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Bunnoy A, Na-Nakorn U, Srisapoome P. Mystifying Molecular Structure, Expression and Repertoire Diversity of IgM Heavy Chain Genes (Ighμ) in Clarias Catfish and Hybrids: Two Novel Transcripts in Vertebrates. Front Immunol 2022; 13:884434. [PMID: 35784299 PMCID: PMC9247300 DOI: 10.3389/fimmu.2022.884434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Two novel immunoglobulin heavy chain (Ighμ) transcripts encoding membrane-bound forms of IgM (mIgM) were discovered in bighead catfish, Clarias macrocephalus. The first transcript contains four constant and two transmembrane domains [Cμ1-Cμ2-Cμ3-Cμ4-TM1-TM2] that have never been reported in teleosts, and the second transcript is an unusual mIgM that has never been identified in any vertebrate [Cμ1-(Cδ2-Cδ3-Cδ4-Cδ5)-Cμ2-Cμ3-TM1-TM2]. Fluorescence in situ hybridization (FISH) in bighead catfish, North African catfish (C. gariepinus) and hybrid catfish revealed a single copy of Ighμ in individual parent catfish, while two gene copies were found in diploid hybrid catfish. Intensive sequence analysis demonstrated multiple distinct structural variabilities in the VH domain in Clarias, and hybrid catfish were defined and used to generate diversity with various mechanisms. Expression analysis of Ighμ in Aeromonas hydrophila infection of the head kidney, peripheral blood leukocytes and spleen revealed significantly higher levels in North African catfish and hybrid catfish than in bighead catfish.
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Affiliation(s)
- Anurak Bunnoy
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Laboratory of Aquatic Animal Genetics, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- *Correspondence: Prapansak Srisapoome,
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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: 1.5] [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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Rego K, Bengtén E, Wilson M, Hansen JD, Bromage ES. Characterization of immunoglobulin light chain utilization and variable family diversity in rainbow trout. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103566. [PMID: 31837380 DOI: 10.1016/j.dci.2019.103566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/22/2019] [Accepted: 12/05/2019] [Indexed: 06/10/2023]
Abstract
This study characterizes immunoglobulin light chain (IgL) expression and variable family usage in rainbow trout. IgL transcripts were generated by 5' RACE from both immune and TNP-KLH immunized fish. Phylogenetic analysis revealed that the IgL variable regions clustered into seven different families: three kappa families (two newly described in this study), three sigma families, and a single lambda family. IgL1 and IgL3 transcripts expressing identical variable regions were identified and genomic analysis revealed that the two isotypes are co-localized on chromosomes 7, 15, 18, and 21 allowing for potential rearrangement between clusters. Fish were immunized with TNP-KLH (n = 5) and percent expression of IgL1, IgL2, IgL3, and IgL4 measured by qRT-PCR from immune tissues and magnetically sorted TNP-specific lymphocyte populations. In all samples IgL1 constituted 80-95% of the transcripts. The percentage of anti-TNP specific IgL1 transcripts was measured in naïve, unsorted, and TNP-specific cell populations of TNP-KLH fish (n = 3) and found to be significantly higher in the TNP positive cell population (21%) compared to the naïve population (1%; p = 0.02) suggesting that there is a selection of TNP specific IgL sequences.
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Affiliation(s)
- Katherine Rego
- Department of Biology University of Massachusetts Dartmouth, North Dartmouth, MA, USA
| | - Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - John D Hansen
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA; Interdisciplinary Program in Pathobiology, University of Washington, Seattle, WA, USA
| | - Erin S Bromage
- Department of Biology University of Massachusetts Dartmouth, North Dartmouth, MA, USA.
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Magadan S, Krasnov A, Hadi-Saljoqi S, Afanasyev S, Mondot S, Lallias D, Castro R, Salinas I, Sunyer O, Hansen J, Koop BF, Lefranc MP, Boudinot P. Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires. Front Immunol 2019; 10:2541. [PMID: 31798572 PMCID: PMC6866254 DOI: 10.3389/fimmu.2019.02541] [Citation(s) in RCA: 21] [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: 08/30/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022] Open
Abstract
In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.
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Affiliation(s)
- Susana Magadan
- Immunology Laboratory, Biomedical Research Center, University of Vigo, Vigo, Spain
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Aleksei Krasnov
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | - Saida Hadi-Saljoqi
- IMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Stanislas Mondot
- MICALIS, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Lallias
- Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rosario Castro
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Irene Salinas
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Oriol Sunyer
- Pathobiology Department, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - John Hansen
- Western Fisheries Research Center, U.S. Geological Survey, Seattle, WA, United States
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - 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, France
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
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Chappell ME, Epp L, Zwollo P. Sockeye salmon immunoglobulin V H usage and pathogen loads differ between spawning sites. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:297-306. [PMID: 28847679 DOI: 10.1016/j.dci.2017.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
The Immunological Imprinting Hypothesis proposes that juvenile anadromous fish respond to the pathogen fingerprint specific to their natal site by producing protective long lived plasma cells (LLPCs) that constitutively produce antibodies against those pathogens. Hence, fish returning to their natal streams have immunological protection from pathogens at that specific location. Here, we tested the hypothesis through analysis of antibody composition and usage in sockeye salmon populations in Alaska. Spleen and anterior kidney were sampled from salmon from six sites, and relative usage levels of six different Immunoglobulin VH gene families determined using RT-qPCR. Additionally, prevalence and pathogen loads were measured in each fish for Renibacterium salmoninarum, Flavobacterium psychrophilum, and Infectious Hematopoietic Necrosis Virus. Results revealed differences in VH usage, pathogen loads, and infection rates between spawning sites, while probability of infection was dependent on location for each pathogen analyzed. Further, several negative correlations between specific VH usage patterns and pathogen loads were uncovered. Greater understanding of site-dependent VH usage in spawning fish potentially suggests a method of natural immunization against common fish pathogens and thus protection of both farmed and wild populations.
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Affiliation(s)
- Maxwell E Chappell
- Department of Biology, The College of William and Mary, Williamsburg, VA, 23185, United States
| | - Lidia Epp
- Department of Biology, The College of William and Mary, Williamsburg, VA, 23185, United States
| | - Patty Zwollo
- Department of Biology, The College of William and Mary, Williamsburg, VA, 23185, United States.
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Chiraporn P, Sasimanas U, Prapansak S. Diversity analysis of the immunoglobulin M heavy chain gene in Nile tilapia, Oreochromis niloticus (Linnaeus). ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajb2014.14001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Abstract
As in mammals, cartilaginous and teleost fishes possess adaptive immune systems based on antigen recognition by immunoglobulins (Ig), T cell receptors (TCR), and major histocompatibility complex molecules (MHC) I and MHC II molecules. Also it is well established that fish B cells and mammalian B cells share many similarities, including Ig gene rearrangements, and production of membrane Ig and secreted Ig forms. This chapter provides an overview of the IgH and IgL chains in cartilaginous and bony fish, including their gene organizations, expression, diversity of their isotypes, and development of the primary repertoire. Furthermore, when possible, we have included summaries of key studies on immune mechanisms such as allelic exclusion, somatic hypermutation, affinity maturation, class switching, and mucosal immune responses.
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Affiliation(s)
- Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, 39216-4505, USA.
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Coscia MR, Varriale S, Giacomelli S, Oreste U. Antarctic teleost immunoglobulins: more extreme, more interesting. FISH & SHELLFISH IMMUNOLOGY 2011; 31:688-696. [PMID: 21044686 DOI: 10.1016/j.fsi.2010.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 10/12/2010] [Accepted: 10/22/2010] [Indexed: 05/30/2023]
Abstract
We have investigated the immunoglobulin molecule and the genes encoding it in teleosts living in the Antarctic seas at the constant temperature of -1.86 °C. The majority of Antarctic teleosts belong to the suborder Notothenioidei (Perciformes), which includes only a few non-Antarctic species. Twenty-one Antarctic and two non-Antarctic Notothenioid species were included in our studies. We sequenced immunoglobulin light chains in two species and μ heavy chains, partially or totally, in twenty species. In the case of heavy chain, genomic DNA and the cDNA encoding the secreted and the membrane form were analyzed. From one species, Trematomus bernacchii, a spleen cDNA library was constructed to evaluate the diversity of VH gene segments. T. bernacchii IgM, purified from the serum and bile, was characterized. Homology Modelling and Molecular Dynamics were used to determine the molecular structure of T. bernacchii and Chionodraco hamatus immunoglobulin domains. This paper sums up the previous results and broadens them with the addition of unpublished data.
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Affiliation(s)
- Maria Rosaria Coscia
- Institute of Protein Biochemistry, CNR, Via P. Castellino 111, 80131 Naples, Italy.
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Yasuike M, de Boer J, von Schalburg KR, Cooper GA, McKinnel L, Messmer A, So S, Davidson WS, Koop BF. Evolution of duplicated IgH loci in Atlantic salmon, Salmo salar. BMC Genomics 2010; 11:486. [PMID: 20813058 PMCID: PMC2996982 DOI: 10.1186/1471-2164-11-486] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 09/02/2010] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The Atlantic salmon (Salmo salar) immunoglobulin heavy chain (IgH) locus possesses two parallel IgH isoloci (IGH-A and IGH-B), that are related to the genomic duplication event in the family Salmonidae. These duplicated IgH loci in Atlantic salmon provide a unique opportunity to examine the mechanisms of genome diversity and genome evolution of the IgH loci in vertebrates. In this study, we defined the structure of these loci in Atlantic salmon, and sequenced 24 bacterial artificial chromosome (BAC) clones that were assembled into the IGH-A (1.1 Mb) and IGH-B (0.9 Mb) loci. In addition, over 7,000 cDNA clones from the IgH variable (VH) region have been sequenced and analyzed. RESULTS The present study shows that the genomic organization of the duplicated IgH loci in Atlantic salmon differs from that in other teleosts and other vertebrates. The loci possess multiple Cτ genes upstream of the Cμ region, with three of the Cτ genes being functional. Moreover, the duplicated loci possess over 300 VH segments which could be classified into 18 families. This is the largest number of VH families currently defined in any vertebrate. There were significant structural differences between the two loci, indicating that both IGH-A and -B loci have evolved independently in the short time after the recent genome duplication approximately 60 mya. CONCLUSIONS Our results indicate that the duplication of the IgH loci in Atlantic salmon significantly contributes to the increased diversity of the antibody repertoire, as compared with the single IgH locus in other vertebrates.
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Affiliation(s)
- Motoshige Yasuike
- Department of Biology, University of Victoria,Victoria, British Columbia, Canada
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