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Wei L, Wang M, Xiang H, Jiang Y, Gong J, Su D, Al Azad MAR, Dong H, Feng L, Wu J, Chan LL, Yang N, Shi J. Bamboo Shark as a Small Animal Model for Single Domain Antibody Production. Front Bioeng Biotechnol 2021; 9:792111. [PMID: 34957081 PMCID: PMC8692893 DOI: 10.3389/fbioe.2021.792111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
The development of shark single domain antibodies (sdAbs) is hindered by the high cost and tediousness of large-sized shark farming. Here, we demonstrated white-spotted bamboo sharks (Chiloscyllium plagiosum) being cultivated commercially as a promising small animal model to produce sdAbs. We found that immunoglobulin new antigen receptor (IgNAR) presented in bamboo shark genome, transcriptome, and plasma. Four complete IgNAR clusters including variable domains (vNARs) were discovered in the germline, and the Variable–Joining pair from IgNAR1 cluster was dominant from immune repertoires in blood. Bamboo sharks developed effective immune responses upon green fluorescent protein (GFP), near-infrared fluorescent protein iRFP713, and Freund’s adjuvant immunization revealed by elevated lymphocyte counts and antigen specific IgNAR. Before and after immunization, the complementarity determining region 3 (CDR3) of IgNAR were the major determinant of IgNAR diversity revealed by 400-bp deep sequencing. To prove that bamboo sharks could produce high-affinity IgNAR, we isolated anti-GFP and anti-iRFP713 vNARs with up to 0.3 and 3.8 nM affinities, respectively, from immunized sharks. Moreover, we constructed biparatopic vNARs with the highest known affinities (20.7 pM) to GFP and validated the functions of anti-GFP vNARs as intrabodies in mammalian cells. Taken together, our study will accelerate the discovery and development of bamboo shark sdAbs for biomedical industry at low cost and easy operation.
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Affiliation(s)
- Likun Wei
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Meiniang Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Jiang
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jinhua Gong
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Dan Su
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - M A R Al Azad
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Hongming Dong
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limin Feng
- Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Complete Genomics Inc., San Jose, CA, United States
| | - Jiahai Shi
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China.,Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Lange MD, Huang L, Yu Y, Li S, Liao H, Zemlin M, Su K, Zhang Z. Accumulation of VH Replacement Products in IgH Genes Derived from Autoimmune Diseases and Anti-Viral Responses in Human. Front Immunol 2014; 5:345. [PMID: 25101087 PMCID: PMC4105631 DOI: 10.3389/fimmu.2014.00345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/06/2014] [Indexed: 11/24/2022] Open
Abstract
VH replacement refers to RAG-mediated secondary recombination of the IgH genes, which renews almost the entire VH gene coding region but retains a short stretch of nucleotides as a VH replacement footprint at the newly generated VH–DH junction. To explore the biological significance of VH replacement to the antibody repertoire, we developed a Java-based VH replacement footprint analyzer program and analyzed the distribution of VH replacement products in 61,851 human IgH gene sequences downloaded from the NCBI database. The initial assignment of the VH, DH, and JH gene segments provided a comprehensive view of the human IgH repertoire. To our interest, the overall frequency of VH replacement products is 12.1%; the frequencies of VH replacement products in IgH genes using different VH germline genes vary significantly. Importantly, the frequencies of VH replacement products are significantly elevated in IgH genes derived from different autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and allergic rhinitis, and in IgH genes encoding various autoantibodies or anti-viral antibodies. The identified VH replacement footprints preferentially encoded charged amino acids to elongate IgH CDR3 regions, which may contribute to their autoreactivities or anti-viral functions. Analyses of the mutation status of the identified VH replacement products suggested that they had been actively involved in immune responses. These results provide a global view of the distribution of VH replacement products in human IgH genes, especially in IgH genes derived from autoimmune diseases and anti-viral immune responses.
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Affiliation(s)
- Miles D Lange
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Lin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Song Li
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Hongyan Liao
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg , Marburg , Germany
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA ; The Eppley Cancer Institute, University of Nebraska Medical Center , Omaha, NE , USA ; Department of Internal Medicine, University of Nebraska Medical Center , Omaha, NE , USA
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center , Omaha, NE , USA ; The Eppley Cancer Institute, University of Nebraska Medical Center , Omaha, NE , USA
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Huang L, Lange MD, Yu Y, Li S, Su K, Zhang Z. Contribution of V(H) replacement products in mouse antibody repertoire. PLoS One 2013; 8:e57877. [PMID: 23469094 PMCID: PMC3585286 DOI: 10.1371/journal.pone.0057877] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
VH replacement occurs through RAG-mediated recombination between the cryptic recombination signal sequence (cRSS) near the 3′ end of a rearranged VH gene and the 23-bp RSS from an upstream unrearranged VH gene. Due to the location of the cRSS, VH replacement leaves a short stretch of nucleotides from the previously rearranged VH gene at the newly formed V-D junction, which can be used as a marker to identify VH replacement products. To determine the contribution of VH replacement products to mouse antibody repertoire, we developed a Java-based VH Replacement Footprint Analyzer (VHRFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify VH replacement products. The overall frequency of VH replacement products in these IgH genes is 5.29% based on the identification of pentameric VH replacement footprints at their V-D junctions. The identified VH replacement products are distributed similarly in IgH genes using most families of VH genes, although different families of VH genes are used differentially. The frequencies of VH replacement products are significantly elevated in IgH genes derived from several strains of autoimmune prone mice and in IgH genes encoding autoantibodies. Moreover, the identified VH replacement footprints in IgH genes from autoimmune prone mice or IgH genes encoding autoantibodies preferentially encode positively charged amino acids. These results revealed a significant contribution of VH replacement products to the diversification of antibody repertoire and potentially, to the generation of autoantibodies in mice.
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Affiliation(s)
- Lin Huang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Miles D. Lange
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yangsheng Yu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Song Li
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Zhixin Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- The Eppley Cancer Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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