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Park M, de Villavicencio Diaz TN, Lange V, Wu L, Le Bihan T, Ma B. Exploring the sheep (Ovis aries) immunoglobulin repertoire by next generation sequencing. Mol Immunol 2023; 156:20-30. [PMID: 36867981 DOI: 10.1016/j.molimm.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized the way we determine the antibody repertoires encoded by B cells in the blood or lymphoid organs and transformed our understanding of adaptive immune responses in many species. Sheep (Ovis aries) have been widely used as a host for therapeutic antibody production since the early 1980s, however, little is known about their immune repertoires or immunological processes affecting the antibody generation. The objective of this study was to employ NGS for a comprehensive analysis of immunoglobulin heavy and light chain repertoires in four healthy sheep. We obtained > 90 % complete antibody sequences and nearly 130,000, 48,000 and 218,000 unique CDR3 reads for the heavy chain (IGH), kappa chain (IGK), and lambda chain (IGL) loci, respectively. Consistent with other species, we observed biased usage of germline variable (V), diversity (D) and joining (J) genes in the heavy and kappa loci, but not in the lambda loci. Moreover, the enormous diversity of CDR3 sequences was observed through sequence clustering and convergent recombination. These data will build a foundation for future studies investigating immune repertoires in health and disease as well as contribute to further refinement of ovine-derived therapeutic antibody drugs.
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Affiliation(s)
| | | | | | - Lin Wu
- Rapid Novor Inc., Kitchener, Ontario, Canada
| | | | - Bin Ma
- Rapid Novor Inc., Kitchener, Ontario, Canada
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Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
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Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
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3
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Çakan E, Gunaydin G. Activation induced cytidine deaminase: An old friend with new faces. Front Immunol 2022; 13:965312. [PMID: 36405752 PMCID: PMC9670734 DOI: 10.3389/fimmu.2022.965312] [Citation(s) in RCA: 7] [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: 06/09/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Activation induced cytidine deaminase (AID) protein is a member of APOBEC family. AID converts cytidine to uracil, which is a key step for somatic hypermutation (SHM) and class switch recombination (CSR). AID also plays critical roles in B cell precursor stages, removing polyreactive B cells from immune repertoire. Since the main function of AID is inducing point mutations, dysregulation can lead to increased mutation load, translocations, disturbed genomic integrity, and lymphomagenesis. As such, expression of AID as well as its function is controlled strictly at various molecular steps. Other members of the APOBEC family also play crucial roles during carcinogenesis. Considering all these functions, AID represents a bridge, linking chronic inflammation to carcinogenesis and immune deficiencies to autoimmune manifestations.
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Affiliation(s)
- Elif Çakan
- Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University Cancer Institute, Sihhiye, Ankara, Turkey
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4
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Furukawa M, Ito S, Suzuki S, Fuchimoto D, Onishi A, Niimi K, Usami K, Wu G, Bazer FW, Ogasawara K, Watanabe K, Aso H, Nochi T. Organogenesis of Ileal Peyer's Patches Is Initiated Prenatally and Accelerated Postnatally With Comprehensive Proliferation of B Cells in Pigs. Front Immunol 2020; 11:604674. [PMID: 33424851 PMCID: PMC7793923 DOI: 10.3389/fimmu.2020.604674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/05/2020] [Indexed: 11/21/2022] Open
Abstract
Morphogenesis and differentiation of organs is required for subsequent functional maturation. The morphological features of Peyer's patches vary among species. In pigs, they develop extensively in the ileum as ileal Peyer's patches (IPPs). However, the role of IPPs in the porcine immune system remains to be elucidated because of a lack of complete understanding of IPP organogenesis. Results of the present study revealed that development of porcine IPPs is initiated prenatally between embryonic days 76 and 91. The process of IPP organogenesis is concomitant with increased transcriptional patterns of CXCL13 and CCL19. IPPs undergo further development postnatally by forming central, marginal, and subepithelial zones. Importantly, a large number of proliferating B cells and apoptotic cells are found in porcine IPPs postnatally, but not prenatally. The expression level of IgM in proliferating B cells depends on the zone in which distinct B cells are separately localized after birth. Specifically, IgM+ cells are predominantly found in the central zone, whereas IgM-/low cells are abundant in the marginal zone. Importantly, the cellular feature of IPPs differs from that of mesenteric lymph nodes (MLNs) where such distinct zones are not formed both prenatally and postnatally. Our findings suggest that IPPs (not MLNs) in postnatal pigs are involved in complementing functions of the primary lymphoid tissue that promotes the differentiation and maturation of B cells.
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Affiliation(s)
- Mutsumi Furukawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shun Ito
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shunichi Suzuki
- Division of Animal Science, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Daiichiro Fuchimoto
- Division of Animal Science, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Akira Onishi
- Department of Animal Science and Resources, Nihon University College of Bioresource Sciences, Fujisawa, Japan
| | - Kanae Niimi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Katsuki Usami
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Fuller W Bazer
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Kouetsu Ogasawara
- Department of Immunobiology, Tohoku University Institute of Development, Aging and Cancer, Sendai, Japan
| | - Kouichi Watanabe
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hisashi Aso
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tomonori Nochi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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5
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Comparative analysis of the feline immunoglobulin repertoire. Biologicals 2017; 46:81-87. [PMID: 28131552 DOI: 10.1016/j.biologicals.2017.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/19/2022] Open
Abstract
Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets. In this study 4 individual domestic cats (Felis catus) were subjected to antibody repertoire sequencing with total number of sequences generated 1079863 for VH for IgG, 1050824 VH for IgM, 569518 for VK and 450195 for VL. Our analysis suggests that a similar VDJ expression patterns exists across all cats. Similar to the canine repertoire, the feline repertoire is dominated by a single subgroup, namely VH3. The antibody paratope of felines showed similar amino acid variation when compared to human, mouse and canine counterparts. All animals show a similarly skewed VH CDR-H3 profile and, when compared to canine, human and mouse, distinct differences are observed. Our study represents the first attempt to characterize sequence diversity in the expressed feline antibody repertoire and this demonstrates the utility of using NGS to elucidate entire antibody repertoires from individual animals. These data provide significant insight into understanding the feline immune system function.
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6
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Butler JE, Santiago-Mateo K, Wertz N, Sun X, Sinkora M, Francis DL. Antibody repertoire development in fetal and neonatal piglets. XXIV. Hypothesis: The ileal Peyer patches (IPP) are the major source of primary, undiversified IgA antibodies in newborn piglets. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 65:340-351. [PMID: 27497872 DOI: 10.1016/j.dci.2016.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/27/2016] [Accepted: 07/30/2016] [Indexed: 06/06/2023]
Abstract
The ileal Peyers patches (IPP) of newborn germfree (GF) piglets were isolated into blind loops and the piglets colonized with a defined probiotic microflora. After 5 weeks, IgA levels in the intestinal lavage (IL) of loop piglets remained at GF levels and IgM comprised ∼70% while in controls, IgA levels were elevated 5-fold and comprised ∼70% of total Igs. Loop piglets also had reduced serum IgA levels suggesting the source of serum IgA had been interrupted. The isotype profile for loop contents was intermediate between that in the IL of GF and probiotic controls. Surprisingly, colonization alone did not result in repertoire diversification in the IPP. Rather, colonization promoted pronounced proliferation of fully switched IgA(+)IgM(-) B cells in the IPP that supply early, non-diversified "natural" SIgA antibodies to the gut lumen and a primary IgA response in serum.
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Affiliation(s)
- John E Butler
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| | | | - Nancy Wertz
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A & F University, Yangling, China
| | - Marek Sinkora
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, Novy Hradek, Czech Republic.
| | - David L Francis
- Department of Veterinary Sciences, South Dakota State University, Brooking, SD, USA
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7
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Qin T, Liu Z, Zhao H. Organization and genomic complexity of sheep immunoglobulin light chain gene loci. Immunol Lett 2015; 168:313-8. [DOI: 10.1016/j.imlet.2015.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 10/09/2015] [Accepted: 10/15/2015] [Indexed: 01/06/2023]
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8
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Antibody Affinity Maturation in Fishes-Our Current Understanding. BIOLOGY 2015; 4:512-24. [PMID: 26264036 PMCID: PMC4588147 DOI: 10.3390/biology4030512] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/13/2015] [Accepted: 07/23/2015] [Indexed: 12/15/2022]
Abstract
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes.
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9
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Nowland MH, Brammer DW, Garcia A, Rush HG. Biology and Diseases of Rabbits. LABORATORY ANIMAL MEDICINE 2015. [PMCID: PMC7150064 DOI: 10.1016/b978-0-12-409527-4.00010-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Beginning in 1931, an inbred rabbit colony was developed at the Phipps Institute for the Study, Treatment and Prevention of Tuberculosis at the University of Pennsylvania. This colony was used to study natural resistance to infection with tuberculosis (Robertson et al., 1966). Other inbred colonies or well-defined breeding colonies were also developed at the University of Illinois College of Medicine Center for Genetics, the Laboratories of the International Health Division of The Rockefeller Foundation, the University of Utrecht in the Netherlands, and Jackson Laboratories. These colonies were moved or closed in the years to follow. Since 1973, the U.S. Department of Agriculture has reported the total number of certain species of animals used by registered research facilities (1997). In 1973, 447,570 rabbits were used in research. There has been an overall decrease in numbers of rabbits used. This decreasing trend started in the mid-1990s. In 2010, 210,172 rabbits were used in research. Despite the overall drop in the number used in research, the rabbit is still a valuable model and tool for many disciplines.
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10
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Abstract
Animals and many of their chronic microbial inhabitants form relationships of symbiotic mutualism, which occurs when coexisting life-forms derive mutual benefit from stable associations. While microorganisms receive a secure habitat and constant food source from vertebrate hosts, they are required for optimal immune system development and occupy niches otherwise abused by pathogens. Microbes have also been shown to provide vertebrate hosts with metabolic capabilities that enhance energy and nutrient uptake from the diet. The immune system plays a central role in the establishment and maintenance of host-microbe homeostasis, and B lineage cells play a key role in this regulation. Here, I reviewed the structure and function of the microbiota and the known mechanisms of how nonpathogenic microbes influence B cell biology and immunoglobulin repertoire development early in life. I also discuss what is known about how B lineage cells contribute to the process of shaping the composition of commensal/mutualistic microbe membership.
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Affiliation(s)
- Duane R Wesemann
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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11
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Liljavirta J, Niku M, Pessa-Morikawa T, Ekman A, Iivanainen A. Expansion of the preimmune antibody repertoire by junctional diversity in Bos taurus. PLoS One 2014; 9:e99808. [PMID: 24926997 PMCID: PMC4057420 DOI: 10.1371/journal.pone.0099808] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/19/2014] [Indexed: 12/15/2022] Open
Abstract
Cattle have a limited range of immunoglobulin genes which are further diversified by antigen independent somatic hypermutation in fetuses. Junctional diversity generated during somatic recombination contributes to antibody diversity but its relative significance has not been comprehensively studied. We have investigated the importance of terminal deoxynucleotidyl transferase (TdT) -mediated junctional diversity to the bovine immunoglobulin repertoire. We also searched for new bovine heavy chain diversity (IGHD) genes as the information of the germline sequences is essential to define the junctional boundaries between gene segments. New heavy chain variable genes (IGHV) were explored to address the gene usage in the fetal recombinations. Our bioinformatics search revealed five new IGHD genes, which included the longest IGHD reported so far, 154 bp. By genomic sequencing we found 26 new IGHV sequences that represent potentially new IGHV genes or allelic variants. Sequence analysis of immunoglobulin heavy chain cDNA libraries of fetal bone marrow, ileum and spleen showed 0 to 36 nontemplated N-nucleotide additions between variable, diversity and joining genes. A maximum of 8 N nucleotides were also identified in the light chains. The junctional base profile was biased towards A and T nucleotide additions (64% in heavy chain VD, 52% in heavy chain DJ and 61% in light chain VJ junctions) in contrast to the high G/C content which is usually observed in mice. Sequence analysis also revealed extensive exonuclease activity, providing additional diversity. B-lymphocyte specific TdT expression was detected in bovine fetal bone marrow by reverse transcription-qPCR and immunofluorescence. These results suggest that TdT-mediated junctional diversity and exonuclease activity contribute significantly to the size of the cattle preimmune antibody repertoire already in the fetal period.
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Affiliation(s)
- Jenni Liljavirta
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Anna Ekman
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
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12
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Fundamental characteristics of the expressed immunoglobulin VH and VL repertoire in different canine breeds in comparison with those of humans and mice. Mol Immunol 2014; 59:71-8. [DOI: 10.1016/j.molimm.2014.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 11/19/2022]
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13
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Butler JE, Sinkora M. The enigma of the lower gut-associated lymphoid tissue (GALT). J Leukoc Biol 2013; 94:259-70. [PMID: 23695307 DOI: 10.1189/jlb.0313120] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Artiodactyls possess GALT that appears in fetal life and is located at the extreme end of the ileum. These IPP contain mostly B cells and involute early in postnatal life. Rabbits have a similarly located lymphoid organ, called the sacculus rotundus. Studies in sheep and rabbits have led to the concept that the lower hindgut GALT represents primary lymphoid tissue for B cells and is necessary for normal B cell development, analogous to the bursa of Fabricius. This review traces the history of the observations and theories that have led to the existing concept concerning the role of lower GALT. We then review recent data from piglets with resected IPP that challenges the concept that the IPP is primary B cell lymphoid tissue and that artiodactyls and rabbits are members of the GALT group in the same context as gallinaceous birds. Eliminating the IPP as the primary lymphoid tissue for B cells leads to the hypothesis that the IPP acts as first-responder mucosal lymphoid tissue.
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Affiliation(s)
- John E Butler
- Institute of Microbiology AS CR, v.v.i., Doly 183, 54922 Novy Hradek, Czech Republic.
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The evolutionary basis for differences between the immune systems of man, mouse, pig and ruminants. Vet Immunol Immunopathol 2012; 152:13-9. [PMID: 23078904 DOI: 10.1016/j.vetimm.2012.09.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Studying the pathogenesis of an infectious disease like colibacillosis requires an understanding of the responses of target hosts to the organism both as a pathogen and as a commensal. The mucosal immune system constitutes the primary line of defence against luminal micro-organisms. The immunoglobulin-superfamily-based adaptive immune system evolved in the earliest jawed vertebrates, and the adaptive and innate immune system of humans, mice, pigs and ruminants co-evolved in common ancestors for approximately 300 million years. The divergence occurred only 100 mya and, as a consequence, most of the fundamental immunological mechanisms are very similar. However, since pressure on the immune system comes from rapidly evolving pathogens, immune systems must also evolve rapidly to maintain the ability of the host to survive and reproduce. As a consequence, there are a number of areas of detail where mammalian immune systems have diverged markedly from each other, such that results obtained in one species are not always immediately transferable to another. Thus, animal models of specific diseases need to be selected carefully, and the results interpreted with caution. Selection is made simpler where specific host species like cattle and pigs can be both target species and reservoirs for human disease, as in infections with Escherichia coli.
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15
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Gloria-Soria A, Moreno MA, Yund PO, Lakkis FG, Dellaporta SL, Buss LW. Evolutionary genetics of the hydroid allodeterminant alr2. Mol Biol Evol 2012; 29:3921-32. [PMID: 22855537 DOI: 10.1093/molbev/mss197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We surveyed genetic variation in alr2, an allodeterminant of the colonial hydroid Hydractinia symbiolongicarpus. We generated cDNA from a sample of 239 Hydractinia colonies collected at Lighthouse Point, Connecticut, and identified 473 alr2 alleles, 198 of which were unique. Rarefaction analysis suggested that the sample was near saturation. Most alleles were rare, with 86% occurring at frequencies of 1% or less. Alleles were highly variable, diverging on average by 18% of the amino acids in a predicted extracellular domain of the molecule. Analysis of 152 full-length alleles confirmed the existence of two structural types, defined by exons 4-8 of the gene. Several residues of the predicted immunoglobulin superfamily-like domains display signatures of positive selection. We also identified 77 unique alr2 pseudogene sequences from 85 colonies. Twenty-seven of these sequences matched expressed alr2 sequences from other colonies. This observation is consistent with pseudogenes contributing to alr2 diversification through sequence donation. A more limited collection of animals was made from a distant, relict population of H. symbiolongicarpus. Sixty percent of the unique sequences identified in this sample were found to match sequences from the Lighthouse Point population. The large number of alr2 alleles, their degree of divergence, the predominance of rare alleles in the population, their persistence over broad spatial and temporal scales, and the signatures of positive selection in multiple residues of the putative recognition domain paint a consistent picture of negative-frequency-dependent selection operating in this system. The genetic diversity observed at alr2 is comparable to that of the most highly polymorphic genetic systems known to date.
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Butler JE, Santiago-Mateo K, Sun XZ, Wertz N, Sinkora M, Francis DH. Antibody Repertoire Development in Fetal and Neonatal Piglets. XX. B Cell Lymphogenesis Is Absent in the Ileal Peyer’s Patches, Their Repertoire Development Is Antigen Dependent, and They Are Not Required for B Cell Maintenance. THE JOURNAL OF IMMUNOLOGY 2011; 187:5141-9. [DOI: 10.4049/jimmunol.1101871] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Sinkora M, Stepanova K, Butler JE, Francis D, Santiago-Mateo K, Potockova H, Karova K, Sinkorova J. Ileal Peyer's patches are not necessary for systemic B cell development and maintenance and do not contribute significantly to the overall B cell pool in swine. THE JOURNAL OF IMMUNOLOGY 2011; 187:5150-61. [PMID: 22013120 DOI: 10.4049/jimmunol.1101879] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Based on studies of sheep, ileal Peyer's patches (IPP) have been regarded as a type of primary lymphoid tissue similar to the bursa of Fabricius in chicken. Because bursectomy results in B cell deficiency, we wondered whether resection of the IPP of piglets would have a similar effect. Comparison of IPP-resected, surgical shams and untreated germ-free piglets, all of which were later colonized with a defined commensal flora, demonstrated that resection of the IPP did not alter the level and phenotype of B and T cells in lymphoid tissues and the blood 10 wk after surgery. Additionally, colonization of IPP caused a shift from the fetal type of lymphocyte distribution to the adult type that is characterized by prevalence of B cells, with many of them representing IgA(+) switched B cells or displaying a more mature CD2(-)CD21(+) and CD2(-)CD21(-) phenotype. Moreover, colonization leads to appearance of effector CD4(+)CD8(+) αβ T helper and CD2(+)CD8(-) γδ T cells. Comparison of germ-free with colonized pigs and experiments utilizing surgical transposition of jejunal Peyer's patch into terminal ileum or construction of isolated ileal loops indicated that lymphocyte development in IPP is dependent on colonization. Although our studies confirmed higher mitotic and apoptotic rates in IPP, they failed to identify any cell populations that resemble developing B lineage cells in the bone marrow. These results indicate that porcine IPP are not required for systemic B cell generation or maintenance, but they are secondary lymphoid tissue that appears important in immune responses to colonizing bacteria.
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Affiliation(s)
- Marek Sinkora
- Department of Immunology and Gnotobiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, 549 22 Nový Hrádek, Czech Republic.
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18
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Ekman A, Niku M, Liljavirta J, Iivanainen A. Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle. BMC Immunol 2009; 10:22. [PMID: 19405939 PMCID: PMC2686674 DOI: 10.1186/1471-2172-10-22] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 04/30/2009] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The assortment of cattle immunoglobulin and surrogate light chain genes has been extracted from the version 3.1 of Bos taurus genome sequence as a part of an international effort to sequence and annotate the bovine genome. RESULTS 63 variable lambda chain and 22 variable kappa chain genes were identified and phylogenetically assigned to 8 and 4 subgroups, respectively. The specified phylogenetic relationships are compatible with the established ruminant light chain variable gene families or subgroups. Because of gaps and uncertainties in the assembled genome sequence, the number of genes might change in the future versions of the genome sequence. In addition, three bovine surrogate light chain genes were identified. The corresponding cDNAs were cloned and the expression of the surrogate light chain genes was demonstrated from fetal material. CONCLUSION The bovine kappa gene locus is compact and simple which may reflect the preferential use of the lambda chain in cattle. The relative orientation of variable and joining genes in both loci are consistent with a deletion mechanism in VJ joining. The orientation of some variable genes cannot be determined from the data available. The number of functional variable genes is moderate when compared to man or mouse. Thus, post-recombinatorial mechanisms might contribute to the generation of the bovine pre-immune antibody repertoire. The heavy chains probably contribute more to recombinational immunoglobulin repertoire diversity than the light chains but the heavy chain locus could not be annotated from the version 3.1 of Bos taurus genome.
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Affiliation(s)
- Anna Ekman
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
| | - Mikael Niku
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki, Finland
| | - Jenni Liljavirta
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
| | - Antti Iivanainen
- Department of Basic Veterinary Sciences, University of Helsinki, Helsinki, Finland
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19
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Antigen-specific human polyclonal antibodies from hyperimmunized cattle. Nat Biotechnol 2009; 27:173-81. [DOI: 10.1038/nbt.1521] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Accepted: 12/23/2008] [Indexed: 11/09/2022]
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20
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Wilson S, Norton P, Leigh J, Bailey M. Early, microbially driven follicular reactions in the neonatal piglet do not contribute to expansion of the immunoglobulin heavy chain V-D-J repertoire. Vet Immunol Immunopathol 2007; 118:105-12. [PMID: 17560662 DOI: 10.1016/j.vetimm.2007.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2007] [Revised: 04/18/2007] [Accepted: 04/26/2007] [Indexed: 11/16/2022]
Abstract
Selective microbial colonisation of germ-free piglets is reported to result in expansion of immunoglobulin V(H)- and D(H)-segment usage from an initially limited repertoire. Here, the response of the palatine tonsil to microbial colonisation was compared in age-matched conventionally reared and germ-free piglets. At 3 and 5 days after birth an expansion in the B-cell follicle area was observed in the conventional, microbially colonised animals, which was not seen in the germ-free piglets. Consistent with this observation, sequencing of re-arranged heavy chain V-D-J units demonstrated accumulation of point mutations indicating somatic hypermutation in the conventional, microbially colonised piglets but not in the germ-free animals. However, V(H)- and D(H)-segment usage and CDR3 length did not differ between the groups. The results suggest that the follicle reaction observed occurs in response to microbial challenge, involves proliferation and somatic hypermutation of B-cells but does not expand repertoire or generate classical, isotype-switched memory B-cells. We suggest that microbial colonisation of neonatal piglets drives immunological competence in two stages: first, an antigen non-specific, follicular reaction which expands immunological compartments; and second, microbe driven changes in V-segment usage which expand immunological repertoire.
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Affiliation(s)
- Stephen Wilson
- Division of Molecular and Cellular Biology, Department of Clinical Veterinary Science, University of Bristol, Langford House, Bristol, United Kingdom.
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21
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Butler JE, Weber P, Wertz N. Antibody repertoire development in fetal and neonatal piglets. XIII. Hybrid VH genes and the preimmune repertoire revisited. THE JOURNAL OF IMMUNOLOGY 2007; 177:5459-70. [PMID: 17015732 DOI: 10.4049/jimmunol.177.8.5459] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The expressed porcine VH genes belong to the VH3 family (clan), four of which, VHA, VHB, VHC, and VHE, alone comprise approximately 80% of the preimmune repertoire. However, so-called "hybrid" VH genes that use CDR1 of one VH gene and the CDR2 of another are frequently encountered. We studied > 3000 cloned VDJs and found that such hybrids can contribute up to 10% of the preimmune repertoire. Based on the 1) recovery of hybrid VH genes from bacterial artificial chromosome clones, 2) frequency of occurrence of certain hybrids in the preimmune repertoire, and 3) failure to recover equal numbers of reciprocal hybrids, we concluded that some chimeric genes are present in the genome and are not PCR artifacts. Two chimeric germline genes (VHZ and VHY), together with VHF and the four genes mentioned above, constitute the major VH genes and these account for > 95% of the preimmune repertoire. Diversification of the preimmune IgG and IgM repertoires after environmental exposure was mainly due to somatic hypermutation of major VH genes with no evidence of gene conversion. Somatic hypermutation was 3- to 10-fold higher in CDRs than in framework regions, most were R mutations and transversions and transitions equally contributed. Data were used to 1) develop an index to quantify the degree of VH repertoire diversification and 2) establish a library of 29 putative porcine VH genes. One-third of these genes are chimeric genes and their sequences suggest that the porcine VH genome developed by duplication and splicing from a small number of prototypic genes.
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Affiliation(s)
- John E Butler
- Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA.
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22
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Lie KI, Aleksandersen M, Tverdal A, Landsverk T. Reduced apoptosis in sheep ileal Peyer's patch is associated with low levels of follicle centre carbonic anhydrase reactivity. Vet Immunol Immunopathol 2006; 111:127-37. [PMID: 16413061 DOI: 10.1016/j.vetimm.2005.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 11/02/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
Apoptosis in lymphoid follicles of the ileal Peyer's patch (IPP) in 21 sheep of two different age groups was visualized by the TdT-mediated dUTP nick end-labelling (TUNEL) method, and quantified using computer-assisted image analysis. The IPP follicle carbonic anhydrase (CA) reactivity was evaluated in the same samples. No significant differences with respect to apoptosis and CA reactivity were found between sheep aged 5 and 11 months. Individual variation in apoptotic activity correlated with the follicle centre CA reactivity. The group of animals found to have predominantly atypical ileal lymphoid follicles (more than 80% of total number of follicles) with features resembling jejunal Peyer's patch follicles, had lower number of apoptotic cells and reduced CA reactivity compared to the rest of the animals. The differences in CA reactivity in the follicle centres probably represent a variation in the presence of CA rich approximately 50 nm membrane-bounded particles known to be a feature of the sheep IPP. The present results suggest that the particles are involved in the modulation of the lymphocyte proliferation of the IPP follicles.
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Affiliation(s)
- Kai-Inge Lie
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, PO Box 8146 Dep., N-0033 Oslo, Norway.
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23
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Yasuda M, Jenne CN, Kennedy LJ, Reynolds JD. The sheep and cattle Peyer's patch as a site of B-cell development. Vet Res 2006; 37:401-15. [PMID: 16611555 DOI: 10.1051/vetres:2006008] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 11/15/2005] [Indexed: 11/15/2022] Open
Abstract
In sheep and cattle, the ileal Peyer's patch (PP), which extends one-two meters along the terminal small intestine, is a primary lymphoid organ of B-cell development. B-cell diversity in the ileal PP is thought to develop by combinatorial mechanisms, gene conversion and/or point mutation. These species also have jejunal PP that function more like secondary lymphoid tissues concerned with mucosal immune reactions. These two types of PP differ significantly in their histology, ontogeny and the extent of lymphocyte traffic. The prenatal development of follicles in the PP begins first in the jejunum during the middle of gestation and then in the ileum during late gestation. B-cells proliferate rapidly in the ileal PP follicle; up to five percent of these cells survive while the majority dies by apoptosis, perhaps driven by the influence of environmental antigen and/or self-antigen. The surviving cells migrate from the ileal PP and populate the peripheral B-cell compartment. By adolescence, the ileal PP has involuted but the function of jejunal PP, compatible with a role as secondary lymphoid organ, continues throughout life. In this review, we focus on the development of PP as a site of B-cell repertoire generation, positive and negative B-cell selection, and the differences between ileal PP and jejunal PP.
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Affiliation(s)
- Masahiro Yasuda
- Immunology Research Group, Department of Cell Biology and Anatomy, University of Calgary, 3330 Hospital Drive NW, Calgary, Alberta, T2N 4N1, Canada
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24
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Zhao Y, Jackson SM, Aitken R. The bovine antibody repertoire. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:175-86. [PMID: 16054212 DOI: 10.1016/j.dci.2005.06.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cattle are able to produce a full range of Ig classes including the long-elusive IgD through rearrangement of their germline genes. Several IgL groupings have been reported but as in several other livestock species (e.g. sheep, rabbits, chickens), rearrangement per se fails to generate significant IgH diversity. This is largely because of the modest number of bovine VH segments that participate in rearrangement and their conserved sequences. Perhaps in compensation, bovine Ig heavy chains carry CDR3 sequences of exceptional length. Processes that operate post-rearrangement to generate diversity remain ill defined as are the location, timing and triggers to these events. Reagents are needed to understand better the maturation of B lymphocytes, their responses to antigens and cytokines, and to provide standards for the quantitation of Ig responses in cattle; recombinant methods may help meet this need as Ab engineering technologies become more widely used.
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Affiliation(s)
- Yaofeng Zhao
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital at Huddinge, SE-14186 Stockholm, Sweden
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25
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Jenne CN, Kennedy LJ, Reynolds JD. Antibody repertoire development in the sheep. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:165-74. [PMID: 16083958 DOI: 10.1016/j.dci.2005.06.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The model of immunoglobulin (Ig) repertoire diversification in sheep has evolved dramatically in recent years. A process thought to involve the rearrangement of a very limited number of variable (V), diversity (D) and joining (J) segments followed by intense, antigen (Ag)-independent, somatic hypermutation is now known to be less recombinatorially restrictive and to involve fewer mutational events. Although mutation rates are now lower than previously thought, the somatic hypermutation process itself is no less critical to the development of the primary Ig repertoire in sheep. Recent studies have shown that those B cells that fail to mutate will die via apoptosis. Much of the V(D)J rearrangement is thought to occur in the fetal liver and spleen prior to development of the ileal Peyer's patch (PP) at approximately day 100 of gestation. Although de novo Ig rearrangement likely does not occur in the ileal PP, this tissue is a site of massive B-cell proliferation, selection and Ig diversification through somatic hypermutation.
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Affiliation(s)
- Craig N Jenne
- Department of Cell Biology and Anatomy, Immunology Research Group, University of Calgary, 3330 Hospital Dr. N.W., Calgary, Alta., Canada
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26
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Butler JE, Sun J, Wertz N, Sinkora M. Antibody repertoire development in swine. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:199-221. [PMID: 16168480 DOI: 10.1016/j.dci.2005.06.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Swine belong to the Order Artiodactyla and like mice and humans, express IgM, IgD, IgG, IgE and IgA antibodies but a larger number of IgG subclasses. Like rabbits and chickens, expressed V(H) genes belong to the ancestral V(H)3 family and only 5 comprise >80% of the pre-immune repertoire. Since they use primarily two D(H) segments and have a single J(H) like chickens, junctional diversity plays a relatively greater role in repertoire formation than in humans and mice. Proportional light chain usage surprisingly resembles that in humans and is therefore distinctly different from the predominant kappa chain usage (>90%) of lab rodents and predominant lambda chain usage in other ungulates (>90%). The pre-immune V(kappa) repertoire also appears restricted since >95% of V(kappa)J(kappa) rearrangements use only a few members of the IGKV2 family and only J(kappa)2. Two V(lambda) families (IGLV3 and IGLV8) are used in forming the pre-immune repertoire. Antibodies that do not utilize light chains as in camelids, or the lengthy CDR3 regions seen in cattle that use V(H)4 family genes, have not been reported in swine. B cell lymphogenesis first occurs in the yolk sac but early VDJ rearrangements differ from mice and humans in that nearly 100% are in-frame and N-region additions are already present. Swine possess ileal Peyers patches like sheep which may be important for antigen-independent B cell repertoire diversification. The presence of pro B-like cells in interlobular areas of thymus and mature B cells in the thymic medulla that have switched to especially IgA in early gestation, is so far unique among mammals. The offspring of swine are believed to receive no passive immunity in utero and are precosial. Thus, they are a useful model for studies on fetal-neonatal immunological development. The model has already shown that: (a) colonization of the gut is required for responsiveness to TD and TI-2 antigens, (b) responsiveness due to colonization depends on bacterial PAMPs and (c) some viral pathogens can interfere with the establishment of immune homeostasis in neonates. Studies on swine reinforce concerns that caution be used when paradigms arising from studies in one mammal are extrapolated to other mammals, even when similarities are predicted by taxonomy and phylogeny. Swine exemplify a situation in which evolutionary diversification of the immune system is not characteristic of an entire order or even of other related systems in the same species.
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Affiliation(s)
- John E Butler
- Department of Microbiology, The University of Iowa, Iowa City, IA 52242, USA.
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27
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Abstract
Antigen receptor genes exist in the germline in a "split" configuration and are assembled in developing B and T lymphocytes by V(D)J recombination. This site-specific recombination reaction is initiated by a complex containing the RAG1 and RAG2 proteins and completed by general DNA repair factors. RAG1 and RAG2, like the adaptive immune system itself, are found exclusively in jawed vertebrates, and are thought to have entered the vertebrate genome by horizontal transmission as components of a transposable element. This review discusses the structure of antigen receptor genes and the mechanisms by which they are assembled and diversified, and then goes on to consider the evolutionary implications of the arrival of the hypothetical "RAG transposon".
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Affiliation(s)
- David G Schatz
- Section of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06510, USA.
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28
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Gontier E, Ayrault O, Godet I, Nau F, Ladevèze V. Developmental progression of immunoglobulin heavy chain diversity in sheep. Vet Immunol Immunopathol 2005; 103:31-51. [PMID: 15626460 DOI: 10.1016/j.vetimm.2004.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 07/27/2004] [Accepted: 08/18/2004] [Indexed: 11/21/2022]
Abstract
In order to assess the respective impacts of combinatorial rearrangement, junctional diversification, somatic hypermutation and gene conversion in the generation of immunoglobulin heavy chain variable regions diversity, the sequences of 42 variable regions from late fetal, newborn and young sheep were determined and compared to those of adult animals. At earlier stages of development, the use of germline diversity segments appears restricted, junctional variability is already established, and somatic hypermutations are scarce. The sequence diversity in adults is much higher, which we suggest results from a higher hymermutation activity and possibly from the use of a variety of diversity segments. Altogether, this pattern is very reminiscent of the situation observed in cattle, except for the length of the third complementarity determining regions (CDR3) which are shorter in sheep than in bovine. Unlike the chicken and rabbit systems, it seems that new rearrangements continue to occur in sheep for at least several months after birth.
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Affiliation(s)
- Etienne Gontier
- Laboratoire d'Immunologie Moléculaire, Faculté des Sciences, EA 2224, IFR 59, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022 Poitiers Cedex, France
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29
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Butler JE, Wertz N, Sun J, Wang H, Chardon P, Piumi F, Wells K. Antibody repertoire development in fetal and neonatal pigs. VII. Characterization of the preimmune kappa light chain repertoire. THE JOURNAL OF IMMUNOLOGY 2005; 173:6794-805. [PMID: 15557173 DOI: 10.4049/jimmunol.173.11.6794] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Combinatorial diversity is highly restricted in the preimmune porcine H chain repertoire compared with that in humans and mice. This raised the question of whether similar restriction characterized the preimmune L chain repertoire. In this study we present evidence that >90% of all expressed Vkappa genes in the porcine preimmune repertoire belong to three subfamilies of Vkappa genes that share 87% sequence similarity with human IGKV2. This porcine Vkappa family also shares sequence similarity with some, but not all, Vkappa genes from sheep. Hybridization with sperm DNA and sequence analyses of polynucleotides from overlapping bacterial artificial chromosome clones suggest swine possess approximately 60 IGVK2 genes. The latter method also revealed that certain IGKV2 subfamilies are not expressed in the preimmune repertoire. Six members of an IGVK1 family were also expressed as part of the preimmune repertoire, and these shared 87% sequence similarity with human IGVK1. Five Jkappa segments, complete with recombination signal sequences and separated by approximately 300 nt, were identified approximately 3 kb upstream of a single Ckappa. Surprisingly, Jkappa2 accounted for >90% of all framework region 4 sequences in the preimmune repertoire. These findings show that swine use approximately 10 IGVK2 genes from three of six subfamilies and preferentially one Jkappa segment to generate their preimmune kappa repertoire. These studies, like those of porcine Ig constant regions and MHC genes, also indicate unexpected high sequence similarity with their human counterparts despite differences in phylogeny and the mechanism of repertoire diversification.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Motifs/immunology
- Amino Acid Sequence
- Animals
- Animals, Newborn/genetics
- Animals, Newborn/immunology
- Antibody Diversity/genetics
- Base Sequence
- Chromosomes, Artificial, Bacterial
- Cloning, Molecular/methods
- Fetal Development/genetics
- Fetal Development/immunology
- Gene Expression Regulation, Developmental/immunology
- Gene Rearrangement, B-Lymphocyte, Light Chain
- Genes, Overlapping
- Genome
- Humans
- Immunoglobulin J-Chains/biosynthesis
- Immunoglobulin J-Chains/chemistry
- Immunoglobulin J-Chains/genetics
- Immunoglobulin Variable Region/biosynthesis
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/genetics
- Immunoglobulin kappa-Chains/biosynthesis
- Immunoglobulin kappa-Chains/chemistry
- Immunoglobulin kappa-Chains/genetics
- Male
- Molecular Sequence Data
- Multigene Family/immunology
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Swine
- Terminology as Topic
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Affiliation(s)
- John E Butler
- Department of Microbiology and Interdisciplinary Immunology Program, University of Iowa, Iowa City, IA 52242, USA.
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30
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Rhee KJ, Jasper PJ, Sethupathi P, Shanmugam M, Lanning D, Knight KL. Positive selection of the peripheral B cell repertoire in gut-associated lymphoid tissues. ACTA ACUST UNITED AC 2004; 201:55-62. [PMID: 15623575 PMCID: PMC2212770 DOI: 10.1084/jem.20041849] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gut-associated lymphoid tissues (GALTs) interact with intestinal microflora to drive GALT development and diversify the primary antibody repertoire; however, the molecular mechanisms that link these events remain elusive. Alicia rabbits provide an excellent model to investigate the relationship between GALT, intestinal microflora, and modulation of the antibody repertoire. Most B cells in neonatal Alicia rabbits express VHn allotype immunoglobulin (Ig)M. Within weeks, the number of VHn B cells decreases, whereas VHa allotype B cells increase in number and become predominant. We hypothesized that the repertoire shift from VHn to VHa B cells results from interactions between GALT and intestinal microflora. To test this hypothesis, we surgically removed organized GALT from newborn Alicia pups and ligated the appendix to sequester it from intestinal microflora. Flow cytometry and nucleotide sequence analyses revealed that the VHn to VHa repertoire shift did not occur, demonstrating the requirement for interactions between GALT and intestinal microflora in the selective expansion of VHa B cells. By comparing amino acid sequences of VHn and VHa Ig, we identified a putative VH ligand binding site for a bacterial or endogenous B cell superantigen. We propose that interaction of such a superantigen with VHa B cells results in their selective expansion.
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Affiliation(s)
- Ki-Jong Rhee
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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31
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Fleurant M, Changchien L, Chen CT, Flajnik MF, Hsu E. Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains. THE JOURNAL OF IMMUNOLOGY 2004; 173:5574-82. [PMID: 15494507 DOI: 10.4049/jimmunol.173.9.5574] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have characterized a small family of four genes encoding one of the three nurse shark Ig L chain isotypes, called NS5. All NS5 cDNA sequences are encoded by three loci, of which two are organized as conventional clusters, each consisting of a V and J gene segment that can recombine and one C region exon; the third contains a germline-joined VJ in-frame and the fourth locus is a pseudogene. This is the second nurse shark L chain type where both germline-joined and split V-J organizations have been found. Since there are only two rearranging Ig loci, it was possible for the first time to examine junctional diversity in defined fish Ig genes, comparing productive vs nonproductive rearrangements. N region addition was found to be considerably more extensive in length and in frequency than any other vertebrate L chain so far reported and rivals that in H chain. We put forth the speculation that the unprecedented efficiency of N region addition (87-93% of NS5 sequences) may be a result not only of simultaneous H and L chain rearrangement in the shark but also of processing events that afford greater accessibility of the V or J gene coding ends to terminal deoxynucleotidyltransferase.
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Affiliation(s)
- Marshall Fleurant
- Department of Physiology and Pharmacology, State University of New York Health Science Center, Brooklyn, NY 11203, USA
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32
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Casola S, Otipoby KL, Alimzhanov M, Humme S, Uyttersprot N, Kutok JL, Carroll MC, Rajewsky K. B cell receptor signal strength determines B cell fate. Nat Immunol 2004; 5:317-27. [PMID: 14758357 DOI: 10.1038/ni1036] [Citation(s) in RCA: 432] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2003] [Accepted: 12/02/2003] [Indexed: 11/09/2022]
Abstract
B cell receptor (BCR)-mediated antigen recognition is thought to regulate B cell differentiation. BCR signal strength may also influence B cell fate decisions. Here, we used the Epstein-Barr virus protein LMP2A as a constitutively active BCR surrogate to study the contribution of BCR signal strength in B cell differentiation. Mice carrying a targeted replacement of Igh by LMP2A leading to high or low expression of the LMP2A protein developed B-1 or follicular and marginal zone B cells, respectively. These data indicate that BCR signal strength, rather than antigen specificity, determines mature B cell fate. Furthermore, spontaneous germinal centers developed in gut-associated lymphoid tissue of LMP2A mice, indicating that microbial antigens can promote germinal centers independently of BCR-mediated antigen recognition.
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Affiliation(s)
- Stefano Casola
- CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA.
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