1
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van Rijswijck DMH, Bondt A, de Kat N, Lood R, Heck AJR. Direct Comparison of the Hinge-Cleaving Proteases IgdE and BdpK for LC-MS-Based IgG1 Clonal Profiling. Anal Chem 2024; 96:23-27. [PMID: 38105593 PMCID: PMC10782413 DOI: 10.1021/acs.analchem.3c03712] [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: 08/18/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Human antibodies are heterogeneous molecules primarily due to clonal sequence variations. Analytical techniques to assess antibody levels quantitatively, such as ELISA, lack the power to resolve abundances at the clonal level. Recently, we introduced an LC-MS-based approach that can distinguish and quantify antibody clones using the mass and retention time of their corresponding Fab-fragments. We used specific hinge-cleaving protease IgdE (FabALACTICA) to release the Fab-fragments from the constant Fc region of the antibody. Here, we explore an alternative IgG1 hinge-cleaving protease, BdpK (FabDELLO), and compare it directly to IgdE for use in IgG1 repertoire profiling. We used IgdE and BdpK in parallel to digest all IgG1s from the same set of plasma samples. Both proteases cleave IgG1 specifically in the hinge, albeit via different mechanisms and at two distinct cleavage sites. Notwithstanding these differences, the Fab fragments generated by IgdE or BdpK produced highly similar clonal repertoires. However, IgdE required ∼16 h of incubation to digest plasma IgG1s, while BdpK required ∼2 h. We authenticated the similarity of the clones by top-down proteomics using electron transfer dissociation. We conclude that BdpK performs very well in digesting polyclonal plasma IgG1s and that neither BdpK nor IgdE displays detectable biases in cleaving IgG1s. We anticipate that BdpK may emerge as the preferred protease for IgG1 hinge-digestion because it offers a shorter digestion time compared to IgdE, an equally specific digestion site, and no bias against any IgG1 present in plasma.
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Affiliation(s)
- Danique M H van Rijswijck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert Bondt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Naomi de Kat
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Rolf Lood
- Genovis AB, Scheelevägen 2, 223 63 Lund, Sweden
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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2
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Spanov B, Baartmans B, Olaleye O, Nicolardi S, Govorukhina N, Wuhrer M, van de Merbel NC, Bischoff R. Revealing charge heterogeneity of stressed trastuzumab at the subunit level. Anal Bioanal Chem 2023; 415:1505-1513. [PMID: 36693954 PMCID: PMC9974696 DOI: 10.1007/s00216-023-04547-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/24/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
Trastuzumab is known to be heterogeneous in terms of charge. Stressing trastuzumab under physiological conditions (pH 7.4 and 37 °C) increases charge heterogeneity further. Separation of charge variants of stressed trastuzumab at the intact protein level is challenging due to increasing complexity making it difficult to obtain pure charge variants for further characterization. Here we report an approach for revealing charge heterogeneity of stressed trastuzumab at the subunit level by pH gradient cation-exchange chromatography. Trastuzumab subunits were generated after limited proteolytic cleavage with papain, IdeS, and GingisKHAN®. The basic pI of Fab and F(ab)2 fragments allowed to use the same pH gradient for intact protein and subunit level analysis. Baseline separation of Fab subunits was obtained after GingisKHAN® and papain digestion and the corresponding modifications were determined by LC-MS/MS peptide mapping and middle-down MALDI-ISD FT-ICR MS. The described approach allows a comprehensive charge variant analysis of therapeutic antibodies that have two or more modification sites in the Fab region.
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Affiliation(s)
- Baubek Spanov
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Bas Baartmans
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Oladapo Olaleye
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Nico C van de Merbel
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Bioanalytical Laboratory, ICON, Amerikaweg 18, 9407 TK, Assen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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3
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The mosaic puzzle of the therapeutic monoclonal antibodies and antibody fragments - A modular transition from full-length immunoglobulins to antibody mimetics. Leuk Res Rep 2022; 18:100335. [PMID: 35832747 PMCID: PMC9272380 DOI: 10.1016/j.lrr.2022.100335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/09/2022] [Accepted: 06/25/2022] [Indexed: 01/07/2023] Open
Abstract
The use of monoclonal antibodies represents an important and efficient diagnostic and therapeutic tool in disease management and modern science but remains limited by several factors including the uneven distribution in diseased tissues as well as undesired activation of side immune reactions. Major scientific advancements including Recombinant DNA Technology, Hybridoma Technology, and Polymerase Chain Reaction have considerably impacted the use of monoclonal antibodies providing technical and effective solutions to overcome the shortcomings encountered with conventional antibodies. Initially, the introduction of antibody fragments allowed a more uniform and deeper penetration of the targeted tissue and reduced unwanted activation of Fc-mediated immune reactions. On another level, the immunogenicity of murine-derived antibodies was overcome by humanizing their encoding genes with specific sequences of human origin andtransgenic mice able to synthesize fully human antibodies were successfully created. Moreover, the advancement of genetic engineering techniques supported by the modular structure of antibody coding genes paved the way for the development of a new generation of antibody fragments with a wide spectrum of monospecific and bispecific agents. These later could be monovalent, bivalent, or multivalent, and either expressed as a single chain, assembled in multimeric forms or stringed in tandem. This has conferred improved affinity, stability, and solubility to antibody targetting. Lately, a new array of monoclonal antibody fragments was introduced with the engineering of nanobody and antibody mimetics as non-immunoglobulin-derived fragments with promising diagnostic and therapeutic applications. In this review, we decipher the molecular basis of monoclonal antibody engineering with a detailed screening of the antibody derivatives that provides new perspectives to expand the use of monoclonal fragments into previously unexplored fields.
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4
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Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches. Int J Mol Sci 2021; 23:ijms23010412. [PMID: 35008838 PMCID: PMC8745752 DOI: 10.3390/ijms23010412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 01/25/2023] Open
Abstract
Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we revisited this protease through a set of complementary approaches relying on state of-the-art HPLC-MS methods. After conceiving an efficient protocol to recombinantly express SpeB, the zymogen of the protease and its activation were characterized. Employing proteome-derived peptide libraries, a strong preference for hydrophobic and aromatic residues at P2 alongside negatively charged amino acids at P3′ to P6′ was revealed. To identify relevant in vivo substrates, native proteins were obtained from monocytic secretome and plasma to assess their cleavage under physiological conditions. Besides corroborating our findings concerning specificity, more than 200 cleaved proteins were identified, including proteins of the extracellular matrix, proteins of the immune system, and proteins involved in inflammation. Finally, the cleavage of IgG subclasses was studied in detail. This study precisely depicts the proteolytic properties of SpeB and provides a library of potential host substrates, including their exact cleavage positions, as a valuable source for further research to unravel the role of SpeB during streptococcal infection.
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Tandale JB, Badgujar SB, Tandale BU, Angre U, Daftary SB, Lala S, Gaur VP. An improved protocol for large scale production of high purity 'Fc' fragment of human immunoglobulin G (IgG-Fc). J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1159:122400. [PMID: 33126073 DOI: 10.1016/j.jchromb.2020.122400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/30/2020] [Accepted: 09/29/2020] [Indexed: 01/09/2023]
Abstract
We describe a simplified approach for purification and characterization of human 'IgG-Fc' fragment used widely as immunochemical tool and for therapeutic purposes. The 'Fc' fragment was purified from human IgG in a 3-stage column chromatography. The purified 'Fc' fragment appeared as a dimer glycoprotein with an apparent molecular mass of 52,981 Dalton (Ultraflex MALDI TOF/TOF). The Size-exclusion HPLC profile of the purified 'Fc' fragment of human IgG matched that of a commercially procured reference 'Fc' fragment material. The purity of the 'Fc' fragments was >99% by SDS-PAGE and size-exclusion HPLC. The results of Western blotting, immunoelectrophoresis, and mass spectrometry analysis indicate a high purity of the 'Fc' fragment. Peptide mass fingerprint analysis of the purified 'Fc' protein yielded peptides that partially match the known database sequences of FCG3B_HUMAN (Uniprot ID: O75015). This method of purification of the 'Fc' fragment is suitable for achieving high purity level of 'Fc' fragment protein. With this purification approach, the cost of the purified 'Fc' fragment of human IgG is significantly reduced as compared with the current market price of IgG-Fc fragment protein in international market. The purified 'IgG-Fc' fragment protein was found to be negative for major viral markers.
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Affiliation(s)
- Jatin B Tandale
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India
| | - Shamkant B Badgujar
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India.
| | - Babasaheb U Tandale
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India
| | - Unmesh Angre
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India
| | - Siddharth B Daftary
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India
| | - Sanjeev Lala
- Laboratory of Native Antigens, Research and Development Division, Advy Chemical Private Limited, Thane 400604, Maharashtra, India
| | - Vinod P Gaur
- Northwest Lipid Metabolism and Diabetes Research Laboratories (NWRL), Department of Medicine, University of Washington, 401 Queen Anne Ave North, Seattle, WA 98109, USA
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6
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Ye X, Su H, Wrapp D, Freed DC, Li F, Yuan Z, Tang A, Li L, Ku Z, Xiong W, Jaijyan D, Zhu H, Wang D, McLellan JS, Zhang N, Fu TM, An Z. Recognition of a highly conserved glycoprotein B epitope by a bivalent antibody neutralizing HCMV at a post-attachment step. PLoS Pathog 2020; 16:e1008736. [PMID: 32745149 PMCID: PMC7425986 DOI: 10.1371/journal.ppat.1008736] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/13/2020] [Accepted: 06/22/2020] [Indexed: 01/13/2023] Open
Abstract
Human cytomegalovirus (HCMV) is one of the main causative agents of congenital viral infection in neonates. HCMV infection also causes serious morbidity and mortality among organ transplant patients. Glycoprotein B (gB) is a major target for HCMV neutralizing antibodies, yet the underlying neutralization mechanisms remain largely unknown. Here we report that 3–25, a gB-specific monoclonal antibody previously isolated from a healthy HCMV-positive donor, efficiently neutralized 14 HCMV strains in both ARPE-19 cells and MRC-5 cells. The core epitope of 3–25 was mapped to a highly conserved linear epitope on antigenic domain 2 (AD-2) of gB. A 1.8 Å crystal structure of 3–25 Fab in complex with the peptide epitope revealed the molecular determinants of 3–25 binding to gB at atomic resolution. Negative-staining electron microscopy (EM) 3D reconstruction of 3–25 Fab in complex with de-glycosylated postfusion gB showed that 3–25 Fab fully occupied the gB trimer at the N-terminus with flexible binding angles. Functionally, 3–25 efficiently inhibited HCMV infection at a post-attachment step by interfering with viral membrane fusion, and restricted post-infection viral spreading in ARPE-19 cells. Interestingly, bivalency was required for HCMV neutralization by AD-2 specific antibody 3–25 but not the AD-4 specific antibody LJP538. In contrast, bivalency was not required for HCMV binding by both antibodies. Taken together, our results reveal the structural basis of gB recognition by 3–25 and demonstrate that inhibition of viral membrane fusion and a requirement of bivalency may be common for gB AD-2 specific neutralizing antibody. HCMV infection is usually asymptomatic in healthy individuals. However, life-threatening diseases frequently accompany HCMV infection in individuals with under-developed or compromised immune systems. Glycoprotein B antigenic domain 2 (AD-2) is a major target for HCMV-neutralizing antibodies that potentially provide immune protection. We report the structure-based study of gB recognition by a potent neutralizing antibody named 3–25 that binds a highly conserved epitope on AD-2. Functionally, 3–25 efficiently inhibited HCMV infection at a post-attachment step by interfering with viral membrane fusion, and restricted post-infection viral spreading. Furthermore, bivalency of 3–25 is required for viral neutralization but not for binding. Our findings advance understanding of gB antibody-mediated HCMV neutralization and facilitate development of gB-targeted vaccines and antibody drugs against HCMV infection.
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Affiliation(s)
- Xiaohua Ye
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Hang Su
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Daniel C. Freed
- Merck Research Laboratory, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Fengsheng Li
- Merck Research Laboratory, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Zihao Yuan
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Aimin Tang
- Merck Research Laboratory, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Leike Li
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Wei Xiong
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Dabbu Jaijyan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Hua Zhu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Dai Wang
- Merck Research Laboratory, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail: (NZ); (TMF); (ZA)
| | - Tong-Ming Fu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Merck Research Laboratory, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail: (NZ); (TMF); (ZA)
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail: (NZ); (TMF); (ZA)
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7
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Sidorov A, Beduleva L, Menshikov I, Terentiev A, Cherepanov I. Physicochemical characteristics of human IgG Fc fragments that expose regulatory rheumatoid factor neoepitopes and may show promise as antirheumatic agents. Biotechnol Appl Biochem 2020; 67:287-293. [DOI: 10.1002/bab.1849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/05/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Alexandr Sidorov
- Udmurt Federal Research Center UB RAS Izhevsk Russian Federation
- Department of Immunology and Cell BiologyUdmurt State University Izhevsk Russian Federation
| | - Liubov Beduleva
- Udmurt Federal Research Center UB RAS Izhevsk Russian Federation
- Department of Immunology and Cell BiologyUdmurt State University Izhevsk Russian Federation
- Novye Vakciny Ltd. Izhevsk Russian Federation
| | - Igor Menshikov
- Udmurt Federal Research Center UB RAS Izhevsk Russian Federation
- Department of Immunology and Cell BiologyUdmurt State University Izhevsk Russian Federation
- Novye Vakciny Ltd. Izhevsk Russian Federation
| | - Alexey Terentiev
- Udmurt Federal Research Center UB RAS Izhevsk Russian Federation
- Department of Immunology and Cell BiologyUdmurt State University Izhevsk Russian Federation
| | - Igor Cherepanov
- Department of Fundamental ChemistryUdmurt State University Izhevsk Russian Federation
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8
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Nascimento A, Mullerpatan A, Azevedo AM, Karande P, Cramer S. Development of phage biopanning strategies to identify affinity peptide ligands for kappa light chain Fab fragments. Biotechnol Prog 2019; 35:e2884. [DOI: 10.1002/btpr.2884] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 01/28/2023]
Affiliation(s)
- André Nascimento
- iBB – Institute for Bioengineering and Biosciences, Instituto Superior TécnicoUniversidade de Lisboa Lisbon Portugal
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy New York
| | - Akshat Mullerpatan
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy New York
| | - Ana Margarida Azevedo
- iBB – Institute for Bioengineering and Biosciences, Instituto Superior TécnicoUniversidade de Lisboa Lisbon Portugal
| | - Pankaj Karande
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy New York
| | - Steven Cramer
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary StudiesRensselaer Polytechnic Institute Troy New York
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9
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Ulmer N, Ristanovic D, Morbidelli M. Process for Continuous Fab Production by Digestion of IgG. Biotechnol J 2019; 14:e1800677. [PMID: 31169346 DOI: 10.1002/biot.201800677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/21/2019] [Indexed: 11/10/2022]
Abstract
Intensified processing and end-to-end integrated continuous manufacturing are increasingly being considered in bioprocessing as an alternative to the current batch-based technologies. Similar approaches can also be used at later stages of the production chain, such as in the post-translational modifications that are often considered for therapeutic proteins. In this work, a process to intensify the enzymatic digestion of immunoglobulin G (IgG) and the purification of the resulting Fab fragment is developed. The process consists of the integration of a continuous packed-bed reactor into a multicolumn chromatographic process. The integration is realized through the development of a novel multicolumn countercurrent solvent gradient purification (MCSGP) process, which, by adding a third column to the classical two-column MCSGP process, allows for continuous loading and then straight-through processing of the mixture leaving the reactor.
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Affiliation(s)
- Nicole Ulmer
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Dragana Ristanovic
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Massimo Morbidelli
- Department of Chemistry and Applied Bioscience, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
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10
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Bates A, Power CA. David vs. Goliath: The Structure, Function, and Clinical Prospects of Antibody Fragments. Antibodies (Basel) 2019; 8:E28. [PMID: 31544834 PMCID: PMC6640713 DOI: 10.3390/antib8020028] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023] Open
Abstract
Since the licensing of the first monoclonal antibody therapy in 1986, monoclonal antibodies have become the largest class of biopharmaceuticals with over 80 antibodies currently approved for a variety of disease indications. The development of smaller, antigen binding antibody fragments, derived from conventional antibodies or produced recombinantly, has been growing at a fast pace. Antibody fragments can be used on their own or linked to other molecules to generate numerous possibilities for bispecific, multi-specific, multimeric, or multifunctional molecules, and to achieve a variety of biological effects. They offer several advantages over full-length monoclonal antibodies, particularly a lower cost of goods, and because of their small size they can penetrate tissues, access challenging epitopes, and have potentially reduced immunogenicity. In this review, we will discuss the structure, production, and mechanism of action of EMA/FDA-approved fragments and of those in clinical and pre-clinical development. We will also discuss current topics of interest surrounding the potential use of antibody fragments for intracellular targeting and blood-brain barrier (BBB) penetration.
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Affiliation(s)
- Adam Bates
- Biopharm Molecular Discovery, GlaxoSmithKline, Hertfordshire SG1 2NY, UK.
| | - Christine A Power
- Biopharm Molecular Discovery, GlaxoSmithKline, Hertfordshire SG1 2NY, UK.
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11
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Yageta S, Imamura H, Shibuya R, Honda S. C H2 domain orientation of human immunoglobulin G in solution: Structural comparison of glycosylated and aglycosylated Fc regions using small-angle X-ray scattering. MAbs 2018; 11:453-462. [PMID: 30513259 PMCID: PMC6512918 DOI: 10.1080/19420862.2018.1546086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The N-linked glycan in immunoglobulin G is critical for the stability and function of the crystallizable fragment (Fc) region. Alteration of these protein properties upon the removal of the N-linked glycan has often been explained by the alteration of the CH2 domain orientation in the Fc region. To confirm this hypothesis, we examined the small-angle X-ray scattering (SAXS) profile of the glycosylated Fc region (gFc) and aglycosylated Fc region (aFc) in solution. Conformational characteristics of the CH2 domain orientation were validated by comparison with SAXS profiles theoretically calculated from multiple crystal structures of the Fc region with different CH2 domain orientations. The reduced chi-square values from the fitting analyses of gFc and aFc associated with the degree of openness or closure of each crystal structure, as determined from the first principal component that partially governed the variation of the CH2 domain orientation extracted by a singular value decomposition analysis. For both gFc and aFc, the best-fitted SAXS profiles corresponded to ones calculated based on the crystal structure of gFc that formed a "semi-closed" CH2 domain orientation. Collectively, the data indicated that the removal of the N-linked glycan only negligibly affected the CH2 domain orientation in solution. These findings will guide the development of methodology for the production of highly refined functional Fc variants.
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Affiliation(s)
- Seiki Yageta
- a Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan.,b Department of Computational Biology and Medical Sciences , Graduate School of Frontier Sciences, the University of Tokyo , Kashiwa , Chiba , Japan.,c Manufacturing Technology Association of Biologics , Tsukuba , Ibaraki , Japan
| | - Hiroshi Imamura
- a Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan.,d Department of Applied Chemistry , College of Life Sciences, Ritsumeikan University , Kusatsu , Shiga , Japan
| | - Risa Shibuya
- b Department of Computational Biology and Medical Sciences , Graduate School of Frontier Sciences, the University of Tokyo , Kashiwa , Chiba , Japan
| | - Shinya Honda
- a Biomedical Research Institute , National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Ibaraki , Japan.,b Department of Computational Biology and Medical Sciences , Graduate School of Frontier Sciences, the University of Tokyo , Kashiwa , Chiba , Japan.,c Manufacturing Technology Association of Biologics , Tsukuba , Ibaraki , Japan
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12
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Nowak C, Patel R, Liu H. Characterization of recombinant monoclonal IgG2 antibodies using LC-MS and limited Lys-C digestion. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1092:15-18. [DOI: 10.1016/j.jchromb.2018.05.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/08/2018] [Accepted: 05/10/2018] [Indexed: 01/08/2023]
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13
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Spoerry C, Hessle P, Lewis MJ, Paton L, Woof JM, von Pawel-Rammingen U. Novel IgG-Degrading Enzymes of the IgdE Protease Family Link Substrate Specificity to Host Tropism of Streptococcus Species. PLoS One 2016; 11:e0164809. [PMID: 27749921 PMCID: PMC5066943 DOI: 10.1371/journal.pone.0164809] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/30/2016] [Indexed: 12/24/2022] Open
Abstract
Recently we have discovered an IgG degrading enzyme of the endemic pig pathogen S. suis designated IgdE that is highly specific for porcine IgG. This protease is the founding member of a novel cysteine protease family assigned C113 in the MEROPS peptidase database. Bioinformatical analyses revealed putative members of the IgdE protease family in eight other Streptococcus species. The genes of the putative IgdE family proteases of S. agalactiae, S. porcinus, S. pseudoporcinus and S. equi subsp. zooepidemicus were cloned for production of recombinant protein into expression vectors. Recombinant proteins of all four IgdE family proteases were proteolytically active against IgG of the respective Streptococcus species hosts, but not against IgG from other tested species or other classes of immunoglobulins, thereby linking the substrate specificity to the known host tropism. The novel IgdE family proteases of S. agalactiae, S. pseudoporcinus and S. equi showed IgG subtype specificity, i.e. IgdE from S. agalactiae and S. pseudoporcinus cleaved human IgG1, while IgdE from S. equi was subtype specific for equine IgG7. Porcine IgG subtype specificities of the IgdE family proteases of S. porcinus and S. pseudoporcinus remain to be determined. Cleavage of porcine IgG by IgdE of S. pseudoporcinus is suggested to be an evolutionary remaining activity reflecting ancestry of the human pathogen to the porcine pathogen S. porcinus. The IgG subtype specificity of bacterial proteases indicates the special importance of these IgG subtypes in counteracting infection or colonization and opportunistic streptococci neutralize such antibodies through expression of IgdE family proteases as putative immune evasion factors. We suggest that IgdE family proteases might be valid vaccine targets against streptococci of both human and veterinary medical concerns and could also be of therapeutic as well as biotechnological use.
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Affiliation(s)
- Christian Spoerry
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Pontus Hessle
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Melanie J. Lewis
- Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Wellcome Trust Building, Dundee, United Kingdom
| | - Lois Paton
- Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Wellcome Trust Building, Dundee, United Kingdom
| | - Jenny M. Woof
- Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Wellcome Trust Building, Dundee, United Kingdom
| | - Ulrich von Pawel-Rammingen
- Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- * E-mail:
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14
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Abstract
Fragmentation in the hinge region of an IgG1 monoclonal antibody (mAb) can affect product stability, potentially causing changes in potency and efficacy. Metals ions, such as Cu(2+), can bind to the mAb and undergo hydrolysis or oxidation, which can lead to cleavage of the molecule. To better understand the mechanism of Cu(2+)-mediated mAb fragmentation, hinge region cleavage products and their rates of formation were studied as a function of pH with and without Cu(2+). More detailed analysis of the chemical changes was investigated using model linear and cyclic peptides (with the sequence of SCDKTHTC) derived from the upper hinge region of the mAb. Cu(2+) mediated fragmentation was determined to be predominantly via a hydrolytic pathway in solution. The sites and products of hydrolytic cleavage are pH and strain dependent. In more acidic environments, rates of Cu(2+) induced hinge fragmentation are significantly slower than at higher pH. Although the degradation reaction rates between the linear and cyclic peptides are not significantly different, the products of degradation vary. mAb fragmentation can be reduced by modifying His, which is a potential metal binding site and a known ligand in other metalloproteins. These results suggest that a charge may contribute to stabilization of a specific molecular structure involved in hydrolysis, leading to the possible formation of a copper binding pocket that causes increased susceptibility of the hinge region to degradation.
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Affiliation(s)
- Zephania Kwong Glover
- a Late Stage Pharmaceutical Development; Genentech, Inc. ; South San Francisco , CA USA
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15
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Hanson QM, Barb AW. A perspective on the structure and receptor binding properties of immunoglobulin G Fc. Biochemistry 2015; 54:2931-42. [PMID: 25926001 DOI: 10.1021/acs.biochem.5b00299] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recombinant antibodies spurred a revolution in medicine that saw the introduction of powerful therapeutics for treating a wide range of diseases, from cancers to autoimmune disorders and transplant rejection, with more applications looming on the horizon. Many of these therapeutic monoclonal antibodies (mAbs) are based on human immunoglobulin G1 (IgG1) or contain at least a portion of the molecule. Most mAbs require interactions with cell surface receptors for efficacy, including the Fc γ receptors. High-resolution structural models of antibodies and antibody fragments have been available for nearly 40 years; however, a thorough description of the structural features that determine the affinity with which antibodies interact with human receptors has not been published. In this review, we will cover the relevant history of IgG-related literature and how recent developments have changed our view of critical antibody-cell interactions at the atomic level with a nod to outstanding questions in the field and future prospects.
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Affiliation(s)
- Quinlin M Hanson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2214 Molecular Biology Building, Ames, Iowa 50011, United States
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2214 Molecular Biology Building, Ames, Iowa 50011, United States
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16
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Zhuang X, Ahmed F, Zhang Y, Ferguson HJ, Steele JC, Steven NM, Nagy Z, Heath VL, Toellner KM, Bicknell R. Robo4 vaccines induce antibodies that retard tumor growth. Angiogenesis 2014; 18:83-95. [PMID: 25348086 DOI: 10.1007/s10456-014-9448-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 10/13/2014] [Indexed: 01/24/2023]
Abstract
Tumor endothelial specific expression of Robo4 in adults identifies this plasma membrane protein as an anti-cancer target for immunotherapeutic approaches, such as vaccination. In this report, we describe how vaccination against Robo4 inhibits angiogenesis and tumor growth. To break tolerance to the auto-antigen Robo4, mice were immunised with the extracellular domain of mouse Robo4, fused to the Fc domain of human immunoglobulin within an adjuvant. Vaccinated mice show a strong antibody response to Robo4, with no objectively detectable adverse effects on health. Robo4 vaccinated mice showed impaired fibrovascular invasion and angiogenesis in a rodent sponge implantation assay, as well as a reduced growth of implanted syngeneic Lewis lung carcinoma. The anti-tumor effect of Robo4 vaccination was present in CD8 deficient mice but absent in B cell or IgG1 knockout mice, suggesting antibody dependent cell mediated cytotoxicity as the anti-vascular/anti-tumor mechanism. Finally, we show that an adjuvant free soluble Robo4-carrier conjugate can retard tumor growth in carrier primed mice. These results point to appropriate Robo4 conjugates as potential anti-angiogenic vaccines for cancer patients.
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Affiliation(s)
- Xiaodong Zhuang
- Institute for Biomedical Research, Schools of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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17
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Bonewald L, Wang AC, Wang IY, Balch CM, Ades EW. Antigenic determinant(s) shared by the human Thy 1 and human IgG. Immunobiology 1984; 166:428-38. [PMID: 6207102 DOI: 10.1016/s0171-2985(84)80020-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A human T cell differentiation antigen (p25) previously described as being the mouse theta equivalent has been examined for shared antigenic determinants with immunoglobulin. A strong cross-reactivity of an antiserum prepared against p25 antigen was established with human IgG subclasses. This antiserum does not react with human IgM or IgA, nor with primate immunoglobulins. The shared determinants appear to be associated with the disulphide-bonded cysteines in the first and third constant domains of the IgG molecule and the 9-112 disulfide bond of Thy 1.
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18
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Kojima M, Odani S, Ono T. An unusual papain cleavage of a human IgG1 (lambda) myeloma protein (Mot). Mol Immunol 1982; 19:1095-103. [PMID: 6815481 DOI: 10.1016/0161-5890(82)90320-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An IgGl (lambda) protein which showed a unique susceptibility towards papain digestion was isolated from the serum of a patient (Mot) with multiple myeloma. The Fab fragments of this protein were degraded rapidly into smaller peptides via an Fb fragment [Gall & D'Eustachio (1972), Biochemistry 11, 4621-4628], which corresponded to the constant domains (Cl-Chl). Structural analysis of the isolated Fab fragment, which consisted of the intact L-chain, a 17,000 and a 5000 mol. wt peptide fragment, indicated that the initial cleavage site was located in the vicinity of the second hypervariable region of the Fd fragment. Examination of the partial amino acid sequences of the Mot H-chain suggested that the variable region of the H-chain may be a hitherto unknown hybrid of subgroups I and III. This particular structure seems to have made the Fab fragment highly susceptible to papain. In the course of the present study, we also found in the papain digests of several human IgG proteins an 'intermediate' 5S fragment, which had previously been reported exclusively for the papain digest of rabbit IgG.
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19
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Marchalonis JJ, Warr GW, Wang AC, Burns WH, Burton RC. An Fab-related surface component of some normal and neoplastic human and marmoset T cells. Demonstration, functional analysis and partial characterization. Mol Immunol 1980; 17:877-91. [PMID: 6163971 DOI: 10.1016/0161-5890(80)90036-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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20
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Wang AC, Mather S, Tung E, Sarvas H, Rivat C, Rivat L. Serological division of the VHIII subgroup of human immunoglobulins. Mol Immunol 1980; 17:313-8. [PMID: 6777660 DOI: 10.1016/0161-5890(80)90051-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Solomon A, Gramse M, Havemann K. Proteolytic cleavage of human IgG molecules by neutral proteases of polymorphonuclear leukocytes. Eur J Immunol 1978; 8:782-5. [PMID: 102513 DOI: 10.1002/eji.1830081106] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effect on human IgG of the elastase-like (ELP) and chymotrypsin-like (CLP) neutral proteases derived from human polymorphonuclear leukocytes was studied. By incubating ELP with monoclonal IgG proteins, two immunochemically and electrophoretically distinct components were formed which were similar, but not identical, to the Fc and Fab fragments produced by papain digestion. When an IgG protein was incubated under similar conditions with CLP enzyme, no proteolysis was observed. IgG proteins differed in their susceptibility to proteolysis by ELP. These differences were related to the subclasses IgG1-IgG4. The IgG1 and IgG3 proteins were readily cleaved by ELP, but the IgG2 and IgG4 proteins were more resistant. Although free light chains differ in susceptibility to proteolysis by ELP, our studies showed that neither the type (kappa or lambda) nor the subgroup of light chain affected the susceptibility of complete IgG molecules to cleavage by this enzyme.
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22
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Wang AC, Mathur S, Pandey J, Siegel FP, Middaugh CR, Litman GW. Hv(1), a variable-region genetic marker of human immunoglobulin heavy chains. Science 1978; 200:327-9. [PMID: 416494 DOI: 10.1126/science.416494] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new antigenic determinant was discovered with a hemagglutination-inhibition assay system. Designated Hv(1), it is located in the variable region of human immunoglobulin heavy chains of the G, M, and A classes. Pedigree and population analyses suggest that it has an autosomal dominant mode of inheritance. This represents the first description of an allotypic determinant in the variable region of human immunoglobulins.
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