325910 PMCID: PMC7215346 DOI: 10.3390/ijms21082861] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
The bovine immune system is known for its unusual traits relating to immunoglobulin and antiviral responses. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes that cause post-translational deimination, contributing to protein moonlighting in health and disease. PADs also regulate extracellular vesicle (EV) release, forming a critical part of cellular communication. As PAD-mediated mechanisms in bovine immunology and physiology remain to be investigated, this study profiled deimination signatures in serum and serum-EVs in Bos taurus. Bos EVs were poly-dispersed in a 70-500 nm size range and showed differences in deiminated protein cargo, compared with whole sera. Key immune, metabolic and gene regulatory proteins were identified to be post-translationally deiminated with some overlapping hits in sera and EVs (e.g., immunoglobulins), while some were unique to either serum or serum-EVs (e.g., histones). Protein-protein interaction network analysis of deiminated proteins revealed KEGG pathways common for serum and serum-EVs, including complement and coagulation cascades, viral infection (enveloped viruses), viral myocarditis, bacterial and parasitic infections, autoimmune disease, immunodeficiency intestinal IgA production, B-cell receptor signalling, natural killer cell mediated cytotoxicity, platelet activation and hematopoiesis, alongside metabolic pathways including ferroptosis, vitamin digestion and absorption, cholesterol metabolism and mineral absorption. KEGG pathways specific to EVs related to HIF-1 signalling, oestrogen signalling and biosynthesis of amino acids. KEGG pathways specific for serum only, related to Epstein-Barr virus infection, transcription mis-regulation in cancer, bladder cancer, Rap1 signalling pathway, calcium signalling pathway and ECM-receptor interaction. This indicates differences in physiological and pathological pathways for deiminated proteins in serum-EVs, compared with serum. Our findings may shed light on pathways underlying a number of pathological and anti-pathogenic (viral, bacterial, parasitic) pathways, with putative translatable value to human pathologies, zoonotic diseases and development of therapies for infections, including anti-viral therapies.
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Affiliation(s)
- 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
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6XH, UK
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19
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Adaptive immune receptor repertoires, an overview of this exciting field. Immunol Lett 2020; 221:49-55. [PMID: 32113899 DOI: 10.1016/j.imlet.2020.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
The adaptive immune response in jawed vertebrates relies on the huge diversity and specificity of the B cell and T cell antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR), respectively. The high level of diversity has represented a barrier to a comprehensive analysis of the adaptive immune response before the emergence of high-throughput sequencing (HTS) technologies. The size and complexity of HTS data requires the generation of novel computational and analytical approaches, which are transforming how the adaptive immune responses are deciphered to understand the clonal dynamics and properties of antigen-specific B and T cells in response to different kind of antigens. This exciting and rapidly evolving field is not only impacting human and clinical immunology but also comparative immunology. We are now closer to understanding the evolution of adaptive immune response in jawed vertebrates. This review provides an overview about classical and current strategies developed to assess the IG/TR diversity and their applications in basic and clinical immunology.
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