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Qiu Y, Yi X, Tang X, Wei Y, Zhang B, Duan S, Wang S, Sun X. Differential analysis of immunoglobulin gene expression pattern in chickens of distinct breeds and developmental periods. J Anim Sci 2024; 102:skae111. [PMID: 38651250 PMCID: PMC11107122 DOI: 10.1093/jas/skae111] [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: 11/19/2023] [Accepted: 04/20/2024] [Indexed: 04/25/2024] Open
Abstract
Immunoglobulin is an essential component of the body's defense against pathogens, aiding in the recognition and clearance of foreign antigens. Research concerning immunoglobulin gene and its diversity of expression across different breeds within the same species is relatively scarce. In this study, we employed RACE (Rapid Amplification of cDNA Ends) technology, prepared DNA libraries, performed high-throughput sequencing, and conducted related bioinformatics analysis to analyze the differences in immunoglobulin gene diversity and expression at different periods in Hy-line brown hens, Lueyang black-bone chickens, and Beijing-You chickens. The study found that the composition of chicken immunoglobulin genes is relatively simple, with both the light chain and heavy chain having a functional V gene. Additionally, the mechanisms of immunoglobulin diversity generation tended to be consistent among different breeds and periods of chickens, primarily relying on abundant junctional diversity, somatic hypermutation (SHM), and gene conversion (GCV) to compensate for the limitations of low-level V(D)J recombination. As the age increased, the junctional diversity of IgH and IgL tended to diversify and showed similar expression patterns among different breeds. In the three chicken breeds, the predominant types of mutations observed in IGHV and IGLV SHM were A to G and G to A transitions. Specifically, IGLV exhibited a preference for A to G mutations, whereas IGHV displayed a bias toward G to A mutations. The regions at the junctions between framework regions (FR) and complementarity-determining regions (CDR) and within the CDR regions themselves are typically prone to mutations. The locations of GCV events in IGLV and IGHV do not show significant differences, and replacement segments are concentrated in the central regions of FR1, CDR, and FR2. Importantly, gene conversion events are not random occurrences. Additionally, our investigation revealed that CDRH3 in chickens of diverse breeds and periods the potential for diversification through the incorporation of cysteine. This study demonstrates that the diversity of immunoglobulin expression tends to converge among Hy-line brown hens, Lueyang black-bone chickens, and Beijing-You chickens, indicating that the immunoglobulin gene expression mechanisms in different breeds of chickens do not exhibit significant differences due to selective breeding.
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Affiliation(s)
- Yanbo Qiu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Yanpei Wei
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
| | - Beibei Zhang
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
| | - Shunan Duan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
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2
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Wang Y, Zhang S, Yang X, Hwang JK, Zhan C, Lian C, Wang C, Gui T, Wang B, Xie X, Dai P, Zhang L, Tian Y, Zhang H, Han C, Cai Y, Hao Q, Ye X, Liu X, Liu J, Cao Z, Huang S, Song J, Pan-Hammarström Q, Zhao Y, Alt FW, Zheng X, Da LT, Yeap LS, Meng FL. Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation. Cell 2023; 186:2193-2207.e19. [PMID: 37098343 DOI: 10.1016/j.cell.2023.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/06/2023] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Xinrui Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chuanzong Zhan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chong Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huizhi Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Hao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Kindstar Global Precision Medicine Institute, Wuhan 430000, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shaohui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Biosciences, University of Chinese Academy of Sciences, Beijing 101499, China
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yaofeng Zhao
- State Key Laboratory of Farm Animal Biotech Breeding, China Agricultural University, Beijing 100193, China
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Huashen Institute of Microbes and Infections, Shanghai 200052, China.
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Exploiting V-Gene Bias for Rapid, High-Throughput Monoclonal Antibody Isolation from Horses. Viruses 2022; 14:v14102172. [PMID: 36298728 PMCID: PMC9609571 DOI: 10.3390/v14102172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/30/2022] Open
Abstract
Horses and humans share a close relationship that includes both species' viromes. Many emerging infectious diseases can be transmitted between horses and humans and can exhibit mortality rates as high as 90% in both populations. Antibody biologics represents an emerging field of rapidly discoverable and potent antiviral therapeutics. These biologics can be used to provide passive immunity, as well as blueprints for the rational design of novel active vaccine antigens. Here, we exploit the limited diversity of immunoglobulin variable genes used by horses to develop a rapid, high-throughput monoclonal antibody discovery pipeline. The antibodies isolated from two horses in this study were developed with near exclusivity from a few highly related germline genes within a single IgHV and IgλV gene family and could be recovered for cloning with just three primer pairs. This variable gene pairing was compatible with both horse and human immunoglobulin G isotypes, confirming the suitability of an equine antibody discovery pipeline for developing novel therapeutics to meet the One Health approach to infectious diseases.
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4
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The major role of junctional diversity in the horse antibody repertoire. Mol Immunol 2022; 151:231-241. [PMID: 36179605 DOI: 10.1016/j.molimm.2022.09.011] [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: 06/26/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022]
Abstract
The antibody repertoire (Rep-seq) sequencing revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-infected horses using NGS (Next generation sequencing). This study obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 % and 82 % in IgM and IgG isotypes. We observed that besides horses antibody can use all functional IGHV genes, around 80 % of their antibodies use only three IGHV gene segments, and around 55 % use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horse antibodies is widespread, present in more than 90 % of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45 % of the antibody clones have more than ten nucleotides in both the N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and other species to better understand antibody repertoire characteristics.
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5
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Rosenfeld R, Alcalay R, Zvi A, Ben-David A, Noy-Porat T, Chitlaru T, Epstein E, Israeli O, Lazar S, Caspi N, Barnea A, Dor E, Chomsky I, Pitel S, Makdasi E, Zichel R, Mazor O. Centaur antibodies: Engineered chimeric equine-human recombinant antibodies. Front Immunol 2022; 13:942317. [PMID: 36059507 PMCID: PMC9437483 DOI: 10.3389/fimmu.2022.942317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/28/2022] [Indexed: 11/27/2022] Open
Abstract
Hyper-immune antisera from large mammals, in particular horses, are routinely used for life-saving anti-intoxication intervention. While highly efficient, the use of these immunotherapeutics is complicated by possible recipient reactogenicity and limited availability. Accordingly, there is an urgent need for alternative improved next-generation immunotherapies to respond to this issue of high public health priority. Here, we document the development of previously unavailable tools for equine antibody engineering. A novel primer set, EquPD v2020, based on equine V-gene data, was designed for efficient and accurate amplification of rearranged horse antibody V-segments. The primer set served for generation of immune phage display libraries, representing highly diverse V-gene repertoires of horses immunized against botulinum A or B neurotoxins. Highly specific scFv clones were selected and expressed as full-length antibodies, carrying equine V-genes and human Gamma1/Lambda constant genes, to be referred as “Centaur antibodies”. Preliminary assessment in a murine model of botulism established their therapeutic potential. The experimental approach detailed in the current report, represents a valuable tool for isolation and engineering of therapeutic equine antibodies.
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Affiliation(s)
- Ronit Rosenfeld
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- *Correspondence: Ronit Rosenfeld, ; Ohad Mazor,
| | - Ron Alcalay
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Alon Ben-David
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tal Noy-Porat
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Epstein
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noa Caspi
- Veterinary Center for Preclinical Research, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ada Barnea
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Dor
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Chomsky
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shani Pitel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Efi Makdasi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ran Zichel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Mazor
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- *Correspondence: Ronit Rosenfeld, ; Ohad Mazor,
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6
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Wu M, Zhao H, Tang X, Zhao W, Yi X, Li Q, Sun X. Organization and Complexity of the Yak (Bos Grunniens) Immunoglobulin Loci. Front Immunol 2022; 13:876509. [PMID: 35615368 PMCID: PMC9124968 DOI: 10.3389/fimmu.2022.876509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
As important livestock in Qinghai-Tibet Plateau, yak provides meat and other necessities for Tibetans living. Plateau yak has resistance to diseases and stress, yet is nearly unknown in the structure and expression mechanism of yak immunoglobulin loci. Based on the published immunoglobulin genes of bovids (cattle, sheep and goat), the genomic organization of the yak immunoglobulin heavy chain (IgH) and immunoglobulin light chain (IgL) were described. The assemblage diversity of IgH, Igλ and Igκ in yak was similar to that in bovids, and contributes little to the antibody lineage compared with that in humans and mice. Somatic hypermutation (SHM) had a greater effect on immunoglobulin diversity in yak than in goat and sheep, and in addition to the complementarity-determining region (CDR), some loci in the framework region (FR) also showed high frequency mutations. CDR3 diversity showed that immunological lineages in yak were overwhelmingly generated through linkage diversity in IgH rearrangements. The emergence of new high-throughput sequencing technologies and the yak whole genome (2019) publication have greatly improved our understanding of the immune response in yaks. We had a more comprehensive analysis of yak immunoglobulin expression diversity by PE300, which avoided the disadvantage of missing low-frequency recombination in traditional Sanger sequencing. In summary, we described the schematic structure of the genomic organization of yak IgH loci and IgL loci. The analysis of immunoglobulin expression diversity showed that yak made up for the deficiency of V(D)J recombinant diversity by junctional diversity and CDR3 diversity. In addition, yak, like cattle, also had the same ultra-long IgH CDR3 (CDR3H), which provided more contribution to the diverse expression of yak immunoglobulin. These findings might provide a theoretical basis for disease resistance breeding and vaccine development in yak.
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Affiliation(s)
- Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanxia Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- *Correspondence: Xiuzhu Sun,
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Gnanesh Kumar B, Rawal A. Sequence characterization and N-glycoproteomics of secretory immunoglobulin A from donkey milk. Int J Biol Macromol 2020; 155:605-613. [DOI: 10.1016/j.ijbiomac.2020.03.253] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/19/2022]
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Yu X, Du L, Wu M, Wu J, He S, Yuan T, Sun X. The analysis of organization and diversity mechanism in goat immunoglobulin light chain gene loci. Immunobiology 2019; 225:151889. [PMID: 31812342 DOI: 10.1016/j.imbio.2019.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
The genomic organization of goat immunoglobulin light chains (Igλ and Igκ) loci were annotated based on the goat genome database. The goat Igλ chain located on chromosome 17 contains at least 35 Vλ gene fragments (seven potential functional genes, one ORF and 27 pseudogenes), two Jλ-Cλ clusters arranged in a Vλ(35)-Jλ2-Cλ1-Jλ1-Cλ2 pattern, with another Cλ3 on scaffold. The Igκ locus included 11 Vκ (five potential functional genes, two ORFs and four pseudogene fragments), three Jκ genes and a single Cκ gene ordered in Vκ(35)-Jκ(3)-Cκ pattern on chromosome 11. By analyzing the clonies of Igλ and Igκ, we further found Vλ2 (26.23 %) &Vλ3 (73.11 %), Vκ2 (52.07 %) &Vκ4 (46.15 %) were predominately used in the expression of λ and κ chains respectively. λ chain showed more abundance in connective diversity than κ chain. Besides, somatic hypermutation with higher frequency in both immunoglobulin light chains was the major mechanism for the goat repertoire diversity. These results demonstrated goat immunoglobulin light chain variable region genome loci and repertoire diversity.
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Affiliation(s)
- Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lijuan Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuai He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Manso TC, Groenner-Penna M, Minozzo JC, Antunes BC, Ippolito GC, Molina F, Felicori LF. Next-generation sequencing reveals new insights about gene usage and CDR-H3 composition in the horse antibody repertoire. Mol Immunol 2018; 105:251-259. [PMID: 30562645 DOI: 10.1016/j.molimm.2018.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/11/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022]
Abstract
Horse serum antibodies have been used for greater than a century for the treatment and prophylaxis of infectious diseases and envenomations. Little is known, however, about the immunogenetic diversity that produces horse serum antibodies. Here, we employed next-generation sequencing for a first-in-kind comprehensive analysis of the equine B-cell repertoire. Nearly 45,000 and 30,000 clonotypes were obtained for the heavy-chain (IGH) and lambda light-chain (IGL) loci, respectively. We observed skewed use of the common subgroups IGHV2 (92.49%) and IGLV8 (82.50%), consistent with previous reports, but also novel use of the rare genes IGHV6S1 and IGLV4S2. CDR-H3 amino acid composition revealed different amino acid patterns at positions 106 and 116 compared to human, rabbit, and mouse, suggesting that an extended conformation predominates among horse CDR-H3 loops. Our analysis provides new insights regarding the mechanisms employed to generate antibody diversity in the horse, and could be applicable to the optimized design of synthetic antibodies intended for future therapeutic use.
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Affiliation(s)
- Taciana Conceição Manso
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michele Groenner-Penna
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - João Carlos Minozzo
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Bruno Cesar Antunes
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Stop A5000, Austin, TX, 78712, USA
| | | | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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10
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Matsuzawa S, Isobe M, Kurosawa N. Guinea pig immunoglobulin VH and VL naïve repertoire analysis. PLoS One 2018; 13:e0208977. [PMID: 30543679 PMCID: PMC6292586 DOI: 10.1371/journal.pone.0208977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
The guinea pig has been used as a model to study various human infectious diseases because of its similarity to humans regarding symptoms and immune response, but little is known about the humoral immune response. To better understand the mechanism underlying the generation of the antibody repertoire in guinea pigs, we performed deep sequencing of full-length immunoglobulin variable chains from naïve B and plasma cells. We gathered and analyzed nearly 16,000 full-length VH, Vκ and Vλ genes and analyzed V and J gene segment usage profiles and mutation statuses by annotating recently reported genome data of guinea pig immunoglobulin genes. We found that approximately 70% of heavy, 73% of kappa and 81% of lambda functional germline V gene segments are integrated into the actual V(D)J recombination events. We also found preferential use of a particular V gene segment and accumulated mutation in CDRs 1 and 2 in antigen-specific plasma cells. Our study represents the first attempt to characterize sequence diversity in the expressed guinea pig antibody repertoire and provides significant insight into antibody repertoire generation and Ig-based immunity of guinea pigs.
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Affiliation(s)
- Shun Matsuzawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- Medical & Biological Laboratories Co., Ltd., Ina-shi, Nagano, Japan
| | - Masaharu Isobe
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
| | - Nobuyuki Kurosawa
- Laboratory of Molecular and Cellular Biology, Graduate School of Science and Engineering for Research, University of Toyama, Toyama-shi, Toyama, Japan
- * E-mail:
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11
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Collins AM, Watson CT. Immunoglobulin Light Chain Gene Rearrangements, Receptor Editing and the Development of a Self-Tolerant Antibody Repertoire. Front Immunol 2018; 9:2249. [PMID: 30349529 PMCID: PMC6186787 DOI: 10.3389/fimmu.2018.02249] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Discussion of the antibody repertoire usually emphasizes diversity, but a conspicuous feature of the light chain repertoire is its lack of diversity. The diversity of reported allelic variants of germline light chain genes is also limited, even in well-studied species. In this review, the implications of this lack of diversity are considered. We explore germline and rearranged light chain genes in a variety of species, with a particular focus on human and mouse genes. The importance of the number, organization and orientation of the genes for the control of repertoire development is discussed, and we consider how primary rearrangements and receptor editing together shape the expressed light chain repertoire. The resulting repertoire is dominated by just a handful of IGKV and IGLV genes. It has been hypothesized that an important function of the light chain is to guard against self-reactivity, and the role of secondary rearrangements in this process could explain the genomic organization of the light chain genes. It could also explain why the light chain repertoire is so limited. Heavy and light chain genes may have co-evolved to ensure that suitable light chain partners are usually available for each heavy chain that forms early in B cell development. We suggest that the co-evolved loci of the house mouse often became separated during the inbreeding of laboratory mice, resulting in new pairings of loci that are derived from different sub-species of the house mouse. A resulting vulnerability to self-reactivity could explain at least some mouse models of autoimmune disease.
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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, United States
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12
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Transcriptome analysis of immune genes in peripheral blood mononuclear cells of young foals and adult horses. PLoS One 2018; 13:e0202646. [PMID: 30183726 PMCID: PMC6124769 DOI: 10.1371/journal.pone.0202646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 08/07/2018] [Indexed: 12/14/2022] Open
Abstract
During the neonatal period, the ability to generate immune effector and memory responses to vaccines or pathogens is often questioned. This study was undertaken to obtain a global view of the natural differences in the expression of immune genes early in life. Our hypothesis was that transcriptome analyses of peripheral blood mononuclear cells (PBMCs) of foals (on day 1 and day 42 after birth) and adult horses would show differential gene expression profiles that characterize natural immune processes. Gene ontology enrichment analysis provided assessment of biological processes affected by age, and a list of 897 genes with ≥2 fold higher (p<0.01) expression in day 42 when compared to day 1 foal samples. Up-regulated genes included B cell and T cell receptor diversity genes; DNA replication enzymes; natural killer cell receptors; granzyme B and perforin; complement receptors; immunomodulatory receptors; cell adhesion molecules; and cytokines/chemokines and their receptors. The list of 1,383 genes that had higher (p<0.01) expression on day 1 when compared to day 42 foal samples was populated by genes with roles in innate immunity such as antimicrobial proteins; pathogen recognition receptors; cytokines/chemokines and their receptors; cell adhesion molecules; co-stimulatory molecules; and T cell receptor delta chain. Within the 742 genes with increased expression between day 42 foal and adult samples, B cell immunity was the main biological process (p = 2.4E-04). Novel data on markedly low (p<0.0001) TLR3 gene expression, and high (p≤0.01) expression of IL27, IL13RA1, IREM-1, SIRL-1, and SIRPα on day 1 compared to day 42 foal samples point out potential mechanisms of increased susceptibility to pathogens in early life. The results portray a progression from innate immune gene expression predominance early in life to adaptive immune gene expression increasing with age with a putative overlay of immune suppressing genes in the neonatal phase. These results provide insight to the unique attributes of the equine neonatal and young immune system, and offer many avenues of future investigation.
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13
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Du L, Wang S, Zhu Y, Zhao H, Basit A, Yu X, Li Q, Sun X. Immunoglobulin heavy chain variable region analysis in dairy goats. Immunobiology 2018; 223:599-607. [PMID: 30025710 DOI: 10.1016/j.imbio.2018.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/12/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
Based on the goat genome database, we have annotated the genomic organization of the goat immunoglobulin heavy chain variable region. The goat IgH locus is present on seven genome scaffolds, and contains ten VH, three DH and six JH segments. After the exclusion of three shorter segments, the VH genes were divided into two gene families based on sequence similarity. By analyzing the IgH cDNA sequences, we further identified that VH2 (54.2%), DH1 (61.7%) and JH1 (60.5%) segments were most frequently utilized in the expression of the immunoglobulin variable region, and that point mutations introduced by somatic hypermutation were the major mutation present in these expressed variable region. Compared with human and horses, DH-DH fusion occurred at a higher frequency in goat V(D)J recombination. These results provided variable insights into goat immunoglobulin heavy chain variable region genome loci and repertoire diversity.
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Affiliation(s)
- Lijuan Du
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanjiao Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Abdul Basit
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qingwang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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14
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Diesterbeck US. Construction of Bovine Immunoglobulin Libraries in the Single-Chain Fragment Variable (scFv) Format. Methods Mol Biol 2018; 1701:113-131. [PMID: 29116502 DOI: 10.1007/978-1-4939-7447-4_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recombinant immunoglobulins are an excellent tool for diagnosis, treatment, and passive immunization. Phage display offers a robust technique for the selection of recombinant antibodies from immunoglobulin libraries. The construction of immunoglobulin libraries for veterinary purposes was restricted by the lack of knowledge about species-specific diversities.The now available data enable the construction of highly diverse libraries in livestock like cattle. Using diverse primer sets, the immunoglobulin repertoire is amplified and ligated into a phagemid. Infection of E. coli with filamentous phages allows the display of the immunoglobulin fragments on the surface as a fusion protein to the phage's minor coat protein 3.
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Affiliation(s)
- Ulrike S Diesterbeck
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, Bethesda, MD, 20892, USA.
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15
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Tallmadge RL, Miller SC, Parry SA, Felippe MJB. Antigen-specific immunoglobulin variable region sequencing measures humoral immune response to vaccination in the equine neonate. PLoS One 2017; 12:e0177831. [PMID: 28520789 PMCID: PMC5433778 DOI: 10.1371/journal.pone.0177831] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/03/2017] [Indexed: 12/16/2022] Open
Abstract
The value of prophylactic neonatal vaccination is challenged by the interference of passively transferred maternal antibodies and immune competence at birth. Taken our previous studies on equine B cell ontogeny, we hypothesized that the equine neonate generates a diverse immunoglobulin repertoire in response to vaccination, independently of circulating maternal antibodies. In this study, equine neonates were vaccinated with 3 doses of keyhole limpet hemocyanin (KLH) or equine influenza vaccine, and humoral immune responses were assessed using antigen-specific serum antibodies and B cell Ig variable region sequencing. An increase (p<0.0001) in serum KLH-specific IgG level was measured between days 21 and days 28, 35 and 42 in vaccinated foals from non-vaccinated mares. In vaccinated foals from vaccinated mares, serum KLH-specific IgG levels tended to increase at day 42 (p = 0.07). In contrast, serum influenza-specific IgG levels rapidly decreased (p≤0.05) in vaccinated foals from vaccinated mares within the study period. Nevertheless, IGHM and IGHG sequences were detected in KLH- and influenza- sorted B cells of vaccinated foals, independently of maternal vaccination status. Immunoglobulin nucleotide germline identity, IGHV gene usage and CDR length of antigen-specific IGHG sequences in B cells of vaccinated foals revealed a diverse immunoglobulin repertoire with isotype switching that was comparable between groups and to vaccinated mares. The low expression of CD27 memory marker in antigen-specific B cells, and of cytokines in peripheral blood mononuclear cells upon in vitro immunogen stimulation indicated limited lymphocyte population expansion in response to vaccine during the study period.
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Affiliation(s)
- Rebecca L. Tallmadge
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Steven C. Miller
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Stephen A. Parry
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, New York, United States of America
| | - Maria Julia B. Felippe
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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16
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Prieto JMB, Tallmadge RL, Felippe MJB. Developmental expression of B cell molecules in equine lymphoid tissues. Vet Immunol Immunopathol 2016; 183:60-71. [PMID: 28063478 DOI: 10.1016/j.vetimm.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 01/01/2023]
Abstract
Identification and classification of B cell subpopulations has been shown to be challenging and inconsistent among different species. Our study tested aspects of ontogeny, phenotype, tissue distribution, and function of equine CD5hi B cells, which represented a greater proportion of B cells early in development and in the peritoneal cavity. CD5hi and CD5lo B cells differentially expressed B cell markers (CD2, CD21, IgM) measured using flow cytometry, but similar mRNA expression of signature genes (DGKA, FGL2, PAX5, IGHM, IL10) measured using quantitative RT-PCR. Sequencing lambda light chain segments revealed that CD5hi B cells generated diverse immunoglobulin repertoires, and more frequently bound to fluorescence-labeled phosphorylcholine. This study shows developmental characteristics and tissue distribution of a newly described subpopulation of B cells in the horse.
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Affiliation(s)
- J M B Prieto
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
| | - R L Tallmadge
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
| | - M J B Felippe
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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17
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Walther S, Tietze M, Czerny CP, König S, Diesterbeck US. Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds. PLoS One 2016; 11:e0164567. [PMID: 27828971 PMCID: PMC5102495 DOI: 10.1371/journal.pone.0164567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023] Open
Abstract
We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11–47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism.
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Affiliation(s)
- Stefanie Walther
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
| | - Manfred Tietze
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
| | - Claus-Peter Czerny
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
| | - Sven König
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
| | - Ulrike S. Diesterbeck
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
- * E-mail:
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18
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Qin T, Zhao H, Zhu H, Wang D, Du W, Hao H. Immunoglobulin genomics in the prairie vole (Microtus ochrogaster). Immunol Lett 2015; 166:79-86. [PMID: 26073565 DOI: 10.1016/j.imlet.2015.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/15/2015] [Accepted: 06/03/2015] [Indexed: 11/17/2022]
Abstract
In science, the prairie voles are ideal models for studying the regulatory mechanisms of social behavior in humans. The utility of the prairie vole as a biology model can be further enhanced by characterization of the genes encoding components of the immune system. Here, we report the genomic organization of the prairie vole immunoglobulin heavy and light chain genes. The prairie vole IgH locus on chromosome 1 spans over 1600kb, and consists of at least 79 VH segments (28 potentially functional genes, 2 ORFs and 49 pseudogenes), 7 DH segments, 4 JH segments, four constant region genes (μ, γ, ɛ, and α), and two transmembrane regions of δ gene. The Igκ locus, found on three scaffolds (JH996430, JH996605 and JH996566), contains a totle of 124 Vκ segments (47 potentially functional genes, 1 ORF and 76 pseudogenes), 5 Jκ segments and a single Cκ gene. Two different transcriptional orientations were determined for these Vκ gene segments. In contrast, the Igλ locus on scaffold JH996473 and JH996489 includes 21 Vλ gene segments (14 potentially functional genes, 1 ORF and 6 pseudogenes), all with the same transcriptional polarity as the downstream Jλ-Cλ cluster. Phylogenetic analysis and sequence alignments suggested the prairie vole's large germline VH, Vκ and Vλ gene segments appear to form limited gene families. Therefore, this species may generate antibody diversity via a gene conversion-like mechanism associated with its pseudogene reserves.
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Affiliation(s)
- Tong Qin
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China.
| | - Huijing Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Huabin Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Dong Wang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Weihua Du
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Haisheng Hao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, PR China
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19
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Battista JM, Tallmadge RL, Stokol T, Felippe MJB. Hematopoiesis in the equine fetal liver suggests immune preparedness. Immunogenetics 2014; 66:635-49. [PMID: 25179685 PMCID: PMC4198492 DOI: 10.1007/s00251-014-0799-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/19/2014] [Indexed: 01/26/2023]
Abstract
We investigated how the equine fetus prepares its pre-immune humoral repertoire for an imminent exposure to pathogens in the neonatal period, particularly how the primary hematopoietic organs are equipped to support B cell hematopoiesis and immunoglobulin (Ig) diversity. We demonstrated that the liver and the bone marrow at approximately 100 days of gestation (DG) are active sites of hematopoiesis based on the expression of signature messenger RNA (mRNA) (c-KIT, CD34, IL7R, CXCL12, IRF8, PU.1, PAX5, NOTCH1, GATA1, CEBPA) and protein markers (CD34, CD19, IgM, CD3, CD4, CD5, CD8, CD11b, CD172A) of hematopoietic development and leukocyte differentiation molecules, respectively. To verify Ig diversity achieved during the production of B cells, V(D)J segments were sequenced in primary lymphoid organs of the equine fetus and adult horse, revealing that similar heavy chain VDJ segments and CDR3 lengths were most frequently used independent of life stage. In contrast, different lambda light chain segments were predominant in equine fetal compared to adult stage, and surprisingly, the fetus had less restricted use of variable gene segments to construct the lambda chain. Fetal Igs also contained elements of sequence diversity, albeit to a smaller degree than that of the adult horse. Our data suggest that the B cells produced in the liver and bone marrow of the equine fetus generate a wide repertoire of pre-immune Igs for protection, and the more diverse use of different lambda variable gene segments in fetal life may provide the neonate an opportunity to respond to a wider range of antigens at birth.
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Affiliation(s)
- JM Battista
- Equine Immunology Lab, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA,
| | - RL Tallmadge
- Equine Immunology Lab, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA,
| | - T Stokol
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA,
| | - MJB Felippe
- Equine Immunology Lab, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
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20
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Qin T, Zhu H, Wang D, Hao H, Du W. Genomic organization and expression of immunoglobulin genes in the Chinese hamster (Cricetulus griseus). Scand J Immunol 2014; 81:11-22. [PMID: 25271137 DOI: 10.1111/sji.12243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/12/2014] [Indexed: 11/26/2022]
Abstract
In science, the hamsters are widely used as a model for studying the human diseases because they display many features like humans. The utility of the Chinese hamster as a biology model can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization and expression of the Chinese hamster immunoglobulin heavy and light chain genes. The Chinese hamster IgH locus contains 268 VH segments (132 potentially functional genes, 12 ORFs and 124 pseudogenes), 4 DH segments, 6 JH segments, four constant region genes (μ, γ, ε and α) and one reverse δ remnant fragment. The Igκ locus contains only a single Cκ gene, 4 Jκ segments and 48 Vκ segments (15 potentially functional genes and 33 pseudogenes), whereas the Igλ locus contains 4 Cλ genes, but only Cλ 3 and Cλ 4 each preceded by a Jλ gene segment. A total of 49 Vλ segments (39 potentially functional genes, 3 ORFs and 7 pseudogenes) were identified. Analysis of junctions of the recombined V(D)J transcripts reveals complex diversity in both expressed H and κ sequences, but the microhomology-directed VJ recombination obviously results in very limited diversity in the Chinese hamster λ gene despite more potential germline-encoded combinatorial diversity. This is the first study to make a comprehensive analysis of the Ig genes in the Chinese hamster, which provides insights into the Ig genes in placental mammals.
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Affiliation(s)
- T Qin
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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21
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Tallmadge RL, Tseng CT, Felippe MJB. Diversity of immunoglobulin lambda light chain gene usage over developmental stages in the horse. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 46:171-179. [PMID: 24726757 PMCID: PMC4107094 DOI: 10.1016/j.dci.2014.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/31/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
To further studies of neonatal immune responses to pathogens and vaccination, we investigated the dynamics of B lymphocyte development and immunoglobulin (Ig) gene diversity. Previously we demonstrated that equine fetal Ig VDJ sequences exhibit combinatorial and junctional diversity levels comparable to those of adult Ig VDJ sequences. Herein, RACE clones from fetal, neonatal, foal, and adult lymphoid tissue were assessed for Ig lambda light chain combinatorial, junctional, and sequence diversity. Remarkably, more lambda variable genes (IGLV) were used during fetal life than later stages and IGLV gene usage differed significantly with time, in contrast to the Ig heavy chain. Junctional diversity measured by CDR3L length was constant over time. Comparison of Ig lambda transcripts to germline revealed significant increases in nucleotide diversity over time, even during fetal life. These results suggest that the Ig lambda light chain provides an additional dimension of diversity to the equine Ig repertoire.
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Affiliation(s)
- Rebecca L Tallmadge
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
| | - Chia T Tseng
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - M Julia B Felippe
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
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22
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Tallmadge RL, Tseng CT, King RA, Felippe MJB. Developmental progression of equine immunoglobulin heavy chain variable region diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:33-43. [PMID: 23567345 PMCID: PMC3672396 DOI: 10.1016/j.dci.2013.03.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/25/2013] [Accepted: 03/28/2013] [Indexed: 06/02/2023]
Abstract
Humoral immunity is a critical component of the immune system that is established during fetal life and expands upon exposure to pathogens. The extensive humoral immune response repertoire is generated in large part via immunoglobulin (Ig) heavy chain variable region diversity. The horse is a useful model to study the development of humoral diversity because the placenta does not transfer maternal antibodies; therefore, Igs detected in the fetus and pre-suckle neonate were generated in utero. The goal of this study was to compare the equine fetal Ig VDJ repertoire to that of neonatal, foal, and adult horse stages of life. We found similar profiles of IGHV, IGHD, and IGHJ gene usage throughout life, including predominant usage of IGHV2S3, IGHD18S1, and IGHJ1S5. CDR3H lengths were also comparable throughout life. Unexpectedly, Ig sequence diversity significantly increased between the fetal and neonatal age, and, as expected, between the foal and adult age.
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Affiliation(s)
- Rebecca L Tallmadge
- Equine Immunology Laboratory, Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
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23
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Keggan A, Freer H, Rollins A, Wagner B. Production of seven monoclonal equine immunoglobulins isotyped by multiplex analysis. Vet Immunol Immunopathol 2013; 153:187-93. [PMID: 23541920 PMCID: PMC10958203 DOI: 10.1016/j.vetimm.2013.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 11/25/2022]
Abstract
Horses have 11 immunoglobulin isotypes: IgM, IgD, IgA, IgE, and seven IgG subclasses designated as IgG1-IgG7, each of which are distinguished by separate genes encoding the constant heavy chain regions. Immunoglobulin (Ig) isotypes have different functions during the immune response and pathogen-specific isotypes can be used as indicators for immunity and protection from disease. In addition to existing monoclonal antibodies to various equine Igs, quantification of the individual isotypes requires pure isotype standards. In this report, we describe a fusion between X63-Ag8.653 mouse myeloma cells and horse PBMC to create equine-murine heterohybridomas. Initial screening for Ig production was performed by ELISA. Further testing was performed by a new 5-plex fluorescent bead-based assay able to simultaneously detect equine IgM, IgG1, IgG4/7, IgG5, and IgG6. Production of IgG3 and IgE was tested by separate bead assays. Seven stable heterohybridoma clones producing monoclonal equine IgM, IgG1, IgG3, IgG4/7, IgG5, IgG6 and IgE were created. Purified Ig isotypes were then tested by SDS-PAGE. The pure, monoclonal equine Ig isotypes and the new equine Ig multiplex testing developed here are valuable tools to quantify antibody responses and to accurately determine individual isotypes concentrations in horses.
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Affiliation(s)
- Alison Keggan
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Heather Freer
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Alicia Rollins
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Bettina Wagner
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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24
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Walther S, Czerny CP, Diesterbeck US. Exceptionally long CDR3H are not isotype restricted in bovine immunoglobulins. PLoS One 2013; 8:e64234. [PMID: 23717573 PMCID: PMC3661452 DOI: 10.1371/journal.pone.0064234] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/13/2013] [Indexed: 11/30/2022] Open
Abstract
Exceptionally long third complementarity determining regions of the heavy chain (CDR3H) were previously described as a specificity of bovine IgG and IgM immunoglobulins. In addition, the genomic organization of the immunoglobulin heavy chain locus remains to be elucidated with a special focus on the number of variable segments (IGHV). By analyzing the variable regions according to the isotype-specific PCR using cDNA-PCR, we were able to prove the existence of exceptional long CDR3H in all bovine isotypes. The corresponding sequences of three distinct amplicons were grouped according to the length of the CDR3H. Sequences of CDR3H possessed 5 to 10, 12 to 31 or at least 48 amino acid residues. Long and mid-length CDR3H were composed of mainly hydrophilic amino acid residues, while short CDR3H also contained hydrophobic amino acid residues. All sequences with long CDR3H were related to the germline variable segment 10. Using the current genome assembly, Bos taurus NCBI build 6.1, the genomic organization of the bovine immunoglobulin heavy-chain locus was analyzed. A main locus was investigated on BTA21. Exons coding for variable, diversity, and joining segments, as well as for the constant regions of different isotypes, were also localized on BTA7, BTA8, and BTA20. Together with the information from unplaced contigs, 36 IGHV were detected of which 13 are putatively functional. Phylogenetic analysis revealed two bovine IGHV families (boVH1, boVH2). Thus, the existence of the two bovine families suggested was demonstrated, where boVH1 comprises all functional segments. This study substantially improves the understanding of the generation of immunoglobulin diversity in cattle.
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Affiliation(s)
- Stefanie Walther
- Division of Microbiology and Animal Hygiene, Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, Georg-August University Göttingen, Göttingen, Germany
| | - Claus-Peter Czerny
- Division of Microbiology and Animal Hygiene, Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, Georg-August University Göttingen, Göttingen, Germany
| | - Ulrike S. Diesterbeck
- Division of Microbiology and Animal Hygiene, Department of Animal Sciences, Faculty of Agricultural Sciences, Institute of Veterinary Medicine, Georg-August University Göttingen, Göttingen, Germany
- * E-mail:
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Sun Y, Wei Z, Li N, Zhao Y. A comparative overview of immunoglobulin genes and the generation of their diversity in tetrapods. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:103-109. [PMID: 22366185 DOI: 10.1016/j.dci.2012.02.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/17/2012] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
In the past several decades, immunoglobulin (Ig) genes have been extensively characterized in many tetrapod species. This review focuses on the expressed Ig isotypes and the diversity of Ig genes in mammals, birds, reptiles, and amphibians. With regard to heavy chains, five Ig isotypes - IgM, IgD, IgG, IgA, and IgE - have been reported in mammals. Among these isotypes, IgM, IgD, and IgA (or its analog, IgX) are also found in non-mammalian tetrapods. Birds, reptiles, and amphibians express IgY, which is considered the precursor of IgG and IgE. Some species have developed unique isotypes of Ig, such as IgO in the platypus, IgF in Xenopus, and IgY (ΔFc) in ducks and turtles. The κ and λ light chains are both utilized in tetrapods, but the usage frequencies of κ and λ chains differ greatly among species. The diversity of Ig genes depends on several factors, including the germline repertoire and recombinatorial and post-recombinatorial diversity, and different species have evolved distinct mechanisms to generate antibody diversity.
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Affiliation(s)
- Yi Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, PR China.
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Wang T, Sun Y, Shao W, Cheng G, Li L, Cao Z, Yang Z, Zou H, Zhang W, Han B, Hu Y, Ren L, Hu X, Guo Y, Fei J, Hammarström L, Li N, Zhao Y. Evidence of IgY subclass diversification in snakes: evolutionary implications. THE JOURNAL OF IMMUNOLOGY 2012; 189:3557-65. [PMID: 22933626 DOI: 10.4049/jimmunol.1200212] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mammalian IgG and IgE are thought to have evolved from IgY of nonmammalian tetrapods; however, no diversification of IgY subclasses has been reported in reptiles or birds, which are phylogenetically close to mammals. To our knowledge, we report the first evidence of the presence of multiple IgY-encoding (υ) genes in snakes. Two υ genes were identified in the snake Elaphe taeniura, and three υ genes were identified in the Burmese python (Python molurus bivittatus). Although four of the υ genes displayed a conventional four-H chain C region exon structure, one of the υ genes in the Burmese python lacked the H chain C region 2 exon, thus exhibiting a structure similar to that of the mammalian γ genes. We developed mouse mAbs specific for the IgY1 and IgY2 of E. taeniura and showed that both were expressed in serum; each had two isoforms: one full-length and one truncated at the C terminus. The truncation was not caused by alternative splicing or transcriptional termination. We also identified the μ and δ genes, but no α gene, in both snakes. This study provides valuable clues for our understanding of Ig gene evolution in tetrapods.
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Affiliation(s)
- Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100094, People's Republic of China
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Niku M, Liljavirta J, Durkin K, Schroderus E, Iivanainen A. The bovine genomic DNA sequence data reveal three IGHV subgroups, only one of which is functionally expressed. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 37:457-61. [PMID: 22369780 DOI: 10.1016/j.dci.2012.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 05/05/2023]
Abstract
A comprehensive analysis of cattle shotgun sequencing data reveals 36 immunoglobulin heavy chain variable genes. The previously described bovine subgroup IGHV1 contains 10 functional genes with a conserved promoter including the consensus octamer and several other transcription factor binding sites, intact exons and matching cDNA sequences. Subgroups IGHV2 and IGHV3 consist entirely of pseudogenes. Thus, the bovine germline IGHV repertoire is very limited. The IGHV genes are distributed in mammalian clans I and II, while no clan III genes were detected. Clan-specific PCR of genomic DNA from cattle, sheep, Eurasian elk, white-tailed deer, pig and dolphin indicates highly dynamic evolution of IGHV gene usage within Cetartiodactyla. The bovine germline IGHV repertoire was probably generated by recent duplications of an IGHV1-IGHV2 homology unit. Immunoglobulin heavy chain genes are largely incorrectly assembled in the current cattle genome versions Btau_4.2 and UMD_3.1. FISH experiments confirm an IGHV locus close to terminus of BTA21.
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Affiliation(s)
- Mikael Niku
- Department of Veterinary Biosciences, University of Helsinki, PO Box 66, FI-00014 University of Helsinki, Finland
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Guo Y, Bao Y, Meng Q, Hu X, Meng Q, Ren L, Li N, Zhao Y. Immunoglobulin genomics in the guinea pig (Cavia porcellus). PLoS One 2012; 7:e39298. [PMID: 22761756 PMCID: PMC3382241 DOI: 10.1371/journal.pone.0039298] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/17/2012] [Indexed: 01/06/2023] Open
Abstract
In science, the guinea pig is known as one of the gold standards for modeling human disease. It is especially important as a molecular and cellular biology model for studying the human immune system, as its immunological genes are more similar to human genes than are those of mice. The utility of the guinea pig as a model organism can be further enhanced by further characterization of the genes encoding components of the immune system. Here, we report the genomic organization of the guinea pig immunoglobulin (Ig) heavy and light chain genes. The guinea pig IgH locus is located in genomic scaffolds 54 and 75, and spans approximately 6,480 kb. 507 V(H) segments (94 potentially functional genes and 413 pseudogenes), 41 D(H) segments, six J(H) segments, four constant region genes (μ, γ, ε, and α), and one reverse δ remnant fragment were identified within the two scaffolds. Many V(H) pseudogenes were found within the guinea pig, and likely constituted a potential donor pool for gene conversion during evolution. The Igκ locus mapped to a 4,029 kb region of scaffold 37 and 24 is composed of 349 V(κ) (111 potentially functional genes and 238 pseudogenes), three J(κ) and one C(κ) genes. The Igλ locus spans 1,642 kb in scaffold 4 and consists of 142 V(λ) (58 potentially functional genes and 84 pseudogenes) and 11 J(λ) -C(λ) clusters. Phylogenetic analysis suggested the guinea pig's large germline V(H) gene segments appear to form limited gene families. Therefore, this species may generate antibody diversity via a gene conversion-like mechanism associated with its pseudogene reserves.
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Affiliation(s)
- Yongchen Guo
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yonghua Bao
- Department of Basic Immunology, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Qingwen Meng
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Qingyong Meng
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Liming Ren
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, People's Republic of China
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Sun Y, Liu Z, Ren L, Wei Z, Wang P, Li N, Zhao Y. Immunoglobulin genes and diversity: what we have learned from domestic animals. J Anim Sci Biotechnol 2012; 3:18. [PMID: 22958617 PMCID: PMC3487963 DOI: 10.1186/2049-1891-3-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/11/2012] [Indexed: 01/06/2023] Open
Abstract
This review focuses on the diversity of immunoglobulin (Ig) genes and Ig isotypes that are expressed in domestic animals. Four livestock species—cattle, sheep, pigs, and horses—express a full range of Ig heavy chains (IgHs), including μ, δ, γ, ϵ, and α. Two poultry species (chickens and ducks) express three IgH isotypes, μ, υ, and α, but not δ. The κ and λ light chains are both utilized in the four livestock species, but only the λ chain is expressed in poultry. V(D)J recombination, somatic hypermutation (SHM), and gene conversion (GC) are three distinct mechanisms by which immunoglobulin variable region diversity is generated. Different domestic animals may use distinct means to diversify rearranged variable regions of Ig genes.
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Affiliation(s)
- Yi Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences; National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, P, R, China.
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Diesterbeck US, Aboelhassan DM, Stein SK, Czerny CP. Detection of new allotypic variants of bovine λ-light chain constant regions in different cattle breeds. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 36:130-139. [PMID: 21741991 DOI: 10.1016/j.dci.2011.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 06/23/2011] [Indexed: 05/31/2023]
Abstract
In the cattle breeds German Black Pied (GBP), German Simmental (GS), Holstein Friesian (HF), Aubrac (A) three transcribed allotypic variants in isotype IGLC2 and five allotypic variants in isotype IGLC3 were identified. Substitutions within the putative interface to CH1 at position 11 and 79 were noted. In IGLC2(b), K79E led to a charge conversion. In IGLC3(b) and IGLC3(c), the E79N replacement removed the charge while the T11K substitution resulted in a positively charged amino acid residue. In addition, D15 and T16 were found in IGLC2(c), IGLC3(b), and IGLC3(c). Substitutions located on the outer site of the molecule were observed in IGLC2(b) (V40, H45.5), IGLC2(c) (A1, V40, D77), IGLC3(b) (A1, D77, D109, P127), IGLC3(c) (A1, G45.5, D77, D109, P127), IGLC3(d) (D109), and IGLC3(e) (A1). Amino acid residues P83 (IGLC2(c), IGLC3(b), IGLC3(c)), N93 (IGLC2(b)), D93 (IGLC3(b)), and G93 (IGLC3(c)) were positioned in cavities but seemed to be accessible for solvents.
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Affiliation(s)
- Ulrike S Diesterbeck
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Burckhardtweg 2, 37077 Goettingen, Germany.
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Transcriptional analysis of equine λ-light chains in the horse breeds Rhenish-German Coldblood and Hanoverian Warmblood. Vet Immunol Immunopathol 2012; 145:50-65. [DOI: 10.1016/j.vetimm.2011.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/14/2011] [Accepted: 10/17/2011] [Indexed: 11/23/2022]
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Sun Y, Wei Z, Hammarstrom L, Zhao Y. The immunoglobulin δ gene in jawed vertebrates: a comparative overview. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:975-81. [PMID: 21182859 DOI: 10.1016/j.dci.2010.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/11/2010] [Accepted: 12/14/2010] [Indexed: 05/13/2023]
Abstract
Immunoglobulin D (IgD) was recently suggested to be an ancient Ig class, as old as IgM, arising approximately 500 million years ago. Its encoding gene has now been identified in nearly all classes of jawed vertebrates (except birds). Variance in the number of CH encoding exons and alternative RNA splicing confers this Ig class a marked structural plasticity, which differs substantially from IgM. Expression of the δ gene can be achieved through co-transcription with the μ gene or by class switching. Although a recent study has suggested that IgD functions as an immunomodulator in immunity and inflammation in humans, its functions are still far from clear. Further studies at the protein levels in additional species may help answer this question.
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Affiliation(s)
- Yi Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, PR China
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Guo Y, Bao Y, Wang H, Hu X, Zhao Z, Li N, Zhao Y. A preliminary analysis of the immunoglobulin genes in the African elephant (Loxodonta africana). PLoS One 2011; 6:e16889. [PMID: 21364892 PMCID: PMC3045440 DOI: 10.1371/journal.pone.0016889] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 01/06/2011] [Indexed: 11/18/2022] Open
Abstract
The genomic organization of the IgH (Immunoglobulin heavy chain), Igκ (Immunoglobulin kappa chain), and Igλ (Immunoglobulin lambda chain) loci in the African elephant (Loxodonta africana) was annotated using available genome data. The elephant IgH locus on scaffold 57 spans over 2,974 kb, and consists of at least 112 V(H) gene segments, 87 D(H) gene segments (the largest number in mammals examined so far), six J(H) gene segments, a single μ, a δ remnant, and eight γ genes (α and ε genes are missing, most likely due to sequence gaps). The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene. Two different transcriptional orientations were determined for these V(κ) gene segments. In contrast, the Igλ locus on scaffold 68 includes 15 V(λ) gene segments, all with the same transcriptional polarity as the downstream J(λ)-C(λ) cluster. These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex. Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.
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Affiliation(s)
- Yongchen Guo
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yonghua Bao
- Department of Basic Immunology, Xinxiang Medical University, Xinxiang, People's Republic of China
- * E-mail: (YZ); (YB)
| | - Hui Wang
- Department of Basic Immunology, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Zhihui Zhao
- Agricultural Division, College of Animal Science and Veterinary Medicine, Jilin University, Changchun, People's Republic of China
| | - Ning Li
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, People's Republic of China
- * E-mail: (YZ); (YB)
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