1
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Altman PX, Ozorowski G, Stanfield RL, Haakenson J, Appel M, Parren M, Lee WH, Sang H, Woehl J, Saye-Francisco K, Sewall LM, Joyce C, Song G, Porter K, Landais E, Andrabi R, Wilson IA, Ward AB, Mwangi W, Smider VV, Burton DR, Sok D. Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire. PLoS Pathog 2024; 20:e1012042. [PMID: 39250525 PMCID: PMC11412654 DOI: 10.1371/journal.ppat.1012042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 09/19/2024] [Accepted: 08/12/2024] [Indexed: 09/11/2024] Open
Abstract
The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.
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Affiliation(s)
- Pilar X Altman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jeremy Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Applied Biomedical Science Institute, San Diego, California, United States of America
| | - Michael Appel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Huldah Sang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, United States of America
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Karen Saye-Francisco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ian A Wilson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, United States of America
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Applied Biomedical Science Institute, San Diego, California, United States of America
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Global Health Investment Corporation, New York, New York, United States of America
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2
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Altvater-Hughes TE, Hodgins HP, Hodgins DC, Gallo NB, Chalmers GI, Ricker ND, Mallard BA. Estimates of Sequences with Ultralong and Short CDR3s in the Bovine IgM B Cell Receptor Repertoire Using the Long-read Oxford Nanopore MinION Platform. Immunohorizons 2024; 8:635-651. [PMID: 39248806 PMCID: PMC11447701 DOI: 10.4049/immunohorizons.2400050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024] Open
Abstract
Cattle produce Abs with an H chain ultralong CDR3 (40-70 aa). These Abs have been shown to have features such as broad neutralization of viruses and are investigated as human therapeutics. A common issue in sequencing the bovine BCR repertoire is the sequence length required to capture variable (V) and isotype gene information. This study aimed to assess the use of Oxford Nanopore Technologies' MinION platform to perform IgM BCR repertoire sequencing to assess variation in the percentage of ultralong CDR3s among dairy cattle. Blood was collected from nine Holstein heifers. B cells were isolated using magnetic bead-based separation, RNA was extracted, and IgM+ transcripts were amplified using PCR and sequenced using a MinION R10.4 flow cell. The distribution of CDR3 lengths was trimodal, and the percentage of ultralong CDR3s ranged among animals from 2.32 to 20.13% in DNA sequences and 1.56% to 17.02% in productive protein sequences. V segment usage varied significantly among heifers. Segment IGHV1-7, associated with ultralong CDR3s, was used in 5.8-24.2% of sequences; usage was positively correlated with ultralong CDR3 production (r = 0.99, p < 0.01). To our knowledge, this is the first study to sequence the bovine BCR repertoire using Oxford Nanopore Technologies and demonstrates the potential for cost-efficient long-read repertoire sequencing in cattle without assembly. Findings from this study support literature describing the distribution of length and percentage of ultralong CDR3s. Future studies will investigate changes in the bovine BCR repertoire associated with age, antigenic exposure, and genetics.
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Affiliation(s)
- Tess E Altvater-Hughes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Harold P Hodgins
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Douglas C Hodgins
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Natasha B Gallo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Gabhan I Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nicole D Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Bonnie A Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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3
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Trommer J, Lesniowski F, Buchner J, Svilenov HL. Specific features of a scaffolding antibody light chain. Protein Sci 2024; 33:e4990. [PMID: 38607241 PMCID: PMC11010950 DOI: 10.1002/pro.4990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
The antigen-binding sites in conventional antibodies are formed by hypervariable complementarity-determining regions (CDRs) from both heavy chains (HCs) and light chains (LCs). A deviation from this paradigm is found in a subset of bovine antibodies that bind antigens via an ultra-long CDR. The HCs bearing ultra-long CDRs pair with a restricted set of highly conserved LCs that convey stability to the antibody. Despite the importance of these LCs, their specific features remained unknown. Here, we show that the conserved bovine LC found in antibodies with ultra-long CDRs exhibits a distinct combination of favorable physicochemical properties such as good secretion from mammalian cells, strong dimerization, high stability, and resistance to aggregation. These physicochemical traits of the LCs arise from a combination of the specific sequences in the germline CDRs and a lambda LC framework. In addition to understanding the molecular architecture of antibodies with ultra-long CDRs, our findings reveal fundamental insights into LC characteristics that can guide the design of antibodies with improved properties.
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Affiliation(s)
- Johanna Trommer
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Florian Lesniowski
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Johannes Buchner
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
| | - Hristo L. Svilenov
- Center of Functional Protein Assemblies (CPA) and School of Natural Sciences, Department of BiosciencesTechnical University of MunichGarchingGermany
- Present address:
Faculty of Pharmaceutical SciencesGhent UniversityOttergemsesteenweg 460Ghent9000Belgium
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4
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Altman PX, Ozorowski G, Stanfield RL, Haakenson J, Appel M, Parren M, Lee WH, Sang H, Woehl J, Saye-Francisco K, Joyce C, Song G, Porter K, Landais E, Andrabi R, Wilson IA, Ward AB, Mwangi W, Smider VV, Burton DR, Sok D. Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580058. [PMID: 38405899 PMCID: PMC10888833 DOI: 10.1101/2024.02.13.580058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The generation of broadly neutralizing antibodies (bnAbs) to specific HIV epitopes of the HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The current animal models we use have been unable to reliable produce a broadly neutralizing antibody response, with the exception of cows. Cows have rapidly and reliably produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models other engineered immunogens previously have been able to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n=4) with two regiments of V2-apex focusing immunogens to investigate whether antibody responses could be directed to the V2-apex on Env. Group 1 were immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 were immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows respectively. The best bnAbs had both medium breadth and potency. Potent and broad responses developed later than previous CD4bs cow bnAbs and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target multiple broadly neutralizing epitopes on the HIV surface reveals important insight into the generation of immunogens and testing in the cow animal model. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.
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Affiliation(s)
- Pilar X. Altman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeremy Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Michael Appel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative, New York, NY, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Huldah Sang
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, USA
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative, New York, NY, USA
| | - Karen Saye-Francisco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Katelyn Porter
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elise Landais
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative, New York, NY, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A. Wilson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B. Ward
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medical, Kansas State University, Manhattan, Kansas, USA
| | - Vaughn V. Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Applied Biomedical Science Institute, San Diego, CA, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative, New York, NY, USA
- Lead contact
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Ott JA, Mitchell C, Sheppard M, Deiss TC, Horton JMC, Haakenson JK, Huang R, Kelley AR, Davis BW, Derr JN, Smider VV, Criscitiello MF. Evolution of immunogenetic components encoding ultralong CDR H3. Immunogenetics 2023; 75:323-339. [PMID: 37084012 PMCID: PMC10119515 DOI: 10.1007/s00251-023-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023]
Abstract
The genomes of most vertebrates contain many V, D, and J gene segments within their Ig loci to construct highly variable CDR3 sequences through combinatorial diversity. This nucleotide variability translates into an antibody population containing extensive paratope diversity. Cattle have relatively few functional VDJ gene segments, requiring innovative approaches for generating diversity like the use of ultralong-encoding IGHV and IGHD gene segments that yield dramatically elongated CDR H3. Unique knob and stalk microdomains create protracted paratopes, where the antigen-binding knob sits atop a long stalk, allowing the antibody to bind both surface and recessed antigen epitopes. We examined genomes of twelve species of Bovidae to determine when ultralong-encoding IGHV and IGHD gene segments evolved. We located the 8-bp duplication encoding the unique TTVHQ motif in ultralong IGHV segments in six Bovid species (cattle, zebu, wild yak, domestic yak, American bison, and domestic gayal), but we did not find evidence of the duplication in species beyond the Bos and Bison genera. Additionally, we analyzed mRNA from bison spleen and identified a rich repertoire of expressed ultralong CDR H3 antibody mRNA, suggesting that bison use ultralong IGHV transcripts in their host defense. We found ultralong-encoding IGHD gene segments in all the same species except domestic yak, but again not beyond the Bos and Bison clade. Thus, the duplication event leading to this ultralong-encoding IGHV gene segment and the emergence of the ultralong-encoding IGHD gene segment appears to have evolved in a common ancestor of the Bos and Bison genera 5-10 million years ago.
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Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Christian Mitchell
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Morgan Sheppard
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Thad C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - J M Cody Horton
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | | | - Brian W Davis
- Department of Veterinary Integrative Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - James N Derr
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA, 92127, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, 77807, USA.
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6
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Jenkins GW, Safonova Y, Smider VV. Germline-Encoded Positional Cysteine Polymorphisms Enhance Diversity in Antibody Ultralong CDR H3 Regions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2141-2148. [PMID: 36426974 PMCID: PMC9940733 DOI: 10.4049/jimmunol.2200455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/25/2022] [Indexed: 01/04/2023]
Abstract
Ab "ultralong" third H chain complementarity-determining regions (CDR H3) appear unique to bovine Abs and may enable binding to difficult epitopes that shorter CDR H3 regions cannot easily access. Diversity is concentrated in the "knob" domain of the CDR H3, which is encoded by the DH gene segment and sits atop a β-ribbon "stalk" that protrudes far from the Ab surface. Knob region cysteine content is quite diverse in terms of total number of cysteines, sequence position, and disulfide bond pattern formation. We investigated the role of germline cysteines in production of a diverse CDR H3 structural repertoire. The relationship between DH polymorphisms and deletions relative to germline at the nucleotide level, as well as diversity in cysteine and disulfide bond content at the structural level, was ascertained. Structural diversity is formed through (1) DH polymorphisms with altered cysteine positions, (2) DH deletions, and (3) new cysteines that arise through somatic hypermutation that form new, unique disulfide bonds to alter the knob structure. Thus, a combination of mechanisms at both the germline and somatic immunogenetic levels results in diversity in knob region cysteine content, contributing to remarkable complexity in knob region disulfide patterns, loops, and Ag binding surface.
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Affiliation(s)
| | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, La Jolla, CA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD; and
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA
- Department of Molecular Medicine, Scripps Research, La Jolla, CA
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7
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Cordero-Solorzano J, de Koning DJ, Tråvén M, de Haan T, Jouffroy M, Larsson A, Myrthe A, Arts JAJ, Parmentier HK, Bovenhuis H, Wensman JJ. Genetic parameters of colostrum and calf serum antibodies in Swedish dairy cattle. Genet Sel Evol 2022; 54:68. [PMID: 36273117 PMCID: PMC9588213 DOI: 10.1186/s12711-022-00758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Background A sufficient IgG content in the colostrum is essential for the newborn calf, as it provides passive immunity which substantially affects the probability of survival during rearing. Failure of passive transfer (FPT) occurs when a calf does not absorb enough antibodies from the colostrum and is defined by an IgG concentration in calf serum lower than 10 g/L. Apart from delayed access to colostrum, FPT can be due to a low production of IgG in the mother or poor IgG absorption by the calf. The aim of this study was to estimate the genetic background of antibody levels and indicator traits for antibodies in the colostrum and calf serum, and their correlation with milk production. Results Colostrum data were available for 1340 dairy cows with at least one calving and calf serum data were available for 886 calves from these cows. Indicator traits for antibody concentrations were estimated using refractometry (a digital Brix refractometer for colostrum and an optical refractometer for serum), and enzyme-linked immunosorbent assays (ELISA) were used to determine the levels of total IgG and natural antibodies (NAb) of various antibody isotypes in the colostrum and calf serum. Colostrum traits had heritabilities ranging from 0.16 to 0.31 with repeatabilities ranging from 0.21 to 0.55. Brix percentages had positive genetic correlations with all colostrum antibody traits including total IgG (0.68). Calf serum antibody concentrations had heritabilities ranging from 0.25 to 0.59, with a significant maternal effect accounting for 17 to 27% of the variance. When later in life calves produced their first lactation, the lactation average somatic cell score was found to be negatively correlated with NAb levels in calf serum. Conclusions Our results suggest that antibody levels in the colostrum and calf serum can be increased by means of selection.
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Affiliation(s)
- Juan Cordero-Solorzano
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.,Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Animal Health Service of Costa Rica (SENASA), P.O. Box 3-3006, 40104, Heredia, Costa Rica
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Madeleine Tråvén
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden
| | - Therese de Haan
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden
| | - Mathilde Jouffroy
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden.,AgroSup Dijon - National Superior Institute of Agronomic Sciences Food and the Environment, 26 Boulevard Dr Petitjean, 21079, Dijon, France
| | - Andrea Larsson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden
| | - Aline Myrthe
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden.,Superior School of Agricultures (ESA), 55 Rue Rabelais, 49007, Angers, France
| | - Joop A J Arts
- Adaptation Physiology Group, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Henk K Parmentier
- Adaptation Physiology Group, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Henk Bovenhuis
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Jonas Johansson Wensman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, P.O. Box 7054, 750 07, Uppsala, Sweden. .,Department of Disease Control and Epidemiology, National Veterinary Institute, 751 89, Uppsala, Sweden.
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8
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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: 2] [Impact Index Per Article: 1.0] [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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9
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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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10
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Access to ultra-long IgG CDRH3 bovine antibody sequences using short read sequencing technology. Mol Immunol 2021; 139:97-105. [PMID: 34464839 PMCID: PMC8508064 DOI: 10.1016/j.molimm.2021.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022]
Abstract
The advances in high-throughput DNA sequencing and recombinant antibody technologies has presented new methods for characterizing antibody repertoires and significantly increased our understanding on the functional role of antibodies in immunity and their use in diagnostics, vaccine antigen design and as biological therapeutics. A subset of Bos taurus antibodies possesses unique ultra-long third complementary-determining region of the heavy chain (CDRH3) and are of special interest because they are thought to have unique functional abilities of broadly neutralizing properties - a functional role that has not been fully explored in vaccine development. Next generation sequencing technologies that are widely used to profile immunoglobulin (Ig) repertoires are based on short-read methods such as the Illumina technology. Although this technology has worked well in sequencing Ig V-D-J regions of most jawed vertebrates, it has faced serious technical challenges with sequencing regions in bovine Ig bearing ultra-long CDRH3 sequences, which are longer than 120 bp. To overcome this limitation, we have developed a sequencing strategy based on nested PCR products that allows sequence assembly of full-length bovine Ig heavy-chain (IgH) V-D-J regions. We have used this strategy to sequence IgH V-D-J regions of two Bos indicus breeds, Ankole and Boran. We confirm the presence of ultra-long CDRH3 sequences in IgG transcripts in both African cattle breeds, and provide preliminary evidence for differences and preferences in germline VH, DH and JH allele gene usage as well as differences in the length of the VH region in the two bovine breeds. Our method provides tools that should allow more robust analyses of ultra-long CDRH3 sequences aiding antibody and epitope discovery in different cattle breeds and their role in mediating immunity.
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11
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Maina TW, Grego EA, Boggiatto PM, Sacco RE, Narasimhan B, McGill JL. Applications of Nanovaccines for Disease Prevention in Cattle. Front Bioeng Biotechnol 2020; 8:608050. [PMID: 33363134 PMCID: PMC7759628 DOI: 10.3389/fbioe.2020.608050] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Vaccines are one of the most important tools available to prevent and reduce the incidence of infectious diseases in cattle. Despite their availability and widespread use to combat many important pathogens impacting cattle, several of these products demonstrate variable efficacy and safety in the field, require multiple doses, or are unstable under field conditions. Recently, nanoparticle-based vaccine platforms (nanovaccines) have emerged as promising alternatives to more traditional vaccine platforms. In particular, polymer-based nanovaccines provide sustained release of antigen payloads, stabilize such payloads, and induce enhanced antibod- and cell-mediated immune responses, both systemically and locally. To improve vaccine administrative strategies and efficacy, they can be formulated to contain multiple antigenic payloads and have the ability to protect fragile proteins from degradation. Nanovaccines are also stable at room temperature, minimizing the need for cold chain storage. Nanoparticle platforms can be synthesized for targeted delivery through intranasal, aerosol, or oral administration to induce desired mucosal immunity. In recent years, several nanovaccine platforms have emerged, based on biodegradable and biocompatible polymers, liposomes, and virus-like particles. While most nanovaccine candidates have not yet advanced beyond testing in rodent models, a growing number have shown promise for use against cattle infectious diseases. This review will highlight recent advancements in polymeric nanovaccine development and the mechanisms by which nanovaccines may interact with the bovine immune system. We will also discuss the positive implications of nanovaccines use for combating several important viral and bacterial disease syndromes and consider important future directions for nanovaccine development in beef and dairy cattle.
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Affiliation(s)
- Teresia W. Maina
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Elizabeth A. Grego
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States
| | - Paola M. Boggiatto
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Randy E. Sacco
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Balaji Narasimhan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States
| | - Jodi L. McGill
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
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12
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Macpherson A, Scott-Tucker A, Spiliotopoulos A, Simpson C, Staniforth J, Hold A, Snowden J, Manning L, van den Elsen J, Lawson ADG. Isolation of antigen-specific, disulphide-rich knob domain peptides from bovine antibodies. PLoS Biol 2020; 18:e3000821. [PMID: 32886672 PMCID: PMC7498065 DOI: 10.1371/journal.pbio.3000821] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/17/2020] [Accepted: 08/10/2020] [Indexed: 12/25/2022] Open
Abstract
As a novel alternative to established surface display or combinatorial chemistry approaches for the discovery of therapeutic peptides, we present a method for the isolation of small, cysteine-rich domains from bovine antibody ultralong complementarity-determining regions (CDRs). We show for the first time that isolated bovine antibody knob domains can function as autonomous entities by binding antigen outside the confines of the antibody scaffold. This yields antibody fragments so small as to be considered peptides, each stabilised by an intricate, bespoke arrangement of disulphide bonds. For drug discovery, cow immunisations harness the immune system to generate knob domains with affinities in the picomolar to low nanomolar range, orders of magnitude higher than unoptimized peptides from naïve library screening. Using this approach, knob domain peptides that tightly bound Complement component C5 were obtained, at scale, using conventional antibody discovery and peptide purification techniques. This study describes a method for the isolation of knob domains (a disulfide-rich domain found in the ultra-long CDRH3 of a subset of bovine antibodies) to create a uniquely small antibody fragment. With a molecular weight 3-6 KDa, the knob domain fragment is so small as to be considered a peptide. This approach uniquely harnesses the bovine immune system to affinity maturate peptides in vivo.
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Affiliation(s)
- Alex Macpherson
- UCB, Slough, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- * E-mail:
| | | | | | | | | | | | | | | | - Jean van den Elsen
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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13
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Barroso R, Morrison WI, Morrison LJ. Molecular Dissection of the Antibody Response: Opportunities and Needs for Application in Cattle. Front Immunol 2020; 11:1175. [PMID: 32595642 PMCID: PMC7304342 DOI: 10.3389/fimmu.2020.01175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Improving understanding of the bovine adaptive immune response would equip researchers to more efficiently design interventions against pathogens that impact upon food security and animal welfare. There are features of the bovine antibody response that differ substantially from other mammalian species, including the best understood models in the human and mouse. These include the ability to generate a functionally diverse immunoglobulin response despite having a fraction of the germline gene diversity that underpins this process in humans and mice, and the unique structure of a subset of immunoglobulins with "ultralong" HCDR3 domains, which are of significant interest with respect to potential therapeutics, including against human pathogens. However, a more detailed understanding of the B cell response and the production of an effective antibody response in the bovine is currently hampered by the lack of reagents for the B cell lineage. In this article we outline the current state of knowledge and capabilities with regard to B cell and antibody responses in cattle, highlight resource gaps, and summarize recent advances that have the potential to fundamentally advance our understanding of this process in the bovine host.
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Affiliation(s)
- Ruben Barroso
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - W Ivan Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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14
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Smider BA, Smider VV. Formation of ultralong DH regions through genomic rearrangement. BMC Immunol 2020; 21:30. [PMID: 32487018 PMCID: PMC7265228 DOI: 10.1186/s12865-020-00359-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Background Cow antibodies are very unusual in having exceptionally long CDR H3 regions. The genetic basis for this length largely derives from long heavy chain diversity (DH) regions, with a single “ultralong” DH, IGHD8–2, encoding over 50 amino acids. Many bovine IGHD regions have sequence similarity but have several nucleotide repeating units that diversify their lengths. Genomically, most DH regions exist in three clusters that appear to have formed from DNA duplication events. However, the relationship between the genomic arrangement and long CDR lengths is unclear. Results The DH cluster containing IGHD8–2 underwent a rearrangement and deletion event in relation to the other clusters in the region corresponding to IGHD8–2, with possible fusion of two DH regions and expansion of short repeats to form the ultralong IGHD8–2 gene. Conclusions Length heterogeneity within DH regions is a unique evolutionary genomic mechanism to create immune diversity, including formation of ultralong CDR H3 regions.
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Affiliation(s)
- Brevin A Smider
- The Applied Biomedical Science Institute, San Diego, CA, 92127, USA
| | - Vaughn V Smider
- The Applied Biomedical Science Institute, San Diego, CA, 92127, USA. .,The Scripps Research Institute, La Jolla, CA, 92037, USA.
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15
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Burke MJ, Stockley PG, Boyes J. Broadly Neutralizing Bovine Antibodies: Highly Effective New Tools against Evasive Pathogens? Viruses 2020; 12:v12040473. [PMID: 32331321 PMCID: PMC7232318 DOI: 10.3390/v12040473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Potent antibody-mediated neutralization is critical for an organism to combat the vast array of pathogens it will face during its lifetime. Due to the potential genetic diversity of some viruses, such as HIV-1 and influenza, standard neutralizing antibodies are often ineffective or easily evaded as their targets are masked or rapidly mutated. This has thwarted efforts to both prevent and treat HIV-1 infections and means that entirely new formulations are required to vaccinate against influenza each year. However, some rare antibodies isolated from infected individuals confer broad and potent neutralization. A subset of these broadly neutralizing antibodies possesses a long complementarity-determining 3 region of the immunoglobulin heavy chain (CDR H3). This feature generates unique antigen binding site configurations that can engage conserved but otherwise inaccessible epitope targets thus neutralizing many viral variants. Remarkably, ultralong CDR H3s are a common feature of the cow antibody repertoire and are encoded by a single variable, diversity, joining (VDJ) recombination that is extensively diversified prior to antigen exposure. Recently, it was shown that cows rapidly generate a broadly neutralizing response upon exposure to HIV-1 and this is primarily mediated by these novel ultralong antibody types. This review summarises the current knowledge of these unusual CDR H3 structures and discusses their known and potential future uses.
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Affiliation(s)
- Matthew J. Burke
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
| | - Peter G. Stockley
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Correspondence:
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16
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Haakenson JK, Deiss TC, Warner GF, Mwangi W, Criscitiello MF, Smider VV. A Broad Role for Cysteines in Bovine Antibody Diversity. Immunohorizons 2019; 3:478-487. [PMID: 31619454 PMCID: PMC7366855 DOI: 10.4049/immunohorizons.1900058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/29/2019] [Indexed: 01/26/2023] Open
Abstract
Ab diversity in most vertebrates results from the assortment of amino acid side chains on CDR loops formed through V(D)J recombination. Cows (Bos taurus) have a low combinatorial diversity potential because of a small number of highly homologous V, D, and J gene segments. Despite this, a subset of the Ab repertoire (~10%) contains exceptionally long CDR H chain (HC) 3 (H3) regions with a rich diversity of cysteines and disulfide-bonded loops that diversify through a single V-D-J recombination event followed by massive somatic hypermutation. However, the much larger portion of the repertoire, encoding shorter CDR H3s, has not been examined in detail. Analysis of germline gene segments reveals noncanonical cysteines in the HC V regions and significant cysteine content in the HC D regions. Deep sequencing analysis of naturally occurring shorter CDR H3 (<40 aa) Ab genes shows that HC V and HC D regions preferentially combine to form a functional gene with an even number of total cysteines in the final V region, suggesting that disulfide bonds contribute to diversity not only in ultralong CDR H3 bovine Abs but in shorter CDR H3 bovine Abs as well. In addition to germline “hard-coded” cysteines, the bovine Ab repertoire can produce additional cysteine codons through somatic hypermutation, further diversifying the repertoire. Given the limited combinatorial diversity at the bovine Ig loci, this helps to explain how diversity is created in shorter CDR H3 Abs and potentially provides novel structural paratopes in bovine Ab combining sites.
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Affiliation(s)
- Jeremy K Haakenson
- Applied Biomedical Science Institute, San Diego, CA 92127.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Thaddeus C Deiss
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843; and
| | - Gabrielle F Warner
- Applied Biomedical Science Institute, San Diego, CA 92127.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Waithaka Mwangi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506
| | - Michael F Criscitiello
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843; and
| | - Vaughn V Smider
- Applied Biomedical Science Institute, San Diego, CA 92127; .,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
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17
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Cordero-Solorzano J, Parmentier HK, Arts JAJ, van der Poel J, de Koning DJ, Bovenhuis H. Genome-wide association study identifies loci influencing natural antibody titers in milk of Dutch Holstein-Friesian cattle. J Dairy Sci 2019; 102:11092-11103. [PMID: 31548067 DOI: 10.3168/jds.2019-16627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/05/2019] [Indexed: 12/16/2022]
Abstract
Natural antibodies (NAb) are produced without any antigenic stimulation as a part of the innate immune system and provide a first line of defense against pathogens. Hence, they may be a useful trait when estimating an animal's potential immune competence and in selection for disease resistance. The aim of this study was to identify genomic regions associated with different NAb traits in milk and potentially describe candidate genes. Milk samples from 1,695 first-lactation Holstein Friesian cows with titer measurements for keyhole limpet hemocyanin, lipopolysaccharide, lipoteichoic acid, and peptidoglycan-binding total NAb and isotypes IgG1, IgM, and IgA were used. Genome-wide association study analyses were performed using imputed 777K SNP genotypes, accounting for relationships using pedigree information. Functional enrichment analysis was performed on the significantly associated genomic regions to look for candidate genes. For IgM NAb, significant associations (false discovery rate <0.05) were found on Bos taurus autosome (BTA) 17, 18, and 21 with candidate genes related to immunoglobulin structure and early B cell development. For IgG1, associations were found on BTA3, and we confirmed a quantitative trait loci on BTA21 previously reported for IgG NAb in serum. Our results provide new insights into the regulation of milk NAb that will help unravel the complex relationship between milk immunoglobulins and disease resistance in dairy cattle.
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Affiliation(s)
- Juan Cordero-Solorzano
- Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics, Box 7023,750 07, Uppsala, Sweden; Wageningen University and Research, Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Henk K Parmentier
- Wageningen University and Research, Adaptation Physiology Group, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Joop A J Arts
- Wageningen University and Research, Adaptation Physiology Group, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Jan van der Poel
- Wageningen University and Research, Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Dirk Jan de Koning
- Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics, Box 7023,750 07, Uppsala, Sweden
| | - Henk Bovenhuis
- Wageningen University and Research, Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, the Netherlands.
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18
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Haakenson JK, Huang R, Smider VV. Diversity in the Cow Ultralong CDR H3 Antibody Repertoire. Front Immunol 2018; 9:1262. [PMID: 29915599 PMCID: PMC5994613 DOI: 10.3389/fimmu.2018.01262] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023] Open
Abstract
Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique “stalk and knob” structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
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Affiliation(s)
- Jeremy K Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruiqi Huang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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19
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Stanfield RL, Haakenson J, Deiss TC, Criscitiello MF, Wilson IA, Smider VV. The Unusual Genetics and Biochemistry of Bovine Immunoglobulins. Adv Immunol 2018; 137:135-164. [PMID: 29455846 DOI: 10.1016/bs.ai.2017.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antibodies are the key circulating molecules that have evolved to fight infection by the adaptive immune system of vertebrates. Typical antibodies of most species contain six complementarity-determining regions (CDRs), where the third CDR of the heavy chain (CDR H3) has the greatest diversity and often makes the most significant contact with antigen. Generally, the process of V(D)J recombination produces a vast repertoire of antibodies; multiple V, D, and J gene segments recombine with additional junctional diversity at the V-D and D-J joints, and additional combinatorial possibilities occur through heavy- and light-chain pairing. Despite these processes, the overall structure of the resulting antibody is largely conserved, and binding to antigen occurs predominantly through the CDR loops of the immunoglobulin V domains. Bovines have deviated from this general paradigm by having few VH regions and thus little germline combinatorial diversity, but their antibodies contain long CDR H3 regions, with substantial diversity generated through somatic hypermutation. A subset of the repertoire comprises antibodies with ultralong CDR H3s, which can reach over 70 amino acids in length. Structurally, these unusual antibodies form a β-ribbon "stalk" and disulfide-bonded "knob" that protrude far from the antibody surface. These long CDR H3s allow cows to mount a particularly robust immune response when immunized with viral antigens, particularly to broadly neutralizing epitopes on a stabilized HIV gp140 trimer, which has been a challenge for other species. The unusual genetics and structural biology of cows provide for a unique paradigm for creation of immune diversity and could enable generation of antibodies against especially challenging targets and epitopes.
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Affiliation(s)
| | | | - Thaddeus C Deiss
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Michael F Criscitiello
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Ian A Wilson
- The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- The Scripps Research Institute, La Jolla, CA, United States.
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20
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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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21
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Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cell Mol Immunol 2017; 16:53-64. [PMID: 29200193 DOI: 10.1038/cmi.2017.117] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
The antibody repertoire of Bos taurus is characterized by a subset of variable heavy (VH) chain regions with ultralong third complementarity determining regions (CDR3) which, compared to other species, can provide a potent response to challenging antigens like HIV env. These unusual CDR3 can range to over seventy highly diverse amino acids in length and form unique β-ribbon 'stalk' and disulfide bonded 'knob' structures, far from the typical antigen binding site. The genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well understood. Here we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene, IGHV1-7 (VHBUL) rearranged to the longest diversity gene, IGHD8-2. An eight nucleotide duplication at the 3' end of IGHV1-7 encodes a longer V-region producing an extended F β-strand that contributes to the stalk in a rearranged CDR3. A low amino acid variability was observed in CDR1 and CDR2, suggesting that antigen binding for this subset most likely only depends on the CDR3. Importantly a novel, potentially AID mediated, deletional diversification mechanism of the B. taurus VH ultralong CDR3 knob was discovered, in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in place. These deletions serve to further diversify cysteine positions, and thus disulfide bonded loops. Hence, both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.
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22
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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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23
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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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24
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Vadnais ML, Smider VV. Bos taurus ultralong CDR H3 antibodies. Curr Opin Struct Biol 2016; 38:62-7. [PMID: 27295423 PMCID: PMC6667352 DOI: 10.1016/j.sbi.2016.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/14/2016] [Accepted: 05/18/2016] [Indexed: 02/03/2023]
Abstract
Cow antibodies are unusual in having an exceptionally long third complementarity determining region of the heavy chain (CDR H3). These CDR H3s have a multitude of cysteines and form a distinct domain characterized by a β-ribbon 'stalk' and disulfide bonded 'knob'. Cows appear to utilize somatic hypermutation of a single VDJ rearrangement to produce an astounding variety of distinct CDR H3 sequences with different disulfide bonding patterns within the knob. Thus, cows may be unique amongst vertebrates in evolving an antibody system with both a different scaffold for binding antigen as well as an unusual diversity creating process.
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Affiliation(s)
- Melissa L Vadnais
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, United States
| | - Vaughn V Smider
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines, La Jolla, CA 92037, United States.
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25
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Ma L, Qin T, Chu D, Cheng X, Wang J, Wang X, Wang P, Han H, Ren L, Aitken R, Hammarström L, Li N, Zhao Y. Internal Duplications of DH, JH, and C Region Genes Create an Unusual IgH Gene Locus in Cattle. THE JOURNAL OF IMMUNOLOGY 2016; 196:4358-66. [PMID: 27053761 DOI: 10.4049/jimmunol.1600158] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/09/2016] [Indexed: 02/03/2023]
Abstract
It has been suspected for many years that cattle possess two functional IgH gene loci, located on Bos taurus autosome (BTA) 21 and BTA11, respectively. In this study, based on fluorescence in situ hybridization and additional experiments, we showed that all functional bovine IgH genes were located on BTA21, and only a truncated μCH2 exon was present on BTA11. By sequencing of seven bacterial artificial chromosome clones screened from a Hostein cow bacterial artificial chromosome library, we generated a 678-kb continuous genomic sequence covering the bovine IGHV, IGHD, IGHJ, and IGHC genes, which are organized as IGHVn-IGHDn-IGHJn-IGHM1-(IGHDP-IGHV3-IGHDn)3-IGHJn-IGHM2-IGHD-IGHG3-IGHG1-IGHG2-IGHE-IGHA. Although both of two functional IGHM genes, IGHM1 and IGHM2, can be expressed via independent VDJ recombinations, the IGHM2 can also be expressed through class switch recombination. Likely because more IGHD segments can be involved in the expression of IGHM2, the IGHM2 gene was shown to be dominantly expressed in most tissues throughout different developmental stages. Based on the length and identity of the coding sequence, the 23 IGHD segments identified in the locus could be divided into nine subgroups (termed IGHD1 to IGHD9). Except two members of IGHD9 (14 nt in size), all other functional IGHD segments are longer than 30 nt, with the IGHD8 gene (149 bp) to be the longest. These remarkably long germline IGHD segments play a pivotal role in generating the exceptionally great H chain CDR 3 length variability in cattle.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tong Qin
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Dan Chu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xueqian Cheng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jing Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xifeng Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Peng Wang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Robert Aitken
- Faculty of Health and Life Sciences, York St John University, York YO31 7EX, United Kingdom; and
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China;
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26
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de los Rios M, Criscitiello MF, Smider VV. Structural and genetic diversity in antibody repertoires from diverse species. Curr Opin Struct Biol 2015; 33:27-41. [PMID: 26188469 DOI: 10.1016/j.sbi.2015.06.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/09/2015] [Accepted: 06/19/2015] [Indexed: 01/01/2023]
Abstract
The antibody repertoire is the fundamental unit that enables development of antigen specific adaptive immune responses against pathogens. Different species have developed diverse genetic and structural strategies to create their respective antibody repertoires. Here we review the shark, chicken, camel, and cow repertoires as unique examples of structural and genetic diversity. Given the enormous importance of antibodies in medicine and biological research, the novel properties of these antibody repertoires may enable discovery or engineering of antibodies from these non-human species against difficult or important epitopes.
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Affiliation(s)
- Miguel de los Rios
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121, United States
| | - Michael F Criscitiello
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, United States
| | - Vaughn V Smider
- Fabrus Inc., A Division of Sevion Therapeutics, San Diego, CA 92121, United States; Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
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